REVIEW Download: 107| View: 82| Comments: 0 | doi:10.20944/preprints201911.0331.v1
Subject: Life Sciences, Biochemistry Keywords: pH and breast cancer; breast cancer etiology; breast cancer etiopathogenesis; breast cancer treatment; pH-centric anticancer paradigm; hydrogen ion dynamics of cancer; cancer proton reversal; MDR integral approach
Online: 27 November 2019 (04:57:00 CET)
Despite all efforts, the treatment of breast cancer (BC) cannot be considered to be a success story. The advances in surgery, chemotherapy and radiotherapy have not been sufficient. Indeed, the accumulated experience clearly indicates that new perspectives and non-main stream approaches are needed to better characterize the etiopathogenesis and treatment of this disease. This contibution deals with how the new pH-centric anticancer paradigm plays a fundamental role in reaching a more integral understanding of the etiology, etiopathogenesis and treatment of this multifactorial disease. For the first time the armamentarium available for the treatment of the different types and phases of BC is approached here from a Unitarian perspective based upon the hydrogen ion dynamics of cancer. The wide-ranged pH-related molecular, biochemical and metabolic model is able to embrace most the fields and subfields of breast cancer pathology. This single and integrated approach allows to advance a unidirectional program to treatment. Further efforts in this line are likely to first improve the therapeutics of each subtype of this tumor, then every phase of the disease and finally every individual patient.
REVIEW Download: 59| View: 67| Comments: 0
Subject: Life Sciences, Virology Keywords: antioxidation; aryl hydrocarbon receptor; cellular oxidation; nuclear factor E2-related factor 2; reactive oxygen species
Online: 27 November 2019 (04:20:30 CET)
Cellular oxidation is responsive to external and internal stimulation and is generated via signal molecules in defense mechanisms through networks of cell proliferation, differentiation, intracellular detoxification, bacterial infection, and immune reactions. Oxidative stress is not necessarily harmful per se; it depends on the balance between oxidation and antioxidation cascades, which are induced according to stimuli and can maintain oxygen homeostasis. The reactive oxygen species (ROS) that are generated during influenza virus (IV) infection have critical effects on both the virus and host cells. In this review, we outline the link between viral infection and ROS production, using IV as an example. We introduce the current state of knowledge on the molecular relationship between cellular oxidation mediated by ROS production and various effects of IV infection. We also summarize the potential anti-IV agents that act by targeting oxidative stress.
Tue, 26 November 2019
REVIEW Download: 64| View: 65| Comments: 0 | doi:10.20944/preprints201911.0320.v1
Online: 26 November 2019 (15:28:52 CET)
Head and neck cancers arise from mucosa lining the oral cavity, oropharynx, hypopharynx, larynx, sinonasal tract, and nasopharynx and the etiology of head and neck cancers is complex and involves many factors, among which oncogenic viruses are also enumerated. Nevertheless, this type of cancers are among the most common cancers around the world. The thorough knowledge of the pathogenesis of viral infection is needed to fully understand its impact on cancer development.
SHORT NOTE Download: 64| View: 41| Comments: 0
Subject: Life Sciences, Biochemistry Keywords: protein sequencing; nanopore; tRNA; RNA; codon; amino acid charging; optical tag
Online: 26 November 2019 (11:52:57 CET)
A method for indirectly sequencing a protein from a codon sequence is proposed. An unfolded protein molecule is threaded through a nano-sized pore in an electrolytic cell carboxyl end first and held with a voltage such that only the first residue is exposed in the trans chamber of the cell. A tRNA molecule in trans with matching anticodon for the residue binds itself to the latter in the presence of suitable catalysts. It is then cleaved and transferred to an extended electrolytic cell with N pores, 40 ≤ N ≤ 61, in N individual cis chambers and a single trans chamber. Each of the N pores holds an RNA molecule ending in a unique codon that is held exposed in the trans chamber. In the presence of suitable catalysts the anticodon in the transferred tRNA binds with the codon of a matching RNA molecule. By reversing the voltages in the extended electrolytic cell every RNA molecule except the one to which the transferred tRNA is bound recedes into its cis chamber, this identifies the residue unambiguously. The detected residue in the first cell is cleaved and the process repeated. A feasibility analysis is presented for the proposed scheme. The method is suitable for de novo sequencing as no a priori information about the protein is needed.
ARTICLE Download: 82| View: 93| Comments: 0 | doi:10.20944/preprints201911.0305.v1
Subject: Life Sciences, Microbiology Keywords: Moringa oleifera; copper nanoparticles; polyphenolics; anti-bacterial; anti-fungal; antioxidant
Online: 26 November 2019 (03:45:52 CET)
The synthesis of metal nanoparticles using plant extracts is a very promising method in green synthesis. The medicinal value of Moringa oleifera leaves and the anti-microbial activity of metallic copper were combined in the present study to synthesize copper nanoparticles having a desirable added-value inorganic material. The use of a hydroalcoholic extract of M. oleifera leaves for the green synthesis of copper nanoparticles is an attractive method as it leads to the production of harmless chemicals and reduces waste. The total phenolic content in the M. oleifera leaves extract was 23.0 ± 0.3 mg gallic acid equivalent/g of dried M. oleifera leaves powder. The M. oleifera leaves extract was treated with a copper sulphate solution. A color change from brown to black indicates the formation of copper nanoparticles. Characterization of the synthesized copper nanoparticles was performed using UV-Vis spectrophotometer, FT-IR spectrometer, TEM, SEM, and XRD. The synthesized copper nanoparticles have an amorphous nature and particle size of 35.8-49.2 nm. We demonstrate that the M. oleifera leaves extract and the synthesized copper nanoparticles display considerable antioxidant activity. Moreover, the M. oleifera leaves extract and the synthesized copper nanoparticles exert potent anti-bacterial activity against Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Enterococcus faecalis (MIC values for the extract: 500, 250, 250, and 250 μg/mL; MIC values for the cooper nanoparticles: 500, 500, 500, and 250 μg/mL, respectively). Similarly, the M. oleifera leaves extract and the synthesized copper nanoparticles exert relatively more potent anti-fungal activity against Aspergillus niger, Aspergillus flavus, Candida albicans, and Candida glabrata (MIC values for the extract: 62.5, 62.5, 125, and 250 μg/mL; MIC values for the cooper nanoparticles: 125, 125, 62.5, and 31.2 μg/mL, respectively). Our study reveals that the green synthesis of copper nanoparticles using a hydroalcoholic extract of M. oleifera leaves was successful. In addition, the synthesized copper nanoparticles can be potentially employed in the treatment of various microbial infections due to their potent antioxidant, anti-bacterial, and anti-fungal activities.
Sun, 24 November 2019
ARTICLE Download: 40| View: 47| Comments: 0 | doi:10.20944/preprints201911.0301.v1
Subject: Life Sciences, Genetics Keywords: genetic code; DNA; alphabet; amino acids; hypercomplex numbers; double numbers; binary numbers; dyadic groups; dyadic shift; tensor product
Online: 24 November 2019 (17:20:40 CET)
The article shows materials to the question on algebraic features of the genetic code. Presented results testify in favor that the genetic code is an algebraic code related with a wide class of algebraic codes, which are a basis of noise-immune coding of information in communication technologies. Algebraic features of the genetic code are associated with hypercomplex double (or hyperbolic) numbers. The article also presents data on structural relations of some genetically inherited macrobiological phenomena with double numbers and with their algebraic extentions. The received results confirm that multidimensional numerical systems is effective for modeling and revealing the interconnections of structures of biological bodies at various levels of their organization. This allows one to think that living organisms are algebraically encoded entities.
ARTICLE Download: 70| View: 42| Comments: 0 | doi:10.20944/preprints201911.0293.v1
Subject: Life Sciences, Microbiology Keywords: Candida spp; cryptic species; Honduras; PCR-RFLP; hwp1 gene; gpi gene; C. auris
Online: 24 November 2019 (16:05:45 CET)
Candida spp. are the most common cause of fungal infections worldwide. The taxonomy of Candida is controversial and has undergone recent changes due to novel genetically related species. Therefore, some complexes of cryptic species have been proposed. In clinical settings, the correct identification of Candida species is relevant since some species are associated with high resistance to antifungal drugs and increased virulence. This study aimed to identify the species of four Candida complexes (C. albicans, C. glabrata, C. parapsilosis, and C. haemulonii) by molecular methods. This is the first report of six cryptic Candida species in Honduras: C. dubliniensis, C. africana, C. duobushaemulonii, C. orthopsilosis, and C. metapsilosis, and it is also the first report of the allele hwp1-2 of C. albicans sensu stricto. It was not possible to demonstrate the existence of C. auris among the isolates of the C. haemulonii complex. We also propose a simple method based on PCR-RFLP for the discrimination of the multi-resistant pathogen C. auris within the C. haemulonii complex.
ARTICLE Download: 71| View: 194| Comments: 0 | doi:10.20944/preprints201911.0292.v1
Subject: Life Sciences, Genetics Keywords: NHEJ; double-strand breaks; mouse model; lymphocyte; neurodevelopment
Online: 24 November 2019 (15:57:38 CET)
Classical non-homologous end joining (NHEJ) is a molecular pathway that detects, processes and ligates DNA double-strand breaks (DSBs) throughout the cell cycle. Mutations in several NHEJ genes result in neurological abnormalities and immunodeficiency both in humans and mice. The NHEJ pathway is required for the V(D)J recombination in developing B and T lymphocytes, and for class switch recombination in mature B cells. Ku heterodimer formed by Ku70 and Ku80 recognizes DSBs and facilitates the recruitment of accessory factors (e.g., DNA-PKcs, Artemis, Paxx and Mri/Cyren) and downstream core factors subunits XLF, XRCC4 and Lig4. Accessory factors might be dispensable for the process depending on the genetic background and DNA lesion type. To determine the physiological role of Mri in DNA repair and development, we introduced frame-shift mutation in the Mri gene in mice. We then analyzed the development of Mri-deficient mice as well as wild type and immunodeficient controls. Mice lacking Mri possessed reduced levels of class switch recombination in B lymphocytes and slow proliferation of neuronal progenitors when compared to wild type littermates. Human cell lines lacking Mri were as sensitive to DSBs as WT controls. Overall, we concluded that Mri/Cyren is largely dispensable for DNA repair and mouse development.
REVIEW Download: 37| View: 46| Comments: 0 | doi:10.20944/preprints201911.0286.v1
Subject: Life Sciences, Genetics Keywords: diversity; conservation; animal genetic resources; indigenous pigs; southern Africa
Online: 24 November 2019 (14:47:39 CET)
Pig genetic resources in Africa originate from different regions. Genetic analysis has shown a strong phylogeographic pattern with the pigs on the eastern parts showing a high frequency of alleles from the Far East while the ones on the western parts show a strong European influence. This highlights the influence of trade routes on the genetic legacy of African pigs. They have, however, since adapted to the local environments to produce unique populations with unique attributes. Most of the pigs are now reared in resource-constrained smallholdings under free-range conditions. They are largely owned by women who spread ownership of the resource through kinship networks. Very little work has been done to characterize, conserve and sustainably utilize pig genetic resources in Southern Africa. The risk status of the breeds together with population numbers, distribution and other attributes are largely unknown. This paper proposes several strategies for the sustainable utilization of the pig genetic resources: a market-driven in situ conservation program and two complementary ex situ strategies. In addition, the possibility of community-based breed improvement programs is discussed.
ARTICLE Download: 39| View: 31| Comments: 0
Subject: Life Sciences, Molecular Biology Keywords: Kandelia obovata; mangrove; hydrogen sulfide; salt tolerance; comparative proteome
Online: 24 November 2019 (14:25:34 CET)
As a dominant mangrove species, Kandelia obovata is distributed in an intertidal marsh with an active H2S release. Whether H2S participates in the salt tolerance of mangrove plant is still ambiguous although increasing evidence have demonstrated that H2S functions in plant responses to multiple abiotic stresses. In this study, as an H2S donor, NaHS was used to investigate the regulatory mechanism of H2S on salt tolerance of K. obovata seedlings using a combined physiological and proteomic analysis. The results showed that the reduction in photosynthesis (Pn) caused by 400 mM NaCl was recovered by the addition of NaHS (200 μM). Furthermore, the application of H2S enhanced the quantum efficiency of PSII and the membrane lipid stability, implying that H2S is beneficial to the survival of K. obovata seedlings under high salinity. We further identified 37 differentially expressed proteins by proteomic approaches under salinity and NaHS treatment. Among them, the proteins related to photosynthesis, primary metabolism, stress response and hormone biosynthesis were primarily enriched. The physiological and proteomic results highlighted that exogenous H2S up-regulated photosynthesis and energy metabolism to help K. obovata to cope with high salinity. Specifically, H2S increased photosynthetic electron transfer, chlorophyll biosynthesis and carbon fixation in K. obovata leaves under salt stress. Furthermore, the abundances of other proteins related to metabolic pathway, such as antioxidation (APX, CSD2, PDX1), protein synthesis (HSP, Cpn 20), nitrogen metabolism (GS2, GS1:1), glycolysis (PGK, TPI), AsA-GSH cycle were increased by H2S under high salinity. These findings provide new insights into the roles of H2S in the adaptations of mangrove plant K. obovata to high salinity environment.
ARTICLE Download: 49| View: 104| Comments: 0 | doi:10.20944/preprints201911.0271.v1
Subject: Life Sciences, Genetics Keywords: breast cancer risk; GWAS; candidate causal variant; chromatin conformation capture; reporter gene activity; enhancer; promoter
Online: 24 November 2019 (05:12:07 CET)
Genome-wide association studies have revealed a locus at 8p12 that is associated with breast cancer risk. Fine-mapping of this locus identified 16 candidate causal variants (CCVs). However, as these variants are intergenic, their function is unclear. To map chromatin looping from this risk locus to a previously identified candidate target gene, DUSP4, we performed chromatin conformation capture analyses in normal and tumoral breast cell lines. We identified putative regulatory elements, containing CCVs, that loop to the DUSP4 promoter region. Using reporter gene assays, we found that the risk allele of CCV rs7461885 reduced the activity of a DUSP4 enhancer element, consistent with the function of DUSP4 as a tumor suppressor gene. Furthermore, the risk allele of CCV rs12155535, located in another DUSP4 enhancer element, was negatively correlated with looping of this element to the DUSP4 promoter region, suggesting that this allele would be associated with reduced expression. These findings provide the first evidence that CCV risk alleles downregulate DUSP4 expression, suggesting that this gene is a regulatory target of the 8p12 breast cancer risk locus.
REVIEW Download: 87| View: 136| Comments: 0 | doi:10.20944/preprints201911.0265.v1
Subject: Life Sciences, Microbiology Keywords: craft brewing; saccharomyces cerevisiae; saccharomyces eubayanus; hybrids; 4-vinyl guaiacol; non-conventional yeasts; evolutionary engineering; artisanal fermented food; natural biodiversity
Online: 24 November 2019 (04:35:23 CET)
Beer is a fermented beverage with a history as old as human civilization and its productive process has been spread all around the world becoming unique in every country and iconic of entire populations. Ales and lagers are by far the most common beers; however, the combination of raw materials, manufacture techniques and aroma profiles are almost infinite, so it is not surprising to notice that there is a large amount of different beer styles, each of them with unique characteristics. Nowadays, diversification is becoming increasingly important in the brewing market and the brewers are continuously interested in improving and extending the already wide range of products, especially in craft brewery. One of the major components that can have a deep impact on the final product is yeast, since it is able to convert carbohydrates in wort, especially maltose and maltotriose, into ethanol, carbon dioxide and other minor aroma-active compounds. Saccharomyces cerevisiae (top‐fermenting yeasts used to produce ales) and Saccharomyces pastorianus (cryotolerant bottom‐fermenting hybrids between S. cerevisiae and Saccharomyces eubayanus responsible for the fermentation of lagers) are most used in breweries. However, an increasing number of different yeast starter cultures are commercially available, to improve the production efficiency also at relative low temperatures and to obtain desirable and diversified aroma profiles avoiding undesired compounds. Four main genetic engineering-free trends are becoming popular in craft brewing yeast development: 1) the research for novel reservoirs as source of new performant S. cerevisiae yeasts; 2) the creation of synthetic hybrids between S. cerevisiae and Saccharomyces non-cerevisiae in order to mimic lager yeasts by expanding their genetic background; 3) the exploitation of evolutionary engineering approaches; 4) the usage of non-Saccharomyces yeasts either in co-coculture or in sequential fermentation with S. cerevisiae. In the present work we summarized pro and contra of these approaches and provided an overview on the most recent advances on how brewing yeast genome evolved and domestication took place. Finally, we delineated how the correlations maps between genotypes and relevant brewing phenotypes can assist and further improve the search for novel craft beer starter yeasts.
Fri, 22 November 2019
CONCEPT PAPER Download: 35| View: 46| Comments: 0
Subject: Life Sciences, Biophysics Keywords: brain; nervous system; Einstein; relativity; spacetime; mind
Online: 22 November 2019 (06:46:57 CET)
Visual imagery, i.e., the mental experience of an object occurring in the absence of external visual stimulus, might encompass diverse content according to different observers. Further, subjectively experienced time is encoded in the later entorhinal cortex. Starting from these two observations, and considering Einstein’s account of spacetime, we show how, in terms of special relativity, the content of visual imagery is not stationary and fixed, rather depends on the standpoint of the observer. We elucidate how the subjective definition of time (perceived by our mind as static) might give rise to modifications in the length of the imagined object which are experimentally assessable and quantifiable. In particular, based on recent neuroscientific literature, we show how changes in our mental time windows are able to squeeze the visual content of mental imagery.
Thu, 21 November 2019
ARTICLE Download: 70| View: 87| Comments: 0 | doi:10.20944/preprints201911.0251.v1
Subject: Life Sciences, Biotechnology Keywords: endophyte; Trichoderma; fatty acid; antifeedant, myzus persicae; culture media
Online: 21 November 2019 (15:00:33 CET)
Increasing pesticide resistance in plant pathogens is major concern in agriculture production. Research on ecofriendly alternatives of chemical pesticides are more in demand in pesticide industry. In the current study, an ethyl acetate extract from the endophytic fungus Trichoderma sp. EFI 671, isolated from the stem parts of the medicinal plant Laurus sp., was screened for bioactivity against plant pathogens (Fusarium graminearum, Rhizoctonia solani, Sclerotinia sclerotiorum and Botrytis cinerea), insect pests (Spodoptera littoralis, Myzus persicae, Rhopalosiphum padi) and plant parasites (Meloidogyne javanica). The bioactive components have been characterized following a bioassay-guided isolation against M. persicae. The chemical study of this bioactive extract resulted in the isolation of 1-oleoyl-2-linoleoyl-3-palmitoylglycerol (1), eburicol (2), (24R)-stigmast-4-ene-3-one or β-sitostenone (3), ergosterol (4) and ergosterol peroxide (5). The free fatty acids present in compound 1 (oleic, linoleic and palmitic) showed strong dose-dependent aphid antifeedant effects against M. persicae. Liquid (PDB, and SDB) and solid (corn, sorghum, pearl millet and rice) growth media were tested in order to optimize the yield and bioactivity of the fungal extracts. Pearl millet and corn gave the highest extract yields. All the extracts from these solid media had strong effects against M. persicae with sorghum being the most active. Corn increased the content in linolenic, pearl millet the oleic and stearic and sorghum oleic and linolenic acids compared to rice. Their antifeedant effects correlated with linoleic /oleic acids. The phytotoxic effects of these extracts against Lolium perenne and Lactuca sativa varied with culture media, with sorghum being the least toxic.
ARTICLE Download: 60| View: 173| Comments: 0 | doi:10.20944/preprints201911.0246.v1
Subject: Life Sciences, Biochemistry Keywords: bioactive compounds; forest air; forest bathing; forest therapy; hiking trails; human health; monoterpenes; stress; volatile organic compounds
Online: 21 November 2019 (04:19:17 CET)
Forest healing effects are increasingly valued for their contribution to human psychological and physiological health, motivating further advances aimed at improving the knowledge of the relevant forest resources. Biogenic volatile organic compounds, emitted by the plants and accumulating in the forest atmosphere, are essential contributors to the forest healing effects, and represent the focus of this study. Using a photoionization detector, we investigated the high frequency variability, in time and space, of the concentration of total volatile organic compounds, on a hilly site, as well as along forest paths and long hiking trails on Italian northern Apennines. The scale of concentration variability was found to be comparable to absolute concentration levels, within time scales of less than one hour, and spatial scales of several hundred meters. During daylight hours, the concentration peaked from noon to early afternoon, followed by early morning, with lowest levels in late afternoon. Based on a conceptual model, these results were related to meteorological variables, including the atmospheric vertical stability profile. Moreover, preliminary evidence pointed to higher concentration of volatile organic compounds in forests dominated by conifer trees, in comparison with pure beech forests.
Wed, 20 November 2019
ARTICLE Download: 61| View: 62| Comments: 0 | doi:10.20944/preprints201911.0243.v1
Subject: Life Sciences, Genetics Keywords: adrenergic signaling; ankyrin-B; calcium channel; calcium signaling; glycolysis; oxidative phosphorylation; potassium channel; sodium channel
Online: 20 November 2019 (15:58:20 CET)
Myocardium transcriptomes of mouse left and right atria and ventricles were profiled separately to identify the differences that might be responsible for the distinct functional roles of the four heart chambers. In total, 16,886 distinct unigenes have been quantified in all 16 samples collected from four adult male mice from the same litter. 15.76% of the quantified genes on the left and 16.5% on the right exhibited differential expression between the corresponding atrium and ventricle of the same side, while 5.8% in atria and 1.2% in ventricles were differently expressed between the left and the right. Beyond the differentially expressed genes, the study revealed distinct expression control and coordination of ion channels and genes within the cardiac muscle contraction, oxidative phosphorylation, glycolysis/glucogenesis, calcium and adrenergic signaling pathways. Interestingly, while expression of Ank2 (encoding ankyrin-B) oscillates in phase with all its binding partners in the left ventricle, the percentage of synergistically expressed partners of Ank2 is 15% and 37% in the left and right atria and 74% in the right ventricle. The analysis revealed also the high interventricular synchrony of the expression of ion channels.
REVIEW Download: 62| View: 76| Comments: 0 | doi:10.20944/preprints201911.0236.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Hox genes; limb development; main body axis; timing; time space translation
Online: 20 November 2019 (10:31:55 CET)
This article is a tribute to Lewis Wolpert on the occasion of the recent 50th anniversary of the publication of his article ‘Positional Information and the Spatial Pattern of Differentiation’. This tribute relates to another of his ideas: his early ‘Progress Zone’ timing model for limb development. Recent evidence is reviewed that a mechanism sharing features with this model patterns the main body axis in early vertebrate development. This tribute celebrates the golden era of Developmental Biology.
Tue, 19 November 2019
ARTICLE Download: 83| View: 1151| Comments: 1 | doi:10.20944/preprints201909.0273.v2
Subject: Life Sciences, Biophysics Keywords: amyloid; virus; nucleation; loss-of-function; Alzheimer's; Parkinson's; prion; protein-only
Online: 19 November 2019 (03:53:09 CET)
Amyloids are fibrillar protein aggregates that are associated with diseases such as Alzheimer’s disease, Parkinson’s disease, type II diabetes and Creutzfeldt–Jakob disease. The process of amyloid aggregation involves three pathological protein transformations; from natively-folded conformation to the cross-β conformation, from biophysically soluble to insoluble, and from biologically functional to non-functional. While amyloids share a similar cross-β conformation, the biophysical transformation can either take place spontaneously via a homogeneous nucleation mechanism (HON) or catalytically on an exogenous surface via a heterogeneous nucleation mechanism (HEN). Here, we postulate that the different nucleation pathways can serve as a mechanistic basis for an etiological classification of amyloidopathies, where hereditary forms generally follow the HON pathway, while sporadic forms follow surface-induced (including microbially-induced) HEN pathways. Furthermore, the conformational and biophysical amyloid transformation results in loss-of-function (LOF) of the original natively-folded and soluble protein. This LOF can, at least initially, be the mechanism of amyloid toxicity even before amyloid accumulation reaches toxic levels. By highlighting the important role of non-protein species in amyloid formation and LOF mechanisms of toxicity, we propose a generalized mechanistic framework that could help better understand the diverse etiology of amyloid diseases and offer new opportunities for therapeutic interventions including replacement therapies.
ARTICLE Download: 49| View: 56| Comments: 0 | doi:10.20944/preprints201911.0216.v1
Subject: Life Sciences, Other Keywords: amino acid; digestive enzyme; low protein diet; nitrogen balance; pigs
Online: 19 November 2019 (02:56:38 CET)
This study was conducted to determine the dynamic effects of dietary crude protein (CP) intake on nitrogen (N) balance, ileal amino acid digestibility, and gene expression levels of digestive enzymes at three stages in pigs. In Experiment 1, 18 growing pigs (average body weight (BW) = 9.5 kg) were randomly assigned to one of three treatments (n = 6/treatment group), including normal (20% CP), low (17% CP), and very low (14% CP) protein intake. In Experiment 2, 18 growing pigs (average BW = 30 kg) were allotted randomly to one of three treatments (n = 6/treatment group), including normal (18% CP), low (15% CP), and very low (12% CP) protein intake. In Experiment 3, 18 growing pigs (average BW = 45 kg) were assigned randomly to one of three treatments (n = 6/treatment group), including normal (16% CP), low (13% CP), and very low (10% CP) protein intake. Growing pigs fed the 14% CP and 17% CP diets had lower final BW (P < 0.05) and average daily gain (ADG) (P < 0.05) compared to pigs fed the 20% CP diet. Reducing the dietary CP level from 20 to 14% decreased urinary N excretion by 52.8% (P < 0.001) in Experiment 1. Reducing the dietary CP level from 18 to 12% decreased urinary N excretion by 55.3% (P < 0.001) and reduced fecal N excretion by 34% (P < 0.05) in Experiment 2. Reducing the dietary CP level from 16 to 10% decreased urinary N excretion by 56.4% (P < 0.001) and fecal N excretion by 47.1% (P < 0.001) in Experiment 3. Pigs fed the very low (14%, 12%, and 10% CP) diets showed higher digestibility for CP (P < 0.05), His (P < 0.05), Ile (P < 0.05), Phe (P < 0.05), Thr (P < 0.05), Trp (P < 0.05), Glu (P < 0.05), and Ser (P < 0.05) compared to pigs fed the normal (20%, 18%, and 16% CP) diets among the three experiments. Pigs fed the very low (14%, 12%, and 10% CP) diets showed higher mRNA levels for chymotrypsin C (P < 0.01 in Experiment 1 and 2; P < 0.05 in Experiment 3) compared to pigs fed the normal (20%, 18%, and 16% CP) diets among the three experiments. These results indicated that a reduction in dietary CP by 6% limited the growth performance of growing pigs, and a reduction of dietary CP by 3% supplemented with essential amino acids could reduce the excretion of N into the environment without affecting weight gain.
Sun, 17 November 2019
ARTICLE Download: 47| View: 46| Comments: 0 | doi:10.20944/preprints201911.0205.v1
Online: 17 November 2019 (13:44:29 CET)
The frequency of earthquakes in South Korea is increasing. This study aimed to examine and identify the factors influencing the degree of disaster-incident-related shock among Korean nursing students with the disaster experience. The study sample consisted of 153 nursing students who have been living around Phohang-si in Gyeongsang-do, South Korea, and who having the experience of disaster-incident-related shock. Measures were Impact of Event Scale, Perceived health status scale, Psychological Well-Being Scale, and Coping Strategy Indicator in Korean version. The data collection period was from October to December, 2018. The factor that was found to have the most influence on disaster-incident-related shock among Korean nursing students was the perceived health status (β = 0.48), followed by gender (β = -0.28), coping skill (β = 0.18), psychological well-being (β = 0.14), need for disaster education (β = 0.12), and major satisfaction (β = -0.12). This study provides preliminary evidence that perceived health status is a major and primary predictor of disaster-incident-related shock among Korean nursing students, next followed by coping skill, and psychological well-being. The findings can be reflected in the pertinent curriculum by actively considering these influence factors in designing nursing education interventions for disaster-incident-related shock in the Korean nursing students.
Fri, 15 November 2019
ARTICLE Download: 43| View: 44| Comments: 0 | doi:10.20944/preprints201911.0177.v1
Subject: Life Sciences, Molecular Biology Keywords: macrophage migration inhibitory factor; HNSCC cell lines; proliferation; cell cycle; apoptosis
Online: 15 November 2019 (08:48:50 CET)
Macrophage migration inhibitory factor (MIF) is a multifunctional cytokine that contributes to the progression of several cancers. MIF overexpression has been reported in head and neck squamous cell carcinoma (HNSCC) patients. However, the exact role of MIF in HNSCC is not fully understood. Our aim was to evaluate the amount of secreted MIF and the role of MIF in the proliferation, cell cycle, and apoptosis in HNSCC cell lines. The MIF levels in conditioned media from human primary (HN18 and HN30) and metastatic (HN17 and HN31) HNSCC cell lines were evaluated using ELISA. The HNSCC cell lines were treated with recombinant MIF and its effect on proliferation, cell cycle, and apoptotic status was determined by MTT and flow cytometry, respectively. The HNSCC-secreted MIF concentration ranged from 49.33‒860 pg/ml. Exogenous MIF (25 ng/ml) significantly increased HN18, HN30, and HN31 cell proliferation. Moreover, MIF induced cell cycle progression and inhibited apoptosis in these cells. However, MIF did not affect growth or apoptosis in HN17 cell. In conclusion, the HNSCC cell lines were evaluated secrete MIF. Exogenous MIF promotes various effects on proliferation, cell cycle, and apoptosis in HNSCC cells.
Thu, 14 November 2019
ARTICLE Download: 103| View: 120| Comments: 0 | doi:10.20944/preprints201911.0162.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: human pluripotent stem cells; human stem cell-derived hepatocytes; in vitro; metabolic diseases; transcriptomics; maturation; characterization
Online: 14 November 2019 (11:24:24 CET)
There is a strong anticipated future for human pluripotent stem cell-derived hepatocytes (hiPS-HEP), but so far their use has been limited due to insufficient functionality. We investigated the potential of hiPS-HEP as an in vitro model for metabolic diseases by combining transcriptomics with multiple functional assays. The transcriptomics analysis revealed that 86% of the genes were expressed at similar levels in hiPS-HEP as in human primary hepatocytes (hphep). Adult characteristics of the hiPS-HEP were confirmed by the presence of important hepatocyte features, e.g. Albumin secretion and expression of major drug metabolizing genes. Normal energy metabolism is crucial for modeling metabolic diseases, and both transcriptomics data and functional assays showed that hiPS-HEP were similar to hphep regarding uptake of glucose, LDL and fatty acids. Importantly, the inflammatory state of the hiPS-HEP was low under standard conditions, but in response to lipid accumulation and ER stress the inflammation marker TNFα was upregulated. Furthermore, hiPS-HEP could be co-cultured with primary hepatic stellate cells both in 2D and in 3D spheroids, paving the way for using these co-cultures for modeling NASH. Taken together, hiPS-HEP have the potential to serve as an in vitro model for metabolic diseases. Furthermore, differently expressed genes identified in this study can serve as targets for future improvements of the hiPS-HEP.
ARTICLE Download: 19| View: 45| Comments: 0
Subject: Life Sciences, Molecular Biology Keywords: DNA lesions; 7,8-dihydro-8-oxoguanine (8-oxoG); mutagenic activity; method of detection; cell nuclear extracts; mice organs and embryos
Online: 14 November 2019 (09:00:19 CET)
We propose an improved earlier described “mirror” method  for detecting in cell nuclear extracts mutations that arise in DNA during its replication due to misincorporation of deoxyadenosine-5’-monophosphate (dAMP) opposite 7,8-dihydro-8-oxoguanine (8-oxoG). The method is based on the synthesis of a complementary chain (“mirror”) by nuclear extracts of different mice organs on a template containing 8-oxoG inside and dideoxycytidine residue (ddC) at the 3’-end. The “mirror”was amplified by PCR using primers part of which was non-complementary to the template. It allowed obtaining the “framed mirror” products. The misincorporation of dAMP in “framed mirror” products forms an EcoRI restriction site. The restriction analysis of double-stranded “framed mirror” products allows a quantification of the mutation frequency in nuclear extracts. The data obtained showed that the mutagenic potential of 8-oxoG markedly varied in different organs of adult mice and embryos.
Wed, 13 November 2019
ARTICLE Download: 62| View: 66| Comments: 0 | doi:10.20944/preprints201911.0147.v1
Subject: Life Sciences, Microbiology Keywords: endometriosis; microbiome; 16s-rrna sequencing; atopobium
Online: 13 November 2019 (11:42:32 CET)
Abstract Objective: Endometriosis is a chronic disease characterized by the growth of endometrial cells outside the uterine cavity. The dysfunction of the immune system is strongly associated with the progression of endometriosis, and is also correlated to the diversity of microbiota in the genital tract. According to previous studies, the microbiota significantly contributes to multi-systemic function, but the evidence of endometriosis and adenomyosis remains insufficient. Thus, the present study attempted to identify the characteristics of microbiota in endometriosis patients, and the connection between microbiota and immunological dysfunction. Methods: In order to compare and explore the potential microbiota correlated to endometriosis and adenomyosis in the genital tract, 134 samples obtained from the cervical canal, posterior fornix and uterine cavity were analyzed by 16s-rRNA sequencing. The raw data was filtered, analyzed and visualized, and bio-information methods were used to identify the different and distinctive characteristics of microbiota. Results: Two different locations near the cervix, cervical canal and posterior fornix, exhibited no differences in alpha diversity. Among the different disease groups, five microbiota were distinctive in the genus level, and Atopobium presented with the greatest significance in adenomyoisis-endometriosis patients. The LEfSe analysis failed to identify the special biomarkers, while several characteristic functions were identified through PICRUSt. Conclusion: Lactobacillus is dominant in the female lower genital tract, and Atopobium is distinctively higher in patients with endometriosis combined with adenomyosis. Several different functions of microbiota were explored, and these are found to be associated with endometriosis and adenomyosis. These findings may provide a new concept of microbiota/immune system/endometriosis system. There is an urgent need to investigate the potential microbial biomarkers of endometriosis in the future.
ARTICLE Download: 43| View: 87| Comments: 1 | doi:10.20944/preprints201911.0063.v2
Subject: Life Sciences, Microbiology Keywords: contamination; pathogens; bacteria; escherichia coli; staphylococcus aureus; hygiene; shigella; salmonella; milk processing; foodborne infection; cfu
Online: 13 November 2019 (10:37:25 CET)
Pasteurized milks are still causing food borne illness. Milk contamination can occur at any stage from its way from cow to our tables. Usually milk is pure and sterile when produced in udder of a healthy cow. Like humans, cow are reservoirs of bacteria which are harmless to humans and some cows can harbour few bacteria that are harmful to humans even though they are not harmful to the cow. Milk can be contaminated during or after milking. Also, cow feeds can be contaminated with mycotoxins such as aflatoxins produced by the fungi, Aspergillus flavus. Four types of aflatoxins are known which are; aflatoxin B1, B2, G1, G2. Cows comsuming feeds contaminated with aflatoxin B1 leads to secretion in the milk of aflatoxin M1 and M2 causing aflatoxicosis. Microbial contamination of milk and dairy products is a universal problem and foodborne infections accounting for 20 million cases annually in the world have been identified as an important public health and economic problem in developed as well as developing nations. The main objective of this study was to determine milk microbial quality in Kicukiro district. The specific objectives are to identify bacteria pathogens in milk collected in Kicukiro district, to compare milk quality among sectors of Kicukiro district, to compare milk processed by industries and home-processed milk. The methodology employed in this research was cross-sectional and experimental as the study began with collection of raw data and went through laboratory analysis from July–August, 2018. The findings showed that 59.56% of the milk fell within Grade I – Grade III (< 200,000 ≤ 2,000,000 cfu/ml) and 40.42 % of the milk samples were not within the acceptable limit of total count quality as per COMESA and EAS, non-lactobacilli and fungi were present in most samples as examined through microscope and no Staphylococcus aureus was present in any sample as examined by catalase and coagulase tests.
ARTICLE Download: 54| View: 68| Comments: 0 | doi:10.20944/preprints201911.0137.v1
Subject: Life Sciences, Other Keywords: Hibiscus sabdariffa; phenolic compounds; spray-drying; antioxidant capacity
Online: 13 November 2019 (03:15:28 CET)
Aqueous and ethanolic extracts of Hibiscus sabdariffa were spray-drying using maltodextrin (MD) and gum arabic (GA) as carriers agents. An experimental design Taguchi L8 with seven variables was implemented. Physicochemical properties in the encapsulates were evaluated by UV-Vis, XRD, spectroscopy and gravimetric techniques. Treatments with aqueous extracts showed the highest concentration of total soluble polyphenols (TSP) 32.12- 21.23 mg EAG/g DW, and antioxidant capacity (AOX) for ABTS assay. The best treatment for TSP and AOX was T4: 2.5% Hibiscus w/w, aqueous extracts, decoction, extract-to-carrier ratio 1:1 (w/w), proportion to carriers (MD:GA) 80:20 (w/w), 10000 rpm, 150°C. Taguchi L8 model is a tool that allows the use of multiple variables with a low number of treatments that indicate the drying conditions that give the best parameters, focusing mainly on TSP and AOX, in addition, is a good alternative for the preservation and stability of the PC in Hibiscus.
Sun, 10 November 2019
ARTICLE Download: 65| View: 80| Comments: 0 | doi:10.20944/preprints201911.0100.v1
Online: 10 November 2019 (09:24:22 CET)
Paper recycling has increased in recent years. A principal consequence of this process is the problem of addressing polymeric components known as stickies. A deep characterization of stickies sampled over one year in a recycled paper industry in México was performed. Based on their chemical structure, an enzymatic assay was performed using lipases. Compounds found in stickies by Fourier-Transform Infrared spectrometry were poly (butyl-acrylate), dioctyl phthalate, poly (vinyl-acetate), and poly (vinyl-acrylate). Pulp with 4% consistency and pH=6.2 was sampled directly from the mill once macro stickies were removed. Stickies were quantified by counting the tacky macrostructures in the liquid fraction of the pulp using a Neubauer chamber before the paper was made, and they were analyzed with rhodamine dye and a UV lamp. Of the two enzymes evaluated, the best treatment condition used Lipase 30G at a concentration of 0.44 g/L, which produced a 35.59% decrease in stickies. SebOil DG showed a smaller stickies reduction of 21.5% when used at a concentration of 0.33 g/L. Stickies in kraft paper processes were actively controlled by the action of lipases, and future research should focus on how this enzyme recognizes its substrate and should apply synthetic biology to improve lipase specificity.
Fri, 8 November 2019
REVIEW Download: 149| View: 269| Comments: 0 | doi:10.20944/preprints201911.0085.v1
Subject: Life Sciences, Genetics Keywords: mendelian disease; diagnostics; variant interpretation; variant prioritization; rna splicing; bioinformatics; machine learning; genomic medicine; effect prediction
Online: 8 November 2019 (04:07:16 CET)
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient’s variant landscape, the ability to characterize variants causing splicing defects has not progressed with the same speed. To address this, recent years have seen a sharp spike in the number of splice prediction tools leveraging machine learning approaches, leaving clinical geneticists with a plethora of choices for in silico analysis. In this Review, some basic principles of machine learning are introduced in the context of genomics and splicing analysis. A critical comparative approach is then used to describe seven recent machine learning-based splice prediction tools, revealing highly diverse approaches and common caveats. We find that, although great progress has been made in producing specific and sensitive tools, there is still much scope for personalized approaches to prediction of variant impact on splicing. Such approaches may increase diagnostic yields and underpin improvements to patient care.
ARTICLE Download: 104| View: 94| Comments: 0 | doi:10.20944/preprints201911.0081.v1
Subject: Life Sciences, Virology Keywords: Kaposi’s sarcoma-associated herpesvirus (KSHV); human herpesvirus-8; zebrafish; ddPCR; xenotransplantation; primary effusion lymphoma (PEL); hypoxia
Online: 8 November 2019 (03:23:22 CET)
Kaposi’s sarcoma associated-herpesvirus (KSHV, also known as human herpesvirus-8) is a gammaherpesvirus that establishes life-long infection in human B lymphocytes. KSHV infection is typically asymptomatic but immunosuppression can predispose KSHV-infected individuals to primary effusion lymphoma (PEL); a malignancy driven by aberrant proliferation of latently infected B lymphocytes, and supported by pro-inflammatory cytokines and angiogenic factors produced by cells that succumb to lytic viral replication. Here, we report the development of the first in vivo model for a virally-induced lymphoma in zebrafish, whereby KSHV-infected PEL tumour cells engraft and proliferate in the yolk sac of zebrafish larvae. Using a PEL cell line engineered to produce the viral lytic switch protein RTA in the presence of doxycycline, we demonstrate drug-inducible reactivation from KSHV latency in vivo, which enabled real-time observation and evaluation of latent and lytic phases of KSHV infection. In addition, we developed a sensitive droplet digital PCR method to monitor latent and lytic viral gene expression and host cell gene expression in xenografts. The zebrafish yolk sac is not well-vascularized and using fluorogenic assays we confirmed that this site provides a hypoxic environment that may mimic the microenvironment of some human tumors. We found that PEL cell proliferation in xenografts was dependent on the host hypoxia-dependent translation initiation factor, eukaryotic initiation factor 4E2 (eIF4E2). This demonstrates that the zebrafish yolk sac is a functionally hypoxic environment and xenografted cells must switch to dedicated hypoxic gene expression machinery to survive and proliferate. The establishment of the PEL xenograft model enables future studies that exploit the innate advantages of the zebrafish as a model for genetic and pharmacologic screens.
Thu, 7 November 2019
ARTICLE Download: 84| View: 112| Comments: 0 | doi:10.20944/preprints201911.0077.v1
Subject: Life Sciences, Microbiology Keywords: antibiotics; antibiotics resistance; antimicrobial resistance; dispensing; pharmacist; prescription; Tanzania
Online: 7 November 2019 (15:03:56 CET)
Background: Inappropriate use of antibiotics has been reported to contribute to the emergence and increase of antimicrobial resistance (AMR) in the world. Antibiotics are prescription-only medicines to be dispensed to a person with a legal prescription inscribed by a qualified medical practitioner. Enforcing the dispensing of antibiotics with prescription is a way to promote the rational use of antibiotics and preventing the development and spread of AMR. It is, therefore, the responsibility of a pharmacist to dispense or supervise the dispensing of antibiotics in pharmacies and ensure its rational use. This study aimed to assess pharmacists’ knowledge, attitude and practice regarding the dispensing of antibiotics without prescription in Tanzania. Methods: An online semi-structured questionnaire was designed, tested and shared with licensed pharmacists in Tanzania through an invitation link sent in their official WhatsApp groups. A list of names, contacts and emails of licensed pharmacists obtained from the Pharmacy Council was used to directly contact and request pharmacist to fill the questionnaire, in case the pharmacist contact was not on WhatsApp, a text SMS invitation was sent. Study data were collected and managed using REDCap electronic data capture tools hosted at Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania. Data were then downloaded and exported into Statistical Package for Social Sciences (SPSS) version 20 for data analysis; Chi-square test was used to test association for categorical data, where a p-value of less than 0.05 was considered statistically significant. Results: More than 75% of pharmacists had excellent knowledge about the legal requirements for dispensing antibiotics and of the AMR challenge. Of the interviewed pharmacists, seventy-four percent admitted to dispensing antibiotics without prescription in their daily practice. The main reasons for administering antibiotics without prescription were the profitability nature of pharmacy business, a failure of the patient to get a prescription and lack of stringent regulatory authorities. Penicillins, macrolides and floroquinolones were the classes of antibiotics mostly dispensed without a prescription. Conclusion: The study shows that the dispensing of antibiotics without prescription is a common practice in Tanzania. The regulatory authorities should make regular inspections in pharmacies to detect this malpractice. The community should be trained on the importance of taking laboratory tests before getting medications for their sickness by a qualified medical practitioner.
REVIEW Download: 107| View: 104| Comments: 0 | doi:10.20944/preprints201911.0076.v1
Subject: Life Sciences, Genetics Keywords: phase separation; nuclear bodies; self-assembly; genome organization; gene expression
Online: 7 November 2019 (14:48:08 CET)
The importance of genome organization at the supranucleosomal scale in the control of gene expression is increasingly recognized today. In mammals, Topologically Associating Domains (TADs) and the active / inactive chromosomal compartments are two of the main nuclear structures that contribute to this organization level. However, recent works reviewed here indicate that, at specific loci, chromatin interactions with nuclear bodies could also be crucial to regulate genome functions, in particular transcription. They moreover suggest that these nuclear bodies are membrane-less organelles dynamically self-assembled and disassembled through mechanisms of phase separation. We have recently developed a novel genome-wide experimental method, High-salt Recovered Sequences sequencing (HRS-seq), designed to identify chromatin regions associated with large ribonucleoprotein (RNP) complexes and nuclear bodies. We argue that the physical nature of such RNP complexes and nuclear bodies appears to be central in their ability to promote efficient interactions between distant genomic regions. The development of novel experimental approaches, including our HRS-seq method, is opening new avenues to understand how self-assembly of phase separated nuclear bodies possibly contributes to mammalian genome organization and gene expression.
REVIEW Download: 71| View: 100| Comments: 0 | doi:10.20944/preprints201911.0074.v1
Online: 7 November 2019 (09:42:30 CET)
A contrasting empirical evaluation will be provided with the aim of suggesting that the reductionist approach results in experiments that are not reproducible.
Wed, 6 November 2019
ARTICLE Download: 51| View: 482| Comments: 12 | doi:10.20944/preprints201911.0063.v1
Subject: Life Sciences, Microbiology Keywords: contamination; pathogens; bacteria; escherichia coli; staphylococcus aureus; hygiene; shigella; salmonella; milk processing; foodborne infection; cfu
Online: 6 November 2019 (11:35:43 CET)
Pasteurized milks are still causing food borne illness. Milk contamination can occur at any stage from its way from cow to our tables. Usually milk is pure and sterile when produced in udder of a healthy cow. Like humans, cow are reservoirs of bacteria which are harmless to humans and some cows can harbour few bacteria that are harmful to humans even though they are not harmful to the cow. Milk can be contaminated during or after milking. Also, cow feeds can be contaminated with mycotoxins such as aflatoxins produced by the fungi, Aspergillus flavus. Four types of aflatoxins are known which are; aflatoxin B1, B2, G1, G2. Cows comsuming feeds contaminated with aflatoxin B1 leads to secretion in the milk of aflatoxin M1 and M2 causing aflatoxicosis. Microbial contamination of milk and dairy products is a universal problem and foodborne infections accounting for 20 million cases annually in the world have been identified as an important public health and economic problem in developed as well as developing nations. The main objective of this study is to determine milk microbial quality in Kicukiro district. The specific objectives are to identify bacteria pathogens in milk collected in Kicukiro district, to compare milk quality among sectors of Kicukiro district, to compare milk processed by industries and home-processed milk. The methodology employed in this research was cross-sectional and experimental as the study began with collection of raw data and went through laboratory analysis from July – August, 2018. The expected results from this study will be beneficial to four groups; one is to me as this research will help me to put into practice what I have been learning throughout my years in the school and help me acquire the basic knowledge practically in the laboratory, two is to the masses as this research when published, will help people know where to buy quality and healthy milk products, three is to the government as this research with aid the government to monitor milk processors and promulgate a law that will seek to restrict person who process commercial milk in unhygienic environment, four is to the researchers as this research will serve as basis and background knowledge in their subsequent researches. The findings showed that 59.56% of the milk fell within Grade I – Grade III (< 200,000 ≤ 2,000,000 cfu/ml) and 40.42 % of the milk samples were not within the acceptable limit of total count quality as per COMESA and EAS, non-lactobacilli and fungi were present in most samples as examined through microscope and no Staphylococcus aureus was present in any sample as examined by catalase and coagulase tests.
ARTICLE Download: 83| View: 84| Comments: 0 | doi:10.20944/preprints201911.0061.v1
Subject: Life Sciences, Molecular Biology Keywords: rett syndrome; intrinsically disordered region; phylogenetic profile analysis; post-transcriptional modification; methyl-cpg-binding protein 2; cyclin-dependent kinase-like 5; forkhead box protein g1
Online: 6 November 2019 (10:58:54 CET)
Rett syndrome (RTT), a neurodevelopmental disorder, is mainly caused by mutations in methyl CpG-binding protein 2 (MECP2), which alter the functions of domains to either bind to methylated DNA or interact with a transcriptional co-repressor complex. It has been established that alterations in cyclin-dependent kinase-like 5 (CDKL5) or forkhead box protein G1 (FOXG1) correspond to distinct neurodevelopmental disorders, given that a series of studies have indicated that RTT is also caused by alterations in either one of these genes. We tried to elucidate RTT through evolution and structure assessment of MeCP2, CDKL5, and FOXG1, by focusing on their binding partners and disordered structures. Here, we provide insight into the similarities of the FOXG1 and MECP2 binding partners evolution and function. On the other hand, we suggest that CDKL5 could be a potential candidate for a classical RTT treatment, particularly based on its disordered structure that spans after the catalytic domain to the C-terminus, which shows abundant linear motifs that can bind to molecules with divergent structures of similar affinity. Additionally, we provide insight into the relationship between disordered structure and disease.
REVIEW Download: 148| View: 104| Comments: 0 | doi:10.20944/preprints201911.0060.v1
Subject: Life Sciences, Other Keywords: alcohol consumption; Alzheimer's disease; light to moderate wine consumption; neurodegeneration
Online: 6 November 2019 (10:54:00 CET)
Background: Alzheimer’s disease (AD), the most threatening neurodegenerative diseases, is characterized by the loss of memory and language function, an unbalanced perception of space and other cognitive and physical manifestations. Pathology of the AD is characterized by neuronal loss, and the extensive distribution of senile plaques and neurofibrillary tangles (NFTs). The role of environment and the diet in the AD is being studied actively, and nutrition is certainly one of the main factors playing a prominent role in the prevention of neurodegenerative diseases. In this context, the relationship between dementia and wine use/abuse has received increased research interest in recent times, with varying and often conflicting results. Scope and approach: This review aims to critically summarize the most recent studies conducted to clarify the relationship between wine drinking and AD, as well as whether effects are influenced by quantity and/or frequency of drinking. Key findings and Conclusion: Overall, based on the interpretation of various studies, it can be concluded that there is no indication that light to moderate alcohol drinking is detrimental to cognition and dementia, and it is not possible to define whether alcohol could be used as a means to reduce risk of developing AD.
Tue, 5 November 2019
ARTICLE Download: 96| View: 81| Comments: 0 | doi:10.20944/preprints201911.0042.v1
Subject: Life Sciences, Endocrinology & Metabolomics Keywords: olivo-ponto-cerebellar atrophy (OPCA); amyotrophic lateral sclerosis (ALS); tauopathy; leukodystrophy; mass spectrometry; RT-qPCR; Ceramide Synthase (CERS2/CERS1); Serine Palmitoyltransferase 2 (Sptlc2); neutral Sphingomyelinase (Smpd3); neutral Ceramidase (Asah2); Fatty Acid Elongase (Elovl1/4/5); SCA34; SCA38; acid Sphingomyelinase (ASMase, Smpd1)
Online: 5 November 2019 (03:04:02 CET)
Ataxin-2 (ATXN2) acts during stress-responses, modulating mRNA translation and nutrient metabolism. Atxn2 knockout mice exhibit progressive obesity, dyslipidemia and insulin resistance. Conversely, the progressive ATXN2 gain-of-function due to polyGlutamine (polyQ) expansions leads to a dominantly inherited neurodegenerative process named spinocerebellar ataxia type 2 (SCA2), with early adipose tissue loss and late muscle atrophy. We tried to understand lipid dysregulation in a SCA2 patient brain and in an authentic mouse model. Thin layer chromatography of a patient cerebellum was compared to the lipid metabolome of Atxn2-CAG100-KnockIn (KIN) mouse spinocerebellar tissue. The human pathology caused deficits of sulfatide, galactosylceramide, cholesterol, C22/24-sphingomyelin and gangliosides GM1a/GD1b, despite quite normal levels of C18-sphingomyelin. Cerebellum and spinal cord from the KIN mouse showed a consistent decrease of various ceramides, with a significant elevation of sphingosine in the more severely affected spinal cord. Deficiency of C24/26-sphingomyelins contrasted with excess C18/20-sphingomyelin. Spinocerebellar expression profiling revealed consistent reductions of CERS protein isoforms, of Sptlc2 and Smpd3, but upregulation of Cers2 mRNA, as prominent anomalies in the ceramide-sphingosine metabolism. Reduction of Asah2 mRNA correlated to deficient S1P levels. In addition, downregulations for the elongase Elovl1, Elovl4, Elovl5 mRNAs and ELOVL4 protein explain the deficit of very-long-chain sphingomyelin. Reduced ASMase protein levels correlated to the accumulation of long-chain sphingomyelin. Overall, a deficit of myelin lipids was prominent in SCA2 nervous tissue at prefinal stage, not compensated by transcriptional adaptation of several metabolic enzymes. Myelination is controlled by mTORC1 signals, so our human and murine observations are in agreement with the known role of ATXN2 yeast, nematode and mouse orthologs as mTORC1 inhibitors and autophagy promoters.
REVIEW Download: 48| View: 102| Comments: 0
Subject: Life Sciences, Biochemistry Keywords: continuous evolution; protein design; protein engineering; phage; bacterial one-hybrid; plaque assay; mutational analysis; DNA sequencing
Online: 5 November 2019 (02:19:01 CET)
Directed evolution methods are becoming increasingly popular, as they are extremely powerful toward developing new biomolecules with altered/novel activities, e.g., proteins with new catalytic functions or substrate specificities, and nucleic acids that recognize an intended target. Especially useful are systems that have incorporated continuous evolution, where the protein to be evolved undergoes continuous mutagenesis to evolve a desired trait with little to no input from the researcher once the system is started. However, continuous evolution methods can be challenging to implement in the lab and daunting for researchers to invest time and resources. Our intent is to provide basic information and helpful suggestions that we have gained from our experience with bacterial phage-assisted continuous evolution (PACE). Specifically, we review factors to consider before adopting PACE for a given evolution scheme, different types of selection circuits that can be utilized with particular focus on the PACE-B1H selection system, what optimization of a PACE selection circuit may look like using directed evolution of ME47 as a case study, and additional techniques that may be incorporated into a PACE experiment. With this information, researchers will be better equipped to determine if PACE is a valid strategy to use to evolve their proteins and how to set up a valid selection circuit.
Mon, 4 November 2019
REVIEW Download: 111| View: 69| Comments: 0 | doi:10.20944/preprints201911.0031.v1
Subject: Life Sciences, Molecular Biology Keywords: lncRNA; translation; transcription; splicing; brain; cerebral cortex; neurogenesis; synaptic plasticity; neurons
Online: 4 November 2019 (03:06:01 CET)
Mammalian genomes encode tens of thousands of long-noncoding RNAs (lncRNAs), which are capable of interactions with DNA, RNA and protein molecules, thereby enabling a variety of transcriptional and post-transcriptional regulatory activities. Strikingly, about 40% of lncRNAs are expressed specifically in the brain in precisely regulated temporal and spatial expression patterns. In stark contrast to the highly conserved repertoire of protein-coding genes, thousands of new lncRNAs have appeared during primate nervous system evolution with hundreds of human-specific lncRNAs. Their evolvable nature and the myriad of potential functions make lncRNAs ideal candidates for drivers of human brain evolution. The human brain displays the largest relative volume of any animal species and the most remarkable cognitive abilities. In addition to brain size, structural reorganization and adaptive changes represent crucial hallmarks of human brain evolution. LncRNAs are increasingly reported to be involved in neurodevelopmental processes including proliferation, neurite outgrowth and synaptogenesis, as well as in neuroplasticity, suggested to underlie human brain evolution. Hence, evolutionary human brain adaptations are proposed to be essentially driven by lncRNAs, which will be discussed in this review.
ARTICLE Download: 60| View: 51| Comments: 0 | doi:10.20944/preprints201911.0030.v1
Subject: Life Sciences, Other Keywords: walnuts; kidney disease; phytate; dietary intervention; phosphorous
Online: 4 November 2019 (02:59:12 CET)
The aim of this study of patients with chronic kidney disease (CKD) is to assess the safety of daily consumption of walnuts on the physiological levels of phosphorous, potassium, parathyroid hormone (PTH), and fibroblast growth factor 23 (FGF23), and to assess the short-term benefits of this intervention on risk factors associated with cardiovascular events. This led us to perform a prospective, randomized, cross-over, pilot clinical trial examined 13 patients with chronic kidney disease (CKD). Subjects were randomly assigned to a diet of 30 g of walnuts per day or the control diet. After 30 days, each group was given a 30-day washout period, and then switched to the alternate diet for 30 days. Urinary and serum levels of phosphorous and potassium, multiple vascular risk factors, and urinary inositol phosphates (InsPs) were measured at baseline and at the end of the intervention period. Our results showed that the walnut dietary supplement led to reduced blood pressure, LDL cholesterol, and serum albumin, but had no effect on the physiological levels of phosphorous, potassium, PTH, and FGF23. This is the first report to show that daily consumption of walnuts by patients with CKD does not alter their physiological levels of phosphorous, potassium, PTH, and FGF23. Consequently, this dietary supplement may prevent cardiovascular events in patients with CKD.
Sun, 3 November 2019
ARTICLE Download: 87| View: 107| Comments: 0 | doi:10.20944/preprints201911.0023.v1
Subject: Life Sciences, Biotechnology Keywords: monoclonal antibodies; Mabs; fusion; false positives; hapten immunoassays; competitive immunoassays; ELISA; antibody validation; antibody quality; microarray; hybridoma technology; linker recognition; high-throughput screening; HTS; heterology concept
Online: 3 November 2019 (17:00:59 CET)
The primary screening of hybridoma cells is a time-critical and laborious step during the development of monoclonal antibodies. Often critical errors occur in this phase, which supports the notion that the generation of monoclonal antibodies with hybridoma technology is difficult to control and hence a risky venture. We think that it is crucial to improve the screening process to eliminate most of the immanent deficits of the conventional approach. With this new microarray-based procedure, several advances could be achieved: Selectivity for excellent binders, high throughput, reproducible signals, avoidance of misleading avidity (multivalency) effects, and simultaneous performance of competition experiments. The latter can directly be used to select clones of desired cross-reactivity properties. In this paper, a model system with two excellent clones against carbamazepine, two weak clones and blank supernatant has been designed to examine the effectiveness of the new system. The excellent clones could be detected largely independent of the IgG concentration, which is unknown during the clone screening since the determination and subsequent adjustment of the antibody concentration is not possible in most cases. Furthermore, in this approach, the enrichment, isolation, and purification of IgG for characterization is not necessary. Raw cell culture supernatant can be used directly, even when fetal calf serum (FCS) or other complex media had been used. In addition, an improved method for the oriented antibody-immobilization on epoxy-silanized slides is presented. Based on the results of this model system, we conclude that this approach should be preferable to most other protocols leading to many of false positives, causing expensive and lengthy confirmation steps to weed out the poor clones.
TECHNICAL NOTE Download: 48| View: 85| Comments: 0 | doi:10.20944/preprints201911.0014.v1
Online: 3 November 2019 (14:59:55 CET)
miRNA sponges allow the selective blockade of a complete family of associated miRNAs which induce posttranscriptional gene silencing in its target through binding to 3´UTR mRNA. MiRNA-365 and miRNA-145 are down-regulated in colorectal cancer (CRC), but not in health tissues. Based on this, we constructed two vectors by inserting miRNA sponge (one for miRNA-365 and other for miRNA-145), and used EGFP (enhanced green fluorescent protein) as a 3′ UTR reporter gene to analyse the ability of each sponge to catch its respective miRNA. qPCR results corroborated that the expression levels of both miRNAs were lower in CRC cell lines than in normal colon cell line. Flow cytometry analysis revealed a decrease of the EGFP expression levels in the cell lines transfected with both sponges, being higher on the normal cell line while CRC cell lines presented a minimal decline. Also, this decrease was inversely proportional to the levels of expression of both miRNAs obtained by qPCR. These results were corroborated by fluorescence microscopy, showing a similar decrease fluorescence. We propose a new vector system to carry in a specific way the expression of genes to CRC cells without affecting healthy cells, preventing damage to healthy tissues.
Fri, 1 November 2019
ARTICLE Download: 45| View: 69| Comments: 0
Subject: Life Sciences, Microbiology Keywords: h. pylori; restriction modification system; virulence; il-8; apoptosis
Online: 1 November 2019 (12:52:39 CET)
Helicobacter pylori is a common human pathogen that causes gastroduodenal diseases. H. pylori genome consists of numerous restriction-modification (R-M) genes. It is established that N6-adenine methylation plays a crucial role in bacterial gene regulation and virulence, but not much is known about the role of C5-cytosine methylation. In this study, we examined the influence of an orphan cytosine methyltransferase, hpyAVIBM on gastric infection in mice and cultured cells. Histopathological staining showed that the deletion of hpyAVIBM in H. pylori strain SS1 had increased damaging hemorrhagic effects on the mice stomach. The gelatin-zymography result demonstrated that the mice infected with mutant SS1ΔhpyAVIBM had significantly up-regulated pro-MMP-9 than those infected with SS1. Additionally, ELISA results of pro-inflammatory cytokines proved that mutant strain caused significantly more inflammatory effect on mice stomach than its wild-type counterpart. The immunohistochemistry data showed that mutant strain caused attenuated epithelial cell damage. Co-culture studies of H. pylori with AGS (Human Gastric Adenocarcinoma cell line) cells revealed that SS1ΔhpyAVIBM instigated significantly more apoptotic death in the AGS cells compared to the wild-type strain. Our results indicated that DNA methylation by hpyAVIBM plays a crucial role in modulating virulence factors in bacterial cells and their interaction with the host cells.
Thu, 31 October 2019
ARTICLE Download: 70| View: 76| Comments: 1 | doi:10.20944/preprints201910.0307.v2
Subject: Life Sciences, Molecular Biology Keywords: antioxidant activity; cross-tolerance; glycine max; heat stress; proteomics; water stress
Online: 31 October 2019 (05:23:35 CET)
Water stress (WS) and heat stress (HS) have a negative effect on soybean plant growth and crop productivity. During WS, soybean plants opt for survival through ion homeostasis and the conformations of proteins are disconcerted as plant cells lose water while HS leads to difficulties in flowering and fruiting. Some of these changes include oxidative stress leading to the destruction of photosynthetic apparatus, macromolecules within cells and the onset of complex signaling cascades. Changes in the physiological characteristics, proteome, and certain metabolites investigated on molecular and cellular functions were studied in two soybean cultivars exposed to different heat and water stress conditions independently and in combination. Leaf protein composition was studied using 2-DE and complemented with MALDI TOF mass spectrometry. While two cultivars displayed genetic variation in response to water and heat stress, thirty-nine proteins were significantly altered in their relative abundance in response to WS, HS and combined WS+HS in both cultivars; a majority of them involved in metabolism, response to heat and photosynthesis showing significant cross-tolerance mechanisms. Functional analysis revealing a majority of heat responsive-proteins were more abundant during HS and combined stress (WS+HS) whereas these proteins were low to WS in cultivar PI 471938 and heat shock proteins were in low abundance to water, heat and combined stresses in cultivar R95-1705. Most protein abundances were not correlated with their expression at mRNA levels in PI cultivar, however, in cultivar R 95, the expression levels of transcript follow their relative abundance in proteins. Our systems bioinformatics analyses revealed that MED37C, a probable mediator of RNA polymerase transcription II protein showed potential interacting partners in Arabidopsis and our studies signifies the marked impact of this protein in PI cultivar. Elevated activities in antioxidant enzymes indicate that the PI-371938 cultivar has the ability to restore the oxidation levels and sustain the plant during the stress. Our study hypothesizes the plant’s development of cross-stress tolerance which will help foster the ongoing ventures in genetic modifications in stress tolerance.
HYPOTHESIS Download: 45| View: 52| Comments: 1 | doi:10.20944/preprints201904.0210.v2
Subject: Life Sciences, Biochemistry Keywords: regulation; membrane; glycerophospholipid; composition; chemical activity
Online: 31 October 2019 (04:39:47 CET)
Mammalian cells maintain the complex glycerophospholipid (GPL) class compositions of their various membranes within close limits because this is essential to their well-being or viability. Surprisingly, however it is still not understood how those compositions are maintained except that GPL synthesis and degradation closely coordinated. Here, we hypothesize that abrupt changes in the chemical activity of the individual GPL classes coordinate the synthesis and degradation, as well other homeostatic processes. A previously proposed model proposed that in cellular membranes only a limited number of “allowed” or optimal GPL glass compositions exist because they are energetically more favorable than the other compositions, i.e. they represent local free energy minima (Somerharju et al. 2009). This model, however, could not satisfactorily explain how the optimal compositions are sensed by the key homeostatic enzymes i.e., the rate-limiting synthetizing enzymes and the degrading enzymes (i.e., homeostatic phospholipases). We now propose that when the mole fraction of a GPL class exceeds an optimal one, its chemical activity abruptly increases, which (i) increases its propensity to efflux from the membrane thus making it susceptible for hydrolysis by homeostatic phospholipases, (ii) increases its potency to inhibit its own biosynthesis via a feedback mechanism, (iii) enhances its conversion to another GPL class via a novel process termed “head group remodeling” or (iv) enhances its translocation to other subcellular membranes. Accordingly, abrupt changes in the chemical activity of the individual GPL classes is proposed to regulate and coordinate those four processes maintaining GPL class homeostasis in mammalian cells.
ARTICLE Download: 50| View: 60| Comments: 0 | doi:10.20944/preprints201910.0358.v1
Subject: Life Sciences, Other Keywords: epithelial-to-mesenchymal transition; TGF-β1; cAMP; A-kinase anchoring protein; Ezrin; AKAP95; Yotiao; cigarette smoke; COPD
Online: 31 October 2019 (02:15:56 CET)
Epithelial-to-mesenchymal transition (EMT) plays a role in chronic obstructive pulmonary diseases (COPD). Cyclic adenosine monophosphate (cAMP) can inhibit transforming growth factor-β1 (TGF-β1) mediated EMT. Although compartmentalization via A-kinase anchoring proteins (AKAPs) is central to cAMP signaling, functional studies on their therapeutic value in the lung EMT process are lacking. Bronchial epithelial (BEAS-2B, primary HAE cells) were exposed to TGF-β1. Epithelial (E-cadherin, ZO-1) and mesenchymal markers collagen Ӏ (mRNA, protein) were analyzed. St-Ht31 disrupted AKAP-PKA interactions. TGF-β1 release was measured by ELISA. TGF-β1-sensitive AKAPs Ezrin, AKAP95 and Yotiao were silenced using siRNA. Cell migration was analyzed by wound healing assay, xCELLigence, Incucyte. Prior to TGF-β1, dibutyryl-cAMP (dbcAMP), fenoterol, rolipram, cilostamide, forskolin were used to elevate intracellular cAMP. TGF-β1 induced morphological changes, decreased E-cadherin but increased collagen Ӏ and cell migration, a process reversed by PF-670462. TGF-β1 altered (mRNA, protein) expression of Ezrin, AKAP95 and Yotiao. St-Ht31 decreased E-cadherin (mRNA, protein), but counteracted TGF-β1-induced collagen Ӏ upregulation. Cigarette smoke (CS) increased TGF-β1 release, activated TGF signaling, augmented cell migration and reduced E-cadherin expression, a process blocked by TGF-β1 neutralizing antibody. Silencing of Ezrin, AKAP95 and Yotiao diminished TGF-β1-induced collagen Ӏ expression, as well as TGF-β1-induced cell migration. Fenoterol, rolipram, and cilostamide, in AKAP silenced cells pointed to distinct cAMP compartments. We conclude that Ezrin, AKAP95 and Yotiao promote TGF-β1-mediated EMT, linked to a TGF-β1 release by CS. AKAP members define the ability of fenoterol, rolipram and cilostamide to modulate the EMT process, and are potential relevant targets in the treatment of COPD.
Tue, 29 October 2019
ARTICLE Download: 56| View: 54| Comments: 0 | doi:10.20944/preprints201910.0335.v1
Subject: Life Sciences, Microbiology Keywords: lipopolysaccharides; mucin; ileum; MUC2; mucosal barrier; mouse
Online: 29 October 2019 (10:50:10 CET)
The small intestinal villus is covered with a thick layer of mucus that is secreted by goblet cells and functions primarily to first barrier from damage by toxic substance. Recent studies showed that goblet cells and mucins involved in complex immune function. Lipopolysaccharide (LPS) is widespread in the housing of livestock, which can induce bacterial infection symptoms and immunological stress within a short of time. Therefore, we aimed to study the effects of long-term exposure to different doses of LPS on intestinal mucus layer and immune barrier. The result showed that mucus layer thickness and goblet cell functions were significantly increased after low doses of LPS. The intestinal mucosal barrier can block the bacteria of the lumen, but LPS can penetrate this barrier into the blood, putting the body in a state of chronic low-grade inflammation and reducing the body’s immune function. However, after long-term exposure to high doses of LPS, a large number of lysosomes in goblet cells caused loss of function, and mucus layer thickness was significantly decreased. A large amount of LPS stuck to the mucus, leading to normal LPS and inflammatory cytokines level of plasma. The intestinal tissue morphology was damaged, and a number of immune cells were necrosis in the intestine. Collectively, long-term exposure to low doses of LPS lead to chronic low-grade inflammation in the body. Long-term exposure to high doses of LPS can be directly linked to the severity of the immunosuppression in the body.
REVIEW Download: 83| View: 88| Comments: 0
Subject: Life Sciences, Microbiology Keywords: honey; antimicrobials; methylglyoxal; hydrogen peroxide; bee-defensin 1; wound treatment
Online: 29 October 2019 (10:45:51 CET)
Honey is a complex sweet food stuff with well-established antimicrobial and antioxidant properties. It has been used for millennia in a variety of applications, but those most noteworthy include treatment of surface wounds, burns and inflammation. A variety of substances in honey have been suggested as the key component to its antimicrobial potential; polyphenolic compounds, hydrogen peroxide, methylglyoxal and bee-defensin 1. These components vary greatly across honey samples due to botanical origin, geographical location and the individual bee. The use of medical grade honey, Medihoney and Revamil, in the treatment of surface wounds and burns has been seen to improve the healing process, reduce healing time, reduce scarring and prevent microbial contamination. Therefore, medical grade honeys should be used for these treatments and reduce the demand for antibiotic usage. In this review, we aim to outline the constituents of honey and how they affect the antibiotic potential of honeys in a clinical setting.
ARTICLE Download: 53| View: 61| Comments: 0 | doi:10.20944/preprints201910.0330.v1
Online: 29 October 2019 (10:23:19 CET)
Accumulating evidence suggests that mast cells should play critical roles in disruption and maintenance of intestinal homeostasis, although it remains unknown how they affect local microenvironment. Interleukin-9 (IL-9) was found to play critical roles in intestinal mast cell accumulation induced in various pathological conditions, such as parasite infection and oral allergen-induced anaphylaxis. Newly recruited intestinal mast cells trigger inflammatory responses and damage epithelial integrity through release of a wide variety of mediators including mast cell proteases. We established a novel culture model (mucosal mast cell-like cultured mast cells, MMC-like MCs), in which murine IL-3-dependent bone marrow-derived cultured mast cells (BMMCs) were further cultured in the presence of stem cell factor and IL-9. In MMC-like MCs, drastic up-regulation of Mcpt1 and Mcpt2 was found. Although histamine storage and tryptase activity were significantly downregulated in the presence of SCF and IL-9, it was entirely reversed when mast cells were co-cultured with a murine fibroblastic cell line, Swiss 3T3. MMC-like MCs underwent degranulation upon IgE-mediated antigen stimulation, which was found to less sensitive to lower concentrations of IgE in comparison with BMMCs. This model might be useful for investigation of the spatiotemporal changes of newly recruited intestinal mast cells.
ARTICLE Download: 70| View: 92| Comments: 0 | doi:10.20944/preprints201910.0325.v1
Subject: Life Sciences, Microbiology Keywords: AbrB-ParE; c-di-AMP; Geobacillus kaustophilus; Geobacillus thermodenitrificans; Geobacillus thermoleovorans; Geobacillus sp. ZGt-1; GNAT-HTH; (p)ppGpp; MNT-HEPN; XRE-COG2856
Online: 29 October 2019 (09:51:30 CET)
The toxin-antitoxin (TA) systems have been attracting attention due to their role in regulating prokaryotic cell responses to stress and their biotechnological potential. Much recognition has been given to type II TA system of mesophiles, but so far, limited attention has been given to thermophiles. Here, we are presenting the putative type II TA families encoded on the genomes of four Geobacillus strains. We employed the TA finder tool to mine for TA-coding genes and manually curated the results using various tools. We identified 28 putative TA pairs, distributed over 8 TA families. Among the identified TAs, 15 represent putative novel toxins and antitoxins that have been overlooked or annotated as hypothetical proteins in their genome records. We also identified a potentially new TA composite, AbrB-ParE. Furthermore, we are suggesting the Geobacillus acetyltransferase toxin-antitoxin (GacTA) family which potentially represents one of the unique TA families that has a reverse gene order. Moreover, we are proposing a hypothesis on the regulation of the xre-cog2856 gene expression, which seems to involve c-di-AMP. This study aims for highlighting the significance of studying TAs in Geobacillus, since they have special features. It also aims for facilitating future experimental research.
ARTICLE Download: 290| View: 118| Comments: 0 | doi:10.20944/preprints201910.0323.v1
Subject: Life Sciences, Biochemistry Keywords: catalase activity; hydrogen peroxide; hydroquinone; anilinium sulfate; ammonium molybdate
Online: 29 October 2019 (04:04:50 CET)
Background: Catalase is a vital antioxidant enzyme that dismutates H2O2 into water and molecular oxygen. Many protocols have been developed to measure catalase enzyme activity. Spectrophotometric methods are the most common assays that used to assess catalase enzyme activity. Methods: Because the rate-limiting step during catalase enzyme activity depends upon the dissociation of hydrogen peroxide, the developed assay measures the reaction between a hydroquinone/anilinium sulfate/ammonium molybdate reagent and Unreacted Hydrogen Peroxide, which results in the production of a purple, disubstituted quinone compound with a maximum absorbance value at 550 nm. Results: To clarify the precision of the developed method, the coefficients of variation were determined to be 2.6% and 4.7% for within run measurements and between run measurements, respectively. This method returned results that correlated well (r = 0.9982) with the results returned using the peroxovanadate method to assess catalase enzyme activity. Additionally, we examined the use of the newly developed hydroquinone assay to measure catalase enzyme activity in liver and bacterial homogenate samples. Conclusion: These results demonstrated that this assay can be used for scientific research and routine health applications because it is inexpensive, simple, accurate, and rapid. This method is suitable for use in clinical pathology laboratories because it is simple and produces precise and reproducible results.
Sun, 27 October 2019
CONCEPT PAPER Download: 82| View: 73| Comments: 0 | doi:10.20944/preprints201910.0311.v1
Online: 27 October 2019 (15:49:29 CET)
Technological advances made Virtual and Mixed Reality (VMR) accessible at our fingertips. However, only recently VMR has been explored for the teaching of biology. Here, we highlight how VMR applications can be useful in biology education, discuss about caveats related to VMR use that can interfere with learning, and look into the future of VMR applications in the field. We then propose that the combination of VMR with Machine Learning and Artificial Intelligence can provide unprecedented ways to visualise how species evolve in self-sustained immersive virtual worlds, thereby transforming VMR from an educational tool to the centre of biological interest.
ARTICLE Download: 51| View: 85| Comments: 0 | doi:10.20944/preprints201910.0307.v1
Subject: Life Sciences, Molecular Biology Keywords: antioxidant activity; cross-tolerance; glycine max; heat stress; proteomics; water stress
Online: 27 October 2019 (14:24:45 CET)
Water stress (WS) and heat stress (HS) have a negative effect on soybean plant growth and crop productivity. During WS, soybean plants opt for survival through ion homeostasis and the conformations of proteins are disconcerted as plant cells lose water while HS leads to difficulties in flowering and fruiting. Some of these changes include oxidative stress leading to destruction of photosynthetic apparatus, macromolecules within cells and the onset of complex signaling cascades. Changes in the physiological characteristics, proteome, and certain metabolites were investigated on molecular and cellular functions, two soybean cultivars were exposed to different heat and water stress conditions independently and in combination. Leaf protein composition was studied using 2-DE and complemented with MALDI TOF mass spectrometry. Thirty-nine proteins were significantly altered in their relative abundance in response to WS, HS and combined WS+HS in both cultivars. Functional analysis revealed a majority of heat responsive-proteins were up regulated during HS and combined stress (WS+HS) while these proteins were down regulated to WS in tolerant cultivar with heat shock proteins generally down regulated to all levels of stress in DS cultivar. Protein MED37C, a probable mediator of RNA polymerase transcription II yielded potential protein interactors partners in Arabidopsis and our studies documents the significant impact of the protein in PI cultivar. Our study hypothesizes the plant’s development of cross-stress tolerance and will help foster the ongoing ventures in genetic modifications in stress tolerance.
Thu, 24 October 2019
ARTICLE Download: 63| View: 89| Comments: 0 | doi:10.20944/preprints201910.0281.v1
Subject: Life Sciences, Biophysics Keywords: protein structural dynamics; NQO1; ligand binding; protein stability; allostery; protein degradation
Online: 24 October 2019 (15:41:46 CEST)
Human NAD(P)H:quinone oxidoreductase 1 (NQO1) is a multi-functional protein whose alteration is associated with cancer, Parkinson´s and Alzheimer´s diseases. NQO1 displays a remarkable functional chemistry, capable of binding different functional ligands that modulate its activity, stability and interaction with proteins and nucleic acids. Our understanding on this functional chemistry is limited by the difficulty of obtaining structural and dynamic information on many of these states. Herein, we have used hydrogen/deuterium exchange monitored by mass-spectrometry (HDXMS) to investigate the structural dynamics of NQO1 in three ligation states: without ligands (NQO1apo), with FAD (NQO1holo) and with FAD and the inhibitor dicoumarol (NQO1dic). We show that NQO1apo has a minimally stable folded core holding the protein dimer and with FAD and dicoumarol ligand binding sites populating binding non-competent conformations. Binding of FAD significantly decreases protein dynamics and stabilizes the FAD and dicoumarol binding sites as well as the monomer:monomer interface. Dicoumarol binding further stabilizes all three functional sites, a result not previously anticipated by available crystallographic models. Our work provides an experimental perspective into the communication of stability effects through the NQO1 dimer, valuable to understand at the molecular level the effects of disease-associated variants, post-translation modifications and ligand binding cooperativity in NQO1.
ARTICLE Download: 92| View: 77| Comments: 0 | doi:10.20944/preprints201910.0271.v1
Subject: Life Sciences, Microbiology Keywords: genome assembly; monoxenous trypanosomatids; insect trypanosomatids; trypanosomatidae; whole genome
Online: 24 October 2019 (05:20:52 CEST)
We presented here the first draft genome sequence of the trypanosomatid Herpetomonas muscarum ingenoplastis. This parasite was isolated repeatedly in the black blowfly, Phormia regina. This is the first draft genome of a flagellate from the phylogenetically distinct clade of Trypanosomatidae.
Wed, 23 October 2019
REVIEW Download: 86| View: 81| Comments: 0 | doi:10.20944/preprints201910.0268.v1
Subject: Life Sciences, Other Keywords: Citrus spp.; endophytes; antagonism; defensive mutualism; plant growth promotion; bioactive compounds
Online: 23 October 2019 (10:15:09 CEST)
Besides a diffuse research activity on drug discovery and biodiversity carried out in natural contexts, more recently investigations concerning endophytic fungi have started considering their occurrence in crops based on the major role that these microorganisms have been recognized to play in plant protection and growth promotion. Fruit growing is particularly involved in this new wave, by reason that the pluriannual crop cycle implies a likely higher impact of these symbiotic interactions. Aspects concerning occurrence and effects of endophytic fungi associated with citrus species are revised in the present paper.
Tue, 22 October 2019
REVIEW Download: 126| View: 71| Comments: 0 | doi:10.20944/preprints201910.0255.v1
Subject: Life Sciences, Microbiology Keywords: antimicrobial resistance; biofilm; efflux pump inhibitors; antibiotic potentiation; eskapee pathogens; gram-negative bacteria
Online: 22 October 2019 (10:22:56 CEST)
Antibiotic resistance represents a significant threat to the modern healthcare provision. The ESKAPEE pathogens, in particular, have proven to be especially challenging to treat, due to their intrinsic and acquired ability to rapidly develop resistance mechanisms in response to environmental threats. The development of biofilm has been characterised as an essential contributing factor towards antimicrobial-resistance and tolerance. Several studies have implicated the involvement of efflux pumps in antibiotic resistance, both directly, via drug extrusion and indirectly, through the formation of biofilm. As a result, the underlying mechanism of these pumps has attracted considerable interest due to the potential of targeting these protein structures and developing novel adjunct therapies. Subsequent investigations have revealed the ability of efflux pump-inhibitors (EPIs) to block drug-extrusion and disrupt biofilm formation, thereby, potentiating antibiotics and reversing resistance of pathogen towards them. This review will discuss the potential of EPIs as a possible solution to antimicrobial resistance, examining different challenges to the design of these compounds, with an emphasis on Gram-negative ESKAPEE pathogens.
REVIEW Download: 84| View: 80| Comments: 0 | doi:10.20944/preprints201910.0253.v1
Subject: Life Sciences, Biotechnology Keywords: tropical cash crops; coffee; cacao; papaya; chromosome engineering; synthetic biology
Online: 22 October 2019 (05:32:50 CEST)
Background Tropical and subtropical crops such as coffee, cacao, and papaya are valuable commodities and its consumption is a seemingly indispensable part of the daily lives of billions of people across the world. Conventional breeding in these crops is lengthy and yields are threatened by runaway global warming. In this review we propose the application of chromosome engineering and synthetic biology principles in order to enhance synthesis of key metabolites, and transmission of wild traits for resistance to stress and disease. Conclusions It is hoped that the adoption of such technological approaches may enhance the resilience of agricultural communities, lead to economic growth and secure the availability of key resources for generations to come.
ARTICLE Download: 92| View: 89| Comments: 0 | doi:10.20944/preprints201910.0252.v1
Subject: Life Sciences, Molecular Biology Keywords: ferric ammonium citrate; deferoxamine; 2,2′-bipyridine; iron homeostasis; ISC; mitochondrial clearance; longevity; starvation; Parkinson’s disease
Online: 22 October 2019 (05:01:43 CEST)
Lifespan extension was recently achieved in Caenorhabditis elegans nematodes by mitochondrial stress and mitophagy, triggered via iron depletion. Conversely in man, deficient mitophagy due to Pink1/Parkin mutations triggers iron accumulation in patient brain and limits survival. We now aimed to identify murine fibroblast factors, which adapt their mRNA expression to acute iron manipulation, relate to mitochondrial dysfunction and may influence survival. After iron depletion, expression of the plasma membrane receptor Tfrc with its activator Ireb2, the mitochondrial membrane transporter Abcb10, the heme-release factor Pgrmc1, the heme-degradation enzyme Hmox1, the heme-binding cholesterol metabolizer Cyp46a1, as well as the mitophagy regulators Pink1 and Parkin showed a negative correlation to iron levels. After iron overload, these factors did not change expression. Conversely, a positive correlation of mRNA levels with both conditions of iron availability was observed for the endosomal factors Slc11a2 and Steap2, as well as for the iron-sulfur-cluster (ISC)-containing factors Ppat, Bdh2 and Nthl1. Positive correlation only after iron depletion was observed for the iron export factor Slc40a1, mitochondrial iron transporters Slc25a28, Abcb7 and Abcb8, mitochondrial ISC-containing factors Glrx5, Nfu1, Bola1 and Abce1, cytosolic Aco1 and Tyw5, as well as nuclear Dna2, Elp3, Pold1 and Prim2. The latter are regulators of nucleotide synthesis and DNA quality control, which have known importance for growth and lifespan. The only Pink1-/- triggered transcript modulation was the reduced expression of the ISC-containing ribosomal factor Abce1. These mammalian findings support previous fly data that Pink1 influences co-translational quality control via Abce1, as well as mitophagy. Our findings provide the first systematic survey how iron dosage triggers homeostatic transcriptional regulations and elucidate how iron deprivation results in mitophagy.
ARTICLE Download: 40| View: 90| Comments: 0 | doi:10.20944/preprints201910.0249.v1
Subject: Life Sciences, Molecular Biology Keywords: repeats blocks; repeater finder regular expression; tandem repeats of human coronavirus
Online: 22 October 2019 (04:11:40 CEST)
A lot of research studies have been surveyed the completed genomes of prokaryotic and eukaryotic and focused on the correlation between the percentage of microsatellite sequences in completed genomes and the whole size of the organism genomes. There are fewer studies made in repetitive sequences otherwise simple sequence repeats or long tandem repeats of virus genomes. simple sequence repeats (SSRs) are the most important regions for recombination and moving repeats blocks from site to another site in the genomes. A tool was programmed and designed by visual basic 6.0 to find the long tandem repeats in DNA sequences of the small genomes. The tool named “Repeater Finder Regular Expression”, (RFRE) Version 1.0, 2016. The tool was utilized to discover different pattern of long tandem repeats (LTR) motifs on the completed genomes of human corona virus strains by using a joined regular expression language. In this study, a twenty-nine accession numbers of human coronavirus completed genomes, (hku1) strains were retrieved from the Genbank. The researcher can write a different regular expression patterns and joined regular expression patterns through the designed tool to search and find a specific motif of nucleotide sequences inside the complete genomes. The RFRE tool searched and found three different total lengths of a perfect long tandem repeats (240bp, 300bp and 480bp). A Dot plot gave a picture view for the long tandem repeat sequences in the completed genome sequence (KF430201.1) of human coronavirus. The genomic dot plot tool YASS was used as a genomic similarity searching tool to check for the uninterrupted repeats and confirm the sensitivity of the (RFRE) tool. To identify the recombination site in the genomes of human coronavirus the RAT tool was applied to find the recombination sites between the completed genomes of human corona viruses .The RAT tool recognized the recombination site in the nucleotide position (3012) and at the same time this recombination site position (3012) was also recognized as a beginning position of a long tandem repeat. A precise motif was predicted from the translated repeats of Human Corona Virus which found by PRATT tool. There was a relationship between the total length of long tandem repeats and genome size of Human Corona Virus and the correlation value R2 was equal to (0,451). In conclusion, this study presented the importance of finding the long tandem repeats of human coronavirus and gives a relationship between the completed genome size of human coronavirus types and long tandem repeats. The nucleotide position (3012) was a hot spot site for a recombination among the complete genomes of human coronavirus and also identified as a repetitive site in the genomes of human corona virus (hku1). The repeats in human coronavirus (hku1) were predicated to be a main major role of virus evolution.
HYPOTHESIS Download: 55| View: 80| Comments: 0 | doi:10.20944/preprints201910.0248.v1
Subject: Life Sciences, Microbiology Keywords: Vibrio cholerae; cholera toxin gene; low ionic strength aquatic solution; viability
Online: 22 October 2019 (04:00:54 CEST)
It has been regarded that Vibrio cholerae O1 inhabit in environmental water. As many cholera patients emerge in Kolkata, it has been thought that V. cholerae O1 is easily detected in environmental water in Kolkata. However, the detection of V. cholerae O1 is rare, though other V. cholerae (NAG Vibrio) is constantly detected. To clear the reason for the difference of the detection rate of two Vibrios, we examined the viability of V. cholera O1 and NAG Vibrios in low ionic strength aquatic medium. We observed greater declining viability of V. cholerae O1 possessing cholera toxin gene (ctx) in low ionic strength solution, but the decline of NAG Vibrios non-possessing ctx is small. To evaluate the concerning of ctx in the viability, we examined the viabilities of V. cholerae O1which do not possess ctx and NAG Vibrios possessing ctx under the same condition. The result indicated that the existence of the ctx induces the decrease the viability of the host in low ionic strength solution. The decrease observed in this experiment might relate with the low detection of V. cholerae O1 possessing ctx in environmental water, though NAG Vibrio is constantly detected.
Sun, 20 October 2019
ARTICLE Download: 76| View: 103| Comments: 0 | doi:10.20944/preprints201910.0235.v1
Subject: Life Sciences, Genetics Keywords: African locust bean; climate change; cluster analysis; genetic intra-specific diversity; polymorphic information content; food and nutrition security
Online: 20 October 2019 (16:01:21 CEST)
African locust bean (Parkia biglobosa (Jacq.) is a multi-purpose economic tree with genetic potentials in sub-Saharan Africa. Its cultivation and production is declining with increased aging and genetically threatened throughout its natural ranges. Research efforts are needed to change the present scenario to sustainable cultivation and utilization, hence this present study. This study was aimed at evaluating genetic diversity and geographical spread relationships of twenty landraces collected from different ecological zones of Nigeria using simple sequence repeat (SSR) markers. Ten SSR markers were screened and five primers (PbL02, PbL03, PbL04, PbL05 and PbL09) were selected based on clear amplification products and reproducible scorable bands. The SSR primers detected a total of 55 alleles ranged from 10 to 14 alleles with a mean of 11. The percentage polymorphisms were high and ranged from 68.75 % in PbL04 to 84.21 % in PbL05 with a mean of 74.16 %. The polymorphic information content (PIC) was in the range of 0.31 in PbL02 to 0.37 in PbL09. The genetic diversity and heterozygosity values ranged from 0.39 to 0.50 and 0.00 to 0.68 while the average genetic distance for all pair wise comparisons was 0.31.The first five Principal Component (PC) accounted for 70.20 % of the total variation out of which PC1 (31.50%) and PC2 (19.20%) extracted 49.70% molecular similarity. The dendrogram resulted in separation of the 19 landraces into three major clusters based on unweighted pair group method with arithmetic average. Cluster I comprised of five landraces: ABNo130 and BENo023; OYNo11, KANo125 and NiNo262 while cluster II had only one (BANo116). Cluster III was diverse comprising 13 landraces: ZANo188, KNNo162, KENo220, GMNo076 and EbNo260, ADNo64, EdNo164, KANo137, KENo217, KwNo270, NiNo241, OsNo206 and PLNo120. The homogeneity of alleles among the studied landraces suggested suspicion of loss of genetic intra-specific variation among the landraces of P. biglobosa which calls for concerted efforts toward better cultivation, conservation, management, utilization and genetic improvement of the species in Nigeria.
Sat, 19 October 2019
ARTICLE Download: 59| View: 107| Comments: 0 | doi:10.20944/preprints201910.0223.v1
Subject: Life Sciences, Biochemistry Keywords: α-glucosidase; glyceollin; genistein; luteolin; daidzein; phytoalexins; enzyme kinetics; combination index
Online: 19 October 2019 (02:20:45 CEST)
To determine the mode of action of the effects of phytoalexins in soybeans, we analyzed enzyme inhibition kinetics using Michaelis–Menten plots and the Lineweaver–Burk plots. The results showed that glyceollin showed competitive inhibition, genistein showed noncompetitive, daidzein was uncompetitive, and luteolin showed a mixed mode of action. The Ki values were determined using a Dixon plot as: glyceollin, 18.99; genistein, 15.42; luteolin, 16.81; and daidzein, 9.99 μM, respectively. Furthermore, potential synergistic effects between glyceollin and the three designated polyphenols were investigated. A combination of glyceollin and luteolin (the ratio of 3:7 of glyceollin and luteolin) had synergistic effects on α-glucosidase inhibition according to combination index (CI)-isobologram equation. Collectively, these results showed that a combination of glyceollin and luteolin has the potential to inhibit α-glucosidase activity via a synergistic mode of action.
Fri, 18 October 2019
ARTICLE Download: 72| View: 116| Comments: 0 | doi:10.20944/preprints201910.0209.v1
Subject: Life Sciences, Genetics Keywords: agronomic practices; agrobiodiversity; aflp; climate change; cluster analysis; genetic diversity; moringa oleifera; food and nutrition security
Online: 18 October 2019 (07:34:50 CEST)
Evaluation of agronomic practices, genetic diversity and population structure of Moringa oleifera (Lam.) is crucial to its sustainable utilization to ensure food and nutritional security. Four agronomic practices of field preparation and soil analysis, regeneration, weeding and pruning, as well as harvesting, were adopted. Genetic diversity and population structure of 20 populations were evaluated using amplified fragment length polymorphism (AFLP) primer pairs (E-ACC/M-CAC and E-ACA/M-CAG). The effects of agronomic practices on leaf quantity production were evaluated using standard procedures. The physico-chemical and morphological data were analyzed using descriptive statistics, while genetic diversity, population structure, dendrogram reconstruction, and Principal Component Analysis (PCA) were analyzed from the AFLP genetic data. Significant effects (P ≤ 0.05) of agronomic practices on the quantity of leaf production were recorded across the accessions. The two primer pairs generated a total of 80 alleles with a mean major allele frequency of 0.0250. Gene diversity and polymorphic information content (PIC) values were high with a mean of 0.98 and 0.974, respectively. The Gst value of 0.0490 indicated that 5 % of the total genetic divergence was among the population while 95 % within the population. Dendrogram reconstruction with genetic distance ranging from 0.87 to 0.96 segregated the accessions into eleven clusters while PCA generated six cluster groups. Field preparation and physico-chemical soil properties, regeneration, weeding and pruning, and stand development, as well as harvesting, influenced the leaf yield and genetic diversity observed in this study. The genetic data revealed that some accessions were clustered along eco-geographical lines while others grouped disparately. Identified potential parent genotypes with valuable and desirable genetic traits can be exploited for commercial, breeding and conservation purposes to ensure sustainable utilization of the species in Nigeria.
Thu, 17 October 2019
ARTICLE Download: 89| View: 152| Comments: 0 | doi:10.20944/preprints201910.0193.v1
Subject: Life Sciences, Molecular Biology Keywords: antioxidant enzymes; lipid peroxidation; NaCl; Pistacia vera; rootstock; salinity stress
Online: 17 October 2019 (11:53:12 CEST)
Salinity substantially affects plant growth and crop productivity worldwide. Plants adopt several biochemical mechanisms including regulation of antioxidant biosynthesis to protect themselves against the toxic effects induced by the stress. One-year-old Pistachio rootstock exhibiting different degrees of salinity tolerance were subjected to sodium chloride induced salt stress to identify genetic diversity among cultivated pistachio rootstock for their antioxidant responses, and to determine the correlation of these enzymes to salinity stress. Leaves and roots were harvested following NaCl-induced stress. Results show that a higher concentration of NaCl treatment induced oxidative stress in the leaf tissue and to a lesser extent in the roots. Both tissues showed an increase in ascorbate peroxidase, superoxide dismutase, catalase, glutathione reductase, peroxidase and malondialdehyde. Responses of antioxidant enzymes were cultivar dependent, as well as temporal and dependent on the salinity level. Linear and quadratic regression model analysis revealed significant correlation of enzyme activities to salinity treatment in both tissues. The variation in salinity tolerance reflected their capabilities in orchestrating antioxidant enzymes at the roots and harmonized across the cell membranes of the leaves. The study provides a better understanding of root and leaf coordination in regulating the antioxidant enzymes to NaCl induced oxidative stress.
REVIEW Download: 113| View: 116| Comments: 0 | doi:10.20944/preprints201910.0189.v1
Subject: Life Sciences, Microbiology Keywords: microbiome; microbiota-gut-brain axis; ADHD; attention-deficit-hyperactive-disorder
Online: 17 October 2019 (09:04:10 CEST)
The latest research cumulates staggering information about the correlation between the microbiota-gut-brain axis and neurodevelopmental disorders. This review aims to shed light on the potential influence of the microbiome on the development of the most prevalent neurodevelopmental disease, attention-deficit-hyperactive disorder (ADHD). As the etiology and pathophysiology of ADHD are still unclear, finding viable biomarkers and effective treatment still represent a challenge. Therefore, we focused on factors that have been associated with a higher risk of developing ADHD while simultaneously influencing the microbial composition. We reviewed the effect of a differing microbial composition on neurotransmitter concentrations important in the pathophysiology of ADHD. Additionally, we deduced factors that correlate with a high prevalence of ADHD while simultaneously affecting the gut microbiome such as emergency c-sections, and premature birth as the former leads to a decrease of the gut microbial diversity and the latter causes neuroprotective Lactobacillus levels to be reduced. Also, we assessed nutritional influences such as breastfeeding, ingestion of short-chain fatty acids (SCFAs) and polyunsaturated fatty acids (PUFAs) on the host’s microbiome and development of ADHD. Finally, we discussed the potential significance of Bifidobacterium as a biomarker for ADHD, the importance of preventing premature birth as prophylaxis and nutrition as a prospective therapeutic measurement against ADHD.
Tue, 15 October 2019
ARTICLE Download: 176| View: 152| Comments: 0
Subject: Life Sciences, Molecular Biology Keywords: protein/rna world; plasma membrane; cytoplasm; virus world; pre-retro virus; emergence of dna; transcription and replication; first cells; hyperthermophiles; luca; bacteria and archaea; anoxygenic bacteria; oxygenic bacteria; global distribution of cyanobacteria
Online: 15 October 2019 (11:18:58 CEST)
The transition from the Peptide/RNA world to the Protein/RNA world in the hydrothermal vent environment was a major event in the history of life. The advent of proteins utterly changed the conditions of emerging life, representing a watershed in its development. During subsequent translation various protein enzymes emerged driving protocells into a more complex and interconnected system. With their astonishing versatility, the protein enzymes catalyzed crucial biochemical reactions within protocells into more complex biomolecules in diverse metabolic pathways, whereas structural proteins provided strength and permeability in the cell membrane. Four major events followed after availability of various kinds of protein molecules during prebiotic synthesis. These are: (1) the modification of the phospholipid membrane into the plasma membrane; (2) the origin of primitive cytoplasm; (3) the beginnings of the virus world; and (4) the advent of DNA. The first innovation mediated by proteins was the improvement of the cell membrane. The phospholipid membrane was initially evolved in a vent environment from the gradual modification of a fatty acid membrane via an intermediate phosphatidate acid by non-enzymatic reactions. The phospholipid is then synthesized from phosphatidate acid by a series of enzymes. To make the phospholipid membrane more permeable, various protein molecules interacted with the cell membrane. Proteins not only stabilized the wall membrane, but also acted as pumps, preventing some molecules from the protocells from crossing the membrane barriers, while permitting other selected molecules and ions to enter and leave the protocell. The second modification led by proteins is the gradual conversion of the interior of the protocell from a water-like medium into a gel-like cytoplasm, which became the storehouse of a wide range of biomolecules including amino acids, proteins, nucleic acids, ribosomes, as well as salt and water. The third innovation utilizing the newly synthesized proteins was the emergence of the ancient virus world. In the milieu of different kinds of mRNAs in the prebiotic soup, jelly-roll capsid genes originated de novo within genomes of nonviral mRNAs by overprinting. These fragile capsid genes were possibly coated by proteins on the mineral substrate for stability and durability, transforming them into ancient viral particles. These protein coats were random and were not encoded by encased genes. Some protocells might have engulfed these viral particles, when the capsid genes utilized the ribosomes of the host to translate into the appropriate capsid proteins. These capsid proteins then coated the viral genes to make new copies of primordial viruses inside the protocell. Since then, viruses became capsid-encoding organisms. These primordial mRNA viruses parasitized RNA-based protocells, manipulating them to make new copies of themselves. This was the beginning of a relentless war between viruses and their protocellular hosts. The next stage in viral evolution was the emergence of a primitive retrovirus (pre-retrovirus) with a new kind of replicative strategy in a sense that it could turn its RNA into DNA using its own reverse transcriptase enzyme. This is the beginning of the Retro world that facilitated the transition from RNA to DNA genomes. The infection of RNA protocells with pre-retroviruses progressively transferred the RNA genome to a viral DNA genome by retro-transcription. The advent of DNA by the pre-retrovirus marks the fourth innovation, when a number of enzymes had already developed and were utilized by pre-retroviruses. With continued infection, DNA viruses slowly transferred not only their core replication enzymes, such as helicase, primase, and DNA polymerase, to RNA protocells, but also to their DNAs as well. Thus, began the DNA world, when DNA replaced RNA as the major genome of the protocells. With the advent of DNA, replication of information was entirely dissociated from its expression. Because DNA is much more stable than mRNA with more storage capacity, it is a superb archive for information systems in the form of base sequences. DNA progressively took over the replicative storage function of mRNA, leaving the latter for protein synthesis. The new protocell with the DNA genome will diversify into large populations of DNA protocells that will outcompete populations of RNA protocells. Genetic information began to flow from DNA to mRNA to protein in a two-step process involving transcription and translation. In the biological stage, DNA replication was central to the binary fission of the first cell, orchestrated by the duplication of genomes and then the division of the parent cell into two identical daughter cells. It was carried out by a set of enzymes that formed a Z-ring at the site of replication. With the onset of binary fission, the population of primitive cells grew rapidly in the hydrothermal vent environment, undergoing Darwinian evolution and diversification. These primordial hyperthermophiles, presumably the first life, obtained food and energy directly from the vent environment. However, such a situation was self-limiting, so the early cells evolved their own mechanisms for generating metabolic energy and synthesizing the molecules necessary for their reproduction. The earliest fossil record (≥ 3.5 Ga) of biotic activity is preserved in the Archean hydrothermal and sedimentary rocks of the Nuvvuagittuq Craton of Canada, the Isua Craton of Greenland, the Pilbara Craton of Australia, the Kaapvaal Craton of South Africa, and the Singhbhum Craton of India in the form of the carbonaceous remains of microbial cells, cellular microfossils, and stromatolites. These microscopic fossils provide crucial evidence of the origin and early evolution of prokaryotic cells, beginning with hyperthermophiles. Molecular phylogenetic analysis suggests that both domains of life ¬– Bacteria and Archaea probably split from the last universal common ancestor (LUCA), a hyperthermophilic organism. In the younger sequences of these Archean cratons, two kinds of photosynthetic bacteria, anoxygenic green sulfur bacteria, and oxygenic cyanobacteria, appeared in quick succession from the thermophilic ancestor, indicating a shift of niche from a benthic to a planktonic, with reduced thermotolerance. The development of anoxygenic and oxygenic photosynthesis would have allowed life to escape the hydrothermal setting and invade a newly evolved habitat—broad continental shelves to tap solar energy. Cyanobacteria invaded the global ocean, turned it into blue and green, produced oxygen for the first time, and left their signatures in the carbonates and stromatolites.
BRIEF REPORT Download: 44| View: 143| Comments: 0 | doi:10.20944/preprints201910.0166.v1
Subject: Life Sciences, Microbiology Keywords: Chagas Disease; Trypanosoma cruzi; benznidazole; nifurtimox; antimicrobial susceptibility test
Online: 15 October 2019 (08:26:29 CEST)
We ascertain the in vitro Benznidazole (BZN) and Nifurtimox (NFX) susceptibility pattern of epimastigotes, trypomastigotes, and amastigotes of 21 T. cruzi strains, from patients, reservoir and triatomine bugs of various geographic origin. Using this panel of isolates, we compute the Epidemiological cut off value (COwt). Then, the frequency of the susceptible phenotype (Wild type) towards BZN and nifurtimox (NFX) within this set of strains belonging to 3 discrete typing units (DTUs), TcI, TcII, and TcV was deduced. We have observed that the susceptibility status of individual T. cruzi isolates toward BZN and NFX is related to the genetic background and to underlying factors probably related to the individual life trait history of each strain. Analyzing drug susceptibility in this conceptual framework would offers the possibility to evidence a link between isolates expressing a low susceptibility level (not wild-type) as define by the COwt value and none-curative treatment. It will also permit to tract drug-resistant parasites in T. cruzi population.
ARTICLE Download: 50| View: 94| Comments: 0 | doi:10.20944/preprints201910.0161.v1
Subject: Life Sciences, Virology Keywords: Enterovirus 71; EV71; EV71 non-structural protein 2B; interleukin enhancer binding factor 2; ILF2; virus infection; virus replication
Online: 15 October 2019 (05:37:34 CEST)
Enterovirus 71 (EV71) infection hand-foot-mouth disease (HFMD), meningoencephalitis, neonatal sepsis, and even fatal encephalitis in children, thereby representing a serious public health hazard. It is important to determine the mechanisms underlying the regulation of EV71 infection. In this study, we initially reveal that the interleukin enhancer binding factor 2 (ILF2) down-regulates EV71 50% tissue culture infective dose (TCID50), attenuates EV71 plaque formation unit (PFU), thereby repressing EV71 infection. Moreover, we reveal a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects. Chip data analyses show that ILF2 mRNA is reduced upon EV71 infection. Cellular studies indicate that EV71 infection represses ILF2 mRNA expression and protein production in human leukemic monocytes (THP-1) differentiated macrophages and in human rhabdomyosarcoma (RD) cells. Additionally, EV71 non-structural protein 2B interacts with ILF2 in human embryonic kidney (HEK293T) cells. Interestingly, in the presence of EV71 2B, ILF2 is translocated from the nucleus to the cytoplasm and co-localizes with 2B in the cytoplasm. Therefore, we reveal a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to cytoplasm through its 2B protein.
Mon, 14 October 2019
ARTICLE Download: 62| View: 161| Comments: 1 | doi:10.20944/preprints201909.0001.v2
Subject: Life Sciences, Biochemistry Keywords: treating filler complications; hyaluronidase; red king crab; hepatopancreas; hyaluronic acid (HA); hyaluronidase activity; turbidimetric method; atomic force microscopy (AFM); nuclear magnetic resonance (NMR); Revofil Ultra filler; Hyaluform deep filler; Lydase; Liporase
Online: 14 October 2019 (15:42:23 CEST)
This study focused on hydrolysis of cosmetic fillers hyaluronic acid (HA) and kinetics of the HA hydrolysis using the homogenate of the red king crab hepatopancreas. Turbidimetric analysis of the reaction mixture revealed a bell-shaped time dependence of aggregation formation. It was shown that the obtained homogenate has the similar activity to the commercially available hyaluronidase. The atomic force microscopy (AFM) examination found that the HA fillers were represented by spherical-like structures. These structures were destroyed under the action of the homogenate of the red king crab hepatopancreas. NMR of the reaction mixture showed that HA degradation lasts for some days, but a maximum rate of the reaction is detected in the first hours of incubation. The preparation with hyaluronidase activity obtained from the red king crab hepatopancreas could be used as potentially safe product for treating filler complications.
ARTICLE Download: 36| View: 128| Comments: 1
Subject: Life Sciences, Molecular Biology Keywords: icariin; nicotine; sperm density; testosterone; antioxidant enzyme; male mice
Online: 14 October 2019 (09:58:40 CEST)
Nicotine is a pharmacologically active component of tobacco which adversely affects the male reproductive system and fertility and Icariin (ICA) is the main active ingredient of Epimedium herba which has been used to treat several male reproductive problems. This study was aimed at investigating the protective or ameliorative effect of ICA against reproductive toxicity induced by intraperitoneal injection of nicotine in mice. Forty male mice were randomly divided into 4 groups: control, nicotine (0.75 mg/kg intraperitoneally), icariin (ICA, 75 mg/kg), and icariin plus nicotine (ICA + nicotine) group. After 35 days of treatment, the mice were weighed, sacrificed, and their reproductive organs were collected and examined for further studies. In the nicotine-treated group, epididymal sperm density and serum testosterone concentrations significantly decreased relative to the control group. Nicotine also caused oxidative damage as shown by significant reduction in the activities of antioxidant enzymes and an elevation in Malondialdehyde (MDA) levels. Icariin on the other hand, improved the reduction in sperm characteristics, hormone levels, and activities of antioxidant enzymes alterations observed in the nicotine treated mice. These findings indicate that the nicotine-induced reproductive toxicity and oxidative damages on male reproductive tissues can be effectively attenuated by icariin.
ARTICLE Download: 90| View: 160| Comments: 0 | doi:10.20944/preprints201910.0156.v1
Subject: Life Sciences, Virology Keywords: noni mosaic virus; potyvirus; complete genome; morinda citrifolia l; illumina transcriptomic sequencing
Online: 14 October 2019 (09:29:57 CEST)
An outbreak of a virus-like disease has caused severe damage to noni plants (Morinda citrifolia L.) in Xishuangbanna area of China's southwestern Yunnan province since 2015. The diseased plants displayed typical mosaic symptom with light and dark green patches on leaves. Flexuous filamentous virus particles of about 800 nm in length were observed from the leaf saps by transmission electron microscope. Illumina transcriptomic sequencing further revealed the presence of a potyvirus and its near complete genome was obtained from de novo assembly. The complete genome of 9,659 nts was obtained by Sanger sequencing of eight amplicons generate by RT-PCR and 5’ and 3’ RACE. BLASTp analysis of the polyprotein sequence showed that the virus was most closely related to Tobacco vein banding mosaic virus (TVBMV), but these two viruses only shared 50.7% amino acid sequence similarity. Both phylogenetic analyses of the polyprotein and CP amino acid sequences indicated that this virus is a member of genus Potyvirus. However, the low sequence homology with all known potyviruses established this virus as a new species in the genus, tentatively named as Noni mosaic virus (NoMV). Our field surveys showed that 100% of the symptomatic samples and 28.57% of the asymptomatic samples were infected with this novel potyvirus. Aphids collected from diseased leaves were also detected carrying the virus. In summary, our data indicated that a novel species of potyvirus, NoMV, is prevalent in Yunnan, China and is associated with an emerging mosaic disease on M. citrifolia.
Sun, 13 October 2019
ARTICLE Download: 51| View: 153| Comments: 0 | doi:10.20944/preprints201910.0154.v1
Subject: Life Sciences, Genetics Keywords: papillary thyroid cancer; germline mutations; whole genome sequencing; predisposition markers; pathway analysis
Online: 13 October 2019 (17:07:34 CEST)
Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family. We performed whole genome sequencing on 23 affected and 3 unaffected family members from five NMTC-prone families and prioritized the identified variants using our Familial Cancer Variant Prioritization Pipeline (FCVPPv2). In total, 31 coding variants and 39 variants located in upstream, downstream, 5′ or 3′ untranslated regions passed FCVPPv2 filtering. Altogether, 210 genes affected by variants that passed the first three steps of the FCVPPv2 were analyzed using Ingenuity Pathway Analysis software. These genes were enriched in tumorigenic signaling pathways mediated by receptor tyrosine kinases and G-protein coupled receptors, implicating a central role of PI3K/AKT and MAPK/ERK signaling in familial NMTC. Our approach can facilitate the identification and functional validation of causal variants in each family as well as the screening and genetic counseling of other individuals at risk of developing NMTC.
ARTICLE Download: 82| View: 185| Comments: 0 | doi:10.20944/preprints201910.0147.v1
Subject: Life Sciences, Biotechnology Keywords: blackleg; brassica; diagnosis; effector; genome alignment; leptosphaeria biglobosa; leptosphaeria maculans; marker; PCR
Online: 13 October 2019 (16:08:55 CEST)
Background: Accurate diagnosis of the differentially aggressive fungus Leptosphaeria maculans and Leptosphaeria biglobosa causing Blackleg in crucifers is crucial. Available markers were designed decades ago which may become ineffective due to the ever evolving nature of the fungus, requiring the development of more precise molecular markers. Methods: The whole genomes of available isolates belonging to this two species were aligned using progressive MAUVE tool, species specific genomic regions were extracted and species specific primers were designed from the sequences that encode for effector proteins. Results: Three (Lm1, Lm2 and Lm5) and two (Lb3 and Lb3’) primer sets specifically detected the isolates of target species in PCR based assay, of which the primers Lm5 and Lb3’ were multiplexed for detection of Leptosphaeria maculans and Leptosphaeria biglobosa, generating PCR amplicons of 230 and 834 bp, respectively from a single PCR reaction. The markers were highly sensitive and were able to amplify target species from crude ‘pseudothecia and ascospores suspension’ without requiring DNA extraction. Conclusions: These markers, solitarily or in combination, designed from species specific genomic segments will serve as precise, sensitive and rapid detection of Leptosphaeria maculans and Leptosphaeria biglobosa species and will be helpful for surveillance, management and transboundary quarantine of the devastating disease.
ARTICLE Download: 544| View: 990| Comments: 0 | doi:10.20944/preprints201910.0146.v1
Online: 13 October 2019 (15:51:58 CEST)
Sat, 12 October 2019
ARTICLE Download: 57| View: 198| Comments: 0 | doi:10.20944/preprints201910.0142.v1
Subject: Life Sciences, Other Keywords: Alces alces; aquatic macrophytes; diet; Isle Royale National Park; moose; stable isotope analysis; ungulate
Online: 12 October 2019 (07:04:00 CEST)
Moose (Alces alces) are generalist herbivores but are important aquatic-terrestrial ecotone specialists. Aquatic macrophytes are a high-quality food source for moose during the summer, however their relative importance to moose diet is difficult to study. We used stable isotope analysis of carbon and nitrogen from moose hooves and forage (terrestrial plants, aquatic macrophytes, and arboreal lichen) to estimate the diet of moose at Isle Royale National Park, Michigan, USA, and to evaluate the isotopic variability along chronologies of serially sampled hooves. We hypothesized that aquatic macrophyte consumption and winter body condition (as measured by bone marrow fat content) would be greater at the eastern end of the island where aquatic habitats were most abundant. We were unable to evaluate spatial differences in aquatic macrophyte consumption, but overall, our mixing model results suggest that between 13% and 27% of summer moose diet was from aquatic sources. Among moose that died during winter, body condition was impaired and hoof δ15N (measured at the hairline) was higher at the western end of the island, where aquatic habitats are sparse. Although isotope chronologies preserved in hooves could significantly enhance our understanding of ungulate foraging ecology, interpretation of such chronologies is presently limited by our lack of knowledge pertaining to hoof growth rate and seasonal dynamics in relation to age and health. Significant isotope distinction among terrestrial plants, aquatic macrophytes, and arboreal lichens indicate that continued methodological advances in stable isotope ecology will lead to more precise estimates of the contribution of aquatic feeding to moose population dynamics.
Fri, 11 October 2019
ARTICLE Download: 52| View: 210| Comments: 0 | doi:10.20944/preprints201910.0121.v1
Subject: Life Sciences, Virology Keywords: alphavirus; vaccine; arbovirus; animal models; nonhuman primates; electrocardiography; ecg; aerosol; encephalitis; equine
Online: 11 October 2019 (03:32:33 CEST)
Eastern (EEEV) and Venezuelan (VEEV) equine encephalitis viruses (EEVs) are related, (+)ssRNA arboviruses that can cause severe, sometimes fatal, encephalitis in humans. EEVs are highly infectious when aerosolized, raising concerns for potential use as biological weapons. No licensed medical countermeasures exist; given the severity/rarity of natural EEV infections, efficacy studies require animal models. Cynomolgus macaques exposed to EEV aerosols develop fever, encephalitis, and other clinical signs similar to humans. Fever is nonspecific for encephalitis in macaques. Electrocardiography (ECG) metrics may predict onset, severity, or outcome of EEV-attributable disease. Macaques were implanted with thermometry/ECG radiotransmitters and exposed to aerosolized EEV. Data was collected continuously, and repeated-measures ANOVA and frequency-spectrum analyses identified differences between courses of illness and between pre-exposure and post-exposure states. EEEV-infected macaques manifested widened QRS-intervals in severely ill subjects post-exposure. Moreover, QT-intervals and RR-intervals decreased during the febrile period. VEEV-infected macaques suffered decreased QT-intervals and RR-intervals with fever onset. Frequency-spectrum analyses revealed differences in the fundamental frequencies of multiple metrics in the post-exposure and febrile periods compared to baseline and confirmed circadian dysfunction. Heart rate variability (HRV) analyses revealed diminished variability post-exposure. These analyses support using ECG data alongside fever and clinical laboratory findings for evaluating medical countermeasure efficacy.
Thu, 10 October 2019
REVIEW Download: 64| View: 208| Comments: 0 | doi:10.20944/preprints201910.0120.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: reelin; lis2; adlte; autism; schizophrenia; translational models; gabaergic interneurons; dendritic spines; forebrain; cerebellum
Online: 10 October 2019 (15:31:12 CEST)
The Reeler mutation was described in mouse more than fifty year ago. Later, its causative gene (reln) was discovered in mouse, and its human orthologue (RELN) was demonstrated to be causative of lissencephaly 2 (LIS2) and about 20% of the cases of autosomal-dominant lateral temporal epilepsy (ADLTE). In both human and mice the gene encodes for a glycoprotein referred to as Reelin (Reln) that plays a primary role in neuronal migration during development and synaptic stabilization in adulthood. Besides LIS2 and ADLTE, RELN and/or other genes coding for the proteins of the Reln intracellular cascade have been associated more or less substantially to other conditions such as spinocerebellar ataxia type 7 and 37, VLDLR-associated cerebellar hypoplasia, PAFAH1B1-associated lissencephaly, autism and schizophrenia. According to their modalities of inheritances and with substantial differences among each other, these neuropsychiatric disorders can be modeled in the homozygous (reln-/-) or heterozygous (reln+/-) mouse. The usefulness of these mice as translational models is discussed, with focus on their construct and face validity. The latter is mainly treated directing the attention to the histological, neurochemical and functional observations in the cerebral cortex, hippocampus and cerebellum of Reeler mice and their human counterparts.
CASE REPORT Download: 40| View: 288| Comments: 0 | doi:10.20944/preprints201910.0112.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: heterotaxy syndromes; cardiac isomerism; chick embryo; Pitx2; proepicardium; non-compaction cardiomyopathy
Online: 10 October 2019 (05:54:08 CEST)
Except for a few species, the outer shape of vertebrates normally is characterized by bilateral symmetry. The inner organs, on the other hand, normally are arranged in bilaterally asymmetric patterns, which are of special importance for the normal function of the cardiovascular system of lung-breathing vertebrates. Deviations from the normal organ asymmetry can occur in the form of mirror imagery of the normal arrangement (situs inversus), or in the form of arrangements that have the tendency for development of bilateral symmetry, either in a pattern of bilateral left-sideness (left isomerism) or bilateral right-sidedness (right isomerism). The latter two forms of visceral situs anomalies are called “heterotaxy syndromes”. During the past 30 years, remarkable progress has been made in uncovering of the genetic etiology of heterotaxy syndromes. However, the pathogenetic mechanisms causing the spectrum of cardiovascular defects found in these syndromes remain poorly understood. In the present report, a spontaneous case of left cardiac isomerism found in a HH-stage 23 chick embryo is described. The observations made in this case suggest that hearts with left cardiac isomerism may have the tendency for development of a non-compaction cardiomyopathy caused by defective development of the proepicardium.
COMMUNICATION Download: 19| View: 153| Comments: 0
Subject: Life Sciences, Other Keywords: smoking; air pollution; health communication; population attributable fraction; copd; emphysema; relative risks
Online: 10 October 2019 (04:47:10 CEST)
A recent study found that a 3ppb increase in O3 ambient concentration was associated with an increased progression of 0.18 percentage points in percent emphysema and that such increase was equal to smoking 20 cigarettes per day for 29 years. A simple estimation of population attributable fraction shows that COPD diagnoses due to smoking are actually 30 times more than those attributed to a 3 ppb increment in O3 concentration. Labelling ozone pollution as the new smoking may distort perception of the risks and hinder proper response to real life threatening risk such as smoking.
Wed, 9 October 2019
ARTICLE Download: 71| View: 207| Comments: 0 | doi:10.20944/preprints201910.0103.v1
Subject: Life Sciences, Microbiology Keywords: beta-lactamase; cephalosporin; cefotaxime; transconjugation; plasmid-borne resistance
Online: 9 October 2019 (11:03:44 CEST)
Clinical pathogens especially Gram-negative bacteria developing resistance to third-generation cephalosporins are making the clinical outcome more complicated and serious. This study was undertaken to evaluate the distribution of extended-spectrum beta-lactamases in Tamil Nadu regions in India. For this study, clinical samples were collected from five different hospitals located in Tamil Nadu and ESBL producing Gram-negative isolates were characterized. Minimal inhibitory concentration (MIC) was performed using cefotaxime and ceftazidime. The blaESBL producing genes were screened using multiplex PCR for the genes, CTX-M group-1,-2,-8,-9,-26. Conjugation studies were performed using E. coli AB1157 as a recipient for the isolates harbouring plasmid-borne resistance following broth-mating experiment. In total, 1500 samples were collected and 599 Gram-negative bacteria were isolated that included Escherichia coli (n=233), Klebsiella pneumoniae (n=182), Pseudomonas aeruginosa (n=79), Citrobacter spp. (n=30), Proteus mirabilis (n=28), Salmonella spp. (n=21), Acinetobacter baumannii (n=12), Serratia spp. (n=6), Shigella spp. (n=4), Morganella morganii (n=3) and Providencia spp. (n=1). MIC results showed that 358 isolates were resistant to cefotaxime and ceftazidime. Further, ESBL gene amplification results showed that 19 isolates had CTX-M group-1 gene including E. coli (n=16), K. pneumoniae (n=2) and P. aeruginosa (n=1) whereas one M. morganii isolate had CTX-M group-9 gene in their plasmid. Through conjugation studies, 12/20 isolates were found to be involved in the transformation of its plasmid-borne resistance gene. Our study highlighted the role of horizontal gene transfer in the dissemination of plasmid-borne blaCTX-M resistance genes among ESBL producing isolates.
Tue, 8 October 2019
ARTICLE Download: 49| View: 145| Comments: 0 | doi:10.20944/preprints201910.0092.v1
Online: 8 October 2019 (11:32:24 CEST)
Galdieria maxima is a polyextremophilic alga capable of diverse metabolic processes. Ammonia is widely used in culture media typical of laboratory growth. Recent reports that this species can grow on wastes promote the concept that G. maxima might have biotechnological utility. Accordingly, there is a need to know the range of pH levels that can support G. maxima growth in a given nitrogen source. Here, we examined the combined effect of pH and nitrate/ammonium source on the growth and long-term response of the photochemical process to a pH gradient in different G. maxima strains. All were able to use differing nitrogen sources, despite both the growth rate and photochemical activity were significantly affected by the combination with the pH. All strains acidified the NH4+-medium (pH<3); only G. maxima IPPAS P507 showed reduced capacity in lowering the pH from 6.5. pH was a limiting factor in nitrate uptake at pH≥6.5; noteworthy, at pH 5 on nitrate G. maxima ACUF551 showed a good growth performance, despite the alkalization of the medium.
ARTICLE Download: 19| View: 104| Comments: 0
Subject: Life Sciences, Molecular Biology Keywords: icariin; nicotine; sperm density; testosterone; antioxidant enzyme; male mice
Online: 8 October 2019 (10:30:43 CEST)
Nicotine is a pharmacologically active component of tobacco which adversely affects the male reproductive system and fertility and Icariin (ICA) is the main active ingredient of Epimedium herba which has been used to treat several male reproductive problems. This study was aimed at investigating the protective or ameliorative effect of ICA against reproductive toxicity induced by intraperitoneal injection of nicotine in mice. Forty male mice were randomly divided into 4 groups: control, nicotine (0.75 mg/kg intraperitoneally), icariin (ICA, 75 mg/kg), and icariin plus nicotine (ICA + nicotine) group. After 35 days of treatment, the mice were weighed, sacrificed, and their reproductive parameters were collected and examined for further studies. In the nicotine-treated group, epididymal sperm density and serum testosterone concentrations significantly decreased relative to the control group. Nicotine also caused oxidative damage as shown by significant reduction in the activities of antioxidant enzymes and an elevation in Malondialdehyde (MDA) levels. Icariin on the other hand, improved the reduction in sperm characteristics, hormone levels, and activities of antioxidant enzymes alterations observed in the nicotine treated mice. These findings indicate that the nicotine-induced reproductive toxicity and oxidative damages on male reproductive tissues can be effectively attenuated by icariin.
Mon, 7 October 2019
SHORT NOTE Download: 59| View: 103| Comments: 0 | doi:10.20944/preprints201910.0067.v1
Subject: Life Sciences, Biochemistry Keywords: Calcium; Actomyosin Kinetics; Myosin Binding Protein-C; Hypertrophic Cardiomyopathy
Online: 7 October 2019 (12:12:35 CEST)
In an attempt to correct misunderstandings this article brings together the observations on Calcium, Myosin Binding Protein-C and Hypertrophic Cardiomyopathy in the basic function of cardiac muscle. A finding of many years ago is reiterated in a novel enzyme kinetic format with defined rate limiting step which makes CaATP the apparent substrate of the actomyosin cross-bridge. The relationship of these kinetics to recent observations on disruption of myosin binding protein-C is described along with how this bears on the understanding of the related cardiomyopathies.
Fri, 4 October 2019
REVIEW Download: 62| View: 153| Comments: 0 | doi:10.20944/preprints201910.0048.v1
Online: 4 October 2019 (11:38:23 CEST)
Bone homeostasis depends on the interplay between bone resporption by osteoclasts and bone formation by osteoblasts. Any Imbalance of this tightly regulated process can cause diseases such as osteoporosis. Therefore, the knowledge about the factors that regulate communication between osteoclasts and osteoblasts are critical to bone cell biology.Osteoporosis is a progressive systemic skeletal disease characterized by low bone mass density and deterioration of bone tissue. Mature miRNAs are about 22 nucleotide long non coding RNA molecules that are involved in regulatory processes intracellularly. A number of scientific studies have revealed a comprehensive and evidential knowledge about miRNAs that affect the bone metabolism by influencing bone formation and resorption processes. In this short review we have summrized the regulatory role of some selective miRNAs in bone formation.
Thu, 3 October 2019
REVIEW Download: 54| View: 141| Comments: 1 | doi:10.20944/preprints201907.0134.v2
Subject: Life Sciences, Immunology Keywords: lymphocytic choriomeningitis virus (LCMV); viral infection; autoimmunity; molecular mimicry; bystander activation; immune tolerance
Online: 3 October 2019 (13:51:08 CEST)
Viral infections are a natural part of our existence. They can affect us in many ways that are the result of the interaction between the viral pathogen and our immune system. Most times the resulting immune response is beneficial for the host. The pathogen gets cleared thus protecting our vital organs with no other consequences. Conversely, the reaction of our immune system against the pathogen can cause organ damage (immunopathology) or lead to autoimmune disease. To date, there are several mechanisms for virus-induced autoimmune disease, including molecular mimicry and bystander activation, in support of the “fertile field” hypothesis, terms defined in our review. On the flip side, viral infections have been associated with protection from autoimmunity through mechanisms that include Treg invigoration and immune deviation, in support of the “hygiene hypothesis”, also defined here. Infection with lymphocytic choriomeningitis virus (LCMV) is one of the prototypes showing that the interaction of our immune system with viruses can either accelerate or prevent autoimmunity. Studies using mouse models of LCMV have helped conceive and establish several concepts that we today know and explain how viruses can lead to autoimmune activation or induce tolerance. Some of the most important mechanisms established during the course LCMV are described in this short review.
REVIEW Download: 162| View: 226| Comments: 1 | doi:10.20944/preprints201910.0034.v1
Subject: Life Sciences, Other Keywords: microcystin; cyanobacteria; cyanotoxin; structural elucidation; toxicology
Online: 3 October 2019 (03:43:55 CEST)
Hepatotoxic microcystins (MCs) are the most widespread class of cyanotoxins and the one that has most often been implicated in cyanobacterial toxicosis. One of the main challenges in studying and monitoring MCs is the great structural diversity within the class. The full chemical structure of the first MC was elucidated in the early 1980s and since then the number of reported structural analogues has grown steadily and continues to do so, thanks largely to advances in analytical methodology. The structures of some of these analogues have been definitively elucidated after chemical isolation using a combination of techniques including nuclear magnetic resonance, amino acid analysis and tandem mass spectrometry (MS/MS). Others have only been tentatively identified using liquid chromatography-MS/MS without chemical isolation. An understanding of the structural diversity of MCs, the genetic and environmental controls for this diversity and the impact of structure on toxicity are all essential to the ongoing study of MCs across several scientific disciplines. However, because of the diversity of MCs and the range of approaches that have been taken for characterizing them, comprehensive information on the state of knowledge in each of these areas can be challenging to gather. We have conducted an in-depth review of the literature surrounding the identification and toxicity of known MCs and present here a concise review of these topics. At present, at least 269 MCs have been reported. Among these, about 20% (54 of 269) appear to be the result of chemical or biochemical transformations of MCs that can occur in the environment or during sample handling and extraction of cyanobacterial, including oxidation products, methyl esters, or post-biosynthetic metabolites. The toxicity of many MCs has also been studied using a range of different approaches and a great deal of variability can be observed between reported toxicities, even for the same congener. This review will help clarify the current state of knowledge on the structural diversity of MCs as a class and the impacts of structure on toxicity, as well as to identify gaps in knowledge that should be addressed in future research.
Wed, 2 October 2019
ARTICLE Download: 103| View: 308| Comments: 0 | doi:10.20944/preprints201910.0025.v1
Subject: Life Sciences, Microbiology Keywords: Acinetobacter baumannii; multiresistant; mutant lytic phage; phage therapy; antibiotic-phage synergy.
Online: 2 October 2019 (08:42:31 CEST)
The global health emergency caused by multi-drug resistant bacteria has led to the search for and development of new antimicrobial agents. Phage therapy is an abandoned antimicrobial therapy that has been resumed in recent years. In this study, we mutated a lysogenic phage from Acinetobacter baumannii into a lytic phage (Ab105-2phiΔCI) showing antimicrobial activity against A.baumannii clinical strains (such as Ab177_GEIH-2000 which showed MICs to meropenem and imipenem of 32 µg/ml and 16 µg/ml, respectively as well as belonging to GEIH-REIPI Spanish Multicenter A. baumannii Study II 2000/2010, Umbrella Genbank Bioproject PRJNA422585). We then enhanced the time kill curves (in vitro) and in Galleria mellonella survival assays (in vivo) antimicrobial activity of the new lytic phage by combining it with carbapenem antibiotics (meropenem and imipenem). We observed in vitro, an antimicrobial synergistic effect (from 4 log to 7 log CFU/ml) with meropenem plus lytic phage in all combinations analysed (0.1, 1 and 10 MOI of Ab105-2phiΔCI mutant as well as 1/4 and 1/8 MIC of meropenem). Moreover, we had a decrease in bacterial growth of 8 log CFU/ml for the combination of imipenem at 1/4 MIC plus lytic phage (Ab105-2phiΔCI mutant) and of 4 log CFU/ml for the combination of imipenem at 1/8 MIC plus lytic phage (Ab105-2phiΔCI mutant) in both MOI 1 and 10. These results were confirmed in in vivo (G. mellonella) obtaining a higher effectiveness in the combination of imipenem and Ab105-2phiΔCI mutant (P<0.05 by Log Rank-Matel Cox test). This approach could help to reduce the emergence of phage resistant bacteria and restore sensitivity to the antibiotics when used to combat multiresistant strains of Acinetobacter baumannii.
BRIEF REPORT Download: 99| View: 248| Comments: 0 | doi:10.20944/preprints201910.0024.v1
Online: 2 October 2019 (08:28:09 CEST)
Flaviviruses replicate in membranous factories associated with the endoplasmic reticulum (ER). The replication rate generates a high polyprotein integration that can contribute to ER stress. Therefore, the host cell can develop an Unfolded Protein Response (UPR) to this protein accumulation which will stimulate appropriate cellular responses in the infectious context (Adaptation, autophagy or cell death). These different stress responses can help to overcome the virus and usually support antiviral strategies initiated by infected cells. In the present study, we investigated the capacity of ZIKA virus (ZIKV) to induce ER stress in epithelial A549 cells with a special focus on the causal factors behind it. We observed that the cells respond to ZIKV infection by implementing an UPR through activation of the IRE1 and PERK pathway but surprisingly without activation of the ATF6 branch. When we examined the effects of modulating the ER stress response we found that UPR inducers significantly inhibit ZIKV replication. Interestingly, our findings provide evidence that ZIKV can altered the UPR in order to escape to the host cell defense system.
REVIEW Download: 85| View: 180| Comments: 0 | doi:10.20944/preprints201910.0021.v1
Subject: Life Sciences, Molecular Biology Keywords: PGC-1α; exercise; metabolism; epigenetics; histone modification; DNA methylation; micro RNA; gene regulation; thermogenesis; metabolic diseases
Online: 2 October 2019 (06:23:31 CEST)
Epigenetic changes are a hallmark of short- and long-term transcriptional regulation, and hence instrumental in the control of cellular identity and plasticity. Epigenetic mechanisms leading to changes in chromatin structure, accessibility for recruitment of transcriptional complexes, and interaction of enhancers and promoters all contribute to acute and chronic adaptations of cells, tissues and organs to internal and external perturbations. Similarly, the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) is activated by stimuli that alter the cellular energetic demand, and subsequently controls complex transcriptional networks responsible for cellular plasticity. It thus is of no surprise that PGC-1α is under the control of epigenetic mechanisms, and constitutes a mediator of epigenetic changes in various tissues and contexts. In this review, we summarize the current knowledge of the link between epigenetics and PGC-1α in health and disease.
ARTICLE Download: 66| View: 309| Comments: 0 | doi:10.20944/preprints201910.0010.v1
Subject: Life Sciences, Other Keywords: affect; embodied ways of knowing; inter-corporality; interspecies intimacy; sensory ethnography; movement; rhythm; canine and equine interactions
Online: 2 October 2019 (03:22:40 CEST)
Children’s beneficial relationships with animals are well known. Companion animals, particularly dogs have become an integral part of family life and children’s material culture. Aside the proven physiological benefits there is little research about what children say about their relationships with animals and how they describe them. In this paper we bring together both horse-human and dog-human interactions, finding common ground for understanding the complexity of human development, well-being and flourishing. Dogs in schools are fast becoming a trend in helping support and enhance children’s learning as well as their social and emotional well-being. Studies have shown that the very presence of a dog can increase children’s concentration, executive function and behavior. Also, equine therapy is gaining momentum and empirical studies are showing noteworthy benefits to children and young people. However, the lack of children’s voices means that the mechanisms for these benefits are somewhat unknown and unclear. In seeking to explore this, the authors utilize a visual, sensory and diffractive ethnographic approach to illuminate and illustrate, experiment and re-enact, how the children relate, share spaces and multiple subjectivities with their classroom canine, “Ted” and companion horse “Henry”. ”Henry” is part of a programme in which youngsters care for and engage in activities with horses.
ARTICLE Download: 59| View: 110| Comments: 0 | doi:10.20944/preprints201910.0006.v1
Subject: Life Sciences, Other Keywords: l-type calcium channels; nociception; spinal cord; central sensitization; windup
Online: 2 October 2019 (02:49:04 CEST)
Windup, a progressive increase in spinal response to repetitive stimulations of nociceptive peripheral fibres, is a useful model to study central sensitization to pain. Windup is expressed by neurons in of both dorsal and ventral horn of the spinal cord. In juvenile rats, it has been demonstrated both in vivo and in vitro that windup depends on calcium-dependent intrinsic properties and their modulation by synaptic components. However, the involvement of these two components in the adult remain controversial. In the present study, by means of electromyographic and extracellular recordings, we show that windup in adult, in vivo, depends on a synaptic balance between excitatory NMDA receptors and inhibitory glycinergic receptors. We also demonstrate the involvement of L-type calcium channels in both the dorsal and ventral horn of the spinal cord. These results indicate that windup in adults is similar to juveniles rats and that windup properties are the same regardless spinal network, i.e. sensory or motor.
Mon, 30 September 2019
COMMUNICATION Download: 65| View: 144| Comments: 0 | doi:10.20944/preprints201909.0346.v1
Subject: Life Sciences, Genetics Keywords: neurogenetics; dementia; next-generation sequencing; in silico analysis; genetic variant; phenotypic variability
Online: 30 September 2019 (11:05:36 CEST)
Background: Advancements in the next-generation sequencing (NGS) techniques have allowed for efficient genetic variant detection at reduced costs. Methods: We describe an ad hoc NGS-based custom designed resequencing gene panel to identify genetic variants in 8 patients with dementing disorders. Results: We found variants of TREM2 and APP genes in three patients; these have been previously identified as pathogenic or likely pathogenic and, therefore, considered as “Disease Causing”. In the remaining subjects, the pathogenicity was evaluated on the in silico analysis, according to the guidelines of the American College of Medical Genetics. In one patient, the p.R205W variant was causative of the disease, thus considered as “Possibly Disease Causing”. The variants found from the other four subjects in the CSF1R, SERPINI1, GRN, and APP genes revealed discordant in silico results and, therefore, it was not possible to assign a definitive pathogenicity. Conclusions: Notwithstanding the limitations of a customized panel, we detected some rare genetic variants with a probable disease association. The future application of NGS techniques and the further replication of these experimental data will replace the so-called “gene by gene” approach with a “panel of genes” strategy, that offers promising perspectives in the diagnosis and management of neurodegenerative disorders.
ARTICLE Download: 50| View: 139| Comments: 0
Subject: Life Sciences, Biotechnology Keywords: chalcopyrite bioleaching; low temperature; microbial community; passivation; extracellular polymeric substances; ferric iron
Online: 30 September 2019 (07:56:59 CEST)
Low-temperature biohydrometallurgy is implicated in metal recovery in alpine mining area, but our knowledge on its mechanism has been limited. To this end, an Acidithiobacillus ferrivorans strain and a mixed culture were used for chalcopyrite bioleaching at 6 °C. The passivation of the mineral surface was analyzed using X-ray photoelectron spectroscopy (XPS), the microbial community structure of the mixed culture-mediated system was tested using high-throughput sequencing technology, and the extracellular polymeric substances (EPS) and ferric iron on the microbe-mineral interface were measured. A higher copper extraction rate was achieved using the mixed culture but it did not relieve the passivation of the mineral surface. Acidithiobacillus spp. and Sulfobacillus spp. were the two major lineages in the mixed culture-mediated system. In the fast-leaching stage, more EPS and ferric iron were extracted in the mixed culture-mediated system. In conclusion, Sulfobacillus spp. can relieve the inhibition of organic components to Acidithiobacillus spp., maintaining the robustness of the leaching system and more Fe(III) complexed by elevated EPS can enhance chalcopyrite bioleaching by the mixed culture.
ARTICLE Download: 100| View: 136| Comments: 0 | doi:10.20944/preprints201909.0341.v1
Subject: Life Sciences, Biochemistry Keywords: Covalent labeling; stereoselectivity; electrophile signaling; affinity; mechanism; kinetic control
Online: 30 September 2019 (07:53:42 CEST)
Significance: Electrophile signaling is coming into focus as a bona fide cell signaling mechanism. The electrophilic regulation occurs typically through a sensing event (i.e., labeling of a protein) and a signaling event (the labeling event having an effect of the proteins activity, association, etc.). Recent advances: Herein, we focus on the first step of this process, electrophile sensing. Electrophile sensing is typically a deceptively simple reaction between the thiol of a protein-cysteine, of which there are around 200,000 in the human proteome, and a Michael acceptor, of which there are numerous flavors, including enals and enones. Recent data overall paint a picture that despite being a simple chemical reaction, electrophile sensing is a discerning process, showing labeling preferences that are often not in line with reactivity of the electrophile. Critical issues: With a view to trying to decide what brings about highly electrophile-reactive protein-cysteines, and how reactive these sensors may be, we discuss aspects of the thermodynamics and kinetics of covalent/non-covalent binding. Data made available by several laboratories indicate that it is likely that specific proteins exhibit highly stereo- and chemoselective electrophile sensing, which we take as good evidence for recognition bet