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Life Sciences, Other; Acrylamide, Free Asparagine, Cropping Systems, Organic, Conventional, Agriculture, Cereals, Species, Cultivars
Online: 23 October 2018 (18:19:26 CEST)
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As bakery products contribute considerably to the daily intake of the carcinogen acting substance acrylamide (AA), the aim of this study was to evaluate the impact of the cropping system (conventional vs. organic farming) on AA precursor levels of free asparagine (Asn) across different cultivars of the cereal species, namely winter wheat (Triticum aestivum), winter spelt (Triticum aestivum ssp. spelta) and winter rye (Secale cereale) with simultaneous consideration of gained grain yields and flour qualities. For this purpose, orthogonal field trials were established at two sites in Southwest Germany over two growing seasons (2006-2007 and 2007-2008). The results indicated a significant impact of the cropping system on free Asn contents. Across all species, free Asn contents in the flour were 26 % lower under organic compared to conventional farming. The impact of the cropping system on individual cultivars was obvious with a maximum reduction in free Asn contents of 50 % (e.g. for cultivars Ludwig, Privileg, Capo) if organically produced. For spelt, a significant impact of the cropping system was only found in 2008 with a reduction in free Asn of up to 25 % if organically produced. Across both cropping systems, cultivar Franckenkorn reached the lowest levels of free Asn. For rye, a significant impact of the cropping system was observed only in 2007 with 33 % higher Asn amounts in the conventional cropping system. Independent of the cropping system, rye reached the highest levels of free Asn followed by wheat and spelt. Across both cropping systems, species and cultivars, the amount of free Asn correlated with the AA content in heated flour with R2=0.63***. Furthermore, the results indicated that lower AA contents in bakery products can be achieved by proper selection of species (e.g. 66 % lower if rye is replaced by wheat) and cultivars. With an appropriate choice of the cultivar, a reduction of up to 65 % was possible within wheat, along with a reduction of 44 % within spelt and 12.5 % within rye. In summary, the results indicated that organically produced wheat especially offers the opportunity to significantly lower the AA potential of bread and bread rolls by the choice of raw materials low in free Asn.
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Life Sciences, Biotechnology; mycelium; fungi; biocomposite; foam; sandwich; lignocellulose; physical properties; mechanical properties; thermal properties.
Online: 23 October 2018 (17:53:42 CEST)
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Reducing the use of non-renewable resources is a key strategy of Circular Economy. Mycelium-based foams and sandwich composites are an emerging category of biocomposites relying on the valorization of lignocellulosic wastes and the natural growth of the living fungal organism. While growing, the fungus cements the substrate, that is partially replaced by the tenacious biomass of the fungus itself. The final product can be shaped to produce insulating panels, packaging materials, bricks or new-design objects. Only a few pioneer companies in the world detain a significant know-how as well as the possibility to provide the material characterization. Moreover, several technical details are not revealed due to industrial secrecy. According to the available literature, mycelium-based biocomposites show low density, good insulation properties both as it regards acoustic and thermal aspects. Mechanical properties are apparently inferior in comparison to EPS (expanded polystyrene), that is the major synthetic competitor. Nevertheless, mycelium-based composites can display an enormous variability on the basis of: fungal species and strain; substrate composition and structure; incubation conditions. Aim of the present review is to critically synthetize the available knowledge about the physical, mechanical and thermodynamic characterization of mycelium-based biocomposites with regard to the actual and potential applications.
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Quante Singleton,
Kumar Vaibhav,
Molly Braun,
Andrew Khayrullin,
Bharati Mendhe,
Ravindra Kolhe,
Helen Kaiser,
Mohamed E. Awad,
Tunde Fariyike,
Ranya Elsayed,
Mohammed Elsalanty,
Carlos M. Isales,
Yutao Liu,
Mark W. Hamrick,
Krishnan M. Dhandapani,
Sadanand Fulzele
Life Sciences, Molecular Biology; extracellular vesicles, EVs , traumatic brain injury, bone loss, TBI
Online: 23 October 2018 (10:56:08 CEST)
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Traumatic brain injury (TBI) is a major source of worldwide morbidity and mortality. Patients suffering from TBI exhibit a higher susceptibility to bone loss and an increased rate of bone fractures; however, the underlying mechanisms remain poorly defined. Herein, we observed significantly lower bone quality and elevated levels of inflammation in bone and bone marrow niche after controlled cortical impact-induced TBI in in-vivo CD-1 mice. Further, we identified dysregulated NFB signaling, an established mediator of osteoclast differentiation and bone loss, within the bone marrow niche of TBI mice. Ex vivo studies revealed increased osteoclast differentiation in bone marrow-derived cells from TBI mice, as compared to sham injured mice. Finally, we found bone marrow derived extracellular vesicles (EVs) from TBI mice enhanced the colony forming ability and osteoclast differentiation efficacy of bone marrow cells and activated NFB signaling genes in bone marrow-derived cells. Taken together, we provide evidence that TBI-induced inflammatory stress on bone and the bone marrow niche may activate NFB leading to accelerated bone loss. Targeted inhibition of these signaling pathways may reverse TBI-induced bone loss and reduce fracture rates.
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Life Sciences, Other; acrylamide; free asparagine; agriculture; organic farming; cultivars; cultivar selection; cereal production; cereals
Online: 23 October 2018 (05:57:10 CEST)
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For cereals grown under organic conditions, information on levels of free asparagine (free Asn) as a precursor to acrylamide (AA) formation, is almost completely lacking. This study investigated the impact of organically grown cereal species and cultivars of winter wheat (Triticum aestivum), winter spelt (Triticum aestivum ssp. spelta), winter rye (Secale cereale), winter einkorn (Triticum monococcum) and winter emmer (Triticum dicoccum) on the level of free Asn with simultaneous consideration of grain yields and flour qualities over three growing seasons (2005–2006, 2006–2007 and 2007–2008) in Southwest Germany. Additionally, the relation of free Asn and AA was investigated. Heritability revealed how strongly the level of free Asn was linked to the genotype. In this context free Asn of species and cultivars grown at a second location in Southern Germany were analysed. The level of free Asn was significantly influenced by species and within species by cultivars. Rye was found to exhibit the highest free Asn amount (52 mg 100 g−1), followed by einkorn (32 mg 100 g−1), emmer (16 mg 100 g−1) wheat (10 mg 100 g−1) and spelt (8 mg 100 g−1), which showed the overall lowest free Asn content. Hence, replacing rye with spelt in food products would lead to an 85% reduction of free Asn in raw material. Within species, cultivars differed in their levels of free Asn by up to 67% for wheat, 55% for spelt and 33% for rye. Year also had a significant impact as almost all samples were significantly higher in their level of free Asn in 2008 compared to 2006 and 2007. Rye was most significantly affected by year as the level of free Asn varied by up to 32% between years. In contrast, wheat and spelt were only affected minimally by year. A high heritability was found for wheat (0.79) and spelt (0.91) concerning locations in 2008, meaning that the level of free Asn is mainly determined by the genotype and less influenced by environmental conditions. In contrast, heritability was low for wheat (0.23) but high for spelt (0.71) and rye (0.67) regarding years. As for organically grown cereals the relation between free Asn and AA formation was never investigated before. Correlation of both parameters was calculated. There was also a close correlation between free Asn and AA. Across species and years, the amount of free Asn correlated with the AA content in heated flour with R2 = 0.69***. Thus, free Asn can serve as an indicator for AA formation during processing. In conclusion, the level of free Asn can be highly influenced by proper selection of species and cultivars under organic growing conditions.
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Life Sciences, Molecular Biology; Sinapis alba L.; Sinapis nigra L.; ultrasound-assisted extraction; antiproliferative; proapoptotic; antimicrobial.
Online: 22 October 2018 (18:04:24 CEST)
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High Brassicaceae consumption reduces the risk of developing several cancer types, probably due to their glucosinolate amount. Extracts from Sinapis nigra L. and Sinapis alba L. have been obtained from leaves and seeds under different conditions using ethanol/water mixtures because well accepted by food industry. The EtOH/H2O 8:2 mixture gives better yields in glucosinolate amounts from grinded seeds, mainly sinalbin in S. alba and sinigrin in S. nigra. The highest antiproliferative activity in both non-tumour and tumour cell lines was induced by S. alba seeds extract. To evaluate whether Sinapis spp effect was only due to glucosinolate content or it was influenced by the extracts’ complexity, cells were treated with extracts or glucosinolates, in the presence of myrosinase. Pure sinigrin did not modify cell proliferation, while pure sinalbin was less effective than the extract. The addition of myrosinase increased the antiproliferative effects of the S. nigra extract and sinigrin. Antiproliferative activity was correlated to MAPKs modulation, which was cell and extract-dependent. Cell-cycle analysis evidenced a proapoptotic effect of S. alba on both tumour cell lines and of S. nigra only on HCT 116. Both extracts showed good antimicrobial activity in disc diffusion tests and on ready-to-eat fresh salad. These results underline the potential effects of Sinapis spp in chemoprevention and food preservation.
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Life Sciences, Other; liposomes, exosomes, extracellular vesicles, drug delivery, drug targeting, bioinspired systems, engineered systems.
Online: 22 October 2018 (17:35:20 CEST)
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The similarities between exosomes and liposomes, together with the high organotropism of several types of exosomes, have recently prompted the development of engineered-exosomes or exosome-mimetics, which may be artificial (liposomal) or cell-derived vesicles, as advanced platforms for targeted drug delivery. Here we provide the current state-of-the-art of using exosome or exosome-inspired systems for drug delivery. We review the various approaches investigated and the shortcomings of each approach. Finally the challenges identified up-to-date in this field are summarized.
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Life Sciences, Microbiology; Mucilaginibacer rubeus；Mucilaginibacter kameinonensis; genomic island; evolution; heavy metal resistance; draft genome sequence; CTnDOT
Online: 22 October 2018 (17:21:18 CEST)
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Heavy metals are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu(II), 21 mM Zn(II), 1.2 mM Cd(II), and 10.0 mM As(III). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative P1B-1-ATPase, 5 putative P1B-3-ATPase and 4 putative Zn(II)/Cd(II) P1B-4 type ATPase, and 16 putative RND-type metal transporter systems. Moreover, the four genomes carry a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci include genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system) respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.
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Life Sciences, Cell & Developmental Biology; Arabidopsis; auxin; HD-Zip transcription factors; light environment; photoreceptors
Online: 22 October 2018 (16:22:42 CEST)
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Plants have evolved two opposing strategies in response to competition for light: shade tolerance and shade avoidance. To detect the presence of neighboring vegetation, shade-avoiding plants have evolved the ability to perceive and integrate multiple signals. Among them, changes in light quality and quantity are central to elicit and regulate the shade avoidance response. Here, we describe recent advances in the understanding of photoperception and downstream signaling mechanisms underlying the shade avoidance response, focusing on Arabidopsis because most of our knowledge derives from studies conducted in this model plant. Shade avoidance is an adaptive response, resulting in phenotypes with high relative fitness in natural dense communities. However, it contributes to reduction in crop plant productivity, and the design of new strategies aimed at attenuating shade avoidance in a stage- and/or organ- specific manner in high-density crop plantings is a major challenge for the future. For this reason, in this review, we also report on recent advances in the molecular description of the shade avoidance response in crops, such as maize and tomato, and discuss similarity and differences with Arabidopsis.
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Life Sciences, Other; acrylamide; asparagine; agriculture; nitrogen; sulfur; fertilization; cereals; cropping system
Online: 22 October 2018 (14:57:43 CEST)
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In a two-year field trial, the effect of nitrogen (N) and sulfur (S) fertilization was investigated on grain yield, grain quality parameters, formation of acrylamide (AA), and the precursor free asparagine (Asn) in organically and conventionally produced winter wheat cultivars. In both production systems, different types, amounts, and temporal distributions of N were tested. While the effect of S fertilizer types and amounts on free Asn was only tested in the conventional farming system. Within both cropping systems, grain yield and baking quality were significantly influenced by N treatment while the effect on free Asn was only minor. Especially within the organic farming system, increasing N fertilization levels did not increase free Asn significantly. A slight trend of increasing free Asn levels with an intensified N supply was observed, especially in the presence of crude protein contents of 14% or higher. But only N amounts of 180 kg N ha−1 or higher increased the probability of high free Asn contents considerably, while N supply below that amount led to free Asn values similar to the unfertilized controls. The results indicated that good baking quality can be achieved without significantly increasing free Asn levels. In addition, cultivars affected the levels of free Asn significantly. Compared to cv. “Bussard” and “Naturastar”, cv. “Capo” exhibited the lowest AA formation potential at an N supply of 180 kg N ha−1 while simultaneously reaching a crude protein content > 15% (conventional) and > 12% (organic). Thus, it seems that cultivars differ in their ability to store and incorporate free Asn into proteins. Over all trials, a correlation of free Asn and AA was shown by R2 = 0.77, while a relation of free Asn and protein was only R2 = 0.36. Thus, lowering free Asn by adjusting N treatments should not necessarily affect baking quality. S nutrition within conventional farming did not change free Asn amount or crude protein significantly, probably due to the fact that soil was not sulfate-deficient. In summary, it was evident that free Asn amounts in wheat varied widely both within cultivars and between cropping systems. In order to clearly unravel genotypic differences and their interaction with environmental factors and especially N fertilization, further research is needed.
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Zhi-Qiang Qin,
Jing Xu,
Ting Feng,
Shan Lv,
Yin-Jun Qian,
Li-Juan Zhang,
Yin-Long Li,
Chao lv,
Robert Bergquist,
Shi-Zhu Li,
Xiao-Nong Zhou
Life Sciences, Molecular Biology; Schistosoma japonicum; Oncomelania hupensis; snail; 28S ribosomal DNA; PCR; loop-mediated isothermal amplification (LAMP); pooled samples; China
Online: 22 October 2018 (14:30:26 CEST)
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Schistosoma infection in snails can be monitored by microscopy or indirectly by sentinel mice. As both these approaches sometimes miss infections, more sensitive tests are needed, particularly in low-level transmission settings. In this study, the loop-mediated isothermal amplification (LAMP) technique, designed to detect a specific 28S ribosomal S. japonicum gene with high sensitivity, was compared to microscopy using snail samples from 51 areas endemic for schistosomiasis in five Chinese provinces. The results were compared with those by polymerase chain reaction (PCR) adding DNA sequencing as a reference when needed. The testing of pooled snail samples showed that a dilution factor of 1/50, i.e., one infected snail plus 49 non-infected ones, would still result in a positive reaction after the recommended number of amplification cycles. Testing a total of 232 pooled samples, emanating from 4,006 snail specimens, with the LAMP assay showed a 6.5% rate of infection, while traditional microscopy found only 0.04% positive samples in the same materials. Parallel PCR analysis confirmed the diagnostic accuracy of the LAMP assay, with DNA sequencing even giving LAMP a slight lead. Microscopy and the LAMP test were carried out at local schistosomiasis-control stations demonstrating that the potential of the latter assay to serve as a point-of-care (POC) test with results available within 60–90 minutes, while the more complicated PCR test had to be carried out at the National Institute of Parasitic Diseases (NIPD) in Shanghai, China. In conclusion, LAMP was found to be clearly superior to microscopy and as good as, or better, than PCR. Application of LAMP testing would be useful for surveillance and risk prediction as it requires less time than other techniques and can be used under field conditions, which improves and accelerates schistosomiasis control.
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Life Sciences, Other; drug release simulation; disintegration simulation; poorly water soluble drug; mefenamic acid; Noyes-Whitney equation; cellular automata; synchrotron microtomography
Online: 22 October 2018 (13:38:04 CEST)
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There are numerous approaches to model an influence of manufacturing parameters on the dissolution and disintegration of solid dosage forms. A modern approach for modelling and simulating complex and heterogeneous systems such as pharmaceutical tablets focuses on computationally-intensive finite-element or discreet element methods. Industrial challenges such as Process Analytical Technology (PAT) and Quality by Design are stimulating computer-based technologies to design, control and improve the quality of pharmaceutical compacts and their performance. In this study the disintegration and dissolution model based on the numerical solutions of the Noyes-Whitney equation and cellular automata supported disintegration model are proposed and evaluated. The results from in vitro release studies of the mefenamic acid formulations were compared to the calculated release patterns from the tablet structures obtained from microtomography experiments and the purely algorithmically created virtual tablets.
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Life Sciences, Biotechnology; DNA origami; aptamer; DNA nanotechnology; protein nano array; biosensor; logic gate; enzyme cascade; drug delivery system; targeted therapy; molecular robotics
Online: 22 October 2018 (12:57:21 CEST)
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DNA origami has emerged in recent years as a powerful technique for designing and building 2D and 3D nanostructures. While the breadth of structures that have been produced is impressive, one of the remaining challenges, especially for DNA origami structures intended to carry out useful biomedical tasks in vivo, is to endow them with the ability to detect and respond to molecules of interest. Target molecules may be disease indicators or cell surface receptors, and the responses may include conformational changes leading to release of therapeutically relevant cargo. Nucleic acid aptamers are ideally suited to this task and are beginning to be used in DNA origami designs. In this review we consider examples of uses of DNA aptamers in DNA origami structures and summarise what is currently understood regarding aptamer-origami integration. We review three major roles for aptamers in such applications: protein immobilisation, triggering of structural transformation, and cell targeting. Finally, we consider future perspectives for DNA aptamer integration with DNA origami.
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Life Sciences, Biochemistry; chlorophyll fluorescence; J8-1 plum line; mandelonitrile; Prunus domestica; redox signalling; salicylic acid; salt-stress; soluble nutrients
Online: 19 October 2018 (16:57:02 CEST)
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Salinity is considered as one of the most important abiotic challenges that affect crop productivity. Plant hormones, including salicylic acid (SA), are key factors in the defence signalling output triggered during plant responses against environmental stresses. We have previously reported in peach a new SA biosynthetic pathway from mandelonitrile (MD), the molecule at the hub of the cyanogenic glucoside turnover in Prunus sp. In this work, we have studied whether this new SA biosynthetic pathway is also present in plum and the possible role this pathway plays in plant plasticity under salinity, focusing on the transgenic plum line J8-1, which displays stress tolerance via an enhanced antioxidant capacity.
The SA biosynthesis from MD in non-transgenic and J8-1 micropropagated plum shoots was studied by metabolomics. Then the response of J8-1 to salt stress in presence of MD or Phe (MD precursor) was assayed by measuring: chlorophyll content and fluorescence parameters, stress related hormones, levels of non-enzymatic antioxidants, the expression of two genes coding redox-related proteins, and the content of soluble nutrients.
The results from in vitro assays suggest that the SA synthesis from the MD pathway demonstrated in peach is not clearly present in plum, at least under in vitro conditions. Nevertheless, in J8-1 NaCl-stressed seedlings, an increase in SA was recorded as a result of the MD treatment, suggesting that MD could be involved in the SA biosynthesis under NaCl stress conditions in plum plants. We have also shown that the plum line J8-1 was tolerant to NaCl under greenhouse conditions, and this response was somewhat different in MD-treated plants. In that regards, the MD treatment produced an increase in SA, jasmonic acid (JA) and reduced ascorbate (ASC) contents as well as in the coefficient of non-photochemical quenching (qN) and the gene expression of Non-Expressor of Pathogenesis-Related 1 (NPR1) and thioredoxin H (TrxH) under salinity conditions, suggesting a crosstalk between different signalling pathways (NPR1/Trx and SA/JA) leading to salinity tolerance in the transgenic plum line J8-1.
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Life Sciences, Molecular Biology; CTCF; tumour suppressor gene; haploinsufficiency; zinc finger; CRISPR/Cas9; cancer; endometrial cancer; gene editing
Online: 19 October 2018 (13:29:01 CEST)
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CCCTC-binding factor (CTCF) is a conserved transcription factor that performs diverse roles in transcriptional regulation and chromatin architecture. Cancer genome sequencing reveals diverse acquired mutations in CTCF, which we have shown, functions as a tumour suppressor gene. While CTCF is essential for embryonic development, little is known of its absolute requirement in somatic cells and the consequences of CTCF haploinsufficiency. We examined the consequences of CTCF depletion in immortalised human and mouse cells using shRNA knockdown and CRISPR/Cas9 genome editing and examined the growth and development of heterozygous Ctcf (Ctcf+/-) mice. We also analysed the impact of CTCF haploinsufficiency by examining gene expression changes in CTCF-altered endometrial carcinoma. Knockdown and CRISPR/Cas9-mediated editing of CTCF reduced the cellular growth and colony-forming ability of K562 cells. CTCF knockdown also induced cell cycle arrest and a pro-survival response to apoptotic insult. However, in p53 shRNA-immortalised Ctcf+/- MEFs we observed the opposite: increased cellular proliferation, colony formation, cell cycle progression and decreased survival after apoptotic insult compared to wild type MEFs. CRISPR/Cas9-mediated targeting in Ctcf+/- MEFs revealed a predominance of in-frame microdeletions in Ctcf in surviving clones, however protein expression could not be ablated. Examination of CTCF mutations in endometrial cancers showed locus-specific alterations in gene expression due to CTCF haploinsufficiency, in concert with downregulation of tumour suppressor genes and upregulation of estrogen-responsive genes. Depletion of CTCF expression imparts a dramatic negative effect on normal cell function. However, CTCF haploinsufficiency can have growth-promoting effects consistent with known cancer hallmarks in the presence of additional genetic hits. Our results confirm the absolute requirement for CTCF expression in somatic cells and provide definitive evidence of CTCF’s role as a haploinsufficient tumour suppressor gene. CTCF genetic alterations in endometrial cancer indicate that gene dysregulation is a likely consequence of CTCF loss, contributing to, but not solely driving cancer growth.
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Life Sciences, Biotechnology; green algae; biomass; fatty acids; Tetraselmis straiata; lipids; carotenoids; raceway ponds
Online: 19 October 2018 (13:09:56 CEST)
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In the process of modernization and development, a human being always needed energy, which increased the dependency on the available sources of fossil fuel. Tetraselmis, a green algal genus belong to the order Chlorodendrales, are described by their strong green coloured chloroplast, flagellated cell bodies, and the occurrence of a pyrenoid within the chloroplast. In this study, four different strains of Tetraselmis species were successfully isolated from the saltpans Kovelong, Chennai, Tamil Nadu, India. The isolated strains were cultured in the normal basal medium and their morphological features were subsequently studied. The species of Tetraselmis straiata (T. straiata) Butcher BBRR1 was confirmed using molecular identification of 18S rRNA gene analysis and its observed systematic position. Among the four different isolates, T. straiata Butcher BBRR1 recorded a highest biomass concentration of 0.58 ± 0.021 g L-1, 15% lipids, 19% proteins and 17% carbohydrates when it grown under laboratory condition. Whereas, in open raceway ponds, T. straiata BBRR1 produced 0.95 ± 0.06 g L-1 biomass, 19% lipids, 28% proteins and 21% carbohydrates in an modified CFTRI I medium. The fatty acids profile of T. straiata Butcher BBRR1showed the presence of 33.14 % Palmitic acid, 22.64% 11- Octadecenoic acid and 21.94% Heptadecanoic acid. Since T. straiata BBRR1 can be cultivated in open ponds without a major contaminations, this species can be used as novel biomass feedstock to produce biofuels. This study may suggest the potential of T. straiata BBRR1 for biofuel production and could compete the energy demand in the future. In addition, this species contains healthful components of carotenoids, lipids and proteins, all these may provide a health benefits beyond basic nutrition.
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Life Sciences, Virology; liver stiffness; MERTK; chronic hepatitis C; cirrhosis; SNPs
Online: 19 October 2018 (12:56:19 CEST)
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Background: The myeloid-epithelial-reproductive tyrosine kinase (MERTK) is involved in hepatic steatosis, inflammation and liver fibrosis. Here we evaluated the association between the MERTK rs4374383 single nucleotide polymorphism (SNP) and liver fibrosis progression in hepatitis C virus (HCV)-infected patients. Methods: We performed a retrospective study (repeated measures design) in 208 patients who had liver stiffness measurement (LSM), which was assessed by transient elastography No patient had cirrhosis at baseline (LSM≥12.5 kPa). Results: At baseline, 53.8% were male, the median age was 47.1 years, 13.5% reported a high intake of alcohol, 10.1% were prior injection drug users, 85.3% were infected by HCV genotype 1, and 22.6% had previously failed antiviral therapy (pegylated-interferon-alpha/ribavirin). During a median follow-up of 46.6 months, 26 patients developed cirrhosis. The rs4374383 G carriers had a higher risk of increasing LSM (adjusted arithmetic mean ratio (aAMR)=1.14; p=0.006) and a higher likelihood of having an increase in LSM greater than 5 kPa (ΔLSM≥5 kPa) [adjusted odds ratio (aOR)=2.37; p=0.029], and greater than 7 kPa (ΔLSM≥7 kPa) [aOR=3.24; p=0.032], after controlling for confounding. The SNP’s association with cirrhosis progression was close to statistical significance (aOR=2.18; p=0.070). Conclusions: MERTK rs4374383 A carriers had a lower risk of liver fibrosis progression than G carriers, supporting the hypothesis that this SNP seems to have a critical role in the pathogenesis of liver disease in HCV-infected patients.
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Life Sciences, Microbiology; cholera; Maranta arundinacea L.; phytochemical; Vibrio cholerae; vibriocidal
Online: 18 October 2018 (09:43:58 CEST)
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Globally, the gastroenteritis or diarrhoea has become a more significant problem today due to infection caused by foodborne/ waterborne pathogen Vibrio cholera. In this concern, an investigation was carried out to evaluate the vibriocidal potential of the different solvent extracts of leaf and rhizome of Maranta arundinacea under in vitro condition. For this, aqueous, methanolic, ethanolic and hexane extracts of both leaf and rhizome of M. arundinacea were tested against the pre-isolated strains of Vibrio cholerae such as SPAB1, SPAB4 and SPAB5 by agar well diffusion and minimum inhibitory concentration (MIC) method. All the solvent extracts of both leaf and rhizome were found to be active against the tried strains of V. cholera however, ethanolic extract showed maximum inhibitory effect against SPAB1 strain with an inhibition zone of 26.23 ± 0.53 mm (MIC of 80.00 ± 10.06 µg/ ml) and 24.27 ± 0.12 mm (MIC of 100.00 ± 12.82 µg/ ml) in rhizome and leaf samples, respectively. Then, the effectiveness was followed in SPAB4 and SPAB5 however, it was not much more significant to that of SPAB1. Therefore, it was suggested that the rhizome and leaf extracts which proved to be potentially effective can be used as the natural alternative for the treatment of diarrhoea caused by Vibrio infection.
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Life Sciences, Virology; cytomegalovirus; HCMV; deguelin; ganciclovir
Online: 18 October 2018 (06:49:15 CEST)
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Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus, for which there is no vaccine or cure. This viral infection, once acquired, is life-long, residing latently in hematopoietic cells. However, latently infected individuals with weakened immune systems often undergo HCMV reactivation, which can cause serious complications in immunosuppressed and immunocompromised patients. Current anti-viral therapies target late stages of viral replication, and are often met with therapeutic resistance, necessitating the development of novel therapeutics. In this current study, we identified a naturally occurring flavonoid compound, deguelin, which inhibits HCMV lytic replication. Our findings reveal that nanomolar concentrations of deguelin significantly suppress the production of infectious virus. Further, we show that deguelin inhibits the lytic cycle during the phase of the replication cycle consistent with early (E) gene and protein expression. Importantly, our data reveal that deguelin inhibits replication of a ganciclovir-resistant strain of HCMV. Together, our findings identify a novel, naturally occurring compound that may prove useful in the treatment of HCMV replication.
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Life Sciences, Other; food labeling; portion size; RACC; NANS; Food4Me
Online: 18 October 2018 (06:09:45 CEST)
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The present study set out to explore the option of developing food portion size for nutritional labelling purposes using two European Union (EU) dietary surveys. The surveys were selected as they differed in (a) methodologies (food diary v food frequency questionnaire), (b) populations (Irish National Adult Nutrition Survey: NANS) versus a seven-country based on the pan EU study Food4Me), (c) food quantification (multiple options v, solely photographic album) and (d) duration (4 consecutive days v recent month). Using data from these studies, portion size was determined for 15 test foods, where portion size was defined as the median intake of a target food when consumed. The median values of the portion sizes derived from both the NANS and Food4Me surveys were correlated (r = 0.823; P<0.00) and the mean of the two survey data sets were compared to US values from the Recognized as Customarily Consumed (RACC) database. There was very strong agreement across all food categories between the averaged EU and the US portion size (r = 0.947; P<0.00). It is concluded that notwithstanding the variety of approaches used for dietary survey data in the EU, the present data supports using a standardized approach to food portion size quantification for food labelling in the EU.
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Life Sciences, Other; wheat; alpha-amylase/trypsin inhibitor; heterologous expression; Pichia pastoris; allergy
Online: 17 October 2018 (19:15:23 CEST)
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Although wheat is a staple food for most of human population, some of its components trigger adverse reactions. Among wheat components, the alpha-amylase/trypsin inhibitors (ATI) are important triggers of several allergies and activators of innate immunity. ATI are a group of exogenous protease inhibitors and include several polypeptides. The three ATI polypeptides named CM3, CM16 and 0.28 are considered major allergens, and might also play a role in other common wheat-related pathologies, such as Non Celiac Wheat Sensitivity and even Celiac Disease. On this basis, we pointed to obtain high amounts of them in purity and evaluating their allergenicity potential. We thus isolated the mRNA corresponding to the three ATI genes CM3, CM16 and 0.28 from 28 days post-anthesis wheat kernels and the corresponding cDNAs were used for heterologous expression in Pichia pastoris. The three purified proteins were tested in degranulation assay against human sera of patients with food allergy to wheat. A large range of degranulation values was observed for each protein according to the sera tested. All the three purified proteins CM3, CM16 and 0.28 were active as allergens because able to induce basophils degranulation on wheat allergic patients’ sera, but the highest values of β-hexosaminidase release were observed for CM3 protein.
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Life Sciences, Biotechnology; mini-bioreactors; parallelization; automation; digitalization; multivariate analysis; dynamic processes
Online: 17 October 2018 (08:19:46 CEST)
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Mini-bioreactor systems enabling automatized operation of numerous parallel cultivations have been used to accelerate and optimize bioprocess development. As implementation of fed-batch conditions, multiple options of process control and sample analysis are possible, these systems represent valuable screening tools for large-scale production. However, the dynamic behavior of cultivations has not yet been considered regarding data evaluation and decision making during high-throughput screening in mini-bioreactors. In this study, the characterization of Saccharomyces cerevisiae AH22 secreting recombinant endopolygalacturonase is performed in 48 parallel fed-batch cultivations regarding 16 experimental conditions. Automated parallel process control, frequent sampling and analysis were implemented. Data-driven multivariate methods were developed to allow for fast, automated decision making as well as online predictive data analysis regarding endopolygalacturonase production. Using dynamic process information, a cultivation with abnormal behavior could be detected by principal component analysis as well as two clusters of similarly behaving cultivations, later classified according to the feeding rate. By decision tree analysis, cultivation conditions leading to an optimal recombinant product formation could be identified automatically. The developed method is easily adaptable and suitable for automatized process development reducing the experimental times and costs.
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Life Sciences, Biophysics; Metalloenzymes; Spectroscopy; Small Molecules
Online: 16 October 2018 (18:54:25 CEST)
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[NiFe]-hydrogenases are gas-processing metalloenzymes that catalyze the conversion of dihydrogen (H2) to protons and electrons in a broad range of microorganisms. Within the framework of green chemistry, the molecular proceedings of biological hydrogen turnover inspired the design of novel catalytic compounds for H2 generation. The bidirectional “O2-sensitive” [NiFe]-hydrogenase from Escherichia coli HYD-2 has recently been crystallized; however, a systematic infrared characterization in the presence of natural reactants is not available yet. In this study, we analyze HYD-2 from E. coli by in situ ATR FTIR spectroscopy under quantitative gas control. We provide an experimental assignment of all catalytically relevant redox intermediates alongside the O2- and CO-inhibited cofactor species. Furthermore, the reactivity and mutual competition between H2, O2, and CO was probed in real time, which lays the foundation for a comparison with other enzymes, e.g., “O2-tolerant” [NiFe]-hydrogenases. Surprisingly, only Ni-B was observed in the presence of O2 with no indications for the “unready” Ni-A state. The presented work proves the capabilities of in situ ATR FTIR spectroscopy as an efficient and powerful technique for the analysis of biological macromolecules and enzymatic small molecule catalysis.
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Life Sciences, Immunology; immunity; leukocyte; lymphocyte; flow cytometry; glucose; exercise
Online: 16 October 2018 (10:59:44 CEST)
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Using a randomized, crossover approach, cyclists (N = 20, overnight fasted) engaged in three 75-km time trials while ingesting water (WAT) or carbohydrate (0.2 g/kg every 15 minutes) from bananas (BAN) or a 6% sugar beverage (SUG). Blood samples were collected pre-exercise and 0 h-, 1.5 h-, and 21 h-post-exercise, and analyzed for NK cytotoxicity activity (NKCA) using pure NK cell populations. The two carbohydrate trials (BAN, SUG) compared to WAT were associated with higher post-exercise glucose, and lower cortisol, total blood leukocyte, neutrophil, and NK cell counts (interaction effects, P < 0.001). The immediate post-exercise increase in NK cell counts was higher in WAT (78%) compared to BAN (32%) and SUG (15%) trials (P ≤ 0.017). The 1.5 h post-exercise decrease in NK cell counts did not differ after WAT (−46%), BAN (−46%), and SUG (−51%) trials. The pattern of change in post-exercise NKCA differed between trials (P < 0.001). The 1.5 h post-exercise decreases in NKCA were 23%, 29%, and 33% in the WAT, BAN, and SUG trials, respectively, but trial contrasts did not differ significantly. Carbohydrate ingestion from BAN or SUG attenuated immediate-post-exercise increases in leukocyte, neutrophil, and NK cell counts, but did not counter the 1.5-h decreases in NK cell counts and NKCA.
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Life Sciences, Biotechnology; schistosomiasis; vaccine; Sm14; FABP
Online: 16 October 2018 (07:02:00 CEST)
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Schistosomiasis, a disease historically associated with poverty, lack of sanitation and social inequalities, is a chronic, debilitating parasitic infection, affecting hundreds of millions of people in endemic countries. Although schistosomiasis control approach has shown that chemotherapy is capable of reducing morbidity in humans, rapid re-infection is a reminder that the impact of drug treatment on transmission control or elimination initiatives is marginal. In addition, and regardless of more than two decades of well-executed control activities based on large-scale chemotherapy, the disease is expanding in many areas including Brazil. The development of the Sm14/GLA-SE schistosomiasis vaccine is an emblematic open knowledge innovation that has successfully completed Phase I and Phase IIa clinical trials, with Phase II/III trials underway in the African continent and to be followed in Brazil. Discovery and experimental phases were long term achievements leading to a robust collection of data that are strongly supporting the presently ongoing Clinical Phase. This paper reviews the development of the Sm14 vaccine formulated with GLA-SE (Glucopyranosyl Lipid A), from the earlier experimental developments to clinical trials including the recent status of Phase II studies.
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Life Sciences, Molecular Biology; microRNA; mouth neoplasms; expression profile; microarray analysis.
Online: 15 October 2018 (19:59:55 CEST)
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MicroRNAs are small non-coding RNAs that are implicated in several physiological processes such as cell development, proliferation, differentiation, apoptosis, immune response and angiogenesis. In the last couple of decades, several studies on miRNA profiling in OSCC have tried to associate miRNAs with clinical characteristics such as relapse, metastasis, and survival, however, the results have been found to vary considerably, sometimes even being contradictory. The main objective of our study was to analyse and verify miRNA expression in oral squamous cell carcinoma in a Spanish population. Second, we attempted to associate the identified deregulated miRNAs with molecular pathways. 8 Oral Squamous Cell Carcinoma patients and 8 healthy control samples were analysed by a microarray Affymetrix® miRNA 4.1 array plate and validated with 8 more cases using RT-qPCR. Deregulated miRNAs were studied using Diana Tools miRPath 3.0 to associate miRNA targets with molecular pathways. Microarray analysis identified 80 deregulated miRNAs (35 over-expressed and 45 under-expressed). Only miR-497-5p and miR-4417 maintained its deregulated expression after validation with qPCR. Among the molecular pathways in which deregulated miRNAs could be implicated, the most statistically significant pathway was ‘proteoglycans in cancer’. No relationship was found between miR-497-5p or miR-4417 expression and clinical or pathological parameters except of nodular affectation (high miR-4417 expression in patients with nodular affectation, p = 0.035) and radiotherapy (diminished miR-497-5p expression in patients who needed radiotherapy, p = 0.05). We have verified the altered expression of miR-497-5p and miR-4417 in Oral Squamous Cell Carcinoma samples and related the deregulated miRNAs with the ‘proteoglycans in cancer’ pathway.
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Life Sciences, Molecular Biology; protein dynamics; coarse-grained simulation; Monte-Carlo dynamics; structural flexibility; large-scale dynamics; elastic network model;
Online: 15 October 2018 (19:10:57 CEST)
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Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this mini-review, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions and, on other hand, highly simplified structure-based Elastic Network Models of protein flexibility. In contrast to classical Molecular Dynamics the modeling strategies discussed here allow quite accurate modeling of much larger systems and longer time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.
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Life Sciences, Microbiology; Bifidobacterium breve; probiotics; pediatrics; therapeutic microbiology
Online: 15 October 2018 (19:03:26 CEST)
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The human intestinal microbiota, establishing a symbiotic relationship with the host, plays a significant role for the human health. It is also well known that a disease status is frequently characterized by a dysbiotic condition of the gut. A probiotic treatment can represent an alternative therapy for enteric disorders and human pathologies not apparently linked to the gut environment. Among bifidobacteria, strains of the species Bifidobacterium breve are widely used in pediatrics. B. breve is the dominant species in the gut of breast-fed infants and it has also been isolated from human milk. It has antimicrobial activity against human pathogens, it does not possess transmissible antibiotic resistance traits, it is not cytotoxic and it has immuno-stimulating abilities. This review describes the applications of B. breve strains mainly for the prevention/treatment of pediatric pathologies. The target pathologies range from widespread gut diseases, including diarrhea and infant colics, to celiac disease, obesity, allergic and neurological disorders. Moreover, B. breve strains are used for the prevention of side infections in pre-term newborns and during antibiotic treatments or chemotherapy. With this documentation, we hope to increase knowledge on this species to boost the interest in the emerging discipline known as “therapeutic microbiology”.
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Life Sciences, Other; hepatitis B virus (HBV); cccDNA; basal core promoter; X promoter; single nucleotide polymorphisms; logo analyses; genotype alignments
Online: 15 October 2018 (15:03:06 CEST)
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Over 250 million people are infected chronically with hepatitis B virus (HBV), the leading cause of liver cancer worldwide. HBV persists due in part to its compact, stable minichromosome, the covalently-closed, circular DNA (cccDNA), which resides in the hepatocytes’ nuclei. Current therapies target downstream replication products, however, a true virological cure will require targeting the cccDNA. Finding targets on such a small, compact genome is challenging. For HBV, to remain replication-competent, it needs to maintain nucleotide fidelity in key regions, such as the promoter regions, to ensure that it can continue to utilize the necessary host proteins. HBVdb (HBV database) is a repository of HBV sequences spanning all genotypes (A-H) amplified from clinical samples, and hence implying an extensive collection of replication-competent viruses. Here, we analyzed the HBV sequences from HBVdb using bioinformatics tools to comprehensively assess the HBV core and X promoter regions amongst the nearly 70,000 HBV sequences for highly-conserved nucleotides and variant frequencies. Notably, there is a high degree of nucleotide conservation within specific segments of these promoter regions highlighting their importance in potential host protein-viral interactions and thus the virus’ viability. Such findings may have key implications for designing antivirals to target these areas.
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Life Sciences, Biophysics; lines; brain; topology; curvature; Dickinsonia; fMRI
Online: 15 October 2018 (12:36:18 CEST)
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Geometry deals both with analogical thinking and physical/biological observables. Naïve, common-sense descriptions of objects’ shapes and systems’ trajectories in geometric phase spaces may help experimental investigation. For example, very different biological dynamics, as the developmental growth patterns of the oldest known animal (the extinct Dickinsonia) and the human brain electric oscillations, display a striking analogy: when encompassed in abstract geometric spaces, their paths describe the same changes in curvature: from convex, to flat, to concave and vice versa. This dynamical behavior, anticipated by Nicholas de Cusa in his analogical account of “coincidentia oppositorum” (1440), helps to describe widespread biological paths in the manageable terms of concave, flat and convex curves on donut-like structures. Every trajectory taking place on such toroidal manifolds can be located, through a topological technique called Hopf fibration, into a four-dimensional space. We discuss how the correlation between Hopf fibration and Navier-Stokes equations allows us to treat the above-mentioned biological and neuroscientific curved paths in terms of flows taking place into a viscous fluid medium that can be experimentally assessed and quantified.
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Life Sciences, Biotechnology; PCR; recombination; cloning; engineering; biotechnology; synthetic biology; synthetic nucleotide; plasmids; repository; minimalism; Escherichia coli; mutagenesis
Online: 15 October 2018 (11:22:22 CEST)
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Minimal plasmids play an essential role in many intermediate steps in molecular biology. They can for example be used to assemble building blocks in synthetic biology or be used as intermediate cloning plasmids that are ideal for PCR-based mutagenesis methods. A small backbone also opens up for additional unique restriction enzyme cloning sites. Here we describe the generation of pICOz, a 1185 bp fully functional high-copy cloning plasmid with an extended multiple cloning site (MCS). To our knowledge, this is the smallest high-copy cloning vector ever described.
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Life Sciences, Molecular Biology; red yeast rice; berberis aristate; morus alba; PCSK9
Online: 15 October 2018 (09:49:55 CEST)
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Proprotein convertase subtilisin/kexin type 9 (PCSK9) is the key regulator of low-density lipoprotein cholesterol (LDL-C) plasma levels. We previously observed that treatment of dyslipidemic subjects with nutraceutical combination containing red yeast rice (monacolin K 3.3 mg), Berberis aristata cortex extract (Berberine 531.25 mg) and Morus alba leaves extract (1-deoxynojirimycin 4 mg) (LopiGLIK®) did not alter the plasma PCSK9 levels. Thus, the aim of the present study was to investigate the effect of these three components on PCSK9 expression in HepG2 cell line in relationship to their effects on LDL-C cellular uptake. HepG2 cell line were incubated with Berberis aristata cortex extract (BCE), red yeast rice (RYR) and Morus alba leaves extract (MLE) alone or in combination for 24 h. RYR (50 µg/mL) increased PCSK9 protein expression (WB and ELISA assays), PCSK9 mRNA and its promoter activity. BCE (40 µg/mL) reduced PCSK9 expression, mRNA levels and promoter activity. MLE determined a concentration-dependent inhibition of PCSK9 at mRNA and protein levels, with a maximal reduction at 1 mg/mL; no significant changes in PCSK9 promoter activity were found. MLE also downregulates the expression of fatty acid synthase and HMG-CoA reductase mRNA levels. The combination of RYR, BCE and MLE reduced PCSK9 at mRNA, protein, and promoter activity. Finally, this combination induced the LDL receptor and LDL-C uptake by HepG2 cells. In conclusion, the positive effect of MLE on PCSK9 supports the rational of using this nutraceutical combination to control hyperlipidemic conditions.
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Life Sciences, Other; exercise; polyphenol; metabolite; Hippurate; intestinal tract; colon
Online: 15 October 2018 (09:39:26 CEST)
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Using a randomized, double-blinded, placebo-controlled, parallel group design, this investigation determined if the combination of 2-weeks flavonoid supplementation (329 mg/day, quercetin, anthocyanins, flavan-3-ols mixture) and a 45-minute walking bout (62.2±0.9% VO2max) enhanced the translocation of gut-derived phenolics into circulation in a group of walkers (N = 77). The walkers (flavonoid, placebo groups) were randomized to either sit or walk briskly on treadmills for 45 minutes (thus four groups: placebo-sit, placebo-walk, flavonoid-sit, flavonoid-walk). A comparator group of runners (N = 19) ingested a double flavonoid dose for 2 weeks (658 mg/day) and ran for 2.5 h (69.2±1.2% VO2max). Four blood samples were collected (pre- and post-supplementation, immediately-post- and 24-h post-exercise/rest). Of the 76 metabolites detected in this targeted analysis, 15 increased after the 2.5-h run, and when grouped were also elevated post-exercise (versus placebo-sit) for the placebo- and flavonoid-walking groups (P < 0.05). A secondary analysis showed that pre-study plasma concentrations of gut-derived phenolics in the runners were 40% higher compared to walkers (P = 0.031). These data indicate that acute exercise bouts (brisk walking, intensive running) are linked to an increased translocation of gut-derived phenolics into circulation, an effect that is amplified when combined with a 2-week period of increased flavonoid intake or chronic training as a runner.
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Life Sciences, Other; Autism; polychlorinated biphenyls; environmental chemicals; children; neurodevelopment
Online: 15 October 2018 (08:23:08 CEST)
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Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social communication and repetitive or stereotypic behaviours. In utero exposure to environmental chemicals, such as polychlorinated biphenyls (PCBs), may play a role in the etiology of ASD. We examined the relation between plasma PCB concentrations measured during pregnancy and autistic behaviours in a subset of children aged 3–4 years old in the Maternal-Infant Research on Environmental Chemicals (MIREC) Study, a pregnancy and birth cohort of 546 mother-infant pairs from Canada (enrolled: 2008-2011). We quantified the concentrations of 6 PCB congeners that were detected in >40% of plasma samples collected during the 1st trimester. At age 3–4 years, caregivers completed the Social Responsiveness Scale-2 (SRS), a valid and reliable measure of children’s reciprocal social and repetitive behaviors and restricted interests. We examined SRS scores as both a continuous and binary outcome, and we calculated Bayesian predictive odds ratios for more autistic behaviours based on a latent variable model for SRS scores >60. We found no association between plasma PCB concentrations and autistic behavior, However, we found small and imprecise increases in the mean SRS score and odds of more autistic behaviour for the highest quartile of plasma PCB concentrations compared with the lowest quartile; for instance, an average increase of 1.1 [95%PCI: −0.5, 2.6] in the mean SRS (exposure contrast 4th versus 1st quartile) for PCB138 translated to an odds ratio of 1.6 [95%PCI: 1.0, 2.5]. Our findings illustrate the importance of measuring associations between PCBs and autistic behaviour on both continuous and binary scales.
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Life Sciences, Other; alpha diversity; beta diversity; floristic arrangement; geological landscapes; geomorphology; Ecuador; mountain forests
Online: 15 October 2018 (08:19:16 CEST)
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1) Background: Neotropical montane forests represent one of the most diverse ecosystems; however, they are also the most threatened for deforestation. Our main goal is to evaluate the change in Basal Area (BA), Density and Species Composition of montane forests in the southern Ecuador and to determine the influence on some critical ecological and geomorphological factors. 2) Methods: One hundred thirty-two temporary plots of 400 m2 each were installed; we identified and measured all trees> 10 cm DBH. We modeled species diversity (Fisher’s alpha) change in relation to climatic, elevational and geomorphological gradients with GLM and Kruskall-Wallis analyses. The change in composition was determined using Cluster Analyses (BIOENV analysis followed by a LINKTREE procedure). Non-metric multidimensional scaling (NMDS) was used to analyze changes across climatic and geomorphological gradients. Finally, we used SIMPER analysis to identify the species that contributed most to the dissimilarity among the different elevations. 3) Results: Formation of floristic groups was influenced by altitude, temperature and Isothermality; physiographic province, great landscape, geological landscape and lithology. Plots located in low hills have higher alpha diversity with respect to the high hills and dissected mountains. 4) Conclusions: The elevation is first hierarchical factor responsible of the division of structural and floristic groups. Plots located on the whitish tuff have a higher alpha value diversity compared with plots in andesitic tuffs. Wettest quarter (> 839 mm) and Isothermality (> 90.5) are the climatic factors that driven de floristic divisions.
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Life Sciences, Immunology; antibody; network; sequence; structure; clonality; B cell; systems biology; quantitative biology
Online: 12 October 2018 (19:01:13 CEST)
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Based on the key molecule of humoral adaptive immunity, the antibody, evolution of the system comprises molecular genetic, cell biologic and immunologic mechanisms, and as a network the system is likely governed and can be characterized by physical rules as well. While deep sequencing can provide vast amounts of data related primarily to clonal relationships, functional interpretation of such data is hampered by the inherent limitations of converting sequence to structure to function. In this paper a novel model of structural interaction space, termed radial adjustment of system resolution, or RADARS, is proposed. The model is based on the radial growth of resolution of structural recognition, corresponding to increasing affinity of immune reactivity, and the virtual infinity of directions of growth, corresponding to the ability to respond to almost any molecular structure. Levels of interaction strength appear as shells of the sphere representing the system. B-cell development and immune responses can be readily interpreted in the model and quantitative properties of the antibody network can be inferred from the physical properties of a quasi-spherical system growing multi-radially. The system is described by double-Pareto distribution, sampling the lognormally distributed equilibrium constants at a rate of phi square. Finally, general strategies for merging antibody sequence space into structural space are outlined.
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Life Sciences, Cell & Developmental Biology; 3D models; cartilage; chondrocytes; osteoarthritis (OA)
Online: 12 October 2018 (14:19:01 CEST)
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Osteoarthritis (OA) is a joint disease involving cartilage degeneration. This study aimed to compare properties of chondrocytes from less-affected (LA-Cartilage) and severely-affected (SA-Cartilage) of human OA articular cartilage. Based on Dougados classification, OA cartilage was classified into two groups; less-affected (Grade 0–1) and severely-affected (Grade 2–3). Chondrocytes from each group were cultured until passage (P) 4. Growth, migration, stem cell properties and chondrogenic properties under normal and inflammatory conditions, and the formation of in vitro 3D cartilage tissues were compared between groups. The growth and migratory properties of LA-chondrocytes and SA-chondrocytes were similar, except that the migration rate of SA-chondrocytes was significantly higher at P0 compared to LA-chondrocytes. Both LA-chondrocytes and SA-chondrocytes expressed mesenchymal stem cell markers and tri-lineage differentiation, but the expression of stem cell markers decreased significantly with increasing passage number. Exposure to inflammatory conditions induced distinct morphological changes and significant increases in expression of SOX9 at P4 and MMP3 at P1 for LA-chondrocytes. LA-chondrocytes and SA-chondrocytes able to develop into in vitro 3D constructs, but SA-chondrocytes exhibited superior cartilage-like properties. Chondrocytes from both less- and severely-affected regions are suitable to be used in clinical applications, however, chondrocytes from severely-affected regions could be a more favorable cell source.
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Life Sciences, Genetics; Turner’s syndrome; chromosomal aneuploidy; amniotic fluid; cell-free RNA; ingenuity pathway analysis
Online: 12 October 2018 (14:07:26 CEST)
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Genetic disorders are quite a major topic of discussion and debate in the recent world of biological sciences. Turner’s syndrome is one such disorder caused by a chromosome aneuploidy and it has characteristic symptoms in the patient or the affected individual. The amniotic fluid is a complex biological material found in the amniotic sac of pregnant women and they can provide valuable knowledge and understanding of the pathogenesis of this particular chromosomal abnormality. In this study, global gene expression analysis of cell-free RNA in amniotic fluid supernatant was used to detect genes/organ systems which may be significant in the pathophysiology of Turner’s syndrome. The cell-free RNA from the amniotic fluid of five mid-trimester Turner’s syndrome fetuses and five euploid female fetuses matched for age of gestation were extracted, amplified and hybridized onto Affymetrix U33 Plus 2.0. array. The paired t-test was used to identify the significantly differentially regulated genes. Biological interpretation was conducted using ingenuity pathway analysis and BioGPS gene expression atlas. Of the genes, XIST was especially downregulated and SHOX was not expressed differentially. One of the most highly represented organ systems was the hematologic/immune system, differentiating the transcriptome of Turner’s syndrome from other chromosomal aneuploidies that are discussed in this area of science. The differences in the transcriptome of the Turner’s syndrome are due to genome-wide dysregulation. The hematologic/immune system differences are significant in early-onset autoimmune dysfunction. There are other genes which have been identified that are associated with the cardiovascular and the skeletal system, as these are often seen to be affected in the female patients with turner’s syndrome. Hopefully, such knowledge gained from this study will help us to understand the deeper mechanisms of this disorder and the possible treatments of this disease.
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Life Sciences, Microbiology; catechol 1,2-dioxygenase; homogentisate 1,2-dioxygenase; Pseudomonas chlororaphis; Pseudomonas chlororaphis strain UFB2
Online: 12 October 2018 (05:45:41 CEST)
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Catechol dioxygenases in microorganisms cleave catechol into cis-cis-muconic acid or 2-hydroxymuconic semialdehyde via the ortho- or meta-pathway, respectively. The aim of the study was to purify, characterize and predict template-based three-dimensional structure of catechol 1,2-dioxygenase (C12O) from indigenous Pseudomonas chlororaphis strain UFB2 (PcUFB2). Preliminary studies showed that PcUFB2 could degrade 40 ppm of 2,4-dichlorophenol (2,4-DCP). The crude cell extract showed 10.34 U/mL of C12O activity with a specific activity of 2.23 U/mg of protein. A 35 kDa protein was purified to 1.5-fold with total yield of 13.02 % by applying anion exchange and gel filtration chromatography. The enzyme was optimally active at pH 7.5 and temperature 30 °C. The Lineweaver-Burk plot showed the vmax and Km values of 16.67 µM/min and 35.76 µM, respectively. ES-MS spectra of tryptic digested SDS-PAGE band and bioinformatics studies revealed that C12O share 81% homology to homogentisate 1,2-dioxygenase reported in other Pseudomonas chlororaphis strains. Characterization and optimization of C12O activity can assist in understanding the 2,4-DCP metabolic pathway in PcUFB2 and its possible application in bioremediation strategies.
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Life Sciences, Biochemistry; heart; ursodeoxycholic acid; cardioprotection; signaling
Online: 11 October 2018 (10:35:28 CEST)
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Bile acids (BA) are classically known as an agent important in lipid absorption and cholesterol metabolism. Nowadays, BAs have been found to be involved in various cellular signaling pathways such as protein kinase cascades, cyclic AMP (cAMP) synthesis and calcium mobilization. In addition, they have also been shown to regulate glucose and energy homeostasis. Bile acids are ligands for several nuclear hormone receptors, including FXR. Recently, muscarinic receptor and TGR5, G-protein-coupled receptor (GPCR), have been suggested to play a role in bile acid activity which is independent of nuclear hormone receptors. Moreover, BAs have also been studied in other GPCR associated pathways, namely sphingosine-1-posphate and glucagon receptor. Hydrophobic bile acids have been proven to affect heart rate and its contraction. Elevated bile acids are associated with arrhythmias in adults and fetal heart. Altered ratios of primary and secondary bile acid are reported in chronic heart failure patients. Meanwhile in patients with liver cirrhosis, cardiac dysfunction has been strongly linked to the increase of serum bile acid concentrations. In contrast, the most hydrophilic BA known as ursodeoxycholic acid has been found beneficial in improving peripheral blood flow in chronic heart failure patients and protecting heart against reperfusion injury.
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Life Sciences, Molecular Biology; Boswellia serrata Roxb.; Curcuma longa L.; intestinal bowel diseases (IBD); Caco-2; PBMC; HMC-1.1; mast cells; cytokines; trans epithelial electrical resistance (TEER); reactive oxygen species (ROS)
Online: 11 October 2018 (07:22:37 CEST)
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Inflammatory bowel diseases, which consist of chronic inflammatory conditions of the colon and the small intestine, are considered a global disease of our modern society. Recently, the interest toward the use of herbal therapies for the management of inflammatory bowel diseases has increased because of their effectiveness and favorable safety profile, compared to conventional drugs. Boswellia serrata Roxb. and Curcuma longa L. are amongst the most promising herbal drugs, however, their clinical use in inflammatory bowel diseases is limited and little is known on their mechanism of action. The aim of this work was to investigate the effects of two phytochemically characterized extracts of B. serrata and C. longa in an in vitro model of intestinal inflammation. Their impact on cytokine release and reactive oxygen species production, as well as the maintenance of the intestinal barrier function and on intestinal mucosa immune cells infiltration, has been evaluated. The extracts showed a good protective effect on the intestinal epithelium at 1 µg/ml, with TEER values increasing by approximately 1.5 fold, compared to LPS-stimulated cells. C. longa showed an anti-inflammatory mechanism of action, reducing IL-8, TNF-α and IL-6 production by approximately 30%, 25% and 40%, respectively, compared to the inflammatory stimuli. B. serrata action was linked to its antioxidant effect, with ROS production being reduced by 25%, compared to H2O2-stimulated Caco-2 cells. C. longa and B. serrata resulted to be promising agents for the management of inflammatory bowel diseases by modulating in vitro parameters which have been identified in the clinical conditions.
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Life Sciences, Microbiology; bronchiectasis; FACED score; microbiome
Online: 10 October 2018 (10:14:24 CEST)
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The application of 16S rRNA gene pyrosequencing has expanded our knowledge about the respiratory tract microbiome originally obtained using conventional, culture-based methods. In this study, we employed DNA-based molecular techniques for examining the sputum microbiome in bronchiectasis patients in relation to disease severity. Of 63 study subjects, 42 had mild and 21 had moderate or severe bronchiectasis, which was classified by calculating the FACED score based on FEV1 (forced expiratory volume in 1 s, %) (F, 0–2 points), age (A, 0–2 points), chronic colonization by Pseudomonas aeruginosa (C, 0-1 point), radiographic extension (E, 0–1 point), and dyspnoea (D, 0–1 point). Bronchiectasis was defined as mild at 0–2 points, moderate at 3–4 points, and severe at 5–7 points. The mean age was 68.0 ± 9.3 years; 33 patients were women. Haemophilus (p=0.005) and Rothia (p=0.043) were significantly more abundant in the mild bronchiectasis group, whereas Pseudomonas (p=0.031) was significantly more abundant in the moderate or severe group. However, the alpha or beta diversity did not significantly differ among sputum microbiota, i.e. the same dominating genera were found in all samples. Further large-scale studies are needed to investigate the sputum microbiome in bronchiectasis.
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Life Sciences, Other; hepcidin, iron deficiency anemia, iron dextran, neonatal period, pig, supplementation
Online: 9 October 2018 (17:34:13 CEST)
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In pigs, iron deficiency anemia (IDA) is the most prevalent deficiency disorder during the early postnatal period frequently developing into a critical illness. Meanwhile, in humans, only low-birth-weight infants, including premature infants are especially susceptible to developing IDA. In both human and pig neonates, the initial cause of IDA is low birth iron stores. In piglets this shortage of stored iron results mainly from genetic selection over the past few decades for large litter size and high birth weight. In consequence, pregnant sows cannot provide sufficient amount of iron to the increasing number of developing fetuses. Supplementation with iron is a common practice for the treatment of IDA in piglets. For decades, the preferred procedure for delivering iron supplements during early life stages has been through the intramuscular injection of large amount of iron dextran. However, this relatively simple therapy, which in general, efficiently corrects IDA, may generate toxic effects, and by inducing hepcidin expression, may decrease bioavailability of supplemental iron. New iron supplements are considered now with the aim to combine improvement of hematological status, blunting hepcidin expression, and minimizing toxicity of the administered iron. We propose that iron-deficient piglets constitute a convenient animal model for performing pre-clinical studies with iron supplements.
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Life Sciences, Other; Authorship contributions, Authorship Score, Authorship Conflicts, First Author, Decision Making, Bibliometry
Online: 9 October 2018 (11:45:12 CEST)
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Disputes on authorships or the order of authors on publications are among the most common conflicts in science, particularly where multi-author papers have become the norm. Here, I propose an adaptable and generalizable method to rationalize and democratize decisions about authorships, which can be applied in diverse scientific areas. In the process, the authors of a manuscript collect, discuss, score, and weight their contributions to the final manuscript. The decision process is assisted by a simple spreadsheet-based “authorship matrix”, which helps to break down the complexity of different contributions and their importance. The matrix generates a score s describing the percentage of the author’s total contributions and can be used to determine authorship and their order. The transparency and simplicity score s can reduce conflicts and thus increase productivity in collaborations.
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Life Sciences, Biochemistry; gelatine; marine; by-products; fish; industry; extraction
Online: 9 October 2018 (07:54:23 CEST)
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In recent years, demand for consumption of marine foods, and especially fish, has substantially increased worldwide. The majority of collagen available is sourced from mammalian-derived products. Although fish derived gelatine is a viable alternative to mammalian sourced gelatine, there are some challenges related to the use of fish gelatine including odour, colour, gelling and film forming properties as well as consistency in gelatine amino acid composition. Chemicals used for pre-treatment, as well as extraction conditions such as temperature and time, can influence the length of polypeptide chains that result and the functional properties of the gelatine. Compared to mammalian sources, gelatines derived from fish show notable differences in physical and chemical properties, and great care should be paid to optimization of the production process in order to obtain a product with the best properties for intended applications. The focus of this review is to explore the feasibility of producing gelatine sourced from marine processing by-products using different pre-treatment and extraction strategies with the aim of improving the techno-functional properties of the final product and improving the clean-label status of gelatines. The bioactivities of gelatine hydrolysates are also discussed.
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Life Sciences, Endocrinology & Metabolomics; FTO; liver; gluconeogenesis; lipogenesis; glucose; insulin; type 2 diabetes; non-alcoholic fatty liver disease
Online: 9 October 2018 (05:52:49 CEST)
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Common genetic variants of the fat mass and obesity associated (FTO) gene are strongly associated with obesity and type 2 diabetes. FTO is ubiquitously expressed, but appears to have tissue-specific roles. Earlier studies have focused on the role of hypothlamic FTO in the regulation of metabolism. However, it appears that FTO plays a role in the regulation of metabolism in a tissue-specific manner. Recent studies suggest that expression of hepatic FTO is regulated by metabolic signals such as nutrients and hormones and altered FTO levels in liver affects glucose and lipid metabolism. This review outlines recent findings on hepatic FTO in the regulation of metabolism, with particular focus on hepatic glucose and lipid metabolism. It is proposed that abnormal activity of hepatic signaling pathways involving FTO links metabolic impairments such as obesity, type 2 diabetes and nonalcoholic fatty liver disease (NAFLD). Therefore, a better understanding of these pathways may lead to therapeutic approaches to treat these metabolic diseases by targeting hepatic FTO. The overall goal of this review is to place FTO within the context of hepatic regulation of metabolism.
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Life Sciences, Virology; Hepatitis C virus, Genotyping, Mixed infection, Fluorescence melting curve analysis, Viral Load, Quantification
Online: 8 October 2018 (18:08:48 CEST)
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Hepatitis-C is one of the most common viral diseases caused by hepatitis C virus (HCV). It is responsible for millions of deaths each year in the developing world. The common dissemination paths of HCV include the use of contaminated water and transfusion of infected blood. Control of this virus has become a challenge for scientists and health professionals due to its versatility and adaptability in different host environments. Along with other problems, lack of efficient diagnosis, quantification and genotyping of viral strains are the major hindrances in a management of this notorious epidemic. The knowledge of HCV genotype and an amount of virus in patient’s blood are pre-requisites to determine the duration and method of treatment. In this review, we discuss the implications of HCV molecular diagnostic methods and their clinical applications. We conclude that while, several commercial and home-brewed methods are available for this purpose, and there is a visible vacuum for cost effective, robust, sensitive assays that can detect multiple viral genotypes in a single reaction. We are of the view that the level of sensitivity offered by Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) technique is unequivocal as compared to other techniques. Therefore, researchers may explore further possibilities using this technique in the management of HCV.
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Life Sciences, Cell & Developmental Biology; Nectin-4; metastasis; angiogenesis; circulating tumor cells; cancer relapse
Online: 8 October 2018 (17:52:03 CEST)
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In the present study, we have systematically examined the clinical significance of Nectin-4 (encoded by the PVRL-4 gene), a marker for breast cancer stem cells (CSCs), in cancer metastasis and angiogenesis using a variety of human specimens, including invasive duct carcinoma (IDC) with multiple grades, several types of primary tumors to local and distant relapses, lymph node metastases and circulating tumor cells (CTCs). Nectin-4 was overexpressed in more than 92% of samples with 65.2% Nectin-4 positive cells. The level of expression was increased with increasing tumor grade (GI-III) and size (T1-4) of IDC specimens. More induction of Nectin-4 was noted in relapsed samples from a variety of tumors (colon, tongue, liver, kidney, ovary, buccal mucosa) in comparison to primary tumors, while paired adjacent normal tissues do not express any Nectin-4. A high expression of Nectin-4 along with other representative markers in CTCs and lymph node metastasis was also observed in cancer specimens. An increased level of Nectin-4 along with representative metastatic (CD-44, Sca1, ALDH1, Nanog) and angiogenic (Ang-I, Ang-II, VEGF) markers was noted in metastatic tumors (local and distant) in comparison to primary tumors that were correlated with different grades of tumor progression. In addition, greater expression of Nectin-4 was observed in secondary tumors (distant metastasis, e.g., breast to liver or stomach to gallbladder) in comparison to primary tumors. Nectin-4 was overexpressed at all stages of metastasis and angiogenesis, thus appearing to play a major role in tumor relapse through the PI3K-Akt-NFκβ pathway.
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Life Sciences, Endocrinology & Metabolomics; Alzheimer’s disease; Diabetes; Diet control diet; AMPK; Tau hyperphosphorylation
Online: 8 October 2018 (17:32:11 CEST)
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Alzheimer’s disease (AD) is a chronic neurodegenerative disease, and typical pathologic findings include abnormally hyperphosphorylated tau aggregation and neurofibrillary tangles. Insulin resistance and hyperglycemia have been assessed as risk factors for AD development. As the maintenance of optimal blood glucose levels is an important indicator of diabetes mellitus (DM) treatment, diet control is essential. AMPK is a crucial sensor of cellular bioenergetics for controlling anabolic and catabolic metabolism. Diet restriction to achieve euglycemia can increase AMPK activity in the liver and heart. Since AMPK is a direct regulator of tau phosphorylation, we hypothesized that strict diet control to achieve euglycemia affects tau protein phosphorylation through increased AMPK activity in the hippocampus of DM rats. To confirm this hypothesis, we generated insulin-deficient DM rats by subtotal pancreatectomy. Animals were categorized into the restriction (R) group, control (C) group and ad libitum (AL) group according to the diet. We found that tau phosphorylation was significantly increased in the R group compared with the C or AL group. AMPK activity in the R group significantly increased compared to that of the C group or AL group, as expected. Furthermore, the R group showed more critical tau pathology in the hippocampus than the other groups. These results suggest that diet control to achieve euglycemia in insulin-deficient DM conditions is harmful because of the increased possibility of AD development through increased tau phosphorylation by AMPK activation in the hippocampus. We propose that not only hyperglycemia but also euglycemia, which is beneficial in DM patients, must be considered a potential risk factor for AD development, especially when euglycemia is achieved by diet control during insulin deficiency.
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Life Sciences, Biochemistry; Bale highlands; livestock; methane emissions; mixed farming
Online: 5 October 2018 (17:39:30 CEST)
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The study was conducted in the potential mixed farming areas of Bale highland to estimate livestock methane emissions. Using multi-stage purposive sampling, 156 households of the three wealth groups were selected based on their livelihood assets as described under methodology. Structured questionnaires, focus group discussions, key informants interview and field visits were the employed methods during the study. Feed nutrient balance was estimated based on the demand and supply while the livestock methane emissions were estimated according to the IPCC guidelines. Descriptive statistics and one-way ANOVA tests were used to analyze the data. Cattle were the dominant (84.25%) livestock owned by the households. The estimated enteric CH4 emission rate from mature cattle, growing cattle, sheep >1 year, sheep ≤ 1 year, horse and donkey were significantly (P<0.001) higher for the better wealth group while mature cattle (69.78%) shared the highest rate. Though, higher emission rates credited to the large number of animals in the area, cattle stay crucial to the livelihoods of the households, beside the major sources of CH4. In conclusion, the estimated CH4 emissions should be focus areas of interventions. Therefore, proper husbandry and quality feed supply and promotion of farm level livestock technologies should be practiced wisely to increase productivity and protect the environment from emissions of the livestock sector.
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Life Sciences, Virology; Nipah Virus, outbreak, inhibitors, QSAR, database, prediction algorithm
Online: 5 October 2018 (17:04:23 CEST)
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Nipah virus (NiV) is responsible to cause various outbreaks in Asian countries, with latest from Kerala state of India. Till date there is no drug available despite its urgent requirement. In the current study, we have provided a computational one-stop solution for NiV inhibitors. We have developed “anti-Nipah” web resource, which comprised of a data repository, prediction method, and data visualization modules. The database comprised of 313 (181 unique) inhibitors from different strains and outbreaks of NiV extracted from research articles and patents. However, the quantitative structure–activity relationship (QSAR) based predictors were accomplished using classification approach employing 10-fold cross validation through support vector machine with 120 (68p + 52n) inhibitors. The overall predictor showed the accuracy and Matthew’s correlation coefficient of 88.89% and 0.77 on training/testing dataset respectively. The independent validation dataset also performed equally well. The data visualization modules from chemical clustering and principal component analyses displayed the diversity in the NiV inhibitors. Therefore, our web platform would be of immense help to the researchers working in developing effective inhibitors against NiV. The user-friendly webserver is freely available on URL: http://bioinfo.imtech.res.in/manojk/antinipah/
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Life Sciences, Molecular Biology; children, immunology, miRNA, partial remission phase, type 1 diabetes
Online: 5 October 2018 (11:29:15 CEST)
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The objective of this study was to identify circulating miRNAs affected by disease duration in newly diagnosed children with type 1 diabetes. Forty children and adolescents from The Danish Remission Phase Cohort were followed with blood samples drawn at 1, 3, 6, 12 and 60 months after diagnosis. Pancreatic autoantibodies were measured at each visit. Cytokines were measured only the first year. miRNA expression profiling was performed by RT-qPCR and quantified for 179 human plasma miRNAs. The effect of disease duration was analyzed by mixed models for repeated measurements, adjusted for sex and age. Eight miRNAs (hsa-miR-10b-5p, hsa-miR-17-5p, hsa-miR-30e-5p, hsa-miR-93-5p, hsa-miR-99a-5p, hsa-miR-125b-5p, hsa-miR-423-3p and hsa-miR-497-5p) were found to significantly change expression (adjusted p-value < 0.05) with disease progression. Three pancreatic autoantibodies ICA, IA-2A, GADA65 and 4 cytokines IL-4, IL-10, IL-21, IL-22 were associated with the miRNAs at different time points. Pathway analysis revealed association with various immune-mediated signaling pathways. Eight miRNAs, involved in immunological pathways changed expression levels during the first five years after diagnosis in children with type 1 diabetes, and were associated with variations in cytokine and pancreatic antibodies, suggesting a possible effect on the immunological processes in the early phase of the disease.
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Benita Percival,
Yasan Osman,
Martin Grootveld,
Miles Gibson,
Marco Molinari,
Fereshteh Jafari,
Mark Martin,
Federico Casanova,
Melissa Mather,
Mark Edgar,
Philippe Wilson
Life Sciences, Endocrinology & Metabolomics; Metabolomics; Benchtop NMR; Biomarkers; Biomolecules; Validation; Protocol
Online: 4 October 2018 (18:23:44 CEST)
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Novel sensing technologies for liquid biopsies offer a promising prospect for the early detection of metabolic conditions through -omics techniques. Indeed, high-field NMR facilities are routinely used for metabolomics investigations on a range of biofluids in order to rapidly recognize unusual metabolic patterns in patients suffering from a range of diseases. However, these techniques are restricted by the prohibitively large size and cost of such facilities, suggesting a possible role for smaller, low-field NMR instruments in biofluid analysis. Herein we describe selected biomolecule validation on a low-field benchtop NMR spectrometer (60 MHz), and present an associated protocol for the analysis of biofluids on compact NMR instruments. We successfully detect common markers of diabetic control at low-to-medium concentrations through optimized experiments, including glucose (≤ 2.6 mmol./L) and acetone (25 μmol./L), and additionally in readily-accessible biofluids. We present a combined protocol for the analysis of these biofluids with low-field NMR spectrometers for metabolomics, and offer a perspective on the future of this technique appealing to point-of-care applications.
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Life Sciences, Other; sarcopenia; exercise; receiver operator characteristic curve; criterion referenced standards; physical fitness
Online: 4 October 2018 (15:38:58 CEST)
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This study provides a newly updated perspective of information on severely screened 21 previous studies of the various measurement methods for improving physical fitness and providing determined cutoff values from our reserved elderly human database by based on the above 21 screened precious previous studies. We thus aimed to provide scientific evidence-based information regarding physical fitness standards for developing useful prognostics, promoting and maintaining health programs for sarcopenic elderly. 21 previous studies emphasizing criterion referenced standards and receiver operator characteristic (ROC) curve analyses for improving physical fitness were screened. For predicting the prevalence of sarcopenia, the t-test, logistic regression, linear regression, ROC curve analyses and voluntary categorizations such as twentieth or sixtieth percentile classification were used. Based on these scientific evidences, we determined cutoff values from our reserved DB, and realized that 75 years for men and 70 years for women is the transitional period during which there are large declines in muscle and fat mass (p<0.01), which reflects physical function tests (p<0.01) in both genders. Using the six factors with ideal cutoff thresholds, an individual exercise program can be designed for alleviating symptoms of frailty caused by sarcopenia for the elderly.
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Life Sciences, Biotechnology; nucleotide triphosphate, label-free, K-Ras, apyrase, terbium
Online: 3 October 2018 (19:32:44 CEST)
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A new label-free molecular probe for luminescent nucleotide detection in neutral aqueous solution is presented. Phosphate-containing molecules such as nucleotides possess vital role in cell metabolism, energy economy, and signaling. Thus the monitoring of nucleotide concentration and nucleotide related enzymatic reactions is of high importance. Two component lanthanide complex formed from Tb(III) ion carrier and light harvesting antenna, readily distinguishes nucleotides containing different number of phosphates and enable direct detection of enzymatic reactions converting nucleotide triphosphate (NTP) to nucleotide di/monophosphate or the opposite. Developed sensor enables the detection of enzymatic activity with a low nanomolar sensitivity, as highlighted with K-Ras and apyrase enzymes in there hydrolysis assays performed in high throughput screening compatible 384-well plate format.
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Temitope Faleye,
Moses Olubusuyi Adewumi,
Moses Olubusuyi Adewumi,
Olayinka Oluseyi Adebowale,
Emmanuel Donbraye,
Bolaji Oluremi,
Uwem George,
Oluwadamilola A Arowolo,
Ewean Chukwuma Omoruyi ,
Maryjoy Ijeoma Ifeorah ,
Adefunke Oyewumi Oyero,
Johnson Adekunle Adeniji
Life Sciences, Virology; Bovine enterovirus, EV-E, Nigeria, Sewage, Complete Genome
Online: 3 October 2018 (16:24:49 CEST)
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We describe the draft genome of a Bovine enterovirus (EV) recovered from sewage in Nigeria. The virus replicates on both RD and L20B cell lines, but is negative for all EV screens in use by the GPEI. It contains 7,368nt, with 50.2% G+C content and an ORF with 6,525nt (2,174aa).
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Life Sciences, Other; public engagement on science, science engagement, science communication, public understanding of science, deficit model, informal STEM learning, active learning
Online: 3 October 2018 (15:09:31 CEST)
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Publicly-funded scientists have a responsibility to engage with the public on scientific information, but are lacking a standardized framework and assessment strategy to do it well. The PEPS (Public Engagement Practices for Scientists) Method is an outcomes-centered framework employing standardized pedagogical methods with quantifiable outcomes. This approach reveals that scientists often have unrealistic expectations for achieving affective learning outcomes (i.e. changing views from anti- to pro-vaccine) by solely cognitive learning strategies (i.e. supplying data). The PEPS Method can serve as a roadmap for standardized science communication assessments, complementing existing science communication training programs for the next generation of scientists.
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Life Sciences, Biotechnology; Bio-disinfection, G. latifolium, Water, Z. zanthoxyloides.
Online: 3 October 2018 (14:53:16 CEST)
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Water and sanitation facilities in sub-Saharan Africa and Africa in general are appalling and for the most part absent. Progress continues with respect to the development of plant materials as potent adsorbents, disinfectants, coagulants, flocculants, wetland species and lots more as substitutes for the dangerous chemical disinfectants.
This research presents the potential of phyto-active components of Zanthoxylum zanthoxyloides and Gongronema latifolium as effective biocides against water microbial contaminants. Dry powder of Zanthoxylum zanthoxyloides and Gongronema latifolium were extracted and prepared into different concentrations with ethyl acetate and chloroform, ranging from 25 to 500 mg/ml. These fractions were then examined for antimicrobial activities against inherent bacterial and fungal water contaminants using disc diffusion assay. Fractions were afterwards screened for phytochemical active compounds using standard methods. Crude extracts of the different plant examined selectively comprise saponins, tannins, reducing sugars, anthraquinones, flavonoids, terpenoids, phlobatanins and alkaloids. All plant extracts showed broad spectrum antibiosis against selected gram positive and gram negative bacteria including E. coli, P. aeruginosa, Klebsiella sp, S. pneumoniae and B. cereus, as well as tested fungi, including A. niger, A. flavus, Trichoderma sp and Candida sp. While all extracts exhibited maximum antibiosis at 500 mg/ml, the chloroform extracts compared well than ethyl acetate extracts. The overall results revealed that antimicrobial activities of the plant extracts are dose dependent with comparative activity greater than that of commercial antibiotics at the concentration of extracts tested. E.coli was the most susceptible microbial isolate tested and represents the potential of the extract against a group of coliform which are important indicators of microbial pollution in water. Other microbial isolates also recorded sensitivity to extracts tested at varying degrees. The findings indicate that microbes tested were mostly susceptible to chloroform extract of Z. zanthoxyloides and G. latifolium except for the activity of ethyl acetate extract of Z. zanthoxyloide against E.coli. Results of phytochemical screening of the extract also showed the varied presence of alkaloids, saponins, tannins, flavonoids, terpenoids and anthraquinones The results indicated that plant materials investigated can be developed as effective biocides against water microbial contaminants
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Life Sciences, Other; Copper nanoparticles, nano-fertilizer, soil, nitrification, nitrification kinetics, toxicity
Online: 3 October 2018 (14:46:58 CEST)
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The potential agricultural use of metal nanoparticles (NPs) for slow-release micronutrient fertilizers is beginning to be investigated by both industry and regulatory agencies. However, the impact of such NPs on soil biogeochemical cycles is not clearly understood. In this study, impacts of a commercially-available copper NPs on the soil nitrification kinetics was investigated via batch experiments. The X-ray absorption near edge structure spectroscopy analysis showed that the NPs readily oxidized to Cu(II) and strongly retained in soils with minimum dissolution (<1% of total mass). The Cu2+ (aq) at 1mg/L showed the beneficial effect on the nitrification, an increase in the rate of nitrification kinetics (Vmax). However Vmax was negatively impacted by ionic Cu at 10-100mg/L and CuNP at 1-100 mg/L. The trace metal toxicity of soil nitrifiers seems to be critical in the soil nitrification processes. Among CuNPs, the suppressed nitrification kinetics was concentration dependent at >10mg/L. The reaction products of surface oxidation such as the release of ionic Cu seem to play an important role in suppressing the nitrification process. Considering the potential use of copper NPs as a slow-release micronutrient fertilizer, further studies are needed in heterogeneous soil systems.
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Life Sciences, Immunology; apoptosis; viral persistence, hepatitis C virus; immunity; chronic infection
Online: 2 October 2018 (18:34:19 CEST)
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Hepatitis C virus (HCV) represents a challenging global health threat in ~200 million infected individuals. Clinical data suggests that only ~10-15% of acutely HCV-infected individuals will achieve spontaneous viral clearance despite exuberant virus-specific immune responses, which is largely attributed to difficulties in recognizing the pathognomonic symptoms during the initial stages of exposure to the virus. Given the paucity of a suitable small animal model, it is also equally challenging to study the early phases of viral establishment. Further, the host factors contributing to HCV chronicity in a vast majority of acutely HCV-infected individuals largely remain unexplored. The last few years have witnessed a surge in studies showing that HCV adopts a myriad mechanisms to disconcert virus-specific immune responses in the host to establish persistence that includes, but not limited to viral escape mutations, viral growth at privileged sites, and antagonism. Here, we discussed a few hitherto poorly explained mechanisms employed by HCV that are believed to lead to chronicity in infected individuals. A better understanding of these mechanisms would aid the design of improved therapeutic targets against viral establishment in susceptible individuals.
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Life Sciences, Immunology; TFH, B-cells, Multiple Sclerosis, EAE, TH17
Online: 2 October 2018 (17:36:06 CEST)
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Multiple sclerosis is an autoimmune disorder where both T cells and B cells are implicated in pathology. However, it remains unclear how these two distinct populations cooperate to drive disease. There is ample evidence from studies in both MS patients and mouse models that Th17, B cells, and follicular T helper (TFH) cells contribute to disease. This review article describes the literature that identifies mechanisms by which Th17, TFH, and B cells cooperatively drive disease activity in MS and EAE. The curation of this literature has identified that CNS-infiltrating TFH cells act with TH17 cell to contribute to an inflammatory B cell response in neuroinflammation. This demonstrates that TFH cells and their products are promising targets for therapies in MS.
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Life Sciences, Molecular Biology; Unfolded protein response; ER morphology; Mitochondria-associated ER membrane; ER-PM contact sites
Online: 2 October 2018 (15:41:17 CEST)
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The function of the endoplasmic reticulum (ER) can be impaired by the alternation of the extra- and intracellular environment such as disruption of calcium homeostasis, expression of mutated proteins and oxidative stress. In response to disruptions to ER homeostasis, eukaryotic cells activate canonical branches of signal transduction cascades, collectively termed the unfolded protein response (UPR). The UPR attempts to recover the protein folding capacity and avoid irreversible cellular damage. Additionally, the UPR has been shown to play unique physiological roles in the regulation of diverse cellular events, including cell differentiation and development and lipid biosynthesis. Recent studies have indicated that these important cellular events are also regulated by contact and communication among organelles. These reports suggest strong involvement among the UPR, organelle communication and regulation of cellular homeostasis. However, the precise mechanisms for the formation of contact sites and the regulation of its dynamics by UPR remain unresolved. In this review, we summarized the current understanding of how the UPR regulates morphological changes to the ER and the formation of contact sites between the ER and other organelles. We also review how UPR-dependent connections between the ER and other organelles affect cellular and physiological functions.
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Life Sciences, Endocrinology & Metabolomics; perilipins, milk lipid globules, human breast milk, lipid content, tandem mass spectrometry, ultra-high performance liquid chromatography
Online: 1 October 2018 (14:18:46 CEST)
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Objective: Lipids are secreted into milk as bilayer-coated structures: milk lipid globules (MLGs). Adipophilin (ADRP) and perilipin 3 (TIP47) are associated with MLGs in human breast milk; however, the role of these proteins in milk lipid secretion is not fully understood. The aim of the study was to investigate levels of ADRP, TIP47 and total lipid content in human breast milk, their mutual correlations and dynamics during lactation. Research Methods & Procedures: Milk samples from 22 healthy lactating women (Caucasian, Central European) were collected at five time points during lactation (1–3, 12–14, 29–30, 88–90 and 178–180 days postpartum). Mass spectrometry-based method was used for quantification of ADRP and TIP47 in the samples. The gravimetric method was used to determine milk total lipid content. Results: We observed distinctive trends in ADRP, TIP47 levels and lipid content in human breast milk during the first 6 months of lactation. We also found a significant association between lipid content and ADRP, lipid content and TIP47, and ADRP and TIP47 concentrations in breast milk at all sampling points. Moreover, we derived an equation for estimating the mean lipid content of milk based on ADRP concentration in human breast milk. Conclusions: A mass spectrometry-based method was developed for quantifying ADRP and TIP47 in human breast milk. Strong mutual correlations were found between ADRP, TIP47 and total lipid content in human breast milk.
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Life Sciences, Other; livestock care management; rotational/continuous grazing; technical advice; stocking rate; functional units
Online: 1 October 2018 (13:24:38 CEST)
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The livestock sector can be a major contributor to the mitigation of greenhouse (GHG) emissions. Within the sector, beef production produces the largest proportion of the livestock sector’s direct emissions. The objective of this study was to assess the on-farm GHG emissions in semi-arid rangelands in Argentina and to identify the relationships between emissions and current farm management practices. A survey recorded detailed information on farm management and characteristics. Assessments of GHG emissions were based on the IPCC Tier 2 protocols [1]. The relationships between farm management and GHG emissions were identified using General Linear Models. Cluster analysis was used to identify groups of farms that differed from others in emissions and farm characteristics. Emissions per product sold were low on farms that had improved livestock care management, rotational grazing, received technical advice, and had high animal and land productivities. Emissions per hectare of farmland were low on farms that had low stocking rates, low number of grazing paddocks, little or no land dedicated to improved pastures and forage crops, and low land productivity. Our results suggest that the implementation of realistic, relatively easy-to-adopt farming management practices has considerable potential for mitigating GHG emissions in semi-arid rangelands of central Argentina.
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Life Sciences, Microbiology; Malassezia, Caenorhabditis elegans, Tenebrio molitor
Online: 1 October 2018 (12:12:54 CEST)
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Malassezia species are part of human commensal microbiota and is also related to diseases. Little is known about the interaction of these microorganisms with their host. Here we established two standard culture conditions for Malassezia spp. to perform infection assays using C. elegans and T. molitor. Invertebrate hosts infected by Malassezia spp. cultured in M9M resulted in higher death rate on survival assays when compared to yeasts cultured in standard Dixon medium indicating that M9M cultured Malassezia species have increased virulence. The culture and infection conditions established in this work, using invertebrate alternative models, are valuable tools to understand Malassezia-host interaction.
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Life Sciences, Microbiology; Prebiotics; Infant Nutrition; Infant formula; Gut microbiota; Lactobacillus; Bifidobacterium; Fructo-oligosaccharides; Galacto-oligosaccharides; Polidextrose; Acidic oligosaccharides.
Online: 30 September 2018 (07:42:39 CEST)
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Abstract: Supplementation of infant formula with ingredients potentially able to manage, in a way positive for the host, the gut microbiota of infants, is nowadays widely used by infant food producers. The impact of this class of compounds, named prebiotics, on gut microbiota composition, was initially measured on the enrichment of Bifidobacterium and Lactobacillus spp., but the use of culture-independent analytical techniques has allowed to establish that a larger number of intestinal microorganisms are affected by the ingestion of prebiotics. However, despite a relevant number of scientific publications, actually there is no consensus on the amount of prebiotics to be administered daily, the potentially different actions exerted by prebiotics which differ in biochemical structures, as well as the impact of different percentages of the same prebiotics when used in mixtures and/or combination. This paper is aimed to critically review the available data on the use of prebiotics in infant formula, with special attention paid to identify a link between, the dosage used, the mixture composition and the observed outcomes, keeping in mind the influences in nutrition quality and growth influence.
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Life Sciences, Biochemistry; squaraine dye; near infrared; fluorescence; chloroquine; malaria; Plasmodium falciparium
Online: 29 September 2018 (12:15:33 CEST)
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Chloroquine was among the first of several effective drug treatments against malaria until the onset of chloroquine resistance. In light of diminished clinical efficacy of chloroquine as an antimalarial therapeutic, there is potential in efforts to adapt chloroquine for other clinical applications, such as in combination therapies and in diagnostics. In this context, we designed and synthesized a novel asymmetrical squaraine dye coupled with chloroquine (SQR1-CQ). In this study, SQR1-CQ was used to label live Plasmodium falciparum (P. falciparum) parasite cultures of varying sensitivities towards chloroquine. SQR1-CQ positively stained ring, mature trophozoite and schizont stages of both chloroquine–sensitive and chloroquine–resistant P. falciparum strains. In addition, SQR1-CQ exhibited significantly higher fluorescence, when compared to a chloroquine-BODIPY (borondipyrromethene) conjugate. We also achieved successful SQR1-CQ labelling of P. falciparum directly on thin blood smear preparations. Drug efficacy experiments measuring half-maximal inhibitory concentration (IC50) showed lower concentration of effective inhibition against resistant strain K1 by SQR1-CQ compared to conventional chloroquine. Taken together, the versatile and highly fluorescent labelling capability of SQR1-CQ and promising preliminary IC50 findings potentiates it to be further developed as a promising diagnostic bioimaging tool with drug efficacy against chloroquine-resistant P. falciparum.
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Life Sciences, Other; machine learning; conotoxins; cone snails; venom; drug discovery
Online: 29 September 2018 (09:39:42 CEST)
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Cone snails (genus Conus) are venomous marine snails that inject prey with a lethal cocktail of conotoxins, small, secreted, cysteine-rich peptides. Given the diversity and often high affinity for their molecular targets, consisting of ion channels, receptors or transporters, many conotoxins have become invaluable pharmacological probes, drug leads and therapeutics. Transcriptome sequencing of Conus venom glands followed by de novo assembly and homology-based toxin identification and annotation is currently the state-of-the-art for discovery of new conotoxins. However, homology-based search techniques, by definition, can only detect novel toxins that are homologous to previously reported conotoxins. To overcome these obstacles for discovery we have created ConusPipe, a machine learning tool that utilizes prominent chemical characters of conotoxins to predict whether a certain transcript in a Conus transcriptome, which has no otherwise detectable homologs in current reference databases, is a putative conotoxin. By using ConusPipe on RNASeq data of 10 species, we report 5,230 new putative conotoxin transcripts that have no homologues in current reference databases. 893 of these were identified by at least 3 out of 4 models used. These data significantly expand current publicly available conotoxin datasets and our approach provides a new computational avenue for the discovery of novel toxin families.
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Life Sciences, Molecular Biology; lung cancer; biomarker; proteomics; QSOX1; secretome
Online: 29 September 2018 (08:19:20 CEST)
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As lung cancer shows the highest mortality in cancer related death, serum biomarkers are demanded for the lung cancer diagnosis and its treatment. To discover lung cancer protein biomarkers, secreted proteins from primary cultured lung cancer and adjacent normal tissues from patients were subjected to LC/MS-MS proteomic analysis. Quescin sulfhydryl oxidase (QSOX1) was selected as a biomarker candidate from the proteins enriched in the secretion of lung cancer cells. QSOX1 levels were higher in 82% (51 of 62 tissues) of lung cancer tissues compared to adjacent normal tissues. Importantly, QSOX1 serum levels were significantly higher in cancer patients (p<0.05, AUC=0.89), when measured by multiple reaction monitoring (MRM). Higher levels of QSOX1 are also uniquely detected in lung cancer tissues among several other solid cancers by immunohistochemistry. QSOX1 knock-downed Lewis lung cancer (LLC) cells was less viable from oxidative stress and had reduced migration and invasion. In addition, LLC mouse models with QSOX1 knock-down also proved that QSOX1 functions in promoting cancer metastasis. In conclusion, QSOX1 might be a lung cancer tissue-derived biomarker and involved in the promotion of lung cancers, and thus can be a therapeutic target for lung cancers.
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Life Sciences, Biochemistry; almond; thermal/pressure treatment; autoclave; food allergens; high resolution mass spectrometry (HR-MS); immunoreactivity reduction; in vitro digestion
Online: 29 September 2018 (06:23:32 CEST)
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Almond is worldwide consumed and renowned as a valuable healthy food. In spite of this, it is also a potent source of allergenic proteins able to trigger several mild to life-threatening immunoreactions. Food processing proved to alter biochemical characteristics of proteins, thus affecting the respective allergenicity. In this paper we investigated the effect of autoclaving, preceded or not by a hydration step, on the biochemical and immunological properties of almond proteins. Any variation in the stability and immunoreactivity of almond proteins extracted from the treated materials, were evaluated by total protein quantification, ELISA assay and protein profiling by electrophoresis-based separation (SDS-PAGE). The autoclaving alone was found to weakly affect almond proteins stability, despite what observed for the combination of hydration and autoclaving, which resulted in a loss of approximately 70% of total protein content compared to untreated sample, and in a final negligible immunoreactivity, as well. The final SDS-PAGE protein pattern recorded for almonds hydrated and autoclaved disclosed significant changes. In addition, the same samples were further submitted to in vitro simulated gastro-duodenal (GI) digestion to evaluate potential changes induced by these processing on allergens digestibility. Digestion products were identified by HPLC-HRMS/MS analysis followed by software-based data mining, and complementary information were provided by analyzing the proteolytic fragments lower that 6 kDa in size. The autoclave based treatment was found not to alter the allergens digestibility, whereas an increased susceptibility to proteolytic action of digestive enzymes was observed in almonds subjected to the combination of prehydration and autoclaving. Finally, the residual immunoreactivity of the GI resistant peptides was investigated in-silico by bioinformatic tools, confirming that by following both approaches, no epitopes survived the almond digestion, thus demonstrating the potential effectiveness of these treatments to reduce almond allergenicity.
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Susann Piehler,
Heidi Dähring,
Julia Grandke,
Julia Göring,
Pierre Couleaud,
Antonio Aires,
Aitziber L. Cortajarena,
José Courty,
Alfonso Latorre,
Álvaro Somoza,
Rodolfo Miranda,
Ingrid Hilger
Life Sciences, Biophysics; magnetic hyperthermia, magnetic nanoparticles (MNP), doxorubicin (DOX), NucAnt (N6L), breast cancer, mouse model
Online: 28 September 2018 (15:29:53 CEST)
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Doxorubicin (DOX) is a frequently used chemotherapeutic drug for breast cancer, but its site specificity and local internalization into tumor cells is rather low. In this paper we conjugated magnetic nanoparticles (MNPs) with DOX and/or a pseudopeptide NucAnt (N6L) as modality to enhance DOX-induced antitumor effects in breast cancer cells (BT474). In this context, we determined cellular uptake of MNP formulations, analyzed cell viability and expression of apoptotic and cell cycle proteins after magnetic hyperthermia (43°C, 1 h) in vivo and in vitro. We have shown that i) the presence of N6L on the surface of DOX-functionalized MNPs increases their internalization into a target cells and potentiates the cytotoxic potential of the anticancer drug, ii) in combination with hyperthermia, DOX functionalized MNPs influence the expression of apoptotic and cell cycle proteins, and also favors tumor regression in vivo. Our data show that intratumoral application of DOX coupled MNPs is able to overcome biological barriers to chemotherapeutic drugs, enabling them to penetrate into the target cells. Combined with hyperthermia these MNPs can be an effective method in enhancing the localised delivery and penetration of DOX into breast cancer cells.
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Life Sciences, Virology; Citrus bark cracking viroid; differentially expressed genes; hop; pathogen; transcriptome analysis; viroids
Online: 28 September 2018 (07:26:31 CEST)
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Viroids are smallest pathogen that consist of non-capsidated, single-stranded non-coding RNA replicons and exploits host factors for their replication and propagation. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) is a serious threat, which spread rapidly within hop gardens. In this study, we employed comprehensive transcriptome analyses to dissect host-viroid interactions and identify gene expression changes associated with disease development in hop. Our analysis revealed that CBCVd-infection resulted in the massive modulation of activity of over 2000 genes. Expression of genes associated with plant immune responses (protein kinase and mitogen-activated protein kinase), hypersensitive responses, phytohormone signaling pathways, photosynthesis, pigment metabolism, protein metabolism, sugar metabolism and modification and others were altered, which could be attributed to systemic symptom development upon CBCVd-infection in hop. In addition, genes encoding RNA-dependent RNA polymerase, pathogenesis-related protein, chitinase as well as those related to basal defense responses were up-regulated. The expression levels of several genes identified from RNA sequencing analysis were confirmed by qRT-PCR. Our systematic comprehensive CBCVd-responsive transcriptome analysis provides a better understanding and insights into complex viroid-hop plant interaction. This information will assist further in the development of future measures for the prevention of CBCVd spread in hop fields.
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Life Sciences, Genetics; genetic code, alphabet, unitary matrix, dyadic shift, decomposition, spectral presentation, fractal, tensor product, quantum informatics
Online: 27 September 2018 (15:36:53 CEST)
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Information molecules of DNA and RNA should obey principles of quantum mechanics where unitary operators in form of unitary matrices have key meanings. Unitary matrices are the basis of calculations in quantum computers. This article presents some author's results, which show that matrix forms of the representation of structured systems of molecular-genetic alphabets can be considered as sets of sparse unitary matrices related with phenomenologic features of the degeneracy of the genetic code. These sparse unitary matrices have orthogonal systems of functions in their rows and columns. A complementarity exists among some unitary genetic matrices in relation each other. Decompositions of numeric genetic matrices into sets of sparse unitary matrices are connected with the logical operation of modulo-2 addition used in quantum computers as well. Tensor (or Kronecker) families of unitary genetic matrices with their fractal-like properties are also considered. The described results are discussed in the frame of development of quantum-information approaches for modeling genetic systems.
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Life Sciences, Biotechnology; hemodialysis; end stage renal disease; diabetes; motor performance; gait; balance; wearable; aging; frailty; diabetic peripheral neuropathy
Online: 27 September 2018 (06:19:43 CEST)
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Motor functions are deteriorated by aging. Some conditions may magnify this deterioration. To examine whether hemodialysis (HD) process would negatively impact gait and balance beyond diabetes condition among mid-age adults (48-64 years) and older adults (65+ years). One hundred and ninety-six subjects (age=66.2±9.1 years, body-mass-index=30.1±6.4 kg/m2, female=56%) in 5 groups were recruited: mid-age adults with diabetes undergoing HD (Mid-age HD+, n=38) and without HD (Mid-age HD-, n=40); older adults with diabetes undergoing HD (Older HD+, n=36) and without HD (Older HD-, n=37); and non-diabetic older adults (Older DM-, n=45). Gait parameters (stride velocity, stride length, gait cycle time, and double support) and balance parameters (ankle, hip, and center of mass sways) were quantified using validated wearable platforms. Groups with diabetes had overall poorer gait and balance compared to the non-diabetic group (p<0.050). Among people with diabetes, the HD+ had significantly worsened gait and balance when comparing to the HD- (Cohen’s effect size d=0.63-2.32, p<0.050). Between-group difference was more pronounced among older adults with the largest effect size observed for stride length (d=2.32, p<0.001). Results suggested that deterioration in gait speed among the HD+ was correlated with age (r=-0.440, p<0.001), while this correlation was diminished among the HD-. Interestingly, results also suggested that poor gait in the Older HD- related to poor balance, while no correlation was observed between poor balance and poor gait among the Older HD+. Using objective assessments, results confirmed that the presence of diabetes can deteriorate gait and balance, and this deterioration can be magnified by HD process. Among non-HD people with diabetes, poor static balance described poor gait. However, among people with diabetes undergoing HD, age was a dominate factor describing poor gait irrespective of static balance. Results also suggested feasibility of using wearable platforms to quantify motor performance during routine dialysis clinic visits. These objective assessments may assist in identifying early deterioration in motor function, which in turn may promote timely intervention.
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Life Sciences, Virology; hepatitis E virus; innate immunity; interferon response; JAK/STAT pathway; zoonosis; emerging pathogen
Online: 27 September 2018 (05:34:49 CEST)
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Hepatitis E virus (HEV) is responsible for large waterborne epidemics of hepatitis in endemic countries and is an emerging zoonotic pathogen worldwide. In endemic regions, HEV-1 or HEV-2 genotypes are frequently associated with fulminant hepatitis in pregnant women, while with zoonotic HEV (HEV-3 and HEV-4), chronic cases of hepatitis and severe neurological disorders are reported. Hence, it is important to characterize the interactions between HEV and its host. Here, we investigated the ability of the non-structural polyprotein encoded by the first open reading frame (ORF1) of HEV to modulate the host early antiviral response and in particular the type I interferon (IFN-I) system. We found that the amino-terminal region of HEV-3 ORF1 (MetPCP), containing a putative methyltransferase (Met) and a papain-like cysteine protease (PCP) functional domain, inhibited IFN-stimulated response element (ISRE) promoter activation and the expression of several IFN-stimulated genes (ISGs) in response to IFN-I. We showed that the MetPCP domain interfered with the Janus kinase (JAK)/signal transducer and activator of transcription protein (STAT) signalling pathway by inhibiting STAT1 nuclear translocation and phosphorylation after IFN-I treatment. By contrast, MetPCP had no effect on STAT2 phosphorylation and a limited impact on the activation of the JAK/STAT pathway after IFN-II stimulation. This inhibitory function seemed to be genotype-dependent as MetPCP from HEV-1 had no significant effect on the JAK/STAT pathway. Overall, this study provides evidence that the predicted MetPCP domain of HEV ORF1 antagonises STAT1 activation to modulate the IFN response.
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Life Sciences, Molecular Biology; Unfolded protein response; ER morphology; Mitochondria-associated ER membrane; ER-PM contact sites
Online: 26 September 2018 (17:44:54 CEST)
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The function of the endoplasmic reticulum (ER) can be impaired by the alternation of the extra- and intracellular environment such as disruption of calcium homeostasis, expression of mutated proteins and oxidative stress. In response to disruptions to ER homeostasis, eukaryotic cells activate canonical branches of signal transduction cascades, collectively termed the unfolded protein response (UPR). The UPR attempts to recover the protein folding capacity and avoid irreversible cellular damage. Additionally, the UPR has been shown to play unique physiological roles in the regulation of diverse cellular events, including cell differentiation and development and lipid biosynthesis. Recent studies have indicated that these important cellular events are also regulated by contact and communication among organelles. These reports suggest strong involvement among the UPR, organelle communication and regulation of cellular homeostasis. However, the precise mechanisms for the formation of contact sites and the regulation of its dynamics by UPR remain unresolved. In this review, we summarized the current understanding of how the UPR regulates morphological changes to the ER and the formation of contact sites between the ER and other organelles. We also review how UPR-dependent connections between the ER and other organelles affect cellular and physiological functions.
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Life Sciences, Microbiology; Actinobaculum; urinary tract infection; biofilm; catheter; CAUTI; host-pathogen interaction; proteome; polymicrobial; metabolism; uropathogen
Online: 26 September 2018 (08:07:28 CEST)
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Actinobaculum massiliense, a Gram-positive anaerobic coccoid rod colonizing the human urinary tract, belongs to the taxonomic class of Actinobacteria. We identified A. massiliense as a cohabitant of urethral catheter biofilms (CB). The CBs also harbored common uropathogens such as Proteus mirabilis and Aerococcus urinae, supporting the notion that A. massiliense is adapted to a life style in polymicrobial biofilms. We isolated a strain from an agar colony derived from a clinical sample. Using 16S rRNA gene sequencing and shotgun proteomics, we identified and characterized A. massiliense, comparing the isolate grown in vitro and four clinical ‘in vivo’ samples. Based on abundances of proteins in the in vivo milieu, we assessed their functions related to nutrient import and responses to hostile host conditions characterized by neutrophil infiltration. Two putative subtilisin-like proteases and a heme/oligopeptide transporter were highly expressed in vivo and are perhaps important for survival in the host milieu. The uptake of xylose/glucuronate and oligopeptides apparently enables feeding metabolites into mixed acid fermentation and peptidolysis pathways, respectively, to generate energy. A putative polyketide synthase which may generate a secondary metabolite interacting with either the host or co-colonizing microbes was identified. The enzyme may contribute to A. massiliense persistence in CBs.
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Life Sciences, Other; Phaseolus vulgaris L., yellow beans, Manteca, cooking time, iron, bioavailability, polyphenols
Online: 24 September 2018 (17:24:38 CEST)
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The common dry bean (Phaseolus vulgaris L.) is a nutrient dense food produced globally as a major pulse crop for direct human consumption, and is an important source of protein and micronutrients for hundreds of millions of people across Latin America, the Caribbean and Sub-Saharan Africa. Beans require large amounts of heat energy and time to cook, deterring consumers worldwide from purchasing beans. In regions where consumers rely on expensive fuelwood for food preparation, the yellow bean is often marketed as fast cooking. A Yellow Bean Panel (YBP) was assembled to explore the cooking time and health benefits of the five major seed types within the yellow bean market class (Amarillo, Canary, Manteca, Mayocoba, Njano) over two field seasons. This study shows how the Manteca yellow bean possess a fast cooking phenotype, which could serve a genetic resource for introducing fast cooking properties into a new generation of dry beans with cooking times < 20 minutes when pre-soaked and < 80 minutes unsoaked. Nutritional evaluation revealed fast cooking yellow beans have high iron retention (>80%) after boiling. An in vitro digestion/Caco-2 cell culture bioassay revealed a strong negative association between cooking time and iron bioavailability in the YBP (r values > -0.73). When either pre-soaked or left unsoaked the highest iron bioavailability scores were measured in the fast cooking Manteca genotypes providing evidence that this yellow market class is worthy of germplasm enhancement through the added benefit of improved iron quality after cooking.
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Life Sciences, Other; sugars, fructose, fruit juice, diabetes, overweight
Online: 24 September 2018 (13:51:47 CEST)
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Much epidemiological research confirms a correlation between a high consumption of sugar sweetened beverages and obesity, diabetes and cardiovascular diseases. In many of these studies, soft drinks, fruit drinks with added sugars and 100% fruit juices without added sugars were considered as one separate category and the total consumption was calculated cumulatively. Being able to make statements about the effects of individual types of drinks, as present in these clusters, is therefore impossible. However, recent data from well-controlled studies and meta-analyses on consumption of 100% fruit juice show that there is no effect on diabetes risks. Adults and children who choose to drink 100% juice appear to have a healthier lifestyle, consume better quality food and usually have a more favorable body weight. Although 100% fruit juice in relation to soft drinks contains a range of nutrients that are considered to be beneficial for health, the associated positive effects can be nullified by high sugar intake, in case of excessive consumption. That is why a golden rule can be applied: "100% fruit juice, as part of a healthy diet, is a healthy choice provided that you do not consume more juice than present in max. 1-3 fruits at a time. In the case of orange juice, this corresponds to a champagne glass full of juice (100-150ml). In this respect 100% fruit juice should be perceived as a nutritional drink that can be consumed with a meal and not as a thirst quencher.
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Life Sciences, Biotechnology; Microbial fuel cell; polymer matrix; immobilization of bacterial cells; interaction of cell membranes with carbon nanotubes, boostconverter accumulation
Online: 24 September 2018 (13:06:23 CEST)
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The anode of a microbial fuel cell (MFC) was formed on a graphite electrode and immobilized Gluconobacter oxydans VKM-1280 bacterial cells. Immobilization was performed in chitosan, poly(vinyl alcohol) or N-vinylpyrrolidone-modified poly(vinyl alcohol). Ethanol was used as substrate. The anode was modified using multiwalled carbon nanotubes. The aim of the modification was to create a conductive network between cell lipid membranes, containing exposed PQQ-dependent alcoholdehydrogenases, and the electrode to facilitate electron transfer in the system. The bioelectrochemical characteristics of modified anodes at various cell/polymer ratios were assessed via current density, power density, polarization curves and impedance spectres. MFCs based on chitosan at a matrix/cell volume ratio of 5:1 produced maximal power characteristics of the system (8.3 μW/cm2) at a minimal resistance (1111 Ohm cm2). Modification of the anode by multiwalled carbon nanotubes led to a slight decrease of internal resistance (down to 1078 Ohm cm2) and to an increase of generated power density up to 10.6 μW/cm2. We explored the possibility of accumulating electric energy from an MFC on a 6,800-μF capacitor via a boost converter. Generated voltage was increased from 0.3 V up to 3.2 V. Accumulated energy was used to power a Clark-type biosensor and a bluetooth transmitter with three sensors, a miniature electric motor and a light-emitting diode.
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Life Sciences, Molecular Biology; Dormant origins; replicative stress; replication timing; DNA damage; genome instability; cancer
Online: 21 September 2018 (18:00:30 CEST)
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Maintenance of the human chromosomes stability requires a tight regulation of DNA replication to duplicate once and only once the entire genome of a single cell. In mammalians cells, origin activation is controlled in space and time by a cell specific and robust program called replication timing. About 100 000 of potential origins are loaded onto the chromatin at the G1 phase but only 20-30% are selected and active during the replication of a given cell. When the replication fork is slowed down by exogenous or endogenous sources, the cell need to activate more origins to complete the replication on time. Thus, the large choice of origins that can be activated may be a key player in the protection of the genome. The aim of this review is to discuss about the role of these dormant origins as housekeepers of the human genome in response to replicative stress.
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Life Sciences, Biotechnology; Lignocellulosic biomass; cellulose; hemicellulose; lignin; biofuel
Online: 20 September 2018 (18:16:47 CEST)
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Carbohydrate composition of lignocellulosic biomass is one of the main factors for production of biofuel from the plant biomass. Various methods like Thermogravimetric analysis (TGA), near infrared spectroscopy (NIR) often used in determination of polysaccharide component of the plant biomass. However, used of such tools is based on the prediction and very costly. This paper discussed about the determination of carbohydrate composition (cellulose, hemicellulose and lignin) using the automatic fibre estimation system. The protocol was developed for the estimation of cellulose, hemicellulose and lignin component of lignocellulosic biomass. This protocol explains a simple method to estimate the polysaccharide component of lignocellulosic biomass. This protocol can be used not only lignocellulosic biomass but also for other hardwood biomass. The advantages and techniques, procedures are presented below.
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Life Sciences, Microbiology; Paenibacillus larvae; optimized qPCR; quantification; honey; hive debris
Online: 20 September 2018 (16:13:42 CEST)
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The application of quantitative PCR (qPCR) as a routine method to detect and enumerate Paenibacillus larvae in honey and hive debris could greatly speed up the estimation of prevalence and outbreak risk of the American foulbrood (AFB) disease of Apis mellifera. However, none of the qPCR tests described so far has been officially proposed as a standard procedure for P. larvae detection and enumeration for surveillance purposes. Therefore, in this study inclusivity, exclusivity and sensitivity in detection of P. larvae spores directly in samples of honey and hive debris were re-evaluated for the previously published qPCR methods. To this aim recently acquired P. larvae sequence data were considered to assess inclusivity in silico and more appropriate non-target species were used to verify exclusivity experimentally. This led to the modification of one of the previously described methods resulting in a new test capable to allow the detection of P. larvae spores in honey and hive debris down to 1 CFU/g. The application of the qPCR test optimized in this study can allow to reliably detect and quantify P. larvae in honey and hive debris, thus circumventing the disadvantages of late AFB diagnosis based on clinical symptoms and possible underestimation of spore numbers that is the main drawback of culture-dependent procedures.
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Life Sciences, Other; Nitrogen; transfer; transformation; N uptake; nitrogen use efficiency
Online: 20 September 2018 (15:09:32 CEST)
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A field experiment was conducted in Ninghe, Tianjin, China, using 15N isotope method to evaluate the application of organic fertilizer on N distribution patterns of labelled and unlabeled N fertilizer, ammonium sulfate -15N uptake by rice, N use efficiency (NUE), and the fate of (15NH4)2SO4 applied. The experiment included eight treatments: CK-N (control + no-duck), CK-D (control + ducks), CF-N (chemical fertilizer + no-ducks), CF-D (chemical fertilizer + ducks), CM-N (chemical fertilizer + organic fertilizer + no-ducks), CM-D (chemical fertilizer + organic fertilizer + ducks), CD-N (chemical fertilizer 30% off + organic fertilizer + no-ducks), and CD-D (chemical fertilizer 30% off + organic fertilizer + ducks). The results showed that the application of organic fertilizer whether CM or CD significantly increased N and P concentrations over control (CK) and chemical fertilizer (CF). Moreover, no-significant differences were found in 15N fresh grain and husk concentration. Both organs ranged of 14.2-14.4 g kg-1 and 6.2-6.3 g kg-1, respectively. N derived from the fertilizer and soil significantly affected fresh grain compared to fresh husk. However, N uptake and N use efficiency did not show any differences. We concluded that organic fertilizer has a significant influence on rice growth and promote crop productivity.
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Life Sciences, Cell & Developmental Biology; H2O2, redox signalling, development, regeneration, adult stem cells, metazoan
Online: 19 September 2018 (23:42:44 CEST)
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Reactive oxygen species (ROS), which were originally classified as exclusively deleterious compounds, have gained increasing interest in the recent years given their action as bona fide signalling molecules. The main target of ROS action is the reversible oxidation of cysteines, leading to the formation of disulfide bonds, which modulate protein conformation and activity. ROS endowed with signalling properties are mainly produced by NADPH oxidases at the plasma membrane, but their action also involves a complex machinery of multiple redox-sensitive protein families that differs in their subcellular localization and their activity. Given that the levels and distribution of ROS are highly dynamic in part due to their limited stability, the development of various fluorescent ROS sensors, some of which are quantitative (ratiometric), represents a clear breakthrough in the field and have been adapted to both ex vivo and in vivo applications. The physiological implication of ROS signalling will be presented mainly in the frame of morphogenetics processes, embryogenesis, regeneration, and stem cell differentiation. Gain and loss of function as well as pharmacological strategies have demonstrated the wide but specific requirement of ROS signalling at multiple stages of these processes and its intricate relationship with other well-known signalling pathways.
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Life Sciences, Biochemistry; fragment screening; XChem; protein crystallisation; X-ray crystallography; diamond light source; I04-1; structural genomics consortium
Online: 19 September 2018 (13:37:41 CEST)
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The XChem facility at Diamond Light Source offers fragment screening by X-ray crystallography as a general access user program. The main advantage of X-ray crystallography as a primary fragment screen is that it yields directly the location and pose of the fragment hits, whether within pockets of interest or merely on surface sites: this is the key information for structure-based design and for enabling synthesis of follow-up molecules. Extensive streamlining of the screening experiment at XChem has engendered a very active user programme that is generating large amounts of data: in 2017, 36 academic and industry groups generated 35,000 datasets of uniquely soaked crystals. It has also generated a large number of learnings concerning the main remaining bottleneck, namely obtaining a suitable crystal system that will support a successful fragment screen. Here we discuss the practicalities of generating screen-ready crystals that have useful electron density maps, and how to ensure they will be successfully reproduced and usable at a facility outside the home lab.
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Life Sciences, Other; Performance, Sports, Aortic Valve, Sinus of Valsalva, Echocardiography, Sudden cardiac death
Online: 18 September 2018 (16:40:43 CEST)
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Aortic rupture is known as one of the potential causes of sudden cardiac death in athletes. Nevertheless, adaptation strategies for aortic root dilation in athletes vary. The purpose of this study was to investigate aortic root adaptation to physical workload and to determine if aortic root’s and left ventricle sizes are contingent upon the physical workload. Echocardiography was applied to 151 subjects to measure the aortic root at aortic valve annulus (AA) and at sinus of Valsalva (VS). 122 were athletes (41 females and 81 males) and 29 were non-athletes (14 females and 15 males). Of the 41 female athletes, 32 were endurance athletes, and 9 strength athletes. From 81 male athletes, 56 were endurance athletes, and 25 were strength athletes. AA and VS mean values for the body surface area were presented as rAA and rVS. Left ventricle (LV) meaures incuded LV end-diastolic diameter (LVEDD), interventricular septum thickness in diastole (IVSTd), LV posterior wall thickness in diastole (LVPWTd), LV mass (LVM), LV mass index, LV end-diastolic diameter index (LVEDDI). Results indicated that VS was higher in female athletes (28.9±2.36mm) than in non-athletes (27.19±2.87mm, p=0.03). On the other hand, rAA was higher in strength athletes (12.19±1.48mm/m2) than in endurance athletes (11.12±0.99mm/m2, p=0.04). Additionally, rVS and rAA were higher in female strength athletes (17.19±1.78mm/m2, 12.19±1.48mm/m2) than female basketball players (15.49±1.08mm/m2, p=0.03, 10.75±1.06 mm/m2, p=0.02). Statistically significant positive moderate correlations were found between VS and LVEDD, LVM, IVSTd, LVPWTd, rVS and LVEDDI parameters in all athletes. The diameter of Valsalva sinus was greater in female athletes compared to non-athletes. The rAA mean value for body surface area was greater in female athletes practising strength sports as compared to their counterparts who were practising endurance sports. The diameter of the aortic root at sinuses positively correlated with the LV size in all athletes. Trial was registered at ClinicalTrials.gov Identifier: NCT03656861, September 3, 2018 (retrospectively registered).
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Life Sciences, Microbiology; Genetic tool development, Food fermentation, Biotherapeutics, Phytotherapeutics, Synthetic biology, GMO regulation
Online: 18 September 2018 (16:22:47 CEST)
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This mini-review provides an overview of traditional, emerging, and future applications of lactic acid bacteria (LAB) and discusses how genome editing tools can be used to overcome current challenges in all these applications. It also describes currently available tools and how these can be further developed, and takes current legislation into account. Genome editing tools are necessary for the construction of strains for new applications and products, but can also play a crucial role in traditional ones, such as food and probiotics, as a research tool for understanding mechanistic insights and discovering new properties. Traditionally, recombinant DNA techniques for LAB have strongly focused on being food-grade, but they lack throughput and the number of genetically tractable strains is still rather limited. Further tool development in this direction will enable rapid construction of multiple mutants or mutant libraries on a genomic level in a wide variety of LAB strains. We also propose an iterative Design-Build-Test-Learn workflow cycle for LAB cell factory development based on systems biology, with “cell factory” expanding beyond its traditional meaning of production strains and making use of high-throughput genome editing tools to advance LAB understanding, applications and strain development.
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Life Sciences, Virology; bacteriophage; phage-host interactions; phage receptors; high-throughput screen; tail fibers
Online: 18 September 2018 (12:00:35 CEST)
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Factors affecting the host-virus interaction must be understood for the effective application of bacteriophages to combat bacterial pathogens. Two novel E. coli phages, the T1-like siphophage LL5 and the rV5-like myophage LL12, were subjected to forward genetic screens against the Keio collection, a library of single non-essential gene deletions in E.coli str. BW25113. These genome-wide screens and subsequent experiments identified eight genes required for efficient propagation of phage LL5 and six genes required for propagation of LL12. The majority of the genes identified were involved in production of the phage receptors. E. coli mutants deficient in heptose II and the phosphoryl substituent of heptose I of the inner core lipopolysaccharide (LPS) were unable to propagate phage LL5, as were mutants deficient in the outer membrane protein TolC. Mutants lacking glucose I of the LPS outer core failed to propagate LL12. Two cytoplasmic chaperones, PpiB and SecB, were found to be required for efficient propagation of phage LL5 but not LL12. This approach may be useful for identifying phage receptors and required host factors in other phages, which would provide valuable information for their potential use as therapeutics and for phage engineering.
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Life Sciences, Virology; Echovirus 7; Echovirus 19; Nigeria; Enterovirus Species B; Complete Genome
Online: 18 September 2018 (11:39:11 CEST)
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We describe the genomes of two Echovirus isolates from Nigeria as reference enterovirus species B genomes for the region. These Echovirus 7 and 19 genomes have 7,411nt and 7,426nt, and were recovered from sewage contaminated water (in 2010) and an acute flaccid paralysis case (in 2014), respectively.
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Life Sciences, Molecular Biology; Oxidative stress; blackcurrant; biofunctional cookie; simulated digestion; bioactive metabolites; inflammatory cytokines
Online: 17 September 2018 (17:05:44 CEST)
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The improved understanding of the underlying mechanisms of oxidative damage and/or chronic diseases is of high priority in dietary research. Although the chemical extraction of biofunctional molecules from different fruits and cereals have been studied extensively, the impact of food processing and digestion on bioactivity has not been studied systematically. The aim of this study was to investigate the biofunctional potential of blackcurrant powder incorporated into wholemeal wheat and barley cookies in after simulated in vitro digestion. The incorporation of blackcurrant significantly (p<0.05) increased the total phenolic content (about 60 %), significantly improved oxygen radical absorbance capacity (about 25 %) of the cookie digesta. Additionally cellular antioxidant and anti-proliferative activity (lowest EC₅₀ value 1.02 mg/mL) on human liver cancer cell model, HepG2 was significantly enhanced. Bioactive metabolites of blackcurrant incorporated cookies were significantly supressed the inflammatory cytokine genes IL-1β (about 3-fold), IL-6 (about 0.5-fold) and NF-kB (about 2-fold) regulation and upregulated satiety gene NUCB-2/Nesfatin-1 (about 5-fold) compare with wholemeal wheat and barley control cookies. The exerted synergistic effects of this study suggest that there may be a new and effective option to prevent and control chronic diseases in human.
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Life Sciences, Other; Dryland cropping system; Management practices; Nitrogen budget; Nitrogen input; Nitrogen output.
Online: 17 September 2018 (16:21:48 CEST)
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Studies on N balance due to N inputs and outputs and soil N retention to measure cropping system performance and environmental sustainability are limited due to the complexity of measurements of some parameters. We measured N balance based on N inputs and outputs and soil N retention under dryland agroecosystem affected by cropping system and N fertilization from 2007 to 2011 in the northern Great Plains, USA. Cropping systems were conventional tillage barley (Hordeum vulgaris L.)-fallow (CTB-F), no-tillage barley-fallow (NTB-F), no-tillage barley-pea (Pisum sativum L.) (NTB-P), and no-tillage continuous barley (NTCB). Nitrogen rates to barley were 0, 40, 80, and 120 kg N ha-1. Total N input due to N fertilization, pea N fixation, soil N mineralization, atmospheric N deposition, nonsymbiotic N fixation, and crop seed N and total N output due to grain N removal, denitrification, volatilization, N leaching, gaseous N (NOx) emissions, surface runoff, and plant senescence were 28 to 37% greater with NTB-P and NTCB than CTB-F and NTB-F. Total N input and output also increased with increased N rate. Nitrogen sequestration rate at 0 to 10 cm averaged 22 kg N ha-1 yr-1 for all treatments. Nitrogen deficit ranged from 5 to 16 kg N ha-1 yr-1, with greater deficits for CTB-F and NTB-P and higher N rates. Because of increased grain N removal and reduced N loss to the environment and N fertilizer requirement, NTB-P with 40 kg N ha-1 can enhance agronomic performance and environmental sustainability while reducing N inputs compared to other management practices.
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Life Sciences, Molecular Biology; breast cancer; metastasis; Notch; Jagged-1; Dll4
Online: 17 September 2018 (13:54:19 CEST)
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Metastasis is a major cause factor for breast cancer (BC)-associated mortality. During the metastatic process, disseminated tumor cells (DTCs) detach from the primary sites, and enter the bloodstream and establish the secondary colonies. Recent studies have provided substantial evidence for the importance of Notch signaling in BC metastasis. Therefore, this review focuses on the mechanisms by which Notch contributes to the origin of BC DTCs, increases their motility, regulates their intravasation and extravasation, protects them from host surveillance, and finally facilitates colonization. Identification of the mechanisms underlying Notch-related BC metastasis will lead to the development of novel Notch-targeted therapeutic strategies to reduce metastasis and significantly improve outcomes.
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Life Sciences, Biotechnology; Mortierella; phytohormones; winter wheat seedlings; psychrotrophs
Online: 17 September 2018 (12:10:24 CEST)
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The endogenous pool of phytoregulators in plant tissues supplied with microbial secondary metabolites may be crucial for the development of winter wheat seedlings during cool springs. Phytohormones may be synthesized by psychrotrophic microorganisms in lower temperatures occurring in temperate climate. Two fungal isolates from the Spitzbergen soils after the microscopic observations and ITS region molecular characterization were identified as Mortierella antarctica (MA DEM 7) and Mortierella verticillata (MV DEM32). To study the synthesis of indoleacetic acid (IAA) and gibberellic acid (GA) Mortierella strains were grown on media supplemented with precursors of phytohormones (tryptophan or methionine) at 9, 15 and 20 °C for 9 days. The highest amount of IAA synthesis was observed in MV DEM 32 9-day culture at 15 °C with 1.5 mM of tryptophan. At the same temperature the significant promoting effect (about 40% root and shoot fresh weight) of this strain on seedlings was observed. However, only MA DEM 7 had the ACC-deaminase activity with the highest efficiency in 9 °C and at this temperature synthesized IAA without tryptophan also at the same conditions the strain confirmed the strong promoting effect (about 40% root and 24% shoot fresh weight) on seedlings. Both strains synthesized GA in all tested terms and temperatures. Tested Mortierella strains had some important traits to consider them as microbial biofertilizers component improving plant growth in difficult temperate climate.
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Life Sciences, Other; monoglyceride colloidal liquid crystals; release profile; mathematical models; drug delivery systems; release kinetic; square root laws
Online: 17 September 2018 (11:33:52 CEST)
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The manuscript studies the release kinetic of fluorescein from colloidal liquid crystals made up from monoglyceride and different non-ionic surfactants. The release experiments were carried out under sink conditions, and mathematical models were described as extrapolations from solutions of diffusion equation in different initial and boundary conditions imposed by pharmaceutical formulations. The diffusion equation was solved, using Laplace and Fourier transformed functions for the release kinetic from infinite reservoirs in a semi-infinite medium. Solutions represents a general square root law and can be applied for the release kinetic of fluorescein from monoglyceride colloidal liquid crystals. Akaike, Schwartz and Imbimbo criteria were used to establish the appropriate mathematical model and the hierarchy of performances of different models applied to the release experiments. The Fisher statistic test was applied to perform significance of differences among mathematical models. Differences evaluated by mathematical criteria demonstrated that small or no significant statistic differences were carried out between various applied models and colloidal formulations. Phenomenological models were preferred over to empirical and semi-empirical ones. The general square root model shows that the diffusion-controlled release of fluorescein is the mathematical models extrapolated for monoglyceride colloidal liquids, in the first part of the process.
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Life Sciences, Immunology; CCR6, CCL20, Inhibitors, TH17, Treg, Inflammatory diseases, Cancer
Online: 17 September 2018 (11:31:43 CEST)
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Prototypical functions of the chemokine receptor CCR6 include immune regulation by manoeuvring cell chemotaxis and selective delimiting of the pro-inflammatory TH17 and regulatory Treg subsets during chronic or acute systemic inflammation. Inhibition of CCR6 is proposed to attenuate disease symptoms and promote recuperation of multiple inflammatory and autoimmune disorders. Prescription medicines with pharmacodynamics involving the inhibition of the chemokine axis CCR6-CCL20 is very limited. Developing such therapeutics is still at an early experimental stage which has mostly utilized pre-clinical models and neutralizing mono or polyclonal antibodies against either partner, CCR6 or CCL20. Other methods have been constitutive use of small molecules as peptide inhibitors or small interfering ribonucleic acid (siRNA) to interfere with transcription at the nuclear level. We in our review aim at introducing the wide array of potential CCR6-CCL20 inhibitors that have been tried to date in the research field with accent on attendant immune-modulator capacity and which are immensely promising compounds as forerunners of future curatives. 16 different tractable inhibitors of the CCR6-CCL20 duo have been identified to possess high medicinal potential to the drug developers worldwide to treat autoimmune and inflammatory diseases. A multitude of antibody preparations are already available in the current pharmaceutical market as patented treatment for diseases in which the CCR6-CCL20 axis is operative, yet must be used only as supplements with existing routinely prescribed medication as they collectively produce adverse side effects. Novel inhibitors are needed to evaluate this invaluable therapeutic target which holds much promise in the research and development of complaisant remedies for inflammatory diseases.
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Life Sciences, Cell & Developmental Biology; axon guidance; growth cone; cytoskeleton; caspases; apoptosis; signal integration; basal level of caspase activity; death associated inhibitor of apoptosis; axon branching; Netrin; DCC; frazzled; slit; robo; Drosophila
Online: 16 September 2018 (11:43:52 CEST)
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Navigating growth cones are exposed to multiple signals simultaneously and have to integrate competing cues into a coherent navigational response. Integration of guidance cues is traditionally thought to occur at the level of cytoskeletal dynamics. Drosophila studies indicate that cells exhibit a low level of continuous caspase protease activation, and that axon guidance cues can activate or suppress caspase activity. We base a model for axon guidance on these observations. By analogy with other systems in which caspase signaling has non-apoptotic functions, we propose that caspase signaling can either reinforce repulsion or negate attraction in response to external guidance cues by cleaving cytoskeletal proteins. Over the course of an entire trajectory, incorrectly navigating axons may pass the threshold for apoptosis and be eliminated, whereas axons making correct decisions will survive. These observations would also explain why neurotrophic factors can act as axon guidance cues and why axon guidance systems such as Slit/Robo signaling may act as tumor suppressors in cancer.
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Life Sciences, Molecular Biology; Keywords: 1; genome 2; epigenetics 3; neurodevelopmental disorders; 4; chromosome anomalies; 5; retrotransposon; 6; chromosome rearrangement; 7; neurologic disease; 8; birth defects; 9; development 10; infection
Online: 15 September 2018 (20:07:03 CEST)
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Abstract: The purpose of this study was to understand the role of infection in the origin of chromosomal anomalies linked to neurodevelopmental disorders. In patients with neurodevelopmental disorders, DNA’s from viruses and bacteria including known teratogens were tested against chromosome anomalies known to cause the disorders. Results support a theory that parental infections disrupt elaborate multi-system gene coordination needed for neurodevelopment. Genes essential for neurons, lymphatic drainage, immunity, circulation, angiogenesis, barriers, structure, and chromatin activity were all found close together in polyfunctional clusters that were deleted in neurodevelopmental disorders. These deletions account for immune, circulatory, and structural deficits that accompany neurologic deficits. In deleted clusters, specific and repetitive human DNA matched infections and passed rigorous artifact tests. In some patients, epigenetic driver mutations were found and may be functionally equivalent to deleting a cluster or changing topologic chromatin interactions because they change access to large chromosome segments. In three families, deleted DNA sequences were associated with intellectual deficits and were not included in any database of genomic variants. These sequences were thousands of bp and unequivocally matched foreign DNAs. Analogous homologies were also found in chromosome anomalies of a recurrent neurodevelopmental disorder. Viral and bacterial DNAs that match repetitive or specific human DNA segments are thus proposed to interfere with highly active break repair during meiosis, and sometimes delete polyfunctional clusters, and disable epigenetic drivers. Mis-repaired gametes produce zygotes containing rare chromosome anomalies which cause neurologic disorders and accompanying non-neurologic signs. Neurodevelopmental disorders may be examples of assault on the human genome by foreign DNA with some infections more likely tolerated because they resemble human DNA segments. Further tests of this model await new technology.
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Life Sciences, Microbiology; L.pneumophila, well water, tap water, ice cubes, hospital water, hotel water
Online: 14 September 2018 (16:24:40 CEST)
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Background Legionella pneumophila is one of the causes of legionellosis. Water environments serve as the natural habitat and the main sources of Legionella pneumophila. Objectives The aims of this study was to understand the differences of Legionella pneumophila serogroups distribution in well water, tap water, ice cubes, hospital and hotel water in East Java-Indonesia. Methods a total of 60 water samples in east java-Indonesia; from well water (n=25), tap water (n=5), ice cubes (n=5), water from the hospital (n=16), and hotel water (n=9) were detected using polymerase chain reaction with mip gene spesific primers and then it was analyzed by phylogenetic tree. Results For the 60 water samples collected in East Java, 12% of the samples (7/60) were positively contaminated by L. pneumophila. In details, there was 8% of the well water samples (2/25), 2% of the tap water samples (1/5), 2% of the ice cubes samples (1/5), 0% of the hospital water samples (0/16) and 33.33% of the hotel water samples (3/9). The phylogenetic tree showed that Legionella pneumophila contaminating well water isolate 1 from Surabaya and tap water isolate from Sidoarjo was closer to L.pneumophila serogroup 2, 4, 6, 8, 10, 12, isolates from Brazil, China, Spain and Australia. L.pneumophila contaminating the ice cubes from Sidoarjo was closer to serogroup 1, 2, 4, 7, 8, 11, 13, 14, while the bacteria contaminating well water isolate 2 from Sidoarjo as well as water in hotel of Surabaya (hotel water isolate 1, 2 and 3) classified into their own group. Conclusion There is a difference in the distribution of L. pneumophila serogroups between well water, tap water, ice cubes, and hotels.
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Life Sciences, Immunology; azaphenothiazine; anti-inflammatory activity; CXCL10; KERTr cells; keratinocytes; IFNβ; TLR3;
Online: 14 September 2018 (14:42:52 CEST)
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An azaphenothiazine derivative, 6-chloroethylureidoethyldiquino[3,2-b;2’,3’-e][1,4]thiazine (DQT) has recently been shown to exhibit immunosuppressive activities in mouse models. It also inhibited the expression of CXCL10 at the protein level, at non-toxic concentrations, in the culture of KERTr cells treated with double-stranded RNA, poly(I:C). In this report, we demonstrated that DQT inhibits the transcription of the CXCL10 gene. Although CXCL10 is an IFNγ-inducible protein, we found that the CXCL10 protein was induced without the detectable release of IFNγ or IκB degradation. Hence, we concluded that IFNγ or NFκB were not involved in the regulation of the CXCL10 gene in KERTr cells transfected with poly(I:C) as well as in the inhibitory activity of DQT. On the other hand, we found that IFNβ was induced under the same conditions and its expression was inhibited by DQT. Kinetic analysis showed that an increase in IFNβ concentrations occurred 4-8 h after poly(I:C) treatment, while the concentration of CXCL10 was undetectable at that time and started to increase later, when IFNβ reached high levels. Therefore, DQT may be regarded as a new promising inhibitor of IFNβ expression and IFNβ-dependent downstream genes and proteins, e.g., CXCL10 chemokine, which is implicated in pathogenesis of autoimmune diseases.
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Life Sciences, Biophysics; molecular dynamics simulation; rare event; string method; multiscale enhanced sampling; weighted ensemble; multidrug transporter; Onsager-Machlup action
Online: 13 September 2018 (14:01:39 CEST)
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To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics are important to be characterized but its atomistic details are hard to obtain both experimentally and computationally. We review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: One is the Onsager-Machlup action method, and the other is the weighted ensemble method. Some applications of above methods to biomolecular systems are also discussed and illustrated.