ARTICLE Download: 617| View: 3121| Comments: 0 | doi:10.20944/preprints201711.0183.v1
Subject: Biology, Anatomy & Morphology Keywords: Dutch Konik; Metacarpal; Metatarsal; primitive horse; splint bones; Tarpan
Online: 29 November 2017 (07:01:17 CET)
The Dutch Konik is valued from a genetic conservation perspective and also for its role in preservation of natural landscapes. The primary management objective for the captive breeding of this primitive horse is to maintain its genetic purity, whilst also maintaining the nature reserves on which they graze. Breeding selection has traditionally been based on phenotypic characteristics consistent with the breed description, and the selection of animals for removal from the breeding program is problematic at times due to high uniformity within the breed. With the objective of identifying an additional non-invasive selection criterion with potential uniqueness to the Dutch Konik, this study investigates the anatomic parameters of the distal equine limb, with a specific focus on the relative lengths of the individual splint bones. Post-mortem dissections performed on distal limbs of Dutch Konik (n = 47) and modern domesticated horses (n = 120) revealed significant differences in relation to the length and symmetry of the 2nd and 4th Metacarpals and Metatarsals. Distal limb characteristics with apparent uniqueness to the Dutch Konik are described which could be an important tool in the selection and preservation of the breed.
Mon, 16 January 2017
ARTICLE Download: 1055| View: 2827| Comments: 0 | doi:10.20944/preprints201701.0073.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: food valuation; food as commons; food as commodity; transition theory; narratives of transition; agency in transition; transformative agency; counter-hegemonic attitudes; gradual reformers
Online: 16 January 2017 (04:17:20 CET)
The food system, the most important driver of planetary transformation, is in a deep crisis. Therefore, seeking a sustainable and socially-fair transition pathway becomes an issue of utmost priority for our own survival. The consideration of food as a commodity, a social construct that played a central role in driving this crisis, remains the uncontested narrative to lead the different transition pathways what seems rather contradictory. By exploring the normative values in the transition landscape, this paper seeks to understand how relevant is the hegemonic narrative of “food as commodity” and its alternative of “food as commons” to determine transition trajectories and food policy beliefs. Applying the Multi-level Perspective framework and developing the ill-studied “agency in transition”, this research enquired food-related professionals that belong to an online community of practice (N=95) on valuation of food dimensions and agency in food transitions to check whether the valuation of food is relevant to explain personal stances in transition. Results suggest the socially-constructed view of food as commodity is positively correlated to the gradual reforming attitude, whereas food as commons is positively correlated to the counter-hegemonic transformers regardless the self-defined position in the transition landscape (regime or niches). At personal level, there are multiple loci of resistance with counter-hegemonic attitudes in varied institutions of the regime and the innovative niches, many of them holding this discourse of food as commons. Conversely, alter-hegemonic attitudes are not positively correlated to this alternative discourse and they may inadvertently or purportedly reinforce the ‘‘neoliberal narrative’’. Food as commons, a different narrative whose rationale is explained in the paper, seems to be a relevant framework that could enrich the multiple transformative constituencies that challenge the industrial food system and therefore facilitate the convergence of movements that reject the commodification of food.
Mon, 14 May 2018
COMMUNICATION Download: 323| View: 1767| Comments: 0 | doi:10.20944/preprints201805.0184.v1
Subject: Biology, Animal Sciences & Zoology Keywords: whale; virome; drone; mammalian host; virosphere
Online: 14 May 2018 (08:25:40 CEST)
There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We characterized the respiratory virome of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome diversity a meta-transcriptomic analysis was performed on 19 pooled whale blow samples collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. Despite the relatively small number of animals surveyed, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, diversity, and evolution.
Wed, 4 April 2018
TECHNICAL NOTE Download: 445| View: 1627| Comments: 0 | doi:10.20944/preprints201804.0047.v1
Online: 4 April 2018 (06:00:40 CEST)
The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabelling encountered when searching for suitable sequences for phylogenetic analysis. These issues include the incorrect identification of sequenced species, non-standardised and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users, among others. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inference, a risk that is likely to increase with the size of phylogenies or the molecular datasets used to generate them. Here we present a software package, phylotaR, that bypasses the above issues by using instead an alignment search tool to identify orthologous sequences. Our package builds on the framework of its predecessor, PhyLoTa, by providing a modular pipeline for identifying overlapping sequence clusters using up-to-date GenBank data and providing new features, improvements and tools. We demonstrate our pipeline’s effectiveness by presenting trees generated from phylotaR clusters for two large taxonomic clades: palms and primates. Given the versatility of this package, we hope that it will become a standard tool for any research aiming to use GenBank data for phylogenetic analysis.
Fri, 24 February 2017
REVIEW Download: 2123| View: 1604| Comments: 0 | doi:10.20944/preprints201702.0083.v2
Subject: Biology, Plant Sciences Keywords: Adaptive mechanisms; antioxidative metabolism; chloroplast; osmotic regulation; oxidative stress; photosynthesis; salinity; water relations
Online: 24 February 2017 (10:21:50 CET)
This review deals with the adaptive mechanisms that plants can implement to cope with the challenge of salt stress. Plants tolerant to NaCl implement a series of adaptations to acclimate to salinity, including morphological, physiological and biochemical changes. These changes include increases in the root/canopy ratio and in the chlorophyll content in addition to changes in the leaf anatomy that ultimately lead to preventing leaf ion toxicity, thus maintaining the water status in order to limit water loss and protect the photosynthesis process. Furthermore, we deal with the effect of salt stress on photosynthesis and chlorophyll fluorescence and some of the mechanisms thought to protect the photosynthetic machinery, including the xanthophyll cycle, photorespiration pathway and water-water cycle. Finally, we also provide an updated discussion on salt-induced oxidative stress at the subcellular level and its effect on the antioxidant machinery in both salt-tolerant and salt-sensitive plants. The aim is to extend our understanding of how salinity may affect the physiological characteristics of plants.
Sun, 18 September 2016
ARTICLE Download: 1573| View: 1436| Comments: 0 | doi:10.20944/preprints201609.0062.v1
Subject: Biology, Plant Sciences Keywords: Nicotiana tabacum; solanesol; RNA-seq; solanesyl diphosphate synthase; gene expression; chlorophyll
Online: 18 September 2016 (10:45:27 CEST)
Solanesol is a noncyclic terpene alcohol composed of nine isoprene units and it mainly accumulates in solanaceous plants, especially tobacco (Nicotiana tabacum L.). Here, RNA-seq analyses of tobacco leaves, stems, and roots were used to identify solanesol biosynthesis genes. Six 1-deoxy-d-xylulose 5-phosphate synthase, two 1-deoxy-d-xylulose 5-phosphate reductoisomerase, two 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase, four 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase, two 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase, four 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, two 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase, six isopentenyl diphosphate isomerase, and two solanesyl diphosphate synthase (SPS) genes were identified to be involved in solanesol biosynthesis. Furthermore, the two N. tabacum SPS (NtSPS1 and NtSPS2), which had two conserved aspartate-rich DDxxD domains, were highly homologous with SPS enzymes from other solanaceous plant species. In addition, the solanesol contents of three organs, and leaves from four growing stages, corresponded with the distribution of chlorophyll. Our findings provide a comprehensive evaluation of the correlation between the expression of different biosynthetic genes and the accumulation of solanesol in tobacco.
Sat, 10 December 2016
REVIEW Download: 678| View: 1388| Comments: 0 | doi:10.20944/preprints201612.0061.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: alcohol; aroma; bioengineering; flavour; synthetic genomics; taste; wine; yeast
Online: 10 December 2016 (09:09:54 CET)
A perfectly balanced wine can be said to create a symphony in the mouth. To achieve the sublime, both in wine and music, requires imagination and skilled orchestration of artistic craftmanship. For wine, inventiveness starts in the vineyard. Similar to a composer of music, the grapegrower produces grapes through a multitude of specifications to achieve a quality result. Different Vitis vinifera grape varieties allow the creation of wine of different genres. Akin to a conductor of music, the winemaker decides what genre to create and considers resources required to realise the grape’s potential. A primary consideration is the yeast: inoculate the grape juice or leave it ‘wild’; which specific or combined Saccharomyces strain(s) should be used; or proceed with a non-Saccharomyces species? Whilst the various Saccharomyces and non-Saccharomyces yeasts perform their role during fermentation, the performance is not over until the ‘fat lady’ (S. cerevisiae) has sung (i.e. the grape sugar has been fermented to specified dryness and alcoholic fermentation is complete). Is the wine harmonious or discordant? Will the consumer demand an encore and make a repeat purchase? Understanding consumer needs lets winemakers orchestrate different symphonies (i.e. wine styles) using single- or multi-species ferments. Some consumers will choose the sounds of a philharmonic orchestra comprising a great range of diverse instrumentalists (as is the case with wine created from spontaneous fermentation); some will prefer to listen to a smaller ensemble (analogous to wine produced by a selected group of non-Saccharomyces and Saccharomyces yeast); and others will favour the well-known and reliable superstar soprano (i.e. S. cerevisiae). But what if a digital music synthesiser ‒ such as a synthetic yeast ‒ becomes available that can produce any music genre with the purest of sounds by the touch of a few buttons? Will synthesisers spoil the character of the music and lead to the loss of the much-lauded romantic mystique? Or will music synthesisers support composers and conductors to create novel compositions and even higher quality performances that will thrill audiences? This article explores these and other relevant questions in the context of winemaking and the role that yeast and its genomics play in the betterment of wine quality.
Fri, 5 August 2016
REVIEW Download: 640| View: 1297| Comments: 0 | doi:10.20944/preprints201608.0054.v1
Subject: Biology, Other Keywords: influenza virus; antiviral agent; proteomics; phosphoproteomics; metabolomics; transcriptomics; genomics; virtual ligand screening
Online: 5 August 2016 (12:41:07 CEST)
Human influenza A viruses (IAVs) cause global pandemics and epidemics. These viruses evolve rapidly, making current treatment options ineffective. To identify novel modulators of IAV-host interactions, we re-analyzed our recent transcriptomics, metabolomics, proteomics, phosphoproteomics, and genomics/virtual ligand screening data. We identified 713 potential modulators targeting 200 cellular and two viral proteins. Anti-influenza activity for 48 of them has been reported previously, whereas the antiviral efficacy of the remaining 665 is unknown. Studying anti-influenza efficacy, immuno-modulating properties and potential resistance of these compounds or their combinations may lead to the discovery of novel modulators of IAV-host interactions, which might be more effective than the currently available anti-influenza therapeutics.
Thu, 13 October 2016
REVIEW Download: 2327| View: 1295| Comments: 0 | doi:10.20944/preprints201610.0049.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: plant extracts; antifungal activity; fungal pathogens
Online: 13 October 2016 (11:50:21 CEST)
Abstract Plant fungal pathogens are frequently found as one of limiting factors for crop production. More than 10,000 species of fungi can cause disease in plants. To control the diseases, many farmers are still rely on the use of chemical fungicides, however most synthetic fungicides can cause acute toxicity, and some cause chronic toxicity as well. Thus, an appropriate technological improvement towards a more effective use of natural resources is required in agriculture to develop environmentally friendly sustainable farming system. This paper highlights the potential of extracts of tropical plants as antifungal agent to control plant fungal diseases. Information and data presented in this paper are mainly derived from selected and related references that previously published in the scientific journals. Many higher plants of tropical origin with fungicidal activities and their potential for fungal disease control of agricultural crops have been studied, however most of the studies have been done under in vitro condition. Some plant extracts showed strong antifungal activities on in vitro as well as in vivo tests, but some plant extracts showed significant antifungal activities on in vitro test, but did not obvious on in vivo tests. A great variation in antifungal activities were shown by plants extracts of different species and plant parts, in one hand, and on the other hand, variation was also observed on the responses of different fungal species to the same plant extract. Since the purpose of the use of plant extract is to control plant fungal diseases, the field trial is needed to ensure the stability of efficacy of certain plant extract. In addition, isolation and identification of active substances in the extracts is needed to assess possible mode of action and side effect of their use.
Fri, 18 January 2019
ARTICLE Download: 97| View: 1276| Comments: 0 | doi:10.20944/preprints201901.0190.v1
Subject: Biology, Physiology Keywords: Sleep, neuronal excitability, central nervous system, sensitivity, cognitive function
Online: 18 January 2019 (12:23:11 CET)
The function of sleep in mammal and other vertebrates is one of the great mysteries of biology. Many hypotheses have been proposed, but few of these have made even the slightest attempt to explain the essence of sleep - the uncompromising need for reversible unconsciousness. During sleep, epiphenomena - often of a somatic character - occur, but these cannot explain the core function of sleep. One answer could be hidden in the observations made for long periods of time of the function of the central nervous system (CNS). The CNS is faced with conflicting requirements on stability and excitability. A high level of excitability is desirable, and is also a prerequisite for sensitivity and quick reaction times; however, it can also lead to instability and the risk of feedback, with life-threatening epileptic seizures. Activity-dependent negative feedback in neuronal excitability improves stability in the short term, but not to the degree that is required. A hypothesis is presented here demonstrating how calibration of individual neurons - an activity which occurs only during sleep - can establish the balanced and highest possible excitability while also preserving stability in the CNS. One example of a possible mechanism is the observation of slow oscillations in EEGs made on birds and mammals during slow wave sleep. Calibration to a genetically determined level of excitability could take place in individual neurons during the slow oscillation, so that action potentials are generated during the oscillations “up-phase”. This can only take place offline, which explains the need for sleep. The hypothesis can explain phenomena such as the need for unconsciousness during sleep, with the disconnection of sensory stimuli, slow EEG oscillations, the relationship of sleep and epilepsy, age, the effects of sleep on neuronal firing rate and the effects of sleep deprivation and sleep homeostasis. This is with regard primarily to mammals, including humans, but also all other vertebrates.
Thu, 25 August 2016
ARTICLE Download: 1502| View: 1252| Comments: 0 | doi:10.20944/preprints201608.0205.v1
Subject: Biology, Ecology Keywords: horizontal subsurface flow wetland; N removal; first-order kinetics; model
Online: 25 August 2016 (08:48:05 CEST)
We monitored the water quality and hydrological conditions of a horizontal subsurface constructed wetland (HSSF-CW) in Beijing, China, for 2 years. We simulated the area rate constant and the temperature coefficient with the first-order kinetic model. We examined the relationships between the nitrogen (N) removal rate, N load, seasonal variations in the N removal rate, and environmental factors, such as the area rate constant, temperature, and dissolved oxygen (DO). The effluent ammonia (NH4+-N) and nitrate (NO3−-N) concentrations were significantly lower than the influent concentrations (p<0.01, n=38). The NO3−-N load was significantly correlated with the removal rate (R2=0.9566, p<0.01), but the NH4+-N load was not correlated with the removal rate (R2=0.0187, p>0.01). The area rate constants of NO3−-N and NH4+-N at 20 °C were 27.01±26.49 and 16.63±10.58 m∙yr−1, respectively. The temperature coefficients for NO3−-N and NH4+-N were estimated at 1.0042 and 0.9604, respectively. The area rate constants for NO3−-N and NH4+-N were not correlated with temperature (p>0.01). The NO3−-N area rate constant was correlated with the corresponding load (R2=0.9625, p<0.01). The NH4+-N area rate was correlated with DO (R2=0.6922, p<0.01), suggesting that the factors that influenced the N removal rate in this wetland met Liebig's law of the minimum.
Sun, 18 September 2016
ARTICLE Download: 1900| View: 1233| Comments: 0 | doi:10.20944/preprints201609.0056.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: green manure; soil microbial communities; crop health; Illumina sequencing
Online: 18 September 2016 (08:56:53 CEST)
Green manure could improve soil nutrients and crop production, playing a significant role in sustainable agriculture. However, the impacts of green manure on crop health and the roles soil microbial communities play in the process haven’t been clarified clearly yet. In this study, we investigated soil microbial community composition and structure in four tobacco farmlands, which were treated with different green manure (control, ryegrass, pea and rape), using 16S rRNA gene amplicons sequencing. Results showed that green manure had significant impacts on soil properties, microbial communities and tobacco health. First, soil total C, N and Ca content increased significantly in groups treated with green manure than control. Second, soil community diversity was significantly higher in groups treated with green manure. Third, green manure especially ryegrass, decreased tobacco disease (bacterial wilt) rate dramatically, and the process might be mediated by soil microbial communities. On the one hand, several microbial populations were found to be potentially disease inducible or suppressive. For example, the abundances of Dokdonella and Rhodanobacter were positively correlated to tobacco disease rate, while Acidobacteira_Gp4 and Gp6 had negative correlations with tobacco disease. On the other hand, soil microbial communities were shaped by soil properties (e.g., pH, C and N content). In conclusion, our research showed that green manure could increase soil nutrients directly, and further improve tobacco health mediated by soil microorganisms, which may shed light on revealing interactions among soil properties, microorganisms and plants.
Mon, 10 October 2016
ARTICLE Download: 1091| View: 1232| Comments: 0 | doi:10.20944/preprints201610.0027.v1
Subject: Biology, Physiology Keywords: Liver X receptor (LXR); Peroxisome proliferator-activated receptor (PPARγ); Adipose expansion; Insulin resistance
Online: 10 October 2016 (07:56:30 CEST)
Liver X receptors (LXR) are deemed as potential drug targets for atherosclerosis, whereas a role in adipose tissue expansion and its relation to insulin sensitivity remains unclear. To assess the metabolic effects of LXR activation, C57BL/6 mice on a high-fat diet (HFD) were treated with the dual LXRα/β agonist T0901317 (30 mg/kg per day) for 3 weeks. Differentiated 3T3-L1 was used for analysing the effect of T0901317 on glucose uptake.T0901317 reduced fat mass, accompanied by a massive fatty liver and lower adipokine levels in circulation of HFD mice. Increased adipocyte apoptosis and macrophage infiltration were found in epididymal fat of T0901317-treated HFD mice. In addition, T0901317 treatment promoted basal lipolysis, but blunted the anti-lipolytic action of insulin. Furthermore, LXR activation antagonized PPARγ target genes in epididymal fat and PPARγ-PPRE binding activity in 3T3-L1 adipocytes. Although the glucose tolerance was comparable to that in vehicle-treated HFD mice, the insulin tolerance was significantly decreased in T0901317-treated HFD mice, indicating decreased insulin sensitivity by T0901317 administration, and which was further supported by impaired insulin signalling found in epididymal fat and decreased insulin-induced glucose uptake in 3T3-L1 by T0901317administration. These findings reveal that LXR activation impairs adipose expansion which contributes to decreased insulin sensitivity.
Sun, 5 February 2017
REVIEW Download: 762| View: 1221| Comments: 0 | doi:10.20944/preprints201702.0016.v1
Subject: Biology, Physiology Keywords: anaphase A; kinetochore; chromosome-to-pole motion; pac-man; microtubule poleward flux; conformational wave; biased diffusion
Online: 5 February 2017 (09:39:32 CET)
The separation of sister chromatids during anaphase is the culmination of mitosis and one of the most strikingly beautiful examples of cellular movement. It consists of two distinct processes: Anaphase A, the movement of chromosomes toward spindle poles via shortening of the connecting fibers, and anaphase B, separation of the two poles from one another via spindle elongation. I focus here on anaphase A chromosome-to-pole movement. The chapter begins by summarizing classical observations of chromosome movements, which support the current understanding of anaphase mechanisms. Live cell fluorescence microscopy studies showed that poleward chromosome movement is associated with disassembly, or ‘melting’ of the kinetochore-attached microtubule fibers that link chromosomes to poles. Microtubule-marking techniques established that kinetochore-fiber disassembly often occurs through a ‘pac-man’ mechanism, where tubulin subunits are lost from kinetochore-attached plus ends and the kinetochore appears to consume its microtubule track as it moves poleward. In addition, kinetochore-fiber disassembly in many cells occurs partly through ‘flux’, where the microtubules flow continuously toward the poles and tubulin subunits are lost from minus ends. Molecular mechanistic models for how load-bearing attachments are maintained to disassembling microtubule ends, and how the forces are generated to drive pac-man and flux-based movements, are discussed.
Wed, 10 August 2016
ARTICLE Download: 1330| View: 1189| Comments: 0 | doi:10.20944/preprints201608.0104.v1
Subject: Biology, Horticulture Keywords: Capsicum annuum L.; capsaicinoid synthesis; gene expression; fruit development; MeJA
Online: 10 August 2016 (10:11:50 CEST)
Background: Capsaicinoid are a group of compounds and widely used in the food, medical, and pharmaceutical industries. Capsaicinoid are unique synthesized and accumulated in the pepper fruits. MeJA can enhance the capsaicinoid production. Temporal and spatial expression of capsaicinoid biosynthetic genes are helpful to understand the molecular mechnism of capsaicinoid biosynthesis in the fruits of pepper. Although some of the capsaicinoid biosynthetic genes in pepper have been identified, the expression of these genes at different developing stages of fruit has not been systemically investigated, and little is known about the molecular basis of MeJA inducing capsaicinoid biosynthesis. Results: HPLC study revealed that the capsaicinoid accumulation in the developing fruit of pepper initially appeared at 24 DAP (day after pollination), was actively development at 36 DAP and peaked at 48 DAP. 11 genes that encoded enzymes involved in capsaicinoid biosynthesis were isolated and characterized. Gene expression with quantitative reverse-transcription polymerase chain reaction analysis demonstrated that the CaCS was unique expressed in placenta and the other 10 genes were expressed in all selected tissues and 9 of 11 genes (except CaCa4H and CaCa3H) were strongly expressed in placenta tissue. Spatial expression analysis demostrated that the 11 gene could be collectively grouped into four categories based on the patterns of relative expression of the genes during fruit development. Category I has 2 and they displayed a bell-shaped expression pattern with the peak expression at 24 DAP, Category II contains 5 genes and expression of the 5 genes was constantly increased from 0 to 36 DAP and peaked at 36 DAP. Category III comprises of 2 genes and both genes reached the peak at 48 DAP. Category IV consists of 2 genes and they showed a high expression at 36 and 48 DAF, but unexpressed from 0 to 12 DAP. The gene expressions of the 11 genes were up-regulated by MeJA. 3 genes showed a high expression at 24 h; 4 genes reached the peak at 12 h; the top expression were observed at 18 h; The last one, CaACYase, achieved the highest level at 8 h. Conclusion: The biosynthesis of capsaicinoid in pepper fruit is developmentally regulated. The expression of the majority of capsaicinoid biosynthetic genes is highly consistent with the development accumulation of capsaicinoid in pepper fruit. These results not only provide the initial information on spatial and temporal expression of capsaicinoid biosynthetic genes in pepper developing fruit, but are also valuable to identify the MeJA-induced genes for capsaicinoid biosynthesis and accumulation during pepper fruit development.
Fri, 30 June 2017
REVIEW Download: 2211| View: 1180| Comments: 0 | doi:10.20944/preprints201706.0127.v1
Subject: Biology, Animal Sciences & Zoology Keywords: sex determination; exual systems; bivalvia; mitochondria
Online: 30 June 2017 (07:28:18 CEST)
In this review, we provide an overview of the current knowledge on the different sexual systems and sex determining mechanisms in bivalves, with a focus on the various epigenetic and genetic factors that may be involved. The final section of the review provides recent discoveries on sex-specific mitochondrial genes in bivalves possessing the unconventional system of doubly uniparental inheritance of mitochondria (which is found in several members of the orders Mytiloida, Unionoida, Veneroida and Nuculanoida). The genes involved in this developmental pathway could represent the first sex determination system in animals in which mitochondrially-encoded genes are directly involved.
Mon, 5 September 2016
ARTICLE Download: 1203| View: 1179| Comments: 0 | doi:10.20944/preprints201609.0009.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Lilium spp.; anthocyanins; purple ovaries; transcriptome; transcriptional network
Online: 5 September 2016 (02:37:09 CEST)
Lily tepals have a short lifespan. Once the tepals senesce, the ornamental value of the flower is lost. Some cultivars have attractive purple ovaries and fruits which greatly enhance the ornamental value of Asiatic hybrid lilies. However, little is known about the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries. To investigate the transcriptional network that governs purple ovary coloration in Asiatic hybrid lilies, we obtained transcriptome data from green ovaries (S1) and purple ovaries (S2) of Asiatic ‘Tiny Padhye’. Comparative transcriptome analysis revealed 4228 differentially expressed genes. Differential expression analysis revealed that nine unigenes including four CHS genes, one CHI gene, one F3H gene, one F3′H gene, one DFR gene, and one UFGT gene were significantly up-regulated in purple ovaries. One MYB gene, LhMYB12-Lat, was identified as a key transcription factor determining the distribution of anthocyanins in Asiatic hybrid lily ovaries. Further qPCR results showed unigenes related to anthocyanin biosynthesis were highly expressed in purple ovaries of Asiatic ‘Tiny Padhye’ at stages 2 and 3, while they showed an extremely low level of expression in ovaries of Asiatic ‘Yellow Pixels’ during all developmental stages. In addition, shading treatment significantly decreased pigment accumulation by suppressing the expression of several unigenes related to anthocyanin biosynthesis in ovaries of Asiatic ‘Tiny Padhye’. These results could further our understanding of the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries.
Tue, 10 January 2017
REVIEW Download: 1905| View: 1175| Comments: 0 | doi:10.20944/preprints201701.0039.v1
Subject: Biology, Other Keywords: apoptosis; autophagy; cancer; crosstalk; curcumin; endoplasmic reticulum; hormatic behavior; lysosomes; mitochondria
Online: 10 January 2017 (03:46:51 CET)
Curcumin, found in the rhizome of turmeric, has extensive therapeutic promises via its antioxidant, anti-inflammatory, and antiproliferative properties. Preclinical in vitro and in vivo data have shown curcumin to be an effective treatment for multiple cancers. These effects are drived by curcumin's ability to induce G2/M cell cycle arrest, induction of autophagy, activation of apoptotic pathways, disruption of molecular signaling, inhibition of invasion and metastasis, and by increasing the efficacy of existing chemotherapeutics. Here we focused on the hormetic behaviour of curcumin. Frequently, low doses of toxins and other stressors not only are harmless but also activate an adaptive stress whereas high dose activates acute responses like autophagy and cell death. This phenomenon is referred to as hormesis. Many molecules that cause cell death elicite an initial autophagic step that is a cytoprotective mechanism relying on elimination of dysfunctional structures intracellular, notably by mitophagy. This phenomenon is considered as a primarily protective mechanism against stressors. At higher doses, cells undergo mitochondrial outer membrane permeabilization due to calcium release from the endoplasmic reticulum and die. Herein, we address the complex crosstalk between the induced mitochondrial biogenesis, mitochondrial destabilization accompanied by mitophagy and cell death that can also be at play.
ARTICLE Download: 854| View: 1173| Comments: 0 | doi:10.20944/preprints201701.0050.v1
Subject: Biology, Anatomy & Morphology Keywords: Interleukin-1 receptor antagonist (IL-1Ra); Interleukin-4 (IL-4); Variable Number Tandem Repeat (VNTR); obesity; adiposity; Malaysia.
Online: 10 January 2017 (10:27:41 CET)
IL1RA intron 2 86-bp repeat and IL4 intron 3 70-bp repeat are VNTRs that have been associated with various diseases, but their role in obesity is elusive. The objective of this study was to investigate the association of IL1RA and IL4 VNTRs with obesity and adiposity in 315 Malaysian subjects (128 M/187 F; 23 Malays/251 ethnic Chinese/41 ethnic Indians). The allelic distributions of IL1RA and IL4 were significantly different among ethnicities, and the alleles were associated with total body fat (TBF) classes. Individuals with IL1RA I/II genotype or allele II had greater risk of having higher adiposity - even after controlling for ethnicity [Odds Ratio (OR) of I/II genotype = 12.21 (CI = 2.54, 58.79; p = 0.002); II allele = 5.78 (CI = 1.73, 19.29; p = 0.004)]. However, IL4 VNTR B2 allele was only significantly associated with overall adiposity status before adjusting for ethnicity [OR = 1.53 (CI = 1.04, 2.23; p = 0.03)]. TBF was also significantly higher in those with IL1RA II allele compared with I allele (31.79 ± 2.52 vs. 23.51 ± 0.40; p = 0.005). Taken together, IL1RA intron 3 VNTR seems to be a genetic marker for overall adiposity status in Malaysian subjects.
Mon, 9 January 2017
ARTICLE Download: 871| View: 1157| Comments: 0 | doi:10.20944/preprints201701.0036.v1
Subject: Biology, Plant Sciences Keywords: Acer truncatum leaves; ultrasonic-assisted extraction; response surface methodology; phenolics; antioxidant activity; UPLC-QTOF-MS/MS
Online: 9 January 2017 (04:16:01 CET)
This study was designed for the first time to improve phenolic yield and antioxidant activity of ultrasonic-assisted extraction from Acer truncatum leaves (ATL) using response surface methodology, and phenolic composition in ATL extracted under the optimized condition were characterized by UPLC-QTOF-MS/MS. Solvent and extraction time were selected based on preliminary experiments, and a four-factors-three-levels central composite design was conducted to optimize solvent concentration (X1), material-to-liquid ratio (X2), ultrasonic temperature (X3) and power (X4) for an optimal total phenol yield (Y1) and DPPH• antioxidant activity (Y2). The results showed that the optimal combination was ethanol: water (v:v) 66.21%, material-to-liquid ratio 1:15.31 g/mL, ultrasonic temperature 60 °C, power 267.30 W, and time 30 min with three extractions, giving a maximal total phenol yield of 7593.62 mg gallic acid equivalent /100 g d.w. and a maximal DPPH• antioxidant activity of 74241.61 μmol Trolox equivalent/100 g d.w.. Furthermore, 22 phenolics were first identified in ATL extract obtained under the optimized conditions, indicating that gallates, gallotannins, quercetin, myricetin and chlorogenic acid derivatives were the main phenolic composition in ATL. What’s more, a gallotannins pathway existing in ATL from gallic acid to penta-O-galloyl-glucoside was interpreted. All these results provided practical information aiming at full utilization of phenolics in ATL, together with fundamental knowledge for further research.
Fri, 8 September 2017
ARTICLE Download: 817| View: 1146| Comments: 0 | doi:10.20944/preprints201709.0031.v1
Subject: Biology, Other Keywords: rice; endophyte; sustainable agriculture; plant microbiome; simplified bacterial community; syncomm; taxonomic profiling; core plant microbiome
Online: 8 September 2017 (14:02:56 CEST)
Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed the isolation of hundreds bacterial isolates obtained from endorhizosphere of two rice cultivars from Venezuela. The validation of plant-growth promoting bacterial activities in vitro has led us to select and characterize 15 isolates for in planta studies such as germination test, endophytism ability and plant growth promotion. Consequently, a set of 10 isolates was selected for the set-up of an endophytic consortium as a simplified model of the natural rice bacterial endomicrobiota. Upon inoculation, the colonization and abundance of each strain within the rice roots was tracked by a culture-independent technique in gnotobiotic conditions in a 30 days period. Four strains belonging to Pseudomonas, Agrobacterium and Delftia genera have shown a promising capacity for colonizing and coexistence in root tissues. On the other hand, a bacterial community taxonomic profiling of the rhizosphere and the endorhizosphere of both cultivars were obtained and are discussed. This study is part of a growing body of research on core crops microbiome and simplified microbiomes, which strengthens the formation process of the endophytic community leading to a better understanding of the rice microbiome.
Mon, 15 August 2016
ARTICLE Download: 1176| View: 1139| Comments: 0 | doi:10.20944/preprints201608.0154.v1
Subject: Biology, Ecology Keywords: carbon stock assessment; protected areas; savannas; degradation; woody vegetation; West Africa
Online: 15 August 2016 (12:06:29 CEST)
Savannas and adjacent vegetation types like gallery forests are highly valuable ecosystems contributing to several ecosystem services including carbon budgeting. Financial mechanisms such as REDD+ have provided an opportunity for developing countries to alleviate poverty through conservation of its forestry resources. For availing this opportunity carbon stock assessments are essential. Therefore, a research study at two protected areas i.e. Nazinga Game Ranch and Bontioli Nature Reserve, in Burkina Faso was conducted with the objective of assessing carbon Mg C ha-1 in aboveground biomass (AGB)dry of trees in different formations of the south-sudanian savanna in Burkina Faso, West Africa. Similarly analysis of various vegetation parameters was also conducted to understand the overall vegetation structure of these two protected areas. For estimating AGBdry, existing allometric equation for dry tropical woody vegetation types was used. The Importance Value Index (IVI) and Family Importance Value (FIV) were estimated through standard procedures. Various linear and non-linear regression analyses were conducted to test the relationships between carbon and other parameters such as DBH, height and basal area (BA). The results showed that both sites collectively contain mean carbon of 3.41 ± 4.98 Mg C ha-1. Amongst different vegetation types, gallery forests recorded the highest mean carbon of 9.38 ± 6.90 Mg C ha-1. The highest IVI of 115.56 at Nazinga Game Ranch was recorded for Anogeissus leiocarpa. Similarly, highest IVI of 98.59 was recorded for Mitragyna inermis at Bontioli Nature Reserve. The highest FIV was recorded for Combretaceae for both of the sites. To our knowledge, this was the first study conducted to assess the carbon stocks at the two protected areas in southern Burkina Faso. The study therefore was an attempt for addressing the knowledge gap particularly on carbon stocks of protected savannas. It could serve as a baseline for carbon stocks for future initiatives such as payment for environmental services and REDD+ at these areas.
Fri, 21 October 2016
ARTICLE Download: 1048| View: 1097| Comments: 0 | doi:10.20944/preprints201610.0088.v1
Online: 21 October 2016 (06:05:11 CEST)
Ecosystem physical structure, defined by the quantity and spatial distribution of biomass, influences a range of ecosystem functions. Remote sensing tools permit the non-destructive characterization of canopy and root features, potentially providing opportunities to link above- and belowground structure at fine spatial resolution in functionally meaningful ways. To test this possibility, we employed ground-based portable canopy lidar (PCL) and ground penetrating radar (GPR) along co-located transects in forested sites spanning multiple stages of ecosystem development and, consequently, of structural complexity. We examined canopy and root structural data for coherence at multiple spatial scales ≤ 10 m within each site using wavelet analysis. Forest sites varied substantially in vertical canopy and root structure, with leaf area index and root mass more evenly distributed by height and depth, respectively, as forests aged. In all sites, above- and belowground structure, characterized as mean maximum canopy height and root mass, exhibited significant coherence at a scale of 3.5-4 meters, and results suggest that the scale of coherence may increase with stand age. Our findings demonstrate that canopy and root structure are linked at characteristic spatial scales, which provides the basis to optimize scales of observation. Our study highlights the potential, and limitations, for fusing lidar and radar technologies to quantitatively couple above- and belowground ecosystem structure.
Fri, 9 September 2016
ARTICLE Download: 586| View: 1096| Comments: 0 | doi:10.20944/preprints201609.0037.v1
Subject: Biology, Plant Sciences Keywords: Consolida orientalis; ethyl acetate extract; antioxidant activity; β-sitosterol
Online: 9 September 2016 (11:18:02 CEST)
General phytochemical screening of the aerial parts of Consolida orientalis revealed the presence of steroids, terpenes, phenolic compounds, saponins, fatty acids, alkaloids. This study was conducted to investigate the bioactivities of extracts, isolation and identification the compounds from aerial parts of C.orientalis. The main goal of the present study is identifying and characterizing the antioxidant activity of the Consolida orientalis and biological isolation of active terpenoid. Aerial parts of the plant were dried at room temperature and reduced to small pieces, followed by using extraction with ethyl acetate percolation. Tree complementary analysis system was used, DPPH free radical scavenging test, total phenolic metabolites and FRAP. The total phenolic content was 38.83±2.09 mg gallic acid corresponding to g-1 extract with regarding to standard curve (y=0.0054x+0.0488, r2=0.995). IC50 value for DPPH radical – scavenging was 987.11±28.66 mgml-1. The extract was exhibited a medium reducing power compared with Vit C. The isolation and purification was afforded white crystalline powder which was subjected to physical, chemical and spectral identification by IR, 1H- and 13C- NMR and GC-MS. Isolated compound was identified as β-sitosterol. That is a terpenoid with melting point 133.4-134.5 ͦ c and with molecular formula C29H50O.
Fri, 7 October 2016
REVIEW Download: 982| View: 1081| Comments: 0 | doi:10.20944/preprints201610.0014.v1
Subject: Biology, Physiology Keywords: Trophic factors; nervous system; development; plasticity; axotomy
Online: 7 October 2016 (09:51:38 CEST)
Neurotrophins play a principal role in neuronal survival and differentiation during development, but also in the maintenance of appropriate adult neuronal circuits and phenotypes. In the oculomotor system, we have demonstrated that neurotrophins are key regulators of developing and adult neuronal properties, but with peculiarities depending on each neurotrophin. For instance, the administration of NGF, BDNF or NT-3 protects neonatal extraocular motoneurons from cell death after axotomy, but only NGF and BDNF prevent the downregulation in ChAT. In the adult, in vivo recordings of axotomized extraocular motoneurons have demonstrated that the delivery of NGF, BDNF or NT-3 recovers different components of the firing discharge activity of these cells, with some particularities in the case of NGF. All neurotrophins have also synaptotrophic activity, although to different degrees. Accordingly, neurotrophins can restore the axotomy-induced alterations acting selectively on different properties of the motoneuron. In this review we summarize these evidences and discuss them in the context of other motor systems.
Tue, 2 October 2018
ARTICLE Download: 161| View: 1079| Comments: 2 | doi:10.20944/preprints201809.0566.v1
Subject: Biology, Plant Sciences Keywords: Montiaceae; life history; climate niche; polyploidy; phylogenetic comparative analysis (PhCA); natural selection (NS); natural drift (ND); chaos; stochasticity; determinism; principle of evolutionary idiosyncraticity (PEI)
Online: 2 October 2018 (12:06:57 CEST)
The present paper reviews evidence for ecological evolution of Montiaceae. Montiaceae (Portulacineae) comprise a family of ca. 275 species and ca. 25 subspecific taxa of flowering plants distributed mainly in extreme western America, with additional endemism elsewhere, including other continents and islands. They have diversified repeatedly across steep ecological gradients. Based on narrative analysis, I argue that phylogenetic transitions from annual to perennial life history have been more frequent than suggested by computational phylogenetic reconstructions. I suggest that a reported phylogenetic correlation between the evolution of life history and temperature niche is coincidental and not causal. I demonstrate how statistical phylogenetic comparative analysis (PhCA) missed evidence for marked moisture niche diversification among Montiaceae. I discount PhCA evidence for the relation between Montiaceae genome duplication and ecological diversification. Based on the present analysis of Montiaceae evolution, I criticize the premise of the prevalent statistical approach to PhCA, which tests Darwinian deterministic hypotheses against stochastic evolutionary null models. I discuss theoretical/empirical evidence that evolution is neither stochastic, nor Darwinistically-determined, but idiosyncratic. Idiosyncraticity describes the outcome of a stochastically perturbed nonlinear chaos-like process. The Principle of Evolutionary Idiosyncraticity (PEI) is based on the evolutionary theory of Natural Drift, which maintains that determinism in evolution is a property of the organism and not, as maintained by the theory of Natural Selection, its traits or its milieu. This determinism is characteristic of chaotic functions, which are absolutely determinate, generate self-similarity, but remain absolutely unpredictable. PEI explains precisely observations that evolution proceeds not linearly, but chaotically, producing both quasi-linear fractal-like patterns and non-linear jumps. PEI has ramifications for all areas of macroevolutionary research. In particular, it demonstrates both the fallacy and futility of the statistical PhCA approach that interprets evolutionary causes in terms of evolutionary correlations. However, statistical methods of PhCA can be applied heuristically and fruitfully to reveal idiosyncraticity and discover evolutionary novelty. This, in turn, is demonstrated by the emergence of statistical anomalies in evolutionary analyses of Montiaceae.
Fri, 30 December 2016
ARTICLE Download: 985| View: 1062| Comments: 0 | doi:10.20944/preprints201612.0151.v1
Online: 30 December 2016 (07:43:42 CET)
Mesial temporal lobe epilepsy (mTLE) is one of the most common and refractory focal epilepsy syndromes. The molecular mechanisms of TLE are not completely understood. The aim of this study was to investigate the expression and potential function of plasma exosomal miRNAs (miR-483-5p, miR-671-5p, and miR-150-3p) in a mouse mode and in temporal lobe epilepsy patients. It was found that exosomal miRNAs were differentially expressed in three phases of the mouse mode, and exosomal miRNAs were down-regulated in mTLE patients compared with healthy controls. A bioinformatics analysis showed that target genes of exosomal miRNAs were significantly involved in the apoptotic process, cell adhesion, nervous system development, neurotrophin signaling pathway, PI3K-Akt signaling pathway, and metabolic pathways. The areas under the curve of miR-483-5p and miR-150-3p were 0.8714 (sensitivity = 75.00%, specificity = 91.65%) and 0.8213 (sensitivity = 67.50%, specificity = 90.00%), respectively. More importantly, the exosomal miRNAs were significantly associated with clinical parameters. Exosomal miRNAs may have the potential to become diagnostic and therapeutic biomarkers.
Tue, 6 September 2016
ARTICLE Download: 1223| View: 1057| Comments: 0 | doi:10.20944/preprints201609.0021.v1
Subject: Biology, Entomology Keywords: lemongrass oil; Ligusticum chuanxiong oil; Aphis citricola van der Goot; botanical aphicides
Online: 6 September 2016 (11:52:51 CEST)
In order to develop novel botanical insecticides, the joint action of Ligusticum chuanxiong oil (LCO) and lemongrass oil (LO) against Aphis citricola van der Goot was determined systematically indoors and outdoors. The chemical profiles of LCO and LO as determined by gas chromatography- mass spectrometry analysis revealed that main compounds from LCO were Z-Ligustilide (44.58%) and Senkyunolide A (26.92%), and that of LO were geranial (42.16%) and neral (32.58%), respectively. The mixture of LCO and LO showed significant synergy against A. citricola, with a common-toxicity coefficient (CTC) value of 221.46 at the optimal ratio of LCO to LO (4: 1, w/w). Based on the results of solvents and emulsifiers screening, L. Chuanxiong oil · Lemongrass oil 20% emulsifiable concentrate (20% LCO · LO EC) was developed, which was confirmed to meet the requirements of a commercial pesticide by quality test. Field trials indicated that the insecticidal activity of the diluted 20% LCO · LO EC (1000 fold dilution) was comparable to conventional pesticide (20% imidacloprid EC) on A. citricola 7 days after application. Thus, the mixture of LCO and LO has the potential to be further developed as a botanical pesticide.
Thu, 13 October 2016
ARTICLE Download: 1504| View: 1056| Comments: 0 | doi:10.20944/preprints201610.0044.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: MODIS; yield; phenology; LAD; logistic function
Online: 13 October 2016 (04:40:10 CEST)
A simple approach was developed to predict corn yields using the MoDerate Resolution Imaging Spectroradiometer (MODIS) data product from two geographically separate major corn crop production regions: Illinois, USA and Heilongjiang, China. The MOD09A1 data product, which are 8-day interval surface reflectance data, were obtained from day of the year (DOY) 89 to 337 to calculate the leaf area index (LAI). The sum of the LAI from early in the season to a given date in the season [end of DOY (EOD)] was well fitted to a logistic function and represented seasonal changes in leaf area duration (LAD). A simple phenology model was derived to estimate the dates of emergence and maturity using the logistic function parameters b1 and b2, which represented the rate of increase in LAI and the date of maximum LAI, respectively. The phenology model predicted emergence and maturity dates fairly well, with root mean square error (RMSE) values of 6.3 and 4.9 days for the validation dataset, respectively. Two simple linear regression models (YP and YF) were established using LAD as the variable to predict corn yield; the yield model (YP) used LAD from predicted emergence to maturity, and the yield model (YF) used LAD for a predetermined period from DOY 89 to a particular EOD. When state/province corn yields for the validation dataset were predicted at DOY 321, near completion of the corn harvest, the YP model performed much better than the YF model, with RMSE values of 0.68 t/ha and 0.66 t/ha for Illinois and Heilongjiang, respectively. The YP model showed a similar or better performance, even for the much earlier yield prediction at DOY 257, compared to that of the YF model. In conclusion, the phenology and yield models were developed based only on logistic changes in remote sensing-derived LAD, and predicted phenological dates and corn yields with considerable accuracy and precision for the two regions selected for this study. However, these models must be examined for spatial portability in more diverse agro-climatic regions.
Tue, 5 February 2019
ARTICLE Download: 602| View: 1054| Comments: 0 | doi:10.20944/preprints201902.0048.v1
Subject: Biology, Ecology Keywords: Sampling methodology; mtDNA; mitochondrial DNA; conservation; biodiversity; populations; genetics
Online: 5 February 2019 (10:03:54 CET)
Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.
Tue, 2 August 2016
ARTICLE Download: 1158| View: 1053| Comments: 0 | doi:10.20944/preprints201608.0018.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: soil tillage; tractors; soil water content; physical soil properties; GPS; energy requirement; CO2 emission
Online: 2 August 2016 (12:50:33 CEST)
In this study the effects of three different main preparatory tillage operations [ploughing at 0.4 m (P40) and 0.20 m (P20) depth and minimum tillage at 0.20 m depth (MT) each of them carried out at two different soil water contents (WC) [low, 58% (LH) and high, 80% (HH) of field capacity] were investigated. The results obtained in this research show high values of soil strength in term of Penetration resistance (CI) and shear strength (SS) particularly in deeper soil layers at lower water content. Fossil-fuel energy requirements both for P40 LH and P20 LH were 25 and 35% higher with respect to the HH treatments and tractor slip were very high (P40 LH = 32.4%) with respect to the P40 HH treatment (16%). Therefore soil water content had significantly influenced tractor performance during soil ploughing, particularly at 0.40 m depth while MT was not influenced at all. A significant correlation between grain yield and soil penetration resistance was found highlighting how soil strength may be good indicator of its productivity. Obtained results during these field tests allowed considering MT and P20 treatments more suitable for this type of soil in climate change scenarios.
Thu, 24 November 2016
ARTICLE Download: 927| View: 1050| Comments: 0 | doi:10.20944/preprints201611.0123.v1
Subject: Biology, Forestry Keywords: co-management; livelihoods; conflicts; biodiversity conservation; sustainable development
Online: 24 November 2016 (11:25:34 CET)
Good governance in natural resource management (NRM) is one of the most challenging issues in developing countries that often inappropriately embedded in national policies and political agendas. It is, in fact, even more important for countries like Bangladesh with exceptionally high pressure and dependence on its natural resources for sustaining rural livelihoods. Globally, nowadays, good governance is considered as one of the key factor for achieving the goal of sustainable development and biodiversity conservation. Bangladesh, of late has responded to that global zeal by involving local communities in the management of country’s declining forest and other natural resources. The colonial legacy of the forestry sector of Bangladesh was planned and, managed as interim projects through donors’ prescriptions. Thus, institutions, management processes and conservation outcomes were problematic. The conventional approach adopted by colonial and post-colonial regimes for forest management also proved to be inefficient due to its top-down management system. The absolute dependency on donor support, and their prescription sometimes worsened the situation both ecologically and socially. Global, regional and local trends supported the need for a different dimension in the governance paradigms. The introduction of a pluralistic approach, known as co-management in protected areas (PAs) is an example of an attempt whereby shared governance mechanism are implemented to attain the desired goals of conservation that will also address the livelihoods and aspirations of communities living in and around PAs of the country. However, in designing future forest and PA regimes the concern of the external aid support and attached conditions remain a reality that needs to be addressed. Adequate attention should be given to our vanishing biodiversity, culture and community livelihoods through devising an appropriate governance mechanism recognizing and supporting local rights, access and participation in the environmental management. It is now time to mainstream the adhoc nature of governance according to our national conservation strategy and policy frameworks in order to achieve the goals and objectives of the Bangladesh NRM sector addressing the human and community right of people in the specific context of forest protected areas management.
Thu, 27 October 2016
ARTICLE Download: 939| View: 1044| Comments: 0 | doi:10.20944/preprints201610.0121.v1
Subject: Biology, Other Keywords: cytokine; gene expression; osteoclast; root resorption; pediatric dentistry; protein expression
Online: 27 October 2016 (12:10:55 CEST)
The present study was performed to examine that transforming growth factor beta (TGF-β) in root-surrounding tissues on deciduous teeth during the physiological root resorption regulates the differentiation induction into odontoclast. We prepared root-surrounding tissues with (R) or without (N) physiological root resorption scraped off at three regions (R1-R3 or N1-N3) from the cervical area to the apical area of the tooth and measured both TGF-β and the tartrate-resistant acid phosphatase (TRAP) activities. The TGF-β activity level was increased in N1-N3, whereas the TRAP activity was increased in R2 and R3. In vitro experiments for RANKL-mediated osteoclast differentiation revealed that TGF-β in N1-N3 and R1-R3 enhanced the TRAP activity in RAW264 cells. A genetic study indicated that the mRNA level of TGF-β1 in N1 and N2 was significantly increased, and corresponded with that of osteoprotegerin (OPG). In contrast, the expression level of receptor activator of NF-κB ligand (RANKL) was increased in R2 and R3. Our findings suggest that TGF-β is closely related to the regulation of OPG induction and RANKL-mediated odontoclast differentiation depending on the timing of RANKL and OPG mRNA expression in the root-surrounding tissues of deciduous teeth during physiological root resorption.
Thu, 25 August 2016
ARTICLE Download: 1143| View: 1043| Comments: 0 | doi:10.20944/preprints201608.0203.v1
Subject: Biology, Entomology Keywords: Sitophilus zeamais; COXⅡ; Soluble proteins; Enzyme activity; AITC
Online: 25 August 2016 (10:11:13 CEST)
COX II containing a dual core CuA active site is one of the three core subunits of mitochondrial Cco, which plays a significant role in the physiological process. In this report, the full-length cDNA of COXⅡ gene was cloned from Sitophilus zeamais, which had an ORF of 684 bp encoding 227 amino acids residues. The predicted COXⅡ protein had a molecular mass of 26.2 kDa with pI value of 6.37, and multiple sequence alignment and phylogenetic analysis indicated that Sitophilus zeamais COXⅡ had high sequence identity 78.51% with the COXⅡ of other insect species, especially similarity to sitophilus oryzae. This gene was subcloned into the prokaryotic expression vector pET-32a, and induced by IPTG in E.coli Transetta (DE3) expression system. Finally the COXⅡ with 6-His tag was purified using affinity chromatography with Ni2+-NTA agarose. WB showed the recombinant COXⅡ was about 44 kD, and the concentration of fusion protein was 50μg/mL. UV-spectrophotometer and infrared spectrometer analysis showed that recombinant COXⅡ could catalyze the oxidation of substrate Cytc, and influenced by AITC. It was found that AITC could form a hydrophobic region with COXⅡ protein via molecular docking, besides, a sulfur atom of AITC structure could form a length of 2.9 Å hydrogen bond with Leu-31. These results will provide valuable information for elucidating the role of COXⅡ in Sitophilus zeamais responses to AITC, meanwhile, it will helpful to carry out a point mutation in AITC binding sites for the future research.
Tue, 20 September 2016
ARTICLE Download: 1384| View: 1042| Comments: 1 | doi:10.20944/preprints201609.0071.v1
Subject: Biology, Plant Sciences Keywords: EST-SSR marker; hexaploid; sweet potato; polymorphic; sequence
Online: 20 September 2016 (11:35:51 CEST)
According to statistics from the Food and Agriculture Organization, the world population will increase to about 91 million (Asia 51 million, Africa 19 million). A rise in the world’s population means an increased need for food. However, climate change has caused desertification and unpredictable weather, creating problems in the supply and demand of food. Sweet potato (Ipomoea batatas) is an alternative to solving the food problem, as it is one of the world’s most important food crops, especially in developing countries. The tuberous roots of sweet potato are usually used as staple food, animal feed, industrial material, or raw material for alcohol production. In the future, more variations of sweet potato will be needed for breeding this crop. Recently, molecular markers developed for sweet potato have demonstrated good potential for use in genetic selection. In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag–simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of full-sequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.
Mon, 14 November 2016
ARTICLE Download: 1054| View: 1036| Comments: 0 | doi:10.20944/preprints201611.0074.v1
Subject: Biology, Ecology Keywords: Acanthaster; coral reefs; food limitation; larval competency; planktonic larval duration (PLD)
Online: 14 November 2016 (07:49:50 CET)
The dispersal potential of crown-of-thorns starfish (CoTS) larvae is important in understanding both the initiation and spread of population outbreaks, and is fundamentally dependent upon how long larvae can persist while still retaining the capacity to settle. This study quantified variation in larval survivorship and settlement rates for CoTS maintained at three different chlorophyll concentrations (0.1, 1.0 or 10.0 µg.L-1), achieved by varying densities of single-celled flagellate phytoplankton, Proteomonas sulcata. Based on the larval starvation hypothesis we expected that low to moderate algal concentrations would significantly constrain both survival and settlement. CoTS larvae were successfully maintained for up to 50 days post-fertilization, but larval survival differed significantly between treatments. Survival was greatest at intermediate (1.0 µg.L-1) chlorophyll concentrations, and lowest at highest (10.0 µg.L-1) chlorophyll concentrations. Rates of settlement were also highest at intermediate (1.0 µg.L-1) chlorophyll concentrations and peaked at 22 days post-fertilization. Peak settlement was delayed at low chlorophyll concentrations, probably reflective of delayed development, but there was no evidence of accelerated development at high chlorophyll concentrations. CoTS larvae were capable of settling 17-43 days post-fertilization, but under optimum conditions with intermediate chlorophyll concentrations, peak settlement occurred at 22 days post-fertilization. Moderate increases in nutrient concentrations and algal densities may increase the number of CoTS that effectively settle, but are unlikely to influence dispersal dynamics.
Thu, 13 April 2017
ARTICLE Download: 823| View: 1033| Comments: 0 | doi:10.20944/preprints201704.0076.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: acne vulgaris; antibiotic resistance; chitosan-phytochemical conjugates; synergistic antibacterial effect
Online: 13 April 2017 (11:19:33 CEST)
The object of this study was to discover an alternative therapeutic agent with fewer side effects against acne vulgaris, which is one of the most common skin diseases. Acne vulgaris often associates with acne-related bacteria such as <i>Propionibacterium acnes</i>, <i>Staphylococcus epidermidis</i>, <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>, some of which exhibit a resistant against commercial antibiotics used in the treatment of acne vulgaris (tetracycline, erythromycin, and lincomycin). In the current study, we evaluated <i>in vitro</i> antibacterial activity of chitosan-phytochemical conjugates against acne-related bacteria. Three of chitosan-phytochemical conjugates used in this study showed stronger antibacterial activity than that of chitosan (unmodified control). Chitosan-caffeic acid conjugate (CCA) exhibited the highest antibacterial activity against acne-related bacteria with minimum inhibitory concentration values of 8 μg/mL to 256 μg/mL. In addition, the MICs of antibiotics against antibiotic resistant <i>P. acnes</i> and <i>P. aeruginosa</i> strains were dramatically reduced in the combination with CCA, suggesting that CCA would restore the antibacterial activity of the antibiotics. The analysis of fractional inhibitory concentration indices clearly revealed a synergistic antibacterial effect between CCA and the antibiotics. Thus, the median ∑FIC values against the antibiotic resistant bacterial strains were ranged from 0.375 to 0.533 in the combination mode of CCA and antibiotics.
Mon, 7 November 2016
ARTICLE Download: 919| View: 1022| Comments: 0 | doi:10.20944/preprints201611.0035.v1
Subject: Biology, Other Keywords: sustainability; resource-dependent city; emergy analysis; IPAT (Human Impact Population Affluence Technology); Taiyuan
Online: 7 November 2016 (05:15:13 CET)
As the natural resources are getting exhausted, the concept of sustainable development of region has received increasing attentions, especially for resource-dependent cities. In this paper an innovative method that emergy analysis and IPAT (Human Impact Population Affluence Technology) model were combined in order to analyze the quantitative relationship of economic growth and energy consumption and further to evaluate its overall sustainability level. Taiyuan, a traditional, resource-dependent city in China, is selected as the case study region. The main results show that total emergy of Taiyuan increased from 9.023× 1023 sej in 2007 to 9.116× 1023sej in 2014, with 38% reduction on non-renewable emergy and 125% growth on imported emergy. Regional emergy money ratio (RMB) was reduced by 48% from 5.31× 1013sej/$ in 2007 to 2.74× 1013sej/$ in 2014, indicating that the increasing speed of consuming resources and energy was faster than the increase of GDP, and that Taiyuan’s money purchasing power declined. The lower emergy sustainability index (ESI) indicates that Taiyuan was explored and produced large quantities of mineral resources, which puts more stress on the environment as a consequence, and that this is not sustainable in the long run. The IPAT analysis demonstrates that Taiyuan sticks to the efforts of energy conservation and environmental protection, in order to promote regional sustainable development, it is necessary to take an integrated effort. Policy insights suggest that resourceful regions should improve include energy and resource efficiency, optimizing energy and resourceful structure.
Sat, 8 October 2016
ARTICLE Download: 1176| View: 1020| Comments: 0 | doi:10.20944/preprints201610.0022.v1
Subject: Biology, Animal Sciences & Zoology Keywords: P. pseudoannulata; Cadmium; Transcriptome; RT-qPCR
Online: 8 October 2016 (11:07:25 CEST)
Pardosa pseudoannulata is one of the most common wandering spiders in agricultural fields and a potentially good bioindicator for heavy metal contamination. However, little is known about the mechanism by which spiders respond to heavy metals at the molecular level. In this study, high-throughput transcriptome sequencing was employed to characterize the de novo transcriptome of the spiders and to identify differentially expressed genes (DEGs) after cadmium exposure. We obtained 60,489 assembled unigenes, 18,773 of which were annotated in the public databases. Ultimately, 3450 cDNA simple sequence repeats were identified and validated as potential molecular markers in the unigenes. A total of 2939, 2491 and 3759 DEGs were detected among the three libraries of two Cd-treated groups and the control. Functional enrichment analysis revealed that metabolism processes and digestive system function were predominately enriched in response to Cd stress. At the cellular and molecular levels, significantly enriched pathways in lysosomes and phagosomes as well as replication, recombination and repair demonstrated that oxidative damage resulted from Cd exposure. Based on the selected DEGs, certain critical genes involved in defence and detoxification were analysed. These results may elucidate the molecular mechanism underlying spiders' responses to heavy metal stress.
Sat, 13 August 2016
ARTICLE Download: 1457| View: 1018| Comments: 0 | doi:10.20944/preprints201608.0141.v1
Online: 13 August 2016 (11:05:38 CEST)
The mechanism of ciprofloxacin action involves interference with transcription and replication of bacterial DNA, which results in elevated oxidative stress, and bacterial cell death. Vorinostat was shown to induce oxidative DNA damage. In the current work, the possibility for interactive effect of vorinotat on ciprofloxacin-induced cytotoxicity against a number of reference bacteria was investigated. Standard bacterial strains were Escherichia coli ATCC 35218, Staphylococcus aureus ATCC29213, Pseudomonas aeruginosa ATCC 9027, Staphylococcus epidermidis ATCC 12228, Acinetobacter baumannii ATCC 17978, Proteus mirabilis ATCC 12459, Klebsiella pneumoniae ATCC 13883, methicillin-resistant Staphylococcus aureus (MRSA) (ATCC 43300), and Streptococcus pneumoniae (ATCC 25923). The antibacterial activity of ciprofloxacin with or without pretreatment of bacterial cells by vorinostat was examined using disc diffusion procedure and determination of the minimum inhibitory concentration (MIC) and zones of inhibition of bacterial growth. All tested bacterial strains showed sensitivity to ciprofloxacin. When pretreated with vorinostat, significantly larger zones of inhibition and smaller MIC values were observed in all bacterial strains compared ciprofloxacin alone. As a conclusion, current results showed the possible agonistic properties for vorinostat when it is used together with ciprofloxacin. Future research will be focus on molecular mechanisms possible for such interactive effect.
Tue, 1 November 2016
ARTICLE Download: 837| View: 1017| Comments: 0 | doi:10.20944/preprints201611.0003.v1
Subject: Biology, Plant Sciences Keywords: calcium; protons; exocytosis; tip growth; Lilium; pollen; respiration; perturbation analysis
Online: 1 November 2016 (05:25:42 CET)
Pollen tubes grow by spatially and temporally regulated expansion of new material secreted into the cell wall at the tip of the tube. A complex web of interactions among cellular components, ions and small molecule provides dynamic control of localized expansion and secretion. Cross-correlation studies on oscillating lily (Lilium formosanum Wallace) pollen tubes showed that an increase in intracellular calcium follows an increase in growth, whereas the increase in the alkaline band and in secretion both anticipate the increase in growth rate. Calcium, as a follower, is unlikely to be a stimulator of growth, whereas the alkaline band, as a leader, may be an activator. To gain further insight herein we reversibly inhibited growth with potassium cyanide (KCN), and followed the re-establishment of calcium, pH and secretion patterns as growth resumed. While KCN markedly slows growth and causes the associated gradients of calcium and pH to sharply decline, its removal allows growth and vital processes to fully recover. The calcium gradient reappears before growth restarts, however it is preceded by both the alkaline band and secretion, in which the alkaline band is slightly advanced over secretion. Thus the pH gradient, rather than the tip-focused calcium gradient, may regulate pollen tube growth.
Mon, 9 January 2017
ARTICLE Download: 562| View: 1009| Comments: 0 | doi:10.20944/preprints201701.0035.v1
Subject: Biology, Other Keywords: QuantiFERON-TB Gold In-Tube test; pulmonary tuberculosis; sensitivity; specificity
Online: 9 January 2017 (03:58:00 CET)
The value of QuantiFERON in the diagnosis of tuberculosis and in the monitoring of the response to anti-tuberculosis treatment is unclear. The aims of this study were to evaluate the accuracy of the QuantiFERON-TB Gold In-Tube (QFT-GIT) test in the diagnosis of tuberculosis and in the monitoring of the response to anti-tuberculosis treatment in patients with active pulmonary tuberculosis (PTB). Between January 2013 and December 2015, 128 cases with active PTB and 128 controls with no mycobacterial infection, matched by age (within 3 years) and by the week that they visited Tainan Chest Hospital, were enrolled in the study. Serial testing by QFT-GIT at baseline and after 2 and 6 months of treatment was performed. At these time points, a comparison of the performance of QFT-GIT with that of sputum culture status among study subjects was conducted. Compared to baseline, 116 (87.2%) cases showed a decreased response, whereas 17 (12.8%) showed persistent or stronger interferon-gamma (IFN-γ) responses at 2 months. Their IFN-γ responses declined significantly from baseline to 2 months (median, 6.32 vs. 4.12; P < 0.005). The sensitivity values of the QFT-GIT test for the detection of pulmonary tuberculosis at cut-off points of 0.35 IU/ml, 0.20 IU/ml, and 0.10 IU/ml were 74.4%, 78.2%, and 80.5%, respectively. The specificity values at cut-off points of 0.35 IU/ml, 0.20 IU/ml, and 0.10 IU/ml were 66.2%, 63.9%, and 57.1%, respectively. Our results support the QFT-GIT assay as a potential tool for diagnosing tuberculosis and for monitoring the efficacy of anti-tuberculosis treatment.
Wed, 24 May 2017
ARTICLE Download: 940| View: 1005| Comments: 0 | doi:10.20944/preprints201705.0178.v1
Subject: Biology, Forestry Keywords: aboveground biomass; GMM; allometry; biomass allocation; machine learning technique
Online: 24 May 2017 (10:28:21 CEST)
This paper presents new above-ground biomass (AGB) and biomass components equations for seventeen forest species in the temperate forests of northwestern Mexico. A data set corresponding to 1336 destructively sampled oak and pine trees was used to fit the models. Generalized method of moments was used to simultaneously fit systems of equations for biomass components and AGB, to ensure additivity. Additionally, the carbon content of each tree component was calculated by the dry combustion method, in a TOC analyser. The fitted equations accounted for on average 91, 83, 84 and 78% of the observed variance in stem wood and stem bark, branch and foliage biomass, respectively, whereas the total AGB equations explained on average 93% of the total observed variance in AGB. The inclusion of h or d2h as additional predictor in the d-only based equations systems slightly improved estimates of stem wood, stem bark and total above-ground biomass, and greatly improved the estimates produced by the branch and foliage biomass equations. The fitted equations were used to estimate AGB stocks at stand level from a database on growing stock from 429 permanent sampling plots. Three machine-learning techniques were used to model the estimated stand level AGB and carbon contents; the selected models were applied to map the AGB and carbon distributions in the study area, which yielded mean values of 129.84 Mg ha-1 and 63.80 Mg ha-1, respectively.
Thu, 15 September 2016
ARTICLE Download: 1268| View: 1002| Comments: 1 | doi:10.20944/preprints201609.0048.v1
Subject: Biology, Plant Sciences Keywords: oligopeptide transporters (OPTs); Medicago truncatula; phylogenetic analysis; gene express
Online: 15 September 2016 (08:39:23 CEST)
Oligopeptide transporters (OPTs) are a group of membrane localized proteins that have a broad range of substrate transport capabilities and contribute to numerous biological processes. However, limited information has been reported on OPTs in higher plants. In this study, a comprehensive analysis of the OPT gene family in Medicago truncatula was performed. A total of 26 OPT genes (MtOPT01-MtOPT26) have been identified in the Medicago truncatula genome. Phylogenetic analyses indicated that MtOPTs consisted of two distinct subgroups, 12 MtOPTs belonged to the peptide transport subgroup (PT-OPT) based on their predicted amino acid sequences containing the two highly conserved motifs (NPG and KIPPR) and 14 MtOPTs belonged to yellow stripe subgroup (YS-OPT). The MtOPTs distributed on each of 8 chromosomes in Medicago truncatula. Sequence analysis verified that MtOPTs significant similar to those in other plants. The copy number of MtOPTs was low and the multiply of MtOPTs was simple relatively. Gene structure analysis showed that most of the MtOPTs have various numbers of introns. The multiple of MtOPTs might play different biological roles which were supported by the fact that MtOPTs have a distinct tissue-specific expression pattern. The data obtained in this study will help to better understand the complexity of the MtOPTs gene family and provide new evidence for the function and evolution of the OPT gene family in higher plants.
Tue, 23 August 2016
ARTICLE Download: 940| View: 1001| Comments: 0 | doi:10.20944/preprints201608.0192.v1
Subject: Biology, Physiology Keywords: trichromacy; opponency; color circularity; spectral images; unique colors; four-color map problem; perception
Online: 23 August 2016 (10:34:13 CEST)
The reasons for the circular sense of human color perception generated by two sorts of color opponent neurons and three cone types are not well understood. Here we use geometrical analysis to examine the hypothesis that opponency, the recursive nature of color perception, and trichromacy arise as the most efficient ways of distinguishing spectrally different points on a plane using a minimum of color classes and receptor types.
Fri, 27 January 2017
ARTICLE Download: 1107| View: 993| Comments: 0 | doi:10.20944/preprints201701.0126.v1
Subject: Biology, Animal Sciences & Zoology Keywords: anemia; iron deficiency; pregnancy; serum ferritin; mean corpuscular volume (mcv); mean corpuscular hemoglobin (MCH); Northern Pakistan
Online: 27 January 2017 (03:46:07 CET)
Abstract: The aim of this study was to find out the incidence of anemia in pregnant women of Swat District; to analyze the iron variations and its dietary effects.Data were collected during the periods of January – September 2016. The study of samples comprised of 250 pregnant women in the different trimester. Blood sample from each woman was collected and full blood count (FBC) was conducted through Mindray BC-3000 plus hem analyzer for all pregnant individuals. Confirmed anemic cases were then examined for IDA with serum ferritin, serum iron, total iron binding capacity (TIBC) through Randox kit and serum transferrin saturation was estimated by formula (serum ferritin saturation =serum iron ×100/TIBC). The total number of participants in the first trimester were 50, among them 26 women were suffer from iron deficiency anemia (IDA) with 52% weightage of prevalence rate, (mean Hb concentration 9.602 ± 0.87 g/dl). The rates of IDA were 63.3%; ( mean Hb concentration 8.48 ± 1.24 g/dl) and 54%; ( mean Hb concentration 9.18 ± 1.28 g/dl), among 150 and 50 participants in the second and third trimester, respectively. A significant correlation was found between serum ferritin and Hb, serum ferritin against MCV and serum ferritin against MCH. The high prevalence of anemia was found 78.2% in the age group from 26-30 followed by 78.2% in the age group 36-40 years compared to those of other age groups in the second trimester. In this study the prevalence of IDA in third trimester is lower compared to first and second trimester.
Wed, 10 August 2016
ARTICLE Download: 1102| View: 989| Comments: 0 | doi:10.20944/preprints201608.0108.v1
Subject: Biology, Anatomy & Morphology Keywords: developmental biology; computational biology; lineage trees; embryogenesis; biological complexity
Online: 10 August 2016 (11:36:39 CEST)
Embryonic development proceeds through a series of differentiation events. The mosaic version of this process (binary cell divisions) can be analyzed by comparing early development of Ciona intestinalis and Caenorhabditis elegans. To do this, we reorganize lineage trees into differentiation trees using the graph theory ordering of relative cell volume. Lineage and differentiation trees provide us with means to classify each cell using binary codes. Extracting data characterizing lineage tree position, cell volume, and nucleus position for each cell during early embryogenesis, we conduct several statistical analyses, both within and between taxa. We compare both cell volume distributions and cell volume across developmental time within and between single species and assess differences between lineage tree and differentiation tree orderings. This enhances our understanding of the differentiation events in a model of pure mosaic embryogenesis and its relationship to evolutionary conservation. We also contribute several new techniques for assessing both differences between lineage trees and differentiation trees, and differences between differentiation trees of different species. The results suggest that at the level of differentiation trees, there are broad similarities between distantly related mosaic embryos that might be essential to understanding evolutionary change and phylogeny reconstruction. Differentiation trees may therefore provide a basis for an Evo-Devo Postmodern Synthesis.
Tue, 31 January 2017
ARTICLE Download: 735| View: 989| Comments: 0 | doi:10.20944/preprints201701.0134.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Triticum aestivum; carbon dioxide; minerals; protein; starch; baking properties; crop quality; food security
Online: 31 January 2017 (11:49:41 CET)
Elevated carbon dioxide (eCO2) stimulates wheat grain yield, but simultaneously reduces protein (N) concentration. Also other essential nutrients are subject to change. This study is a comprehensive synthesis of wheat experiments with eCO2, estimating effects on N, minerals (B, Ca, Cd, Fe, K, Mg, Mn, Na, P, S, Zn), and starch. Analysis was made by i) deriving response functions for the relative effect on element concentration in relation to CO2 concentration, ii) meta-analysis to test the magnitude and significance of observed effects, and iii) relating CO2 effects on minerals to effects on N and grain yield. Responses range from zero to strong negative effects of eCO2 on mineral concentration, with largest reductions for the nutritionally important elements N, Fe, S, Zn and Mg. Together with the positive but small and non-significant effect on starch concentration, the large variation in effects suggests that CO2-induced responses cannot be explained by a simple dilution model. To explain the observed pattern, uptake and transport mechanisms may have to be considered, along with the link of different elements to N uptake. Our study shows that eCO2 has a significant effect on wheat grain stoichiometry, with implications for human nutrition in a world of rising CO2.
Wed, 2 November 2016
ARTICLE Download: 1006| View: 989| Comments: 0 | doi:10.20944/preprints201611.0020.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Verticillium dahliae; VdAAC; RNAi; growth; virulence
Online: 2 November 2016 (16:27:40 CET)
Verticillium dahliae invades the roots of host plants and causes vascular wilt, which seriously diminishes the yield of cotton and other important crops. The protein AAC (ADP, ATP carrier) is responsible for transferring ATP from the mitochondria into the cytoplasm. When V. dahliae protoplasts were transformed with short interfering RNAs (siRNAs) targeting the VdAAC gene, fungal growth and sporulation were significantly inhibited. To further confirm a role for VdAAC in fungal development, we generated knockout mutants (ΔVdACC), which were hypersensitive to stresses such as UV light and high concentrations of NaCl or sorbitol. Compared with wild-type V. dahliae (Vd wt), ΔVdAAC was impaired in germination and virulence; these impairments were rescued in the complementary strains (ΔVdAAC-C). Moreover, when an RNAi construct of VdAAC under the control of the 35S promoter was used to transform Nicotiana benthamiana, the expression of VdAAC was downregulated in the transgenic seedlings, and they had elevated resistance against V. dahliae. The results of this study suggest that VdAAC contributes to fungal development, virulence and response to stresses and is a promising candidate gene to control V. dahliae. In addition, RNAi is a highly efficient way to silence fungal genes and provides a novel strategy to improve disease resistance in plants.
Mon, 24 October 2016
ARTICLE Download: 1048| View: 976| Comments: 0 | doi:10.20944/preprints201610.0103.v1
Subject: Biology, Forestry Keywords: ordinary kriging; geostatistical analysis; spatial variability; Moso bamboo
Online: 24 October 2016 (09:48:08 CEST)
Moso bamboo is famous for fast growing and biomass accumulation, as well as high annual output for timber and bamboo shoots. These high outputs require high nutrient inputs to maintain and improve stand productivity. Soil nitrogen (N), phosphorus (P) and potassium (K) are important micronutrients for plant growth and productivity. Due to high variability of soils, analysing spatial patterns of soil N, P and K stocks is necessary for scientific nutrient management in Moso bamboo forests. In this study, soils were sampled from 138 locations across Yong’an City and ordinary kriging was applied for spatial interpolation of soil N, P and K stocks. Soil N stock showed a strong spatial dependence while soil N and P stocks presented a moderate spatial dependence, indicating soil N was mainly controlled by intrinsic factors while soil N and P stocks were controlled by both intrinsic and extrinsic factors. Different spatial patterns were observed for soil N, P and K stocks across the whole study area, indicating that fertilizations with different ratios of N:P:K should be applied for different sites to maintain and improve stand productivity. The total soil N, P and K stocks within 0-60 cm were 0.624, 0.020 and 0.583 Tg, respectively.
Mon, 8 May 2017
ARTICLE Download: 915| View: 972| Comments: 0 | doi:10.20944/preprints201705.0070.v1
Subject: Biology, Plant Sciences Keywords: Chromatin and transcription dynamics; reproductive development; differentiation; ChIP-seq; RNA-seq
Online: 8 May 2017 (18:25:10 CEST)
Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes, respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related H3K4me3. However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with transcriptional changes, in a developmental series including Arabidopsis leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prime over changes in H3K27me3 and quantitatively correlate with transcription changes, while H3K27me3 changes occur after prolonged expression changes. Notably, early activation of PcG target genes is dominated by increases in H3K4me3 while H3K27me3 remains present at the locus. Our results reveal H3K4me3 as greater predictor over H3K27me3 for transcription dynamics, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.
Wed, 2 November 2016
ARTICLE Download: 853| View: 964| Comments: 0 | doi:10.20944/preprints201611.0016.v1
Online: 2 November 2016 (07:03:29 CET)
We interviewed 48 people including local communities, ex hunters and protected area management professionals. The purpose of the interviews was to understand the motivations for, and the nature of, illegal hunting of prey species of iconic predators - tigers and leopards - in the northern section of Bardia National Park. Participants reported that hunting of prey species occurs mostly in spring and autumn and is less common during the summer. In the past, hunting was primarily for the purposes of obtaining meat for household consumption. Since the introduction of a road network in the region, opportunities to sell wild meat at ad-hoc ‘highway markets’ have developed. The purported medicinal properties of wild meat was also cited as a driver for illegal hunting. Mostly, locally hand-made guns are used for hunting and the use of dogs in hunting was often reported. Protected area managers informed that illegal hunting problems in the study area are associated with a lack of presence of park authorities, remoteness and underdevelopment and poverty of the community. Our study suggested that skills development training for local community members might reduce dependency on wild meat for household consumption and earning thereby reducing illegal hunting.
Wed, 14 December 2016
ARTICLE Download: 800| View: 963| Comments: 0 | doi:10.20944/preprints201612.0074.v1
Subject: Biology, Plant Sciences Keywords: AmRosea1 gene; transcriptome analysis; drought tolerance; salt tolerance; rice
Online: 14 December 2016 (09:16:50 CET)
Ectopic expression of the MYB transcription factor of AmROSEA1 from Antirrhinum majus has been reported to change anthocyanin and other metabolites in several species. In this study, we found that overexpression of AmRosea1 significantly improved the tolerance of transgenic rice to drought and salinity stress. Transcriptome analysis revealed that a considerable amount of stress-related genes were affected by exogenous AmRosea1 during both drought and salinity stress treatments. These affected genes are involved in stress signal transduction, the hormone signal pathway, ion homeostasis and the enzymes that remove peroxides. This work suggests that the AmRosea1 gene is a potential candidate for genetic engineering of crops.
Thu, 24 November 2016
ARTICLE Download: 790| View: 947| Comments: 0 | doi:10.20944/preprints201611.0124.v1
Subject: Biology, Ecology Keywords: electivity; feeding behavior; filtration rate; Great Barrier Reef; phytoplankton
Online: 24 November 2016 (11:27:13 CET)
Outbreaks of the crown-of-thorns seastar (CoTS) represent a major cause of coral loss on the Great Barrier Reef. Outbreaks might be explained by enhanced larval survival supported by higher phytoplankton availability after flood events, yet little is known about CoTS larvae feeding behaviour, in particular their potential for selective feeding. Here, single- and mixed-species feeding experiments were conducted on CoTS bipinnaria larvae using five algae (Phaeodactylum tricornutum, Pavlova lutheri, Tisochrysis lutea , Dunaliella sp. and Chaetoceros sp.) and two algal concentrations (1000 and 2500 algae mL-1). Cell counts using flow-cytometry at the beginning and end of each incubation experiment allowed us to calculate the filtration and ingestion rates of each species by CoTS larvae. In line with previous studies, CoTS larvae ingested more algae when initial algal concentration was higher. We found evidence for the selective ingestion of some species (Chaetoceros sp., Dunaliella sp.) over others (P. lutheri, P. tricornutum). The preferred algal species had the highest energy content, suggesting that CoTS selectively ingested the most energetic algae. Ultimately, combining these results with spatio-temporal patterns in phytoplankton communities will help elucidate the role of larval feeding behaviour in determining the frequency and magnitude of CoTS outbreaks.
Sat, 3 December 2016
ARTICLE Download: 900| View: 940| Comments: 0 | doi:10.20944/preprints201612.0020.v1
Subject: Biology, Forestry Keywords: natural secondary forest; planted forest; vegetation biomass carbon; soil organic carbon
Online: 3 December 2016 (09:25:48 CET)
Forest ecosystems make a greater contribution to carbon (C) stocks than any other terrestrial ecosystem. To understand the role of regional forest ecosystems in global climate change and carbon exchange, forest C stock and its spatial distribution within the small (2,300 km2) Liuxihe River basin were analyzed to determine the different contributors to the C stock. Forest C stocks were quantified by measuring the biomass of trees, understory vegetation, litter and roots, as well as soil organic C, using data from field samples and laboratory experiments. The results showed that forests stored 38.04 Tg C in the entire basin, with secondary and planted forests accounting for 89.82% and 10.18%, respectively, of the stored C. Five types of forests, a subtropical evergreen broad-leaved forest, a subtropical coniferous and broad-leaved mixed forest, a subtropical coniferous forest, a timber forest, and a non-wood forest, stored 257.55 ± 15.01, 218.92 ± 9.59, 195.24 ± 18.29, 177.42 ± 17.55, and 117.86 ± 6.04 Mg C ha−1, respectively. In the forest ecosystem C stocks of the basin, soils averagely contribute about 73.78%, not including root underground biomass. It provides a comprehensive method for forest ecosystem carbon investigation and forest management in small basin scale.
Tue, 16 May 2017
CONCEPT PAPER Download: 658| View: 932| Comments: 0 | doi:10.20944/preprints201705.0121.v1
Subject: Biology, Other Keywords: Genetic code evolution; frozen accident; error minimization; stereochemcial theory; evolution of translation
Online: 16 May 2017 (12:52:10 CEST)
Nearly 50 years ago, Francis Crick propounded the frozen accident scenario for the evolution of the genetic code along with the hypothesis that the early translation system consisted primarily of RNA. Under the frozen accident perspective, the code is universal among modern life forms because any change in codon assignment would be highly deleterious. The frozen accident can be considered the default theory of code evolution because it does not imply any specific interactions between amino acids and the cognate codons or anticodons, or any particular properties of the code. The subsequent 49 years of code studies have elucidated notable features of the standard code, such as high robustness to errors, but failed to develop a compelling explanation for codon assignments. In particular, stereochemical affinity between amino acids and the cognate codons or anticodons does not seem to account for the origin and evolution of the code. Here I expand Crick’s hypothesis on RNA-only translation system by presenting evidence that this early translation already attained high fidelity that allowed protein evolution. I outline an experimentally testable scenario for the evolution of the code that combines a distinct version of the stereochemical hypothesis, in which amino acids are recognized via unique sites in the tertiary structure of proto-tRNAs, rather than by anticodons, expansion of the code via proto-tRNA duplication and the frozen accident.
Tue, 6 June 2017
REVIEW Download: 1972| View: 930| Comments: 0 | doi:10.20944/preprints201706.0035.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: brassica; food odour preference; HIPVs; Plutella xylostella; trap crop
Online: 6 June 2017 (09:00:57 CEST)
The diamondback moth (DBM), Plutella xylostella L. (Lepidoptera: Plutellidae) is very destructive crucifers specialized pest that has resulted in significant crop losses worldwide. The pest is well attracted to glucosinolate-containing crucifers such as; Barbarea vulgaris (Brassicaceae), and generally to other plants in the genus Barbarea. B. vulgaris on their part, build up resistance against DBM and other herbivorous insects using glucosinolates; that are plant secondary metabolites used in plant defense–contained only in plants of the order Brassicales. Aside glucosinolates, plants in this genus Barbarea (Brassicaceae) also contain saponins; which is toxic to insects and act as feeding deterrents for plant herbivores, most importantly, DBM, as it was found to prevent the survival of DBM larvae on the plant. Saponins are plant secondary metabolites have been established in higher concentrations in younger in contrast to older leaves within the same plant. Previous studies have found a relationship between ontogenetical changes in the host plant’s saponin content and attraction/resistance to P. xylostella. The younger leaves recorded higher concentrations of glucosinolates and saponins, which naturally attracts the plant herbivores. DBM was reported to have evolved mechanisms to avoid the toxicity of the former. The plant-herbivore had adapted glucosinolates for host plant recognition, feeding and oviposition stimulants. Despite the adaptation for oviposition by P. xylostella adults, larvae of the insect cannot survive on the same plant. An example is in some varieties of B. vulgaris. The triterpenoid saponins which act as feeding deterrents in larvae are responsible for this direct defense mechanism against P. xylostella. In the future, trials by plant breeders could aim at transferring this insect resistance to other crops. The previous trials had limited because of lack of knowledge on the biosynthetic pathways and regulatory networks of saponins. Herein, we discussed exclusively; saponins mediated plant defense mechanisms against the DBM.
Thu, 16 March 2017
ARTICLE Download: 2801| View: 928| Comments: 0 | doi:10.20944/preprints201703.0116.v1
Subject: Biology, Animal Sciences & Zoology Keywords: In vivo; Alpha-glucosidase; Alpha-amylase; hyperglycemia
Online: 16 March 2017 (09:35:36 CET)
The inhibition of alpha-glucosidase and alpha-amylase is one of clinic strategies for remedy the type II diabetes. Herbal medicines are reported to alleviate hyperglycemia. However, the constituents from those sources whether are targeted to the alpha-glucosidase and alpha-amylase still unexplored. This study attempted to select the compounds for efficacy of hypoglycemia via cellular and mouse levels. The results illustrated that the cytotoxicity in all tested compounds at various concentrations except the concentration of 16-hydroxy-cleroda-3,13-dine-16,15-olide (HCD) at 30 µM were not significant difference (p > 0.05) when compared with the untreated control. Acarbose (reference drug), Antroquinonol, Catechin, Quercetin, Actinodaphnine, Curcumin, HCD, Docosanol, Tetracosanol, Berberine, and Rutin could effectively inhibit the alpha-glucosidase activity of Caco-2 cells when compared with the control (maltose). The compounds (Curcumin, HCD, Tetracosanol, Antroquinonol, Berberine, Catechin, Actinodaphnine, and Rutin) could reduce blood sugar level at 30 min in tested mice. The effects of tested compounds on area under curve (AUC) were significant (p < 0.05) among Acarbose, Tetracosanol, Antroquinonol, Catechin, Actinodaphnine, and Rutin along with Berberine and Quercetin. In in vitro (alpha-glucosidase) with in vivo (alpha-amylase) experiments suggest that bioactive compounds can be a potential inhibitor candidate of alpha-glucosidase and alpha-amylase for the alleviation of type II diabetes.
Fri, 20 January 2017
ARTICLE Download: 922| View: 903| Comments: 0 | doi:10.20944/preprints201701.0088.v2
Subject: Biology, Other Keywords: Adipose derived stem cell (ASC); Regenerative medicine; embryonic stem cell marker network
Online: 20 January 2017 (04:56:06 CET)
The stromal vascular cell fraction (SVF) of visceral and subcutaneous adipose tissue (VAT and SAT) has increasingly come into focus in stem cell research, since these compartments represent a rich source of multipotent adipose-derived stem cells (ASCs). ASCs exhibit a self- renewal potential and differentiation capacity. Our aim was to study the different expression of embryonic stem cell markers NANOG, SOX2 and OCT3/4 and to evaluate if there exists a hierarchal role in this network in ASCs derived from both SAT and VAT. ASCs were isolated from SAT and VAT biopsies of 72 consenting patients (23 men, 47 women; age 45 ± 10; BMI between 25 and 30 range) undergoing elective open-abdominal surgery. Sphere-forming capability was evaluated by plating cells in low adhesion plastic. Stem cell markers CD90 and CD105 were analyzed by flow cytometry and stem cell transcription factors NANOG, SOX2 and OCT3/4 were detected by immunoblotting and Real-Time PCR. NANOG, SOX2 and OCT3/4 interplay was explored by gene silencing. ASCs from VAT and SAT confirmed their mesenchymal stem cell (MSC) phenotype expressing the specific MSC markers CD90, CD105, NANOG, SOX2 and OCT3/4. NANOG silencing induced a significant OCT 3/4 (70% ± 0.05) and SOX2 (75% ± 0.03) down-regulation whereas SOX2 silencing did not affect NANOG gene expression. Adipose tissue is an important source of MSC, and siRNA experiments endorse a hierarchical role of NANOG in the complex transcription network that regulates pluripotency and plasticity.
Tue, 16 May 2017
ARTICLE Download: 725| View: 902| Comments: 0 | doi:10.20944/preprints201705.0126.v1
Subject: Biology, Other Keywords: amyloid peptides; androgen receptor; nuclear receptor; aggregation; atomic force microscopy
Online: 16 May 2017 (17:48:54 CEST)
The human androgen receptor (AR) is a ligand inducible transcription factor harboring an amino terminal domain (AR-NTD) hosting the ligand independent activation function. AR-NTD is intrinsically disordered and display aggregation properties conferred by the presence of a poly-glutamine (polyQ) sequence of 22 residues. The length of the polyQ sequence, as well as the presence of adjacent sequence motifs modulate this aggregation property. AR-NTD contains also a conserved sequence motif KELCKAVSVSM that displays an intrinsic property to form amyloid fibrils under mild oxidative conditions of its conserved cysteine residue. As peptide sequences with intrinsic ability to oligomerize are reported to have an impact on the aggregation of polyQ tract, we determined the effect of the KELCKAVSVSM on the polyQ stretch in the context of the AR NTD, using Atomic Force Microscopy (AFM). Here, we present evidence for a crosstalk between the amyloidogenic properties of the KELCKAVSVSM motif and the polyQ stretch at the AR NTD.
Thu, 9 February 2017
ARTICLE Download: 875| View: 886| Comments: 0 | doi:10.20944/preprints201702.0027.v1
Online: 9 February 2017 (06:56:39 CET)
Atta capiguara is a grass-cutting ant species frequently found in Cerrado biome. However, little is known about the giant nest architecture of this ant. In this study, we investigated the architecture of three A. capiguara nests from the fragment of cerrado in Botucatu, São Paulo, Brazil. Casts were made of the nests by filling them with cement to permit better visualization of internal structures such as chambers and tunnels. After excavation, the depth and dimensions (length, width, and height) of the chambers were measured. The results showed the typical shape of Atta capiguara nests consisting of mounds of loose soil with unique features resembling a conic section. The fungus chambers were found outside the apparent main part of the nest and were spaced apart and distributed laterally at ground level. The waste chambers were located beneath the largest mound of loose soil. Both the fungus and waste chambers exhibited a sectoral distribution. Our study contributes to a better understanding of the so far unknown nest architecture of the grass-cutting ant A. capiguara.
Fri, 23 September 2016
REVIEW Download: 1217| View: 874| Comments: 0 | doi:10.20944/preprints201609.0077.v1
Subject: Biology, Physiology Keywords: glutamate; glutamine; BBB (blood brain-barrier); brain; oxoproline; amino acid transport
Online: 23 September 2016 (03:23:29 CEST)
A facilitative transport system exists on the blood brain barrier (BBB) that has been tacitly assumed to be a path for glutamate entry to brain. But glutamate is a non-essential amino acid whose brain content is much greater than plasma, and studies in vivo show that glutamate does not enter brain in material quantities except in those small regions with fenestrated capillaries (circumventricular organs). The situation became understandable when luminal (blood facing) and abluminal (brain facing) membranes were isolated and studied separately. Facilitative transport of glutamate and glutamine exist only on the luminal membranes whereas Na+-dependent transport systems for glutamate, glutamine and some other amino acids are present only on the abluminal membrane. The Na+-dependent cotransporters of the abluminal membrane are in a position to actively transport amino acids from the extracellular fluid (ECF) into the endothelial cells of the BBB. These powerful secondary active transporters couple the energy of the Na+-gradient to move glutamate and glutamine into the ECF whereupon glutamate can exit to blood on the luminal facilitative glutamate transporter. Glutamine may also exit brain on a separate facilitative transport system that exists on the luminal membranes or glutamine can be hydrolyzed to glutamate within the BBB thereby releasing ammonia that is freely diffusible. The γ-glutamyl participate cycle participates indirectly by producing oxoproline (pyroglutamate) that stimulates almost all secondary active transporters yet discovered in the abluminal membranes of the BBB.
Mon, 28 November 2016
ARTICLE Download: 1112| View: 874| Comments: 0 | doi:10.20944/preprints201611.0140.v1
Subject: Biology, Forestry Keywords: understory species; allometric biomass equation; species-specific and multispecies; temperate coniferous and broadleaved mixed forest; northeastern China
Online: 28 November 2016 (04:41:35 CET)
Understory plants are important components of forest ecosystem productivity and diversity. Compared to biomass models of overstory canopy trees, few are available for understory saplings and shrubs and therefore their roles in estimation of forest carbon pools are often ignored. In this study, we harvested 24 understory species including 4 saplings, 9 tree-like shrubs and 11 typical shrubs in coniferous and broadleaved mixed forest in northeastern China and developed the best fit allometric equations of above- and below-ground and total biomass by species-specific or multispecies using morphological measurements of basal diameter, height and crown area as independent variables. The result showed that single basal diameter, height or crown area had good explanatory power for both species-specific and multispecies (p<0.001). The best-fit models included only basal diameter in sapling and tree-like shrubs, and combinations of crown area, height, and basal diameter in typical shrubs. The logarithmic model was most desired among the 4 model forms of linear, quadratic, multiple linear and logarithmic, for species-specific and multispecies. The models we developed should help the estimation of forest ecosystem carbon stocks, especially for belowground component, and provide tools for quantification of individual species biomass of understory plants.
Tue, 14 February 2017
REVIEW Download: 3472| View: 872| Comments: 0 | doi:10.20944/preprints201702.0045.v1
Online: 14 February 2017 (03:08:37 CET)
Biodiversity has become an issue of global anxiety over the past decades due to its rapid decline worldwide. Bangladesh as one of the most densely populated countries in the world is no more exception. The country, although, was once very rich in biodiversity, during the last few decades as a consequence of the rapid reduction in forest area, urbanisation, habitat modification, unsustainable natural resources use and collection and overall climate change it has decreased alarmingly. Of late, the government, as a signatory of various regional and international conservation treaties, has taken various initiatives to improve country’s dwindling biodiversity. This paper reviews the present situation of biodiversity in Bangladesh, management trends and major causes of biodiversity loss. A separate statutory body is fundamental to ensure conservation, sustainable use and equitable sharing of benefits arisen from biodiversity in the country.
Thu, 23 February 2017
ARTICLE Download: 919| View: 863| Comments: 0 | doi:10.20944/preprints201702.0087.v1
Subject: Biology, Other Keywords: α-C(sp3)–H functionalization; oxidative cyclization; tertiary amine; 6-exo-trig; metal free
Online: 23 February 2017 (10:40:53 CET)
The mechanistic pathway of TEMPO/I2-mediated oxidative cyclization of N,N-diaryl amino alcohols 1 is investigated in this study. Based on our direct empirical experiments, three key intermediates (the aminium radical cation 3, the α-aminoalkyl radical 4, and the iminium 5), four kind reactive species (radical TEMPO, cationic TEMPO, TEMPO-I and iodo radical) and three kind pathways (1. SET/PCET mechanism, 2. HAT/1,6-H transfer mechanism, 3. Ionic mechanism) were assumed. Under the assumption, nine free energy diagrams are acquired through DFT calculation. From the comparison of the solution phase free energy, some possibility can be excluded and then the chosen plausible mechanisms are concretized with the more stable intermediate 7.
Mon, 4 June 2018
ARTICLE Download: 435| View: 858| Comments: 0 | doi:10.20944/preprints201806.0035.v1
Subject: Biology, Other Keywords: origin of life; LUCA; FUCA; RNA World; PTC; Archaea; translation system
Online: 4 June 2018 (11:17:58 CEST)
The existence of a common ancestor to all living organisms in Earth is a necessary corollary of Darwin idea of common ancestry. The Last Universal Common Ancestor (LUCA) has been normally considered as the ancestor of cellular organisms that originated the three domains of life: Bacteria, Archaea and Eukarya. Recent studies about the nature of LUCA indicate that this first organism should present hundreds of genes and a complex metabolism. Trying to bring another of Darwin ideas into the origins of life discussion, we went back into the prebiotic chemistry trying to understand how LUCA could be originated under gradualist assumptions. Along this line of reasoning, it became clear to us that the definition of another ancestral should be of particular relevance to the understanding about the emergence of biological systems. Together with the view of biology as a language for chemical translation, on which proteins are encoded into nucleic acids polymers, we glimpse a point in the deep past on which this Translation mechanism could have taken place. Thus, we propose the emergence of this process shared by all biological systems as a point of interest and propose the existence of this non-cellular entity named FUCA, as the First Universal Common Ancestor. FUCA was born in the very instant on which RNA-world replicators started to be capable to catalyze the bonding of amino acids into oligopeptides. FUCA has been considered mature when the translation system apparatus has been assembled together with the establishment of a primeval, possibly error-prone genetic code. This is FUCA, the great-grandmother of LUCA.
Fri, 17 March 2017
ARTICLE Download: 1835| View: 854| Comments: 0 | doi:10.20944/preprints201703.0131.v1
Subject: Biology, Plant Sciences Keywords: Rhododendron chrysanthum Pall.; cold stress; chlorophyll fluorescence; photosynthesis; antioxidant enzymes
Online: 17 March 2017 (04:46:21 CET)
Rhododendron chrysanthum Pall., live in Changbai Mountain being exposed to chilling temperature, high light intensities and water scarcity condition. To adapt to the harsh environment, the cold resistance mechanisms of R. chrysanthum have been successfully evolved in the long-term adaptive process. In our present work, the methods of proteomics combined with physiological and biochemical analyses were used to investigate the effects of cold stress on the photosynthesis and antioxidant system of Rhododendron chrysanthum Pall. and the molecular mechanisms involved in cold resistance of plants. A total of 153 photosynthesis related proteins were identified in present work, of which 7 proteins including Rubisco large subunit (rbcL) were up-regulated in experiment group (EG) compared with control group (CG). Simultaneously, four chlorophyll fluorescence parameters were measured in present study. The results showed that the maximum photochemical efficiency of photosystem II (Fv/Fm), actual quantum yield of PSII (Y(II)) and photochemical quenching (qP) were significantly higher in EG, whereas the non-photochemical quenching (NPQ) was notably decreased. Cold stress could lead to a significant reduction in electron transport rate (ETR) accompanied with an increase in excitation pressure (1-qP). The abundance of PetE which involved in the plants photosynthetic electron transfer was also significantly influenced by cold stress. Moreover, the up-regulated expressions and higher levels of enzymatic activities of Glutathione peroxidase (GPX) and Ascorbate peroxidases (APXs) were detected in EG. All these changes which can help plants to survive in low temperature are considered as the crucial parts of cold tolerance mechanisms. These results revealed that photosynthesis and redox adjustment play significant roles in the defense of cold-induced damage.
Thu, 30 March 2017
SHORT NOTE Download: 730| View: 853| Comments: 1 | doi:10.20944/preprints201703.0219.v1
Online: 30 March 2017 (16:58:33 CEST)
We cultured Parmelina carporrhizans and P. quercina in Corn Meal Agar and 0.2% glucose Malt Yeast Agar for 160 days. Chemosyndrome of natural thalli and mycobiont cultures were analyzed by HPLC. Lecanoric acid, atranorin, chloratranorin and ergosterol were detected in P. carporrhizans thalli, while lecanoric acid, chloratranorin and aliphates were found in P. quercina thalli. The secondary methabolites pattern between thalli and mycobiont culture was completely different in both species. Both species secreted the phenalenone myeloconone C in culture media and was also detected in P. quercina mycobiont aggregates. Interestingly, the phenolic compounds produced by the mycobiont culture of P. carporrhizans are related to those produced by natural thallus by the same biosynthetic pathway, while the chemosyndrome of P. quercina mycobiont implies switch of biosynthetic pathway from acetate-polymalonate pathway to shikimic acid pathway, with pulvinic acid as major compound of mycobiont culture. The role of Myelochonone C, confluentic acid and pulvinic acid produced by mycobiont culture is discussed as possible adaptive vantage in field as photoprotective agent or as byproduct result of stressing artificial culture conditions.
Fri, 17 March 2017
ARTICLE Download: 975| View: 850| Comments: 0 | doi:10.20944/preprints201703.0139.v1
Subject: Biology, Plant Sciences Keywords: Fritillaria ussuriensis, Fritillaria cirrhosa, Chloroplast genome, Comparative analysis, Highly divergent region
Online: 17 March 2017 (16:30:34 CET)
The genus Fritillaria belongs to the widely distributed family Liliaceae. The bulbs of Fritillaria ussuriensis and Fritillaria cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species is therefore required. Here, we report the complete chloroplast (cp) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria cp genomes were 151,524 and 151,083 bp in length, respectively, including a pair of inverted repeat regions (52,678 and 52,156 bp) separated by a large single copy region (81,732 and 81,390 bp) and small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 protein-coding genes in F. ussuriensis and 78 in F. cirrhosa, 30 tRNA genes, and four rRNA genes. The gene order, content, and orientation of the two Fritillaria cp genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species’ cp genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of two Fritillaria species will be useful genomics resources for identification of Fritillaria species and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae family.
Thu, 1 December 2016
ARTICLE Download: 712| View: 845| Comments: 0 | doi:10.20944/preprints201612.0010.v1
Subject: Biology, Animal Sciences & Zoology Keywords: fertilization; cleavage; gastrulation; sperm motility; temperature; salinity; pH; Acanthaster outbreaks
Online: 1 December 2016 (11:01:19 CET)
For broadcast spawning invertebrates such as the crown-of-thorns starfish, early life history stages (from spawning to settlement) may be exposed to a wide range of environmental conditions, and could have a major bearing on reproductive success and population replenishment. Arrested development in response to multiple environmental stressors at the earliest stages can be used to define lower and upper limits for normal development. Here, we compared sperm swimming speeds and proportion of motile sperm and rates of fertilization and early development under a range of environmental variables (temperature: 20-36°C, salinity: 20-34 psu, and pH: 7.6-8.2) to identify environmental tipping points and thresholds for reproductive success. We also tested the effects of water-soluble compounds derived from eggs on sperm activity. Our results demonstrate that gametes, fertilization, and early development are robust to a wide range of temperature, salinity, and pH levels that are outside the range found at the geographical limits of adult distribution and can tolerate environmental conditions that exceed expected anomalies as a result of climate change. Water-soluble compounds associated with eggs also enhance sperm activity, particularly in environmental conditions where sperm motility is initially limited. These findings suggest that fertilization and embryonic development of crown-of-thorns starfish are tolerant to a wide range of environmental conditions, though environmental constraints on recruitment success may occur at later ontogenic stages.
Thu, 20 October 2016
ARTICLE Download: 1402| View: 838| Comments: 0 | doi:10.20944/preprints201610.0084.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: intra row spacing; intercropping; land equivalent ratio; sorghum (Teshale); groundnut (Fetene)
Online: 20 October 2016 (08:45:36 CEST)
In eastern part of Ethiopia groundnut is very commonly intercropped with sorghum. Even though intercropping of sorghum with groundnut is practiced in the eastern part of Ethiopia the population density at what ratio should not be known. Therefore determining the population ratio is found to be crucial to draw management options. The study was conducted at two locations at Fadis (on station) and Babile (sub- station). Sorghum variety (Teshale) and groundnut (Fetene) were used as planting materials. All agronomic data were collected and analyzed by using GenStat software. Significant different were obtained among the treatments. The research result showed that, there were significance difference for both sorghum and ground nut yield per hectare in the years (2014 and 2015) among treatments. The result over time(in 2014 and 2015) at Fadis and Erer showed that the highest sorghum and groundnut yield per hectare were obtained/harvested from the intra row spacing of 25cmx20cm and 30cmx20cm intercropping sorghum with ground nut system with (1.27 and 1.31) respectively. The highest LER (1.31) and highest GMV (10218.00 ETBr/ha) were obtained from the intercropping of 30cmx20cm (Sorghum & groundnut). Clearly showed that, with intercropping of sorghum and Groundnut, it is possible to produce additional yield of sorghum without significant reduction in groundnut yield. As a result of this, the intra spacing of the main crop (sorghum) 25cm and 30cm and for the subsidiary crop (groundnut) 20cm was recommended for further production in the study areas of eastern Harerghe zone and similar agro-ecologies.
Wed, 24 May 2017
ARTICLE Download: 793| View: 835| Comments: 0 | doi:10.20944/preprints201705.0173.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Echinococcus granulosus; Calmodulin; Ca2+-binding protein; Immunohistochemical localization; Quantitative RT-PCR
Online: 24 May 2017 (08:07:35 CEST)
Echinococcus granulosus is a harmful cestode parasite which could cause Cystic Echinococcosis in humans, various livestock species and wild animals. Calmodulin (CaM), a Ca2+ sensor protein, is widely expressed in eukaryotes and mediates a variety of cellular signaling activities. In our study, the CaM in Echinococcus granulosus (rEgCaM) was successfully cloned and the molecular and biochemical characterizations of rEgCaM were identified. The results showed that rEgCaM was a highly conserved calcium-binding protein, consisting of 149 amino acids. Immunoblot analysis revealed that rEgCaM could be identified using E. granulosus infected sheep serum. The usage of rEgCaM as antigen was evaluated by indirect ELISA which exhibited a high sensitivity of 90.3% but low specificity (47.1%). rEgCaM was mainly located in the tegument tissues and parenchymal region of protoscoleces, the tegument and inner body of adult worm and predominantly expressed in the germinal layer. The mRNA expression of rEgCaM in PSCs were gradually decreased with the increase death of PSCs. In electrophoretic mobility tests and ANS assays, rEgCaM showed a typical calcium-binding protein characteristics. This is the first report on CaM from E. granulosus and rEgCaM is considered to be involved in some important biological function of E. granulosus as a calcium-binding protein.
Thu, 12 April 2018
ARTICLE Download: 230| View: 833| Comments: 0 | doi:10.20944/preprints201804.0160.v1
Online: 12 April 2018 (06:19:14 CEST)
Pheidole oxyops Forel, 1908 is a generalist ant, which forages actively for plant debris to dead arthropods. In addition, its nest has an entrance that allows the ants gather resources passively by capturing falling preys into the nest. Our objective was to verify if different day periods, temperature and residual soil accumulation (ground pile in the side of nest entrance) could influence the patterns of foraging activity. Foraging activities were registered in the morning, afternoon and twilight. We measured direction and vector of trails, air temperature and humidity during foraging events. Our results showed that foraging routes are independent of residual soil accumulation and other nearby nests. However, air temperature and the time daily period are significant factors to foragers’ exits. Higher air temperatures influenced negatively the exits. In the period of the afternoon, the ants do not show any preference for routes, different from the morning and twilight. In addition, foraging activities were significantly more frequent during twilight period. Leaving the nest at twilight could allow ants foraging in an environment with less exposition to potential predators and competitors. Moreover, it may be also related to opportunism to hunt other nocturnal insects.
Thu, 11 August 2016
ARTICLE Download: 913| View: 828| Comments: 0 | doi:10.20944/preprints201608.0118.v1
Subject: Biology, Physiology Keywords: acclimation; coral reefs; endosymbiosis; molecular biology; multivariate statistics; temperature; upwelling
Online: 11 August 2016 (11:03:03 CEST)
Multivariate statistical approaches (MSA), such as principal components analysis and multidimensional scaling, seek to uncover meaningful patterns within datasets by considering multiple response variables in a concerted fashion. Although these techniques are readily used by ecologists to visualize and explain differences between study sites, they could theoretically be employed to differentiate organisms within an experimental framework while simultaneously identifying response variables that drive documented experimental differences. Therefore, MSA were used herein to attempt to understand the response of the common, Indo-Pacific reef coral Seriatopora hystrix to temperature changes using data from laboratory-based temperature challenge studies performed in Southern Taiwan. Gene expression and physiological data partitioned experimental specimens by time of sampling, treatment temperature, and site of origin upon employing MSA, signifying that S. hystrix and its dinoflagellate endosymbionts display physiological and molecular signatures that are characteristic of sampling time, site of colony origin, and/or temperature regime. These findings promote the utility of MSA for documenting biologically meaningful shifts in the physiological and/or sub-cellular response of marine invertebrates exposed to environmental change.
Sun, 18 December 2016
ARTICLE Download: 762| View: 818| Comments: 0 | doi:10.20944/preprints201612.0092.v1
Subject: Biology, Ecology Keywords: Anaea aidea; caterpillar demography; multi-state mark-recapture; state-space model; stage-structured matrix
Online: 18 December 2016 (09:33:13 CET)
Organisms in the wild have cryptic life stages that are sensitive to changing environmental conditions and can be difficult to survey. In this study, I used mark-recapture methods to repeatedly survey Anaea aidea (Nymphalidae) caterpillars in nature, then modeled caterpillar demography as a hidden Markov process to assess if temporal variability in temperature and density influence the survival and growth of A. aidea over time. Individual encounter histories result from the joint likelihood of being alive and observed in a particular stage, and I included hidden states by separating demography and observations into parallel and independent processes. I constructed a demographic matrix containing the probabilities of all possible fates for each stage, including hidden states, e.g., eggs and pupae. I observed both dead and live caterpillars with high probability. Peak caterpillar abundance attracted multiple predators, and survival of fifth instars declined as per capita predation rate increased through spring. A time lag between predator and prey abundance was likely the cause of improved fifth instar survival estimated at high density. Growth rates showed an increase with temperature, but the most likely model did not include temperature. This work illustrates how state-space models can include unobservable stages and hidden state processes to evaluate how environmental factors influence vital rates of cryptic life stages in the wild.
Thu, 17 November 2016
ARTICLE Download: 2001| View: 817| Comments: 2 | doi:10.20944/preprints201611.0091.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: crop coefficient; evapotranspiration; salinity; wheat crop
Online: 17 November 2016 (10:55:59 CET)
A field experiment was conducted for determination of crop coefficient (KC) and water stress coefficient (Ks) for wheat crop under different salinity levels, during 2015-16. Complete randomized block design of five treatments were considered, i.e., 0.51 dS/m (fresh water) as a control treatment and other four saline water treatments (4, 6, 8 and 10 dS/m), for S1, S2, S3 and S4 with three replications. The results revealed that the water consumed by plants during the different crop growth stages follows the order of FW>S1>S2>S3>S4 salinity levels. According to the obtained results, the calculated values of crop coefficients significantly differed from those suggested by FAO No.56 for the crops. The Ks values clearly differ from one stage to another because the salt stress causes both osmotic stress, due to a decrease in the soil water potential, and ionic stress which the average values of water stress coefficient (Ks) follows this order; FW(1.0)=S1(1.0)>S2(1.0)>S3(0.93)>S4(0.82). Overall, it was found the differences are attributed primarily to specific cultivar, the changes in local climatic conditions and seasonal differences in crop growth patterns. Thus, further studies are essential to determine the crop coefficient values under different variables, to make the best management practice (BMP) in agriculture.
Tue, 21 March 2017
ARTICLE Download: 1783| View: 810| Comments: 0 | doi:10.20944/preprints201703.0167.v1
Online: 21 March 2017 (04:23:40 CET)
Diagnosing melanocytic lesions is among the most challenging problems in the practice of pathology. The difficulty of physically masking melanin pigment and the similarity of its color to commonly used chromogens often complicate examination of the cytomorphology and immunohistochemical staining results for tumor cells. Melanin bleach can be very helpful for histopathological diagnosis of heavily pigmented melanocytic lesions. Although various depigmentation methods have been reported, no standardized methods have been developed. This study developed a fully automated platform that incorporates hydrogen peroxide-based melanin depigmentation in an automated immunohistochemical analysis. The utility of the method was tested in one cell block of malignant melanoma cells in pleural effusion, ten ocular melanoma tissue samples, and ten cutaneous melanoma tissue samples. Our results demonstrated that the proposed method, which can be performed in only 3 hours, effectively preserves cell cytomorphology and immunoreactivity. The method is particularly effective for removing melanin pigment to facilitate histopathological examination of cytomorphology and for obtaining an unmasked tissue section for immunohistochemical analysis.
Tue, 4 April 2017
ARTICLE Download: 770| View: 808| Comments: 0 | doi:10.20944/preprints201704.0016.v1
Subject: Biology, Physiology Keywords: periodontitis; the periodontal ligament stem cells; the nuclear factor-erythroid 2-related factor 2; oxidative stress; apoptosis
Online: 4 April 2017 (08:58:13 CEST)
The present study aimed to analyze novel mechanisms underlying Nrf2-mediated anti-apoptosis in periodontal ligament stem cells (PDLSCs) in the periodontitis oxidative microenvironment. We created an oxidative stress model with H2O2-treated PDLSCs. Herein, we used real-time PCR, western blotting, TUNEL staining, fluorogenic assay and transfer genetics to confirm the degree of oxidative stress and apoptosis as well as the Nrf2 function. Surprisingly, we demonstrated that with up-regulated ROS and MDA levels, the effect of oxidative stress was obvious under H2O2 treatment. Anti-oxidative molecules were changed after the H2O2 exposure, whereby the anti-oxidative signaling of Nrf2 was activated with the increase of its downstream effectors, HO-1, NQO1 and γ-GCS. Additionally, the apoptosis levels gradually increased with oxidative stress and changes in the caspase-9, caspase-3, Bax and c-Fos levels, but not with caspase-8 and down-regulated Bcl-2. The enhanced antioxidant effect could not resist the occurrence of apoptosis. Furthermore, Nrf2 overexpression effectively improved the anti-oxidative levels and increased cell proliferation. At the same time, overexpression effectively restrained TUNEL staining and decreased the molecular levels of caspase-9, caspase-3, et al, but not that of caspase-8. By contrast, silencing the expression Nrf2 levels had the opposite effect. Collectively, Nrf2 alleviates PDLSCs via its effects on anti-oxidative and anti-intrinsic apoptosis by the activation of anti-oxidative enzymes.
Fri, 24 March 2017
ARTICLE Download: 796| View: 806| Comments: 0 | doi:10.20944/preprints201703.0182.v1
Subject: Biology, Entomology Keywords: Lauxanioidea; Cyclorrhapha; mitochondrial genome; phylogeny; RNAs; intergenic sequences
Online: 24 March 2017 (08:03:42 CET)
The superfamily Lauxanioidea is a significant dipteran clade including over 2500 known species in three families: Lauxaniidae, Celyphidae and Chamaemyiidae. We sequenced the first five (three complete and two partial) lauxanioid mitochondrial (mt) genomes, and used them to reconstruct the phylogeny of this group. The lauxanioid mt genomes are typical of the Diptera, containing all 37 genes usually present in bilaterian animals. A total of three conserved intergenic sequences have been reported across the Cyclorrhapha. The inferred secondary structure of 22 tRNAs suggested five substitution patterns among the Cyclorrhapha. The control region in the Lauxanioidea has apparently evolved very fast, but four conserved structural elements were detected in all three complete mt genome sequences. Phylogenetic relationships based on the mt genome data were inferred by Maximum Likelihood and Bayesian methods. The traditional relationships between families within the Lauxanioidea, (Chamaemyiidae + (Lauxaniidae + Celyphidae)), was corroborated, however, the higher level relationships between cyclorrhaphan superfamilies are mostly poorly supported.
Thu, 2 March 2017
ARTICLE Download: 633| View: 795| Comments: 0 | doi:10.20944/preprints201703.0018.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Cicer arietimum; Indole Acetic Acid; Bacillus megaterium; Pseudomonas putida; Mesorhizobium ciceri
Online: 2 March 2017 (16:34:44 CET)
Six bacterial strains with differing abilities to produce varying concentrations of Indole Acetic Acid were tested individually and in consortia for plant growth promoting and fitness related traits of Cicer arietinum. In all experiments the presence of the nitrogen fixer Mesorhizobium ciceri resulted in increased biomass production. In the absence of this strain, IAA Psedomonas putida and Bacillus megaterium hinder plant growth and fitness related traits. The application of mixes of the three strains always resulted in better plant performance when M. ciceri was present. Whereas P. putida has a noticeable plant growth-promoting effect B. megaterium resulted less effective. The low levels of IAA produced by the selected strains had a significantly greater positive effect on plant biomass accumulation, flower, pods and seed production as well as on total plant nitrogen and nitrogen concentration in seed than high IAA producer strains.
Mon, 13 February 2017
ARTICLE Download: 749| View: 777| Comments: 0 | doi:10.20944/preprints201701.0009.v2
Subject: Biology, Plant Sciences Keywords: ecosystem services; urban water; Warsaw; Poland; environment
Online: 13 February 2017 (09:30:21 CET)
Urban lakes, especially those of natural origin, provide ecosystem services, recreation being one of the most important and highly valued by the city dwellers. Fulfilling the needs of city residents to relax and have contact with nature has become a priority in urbanized areas and has been proved to positively affect people’s health and well-being. The recreational potential of water bodies was identified to be most important aspect of ecosystem services to the residents of the neighboring areas. An assessment of recreational ecosystem services (RES) provisioning to society based on the real time spent by the citizens and housing values in the rural-urban gradient revealed that the economic benefits of lakes differ in urbanized, suburban and rural landscapes. The growth of cities has led to an increased population density in the surroundings of ecologically valuable areas, resulting in higher pressure from visitors seeking recreational areas. Along with urbanization, the impoverishment of ecosystem functions takes place, limiting their capability to provide ecosystem services. In this work provisioning of recreational ecosystem services of 28 floodplain lakes located along the urban-rural gradient of the Warsaw agglomeration was assessed. The relationship between the ecological value of the water bodies, measured using naturalness indices, and the recreational ecosystem services they can provide was assessed. The results showed that the floodplain lakes located along the urban-rural gradient are of a great importance to the citizens due to their recreational potential. The provisioning of recreational ecosystem services is poorly connected with the ecological characteristics of the floodplain lakes. Only hemeroby, was significantly correlated with provisioning, and there was no relationship with factors such as naturalness of vegetation or water quality, demonstrating that public preference was not generally influenced by high ecological quality. These data should be available to potential buyers and be integrated in spatial planning management plans in order to shape future housing policy.
Fri, 17 March 2017
ARTICLE Download: 689| View: 766| Comments: 0 | doi:10.20944/preprints201703.0128.v1
Subject: Biology, Entomology Keywords: Bti-spraying alternative; Camargue; environmental impacts; mosquito control; Techno Bam traps
Online: 17 March 2017 (03:22:05 CET)
We tested the use of mosquito traps as an alternative to insecticide spraying in Camargue (France) following the significant impacts observed on the non-target fauna through Bti persistence and trophic perturbations. In a village of 600 inhabitants, 16 Techno-Bam traps emitting CO2 and using octenol lures were set from April to November 2016. Trap performance was estimated at 70% overall based on mosquito landing on human baits in areas with and without traps. Reduction of Ochlerotatus caspius and Oc. detritus, the two species targeted by Bti spraying, was respectively 74 and 98%. Traps were less efficient against Anopheles hyrcanus (46%), which was more attracted by lactic-acid than octenol lures based on previous tests. Nearly 300 000 mosquitoes from nine species were captured, with large variations among traps, emphasizing that trap performance is also influenced by surrounding factors. Environmental impact, based on the proportion of non-target insects captured, was mostly limited to small chironomids attracted by street lights. Breeding success of a house martin colony was not significantly affected by trap use, in contrast to Bti spraying. Our experiment confirms that deployment of mosquito traps can offer a cost-effective alternative to Bti spraying for protecting local populations from mosquito nuisance in sensitive natural areas.
Mon, 1 May 2017
REVIEW Download: 742| View: 766| Comments: 0 | doi:10.20944/preprints201705.0019.v1
Subject: Biology, Other Keywords: surrounding microRNAs; low-density lipoprotein; atherosclerosis; APOB; PCSK9; LDLR
Online: 1 May 2017 (11:30:17 CEST)
The atherosclerosis, a chronic and inflammatory disease that occurs when there are high levels of low-density lipoprotein (LDL) on plasma. This important risk factor for development of cardiovascular disease (CVD) is the main cause of death worldwide. MicroRNAs have recently emerged as potential biomarkers and therapeutic target for lipid metabolism disorders. In this review, we will provide profile of surrounding miRNAs that have demonstrated being regulators of PCSK9, LDLR and APOB100 genes. Recent work has identified the mir-148, mir-128, mir-27a/b, mir-185, mir-301, mir-130 as important regulators of this pathway because they decrease supply of LDL receptors through interaction with PCSK9. Inhibition of LDLR expression cause elevation of plasma LDL levels which induces atherosclerosis. While mir-30c, mir-122, mir-34 decrease MTTP, which promotes degradation of APOB100 preventing assembly and secretion of VLDL. We conclude that, when overexpressed, mir-148a, mir128 and mir-27a/b, mir-122 and mir-34 are related to decrease in LDLR, facilitating occurrence of atherosclerosis. While mir-30 has been linked to decreased atherosclerosis. Detection of miRNAs profile could be used in the future as a biomarker for disturbs linked to c-LDL uptake and in future anti-miRNAs therapies may be used in the treatment of atherosclerosis.
Wed, 17 May 2017
ARTICLE Download: 936| View: 762| Comments: 0 | doi:10.20944/preprints201705.0132.v1
Subject: Biology, Plant Sciences Keywords: Pittosporum tobira (Thunb.) Aiton; Essential oils (EOs); Headspace solid-phase microextraction (HS-SPME); Gas chromatography-mass spectrometry (GC-MS); Anticancer activity
Online: 17 May 2017 (13:08:12 CEST)
Background: Pittosporum tobira (Thunb.) Aiton is an aromatic medicinal plant widely cultivated in the world. However, the essential oils (EOs) from P. tobira flowers for anti-cancer potential is still not systematically studied. The present aim to elucidate the phytochemical composition of the EOs and to explore mechanism of anticancer action. Methods: The EOs were extracted and analyzed by headspace solid-phase microextraction (HS-SPME) with gas chromatography-mass spectrometry (GC-MS). Volatile components were identified according to Kovats retention index (KI) and NIST database. The anti-neoplasm mechanisms of the EOs was comprehensively investigated in lung carcinoma A549 and H460 cells. Results: A total of 47 secondary metabolites representing 94.18% of the EOs were successfully identified: monoterpenes and sesquiterpenes were the dominant terpenoids. The EOs exhibited antiproliferative activity on A549 and H460 lung carcinoma cells. Hoechst 33324 fluorescent staining indicated the typical characteristics of apoptosis and induced cycle phase arrest. AnnexinV/PI staining revealed that the number of apoptotic cells was increased. Furthermore, the EOs also induced the caspase-mediated mitochondrial apoptosis pathway. Conclusions: Findings suggest that the full-scale chemical composition and first characterization of anticancer activities of the EOs, it could be used for integrative natural anti-cancer agents in health care should be pay more attention.
Wed, 18 October 2017
ARTICLE Download: 639| View: 758| Comments: 0 | doi:10.20944/preprints201710.0123.v1
Subject: Biology, Plant Sciences Keywords: common bean; soybean; Argonaute5; legume-rhizobia symbiosis
Online: 18 October 2017 (03:20:37 CEST)
The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, is able to bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 hour of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: NUCLEAR FACTOR Y-B (NF-YB), NODULE INCEPTION (NIN) and FLOTILIN2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia in determinate legumes.
Tue, 25 April 2017
REVIEW Download: 1568| View: 753| Comments: 0 | doi:10.20944/preprints201704.0161.v1
Subject: Biology, Other Keywords: Mangifera indica L. fruit; phytochemicals; nutraceutical properties; mangiferin
Online: 25 April 2017 (16:33:54 CEST)
Historically, Mangifera indica L. cultivations have been widely rooted in tropical areas of India, Africa, Asia and Central America. However, at least 20 years ago its spreading allowed the development of some cultivars, also in Sicily, the South of Italy, where the favorable subtropical climate and adapted soils represent the perfect field to create new sources of production for Sicilian agricultural supply chain. Currently, cultivations of Kensington Pride, Keitt, Klenn, Maya and Tommy Atkins varieties are active in Sicilian island and their products meet the requirements of local and European markets. Mango plants produce fleshy stone fruits rich in phytochemicals with an undisputed nutritional value for its high content of flavonoids, vitamins, micro- and macro-elements, vital for maintaining health. This review provides an overview of the antioxidant, anti-inflammatory and anticancer properties of Mango, a fruit that should be included in everyone’s diet for its multifaceted biochemical actions and nutraceutical potential.
Thu, 23 March 2017
ARTICLE Download: 630| View: 753| Comments: 0 | doi:10.20944/preprints201703.0180.v1
Subject: Biology, Other Keywords: Biotransformation; interface-assembling carbonyl reductase; oxcarbazepine; polystyrene; S-licarbazepine
Online: 23 March 2017 (09:33:31 CET)
S-licarbazepine was prepared by asymmetric reduction of oxcarbazepine with interface-assembled carbonyl reductase at the interface of oil/water biphasic system. The carbonyl reductase was conjugated with polystyrene in the surface of toluene/Tris-HCl biphasic system and formed a surfactant-like structure. The conversion and enantiometric excess of S-licarbazepine reached 97.39% and 99.6% when 3.97 mmol/L oxcarbazepine was reduced by interface-assembled carbonyl reductase with 60 g/L ethanol as co-substrate in toluene/Tris-HCl(12.5:10) biphasic system at 30 °C, 180 rpm for 6 h.
Mon, 15 May 2017
ARTICLE Download: 555| View: 752| Comments: 0 | doi:10.20944/preprints201705.0109.v1
Subject: Biology, Plant Sciences Keywords: Turnip mosaic virus; Potyvirus; Genetic structure; Population; China
Online: 15 May 2017 (11:38:11 CEST)
Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis. To understand the genetic structure of TuMV from radish in China, the 3′-terminal genome of 90 TuMV isolates were determined and analyzed with other Chinese isolates available. The results showed that the Chinese TuMV isolates from radish formed three groups: Asian-BR, basal-BR and world-B. More than half of these isolates (52.54%) were clustered to basal-BR group, and could be further divided into three sub-groups. The TuMV basal-BR isolates in the sub-groups I and II were genetically homologous with Japanese ones, while those in sub-group III formed a distinct lineage. Sub-populations of TuMV basal-BR II and III were new emergent and in a state of expansion. The Chinese TuMV radish populations were under negative selection. Gene flow between TuMV populations from Tai’an, Weifang and Changchun was frequent.
Wed, 3 May 2017
ARTICLE Download: 845| View: 746| Comments: 0 | doi:10.20944/preprints201705.0030.v1
Subject: Biology, Ecology Keywords: global warming; nutrients addition; cyanobacterial blooms; eutrophic systems; oligo-mesotrophic systems
Online: 3 May 2017 (09:39:21 CEST)
Global warming, as well as europhication are predicted to promote cyanobacterial blooms, but how tropical phytoplankton communities from different trophic state systems respond to temperature variation is less known. To further explore the effect of temperature changes and nutrient addition on phytoplankton communities and to get insight in possible resistance to these effects, we tested the hypothesis that temperature variation will have a stronger effect on cyanobacteria dominance in eutrophic water than in oligo-mesotrophic. Hereto, we conducted an experiment with phytoplankton communities from two aquatic ecosystems differing in trophic state. Water samples from a eutrophic and an oligo-mesotrophic system were collected and incubated in 25 and 30ºC. Also, treatments that received additional surplus N and P were included that served as eutrophication treatments. Temperature variation itself did not promote cyanobacteria in either water from the oligo-mesotrophic or the eutrophic system. However, nutrient enrichment of water from the eutrophic system significantly boosted cyanobacteria, and biomass increased 10 times in both 25ºC and 30ºC treatments. In contrast, eutrophication of water from the oligo-mesotrophic system did not change the relative contribution of phytoplankton groups and response ratios were much lower than those for water from the eutrophic system. Although using a very simple experimental design, the results suggest that in eutrophic systems cyanobacteria dominance can be favoured by further addition of nutrients, independently of a direct temperature effect and that more pristine environments possess some resistance against eutrophication. Since global warming is assumed to intensify eutrophication symptoms indirectly, our study underscores the importance of nutrient control.
Tue, 27 December 2016
ARTICLE Download: 644| View: 744| Comments: 0 | doi:10.20944/preprints201608.0176.v2
Subject: Biology, Other Keywords: ALP (alkaline phosphatase); OA (osteoarthritis); 5-aza dC (5-aza-2’deoxycytidine); epigenetics
Online: 27 December 2016 (09:36:54 CET)
DNA methylation is one of the epigenetic mechanisms which have been implicated in cellular differentiation, ageing and disease development. The effect of hypomethylating drug 5-aza-2´deoxycytidine (5-aza dC) on the biosynthetic profile of caudal region chondrocytes from chick sternum was studied in detail. The chondrocytes in culture were treated with varying doses of 5-aza dC for 48h and maintained subsequently without the treatment and harvested at selected time points for analysis of growth and differentiation status. 15µg/ml of 5-aza dC showed optimum Concentration at which there was a significant increase in DNA synthesis and RNA synthesis as per cell basis. There was also a significant increase in total protein synthesis and collagen synthesis as per cell basis at this concentration. This optimal concentration also showed to up regulate the gene expression of Type X collagen and alkaline phosphatase, which are the marker of hypertrophic chondrocyte expression. These results further support the notion that methylation is the major epigenetic factor controlling the differentiation and maturation of chondrocytes.
Tue, 24 October 2017
REVIEW Download: 677| View: 742| Comments: 0 | doi:10.20944/preprints201710.0150.v1
Subject: Biology, Animal Sciences & Zoology Keywords: refinement; mouse welfare; mouse husbandry; mouse aggression; male mice; social organisation; group housing; single housing; animal husbandry; animal welfare; animal management
Online: 24 October 2017 (03:29:02 CEST)
It is widely recommended to group house male laboratory mice because they are ‘social animals’, but male mice do not naturally share territories and aggression can be a serious welfare problem. Even without aggression, not all animals within a group will be in a state of positive welfare. Rather, many male mice may be negatively affected by the stress of repeated social defeat and subordination, raising concerns about welfare and also research validity. However, individual housing may not be an appropriate solution, given the welfare implications associated with no social contact. An essential question is whether it is in the best welfare interests of male mice to be group- or singly-housed. This review explores the likely impacts, positive and negative, of both housing conditions, presents results of a survey of current practice and awareness of mouse behaviour, and includes recommendations for good practice and future research. We conclude that whether group- or single-housing is better (or less worse) in any situation is highly context-dependent according to several factors including strain, age, social position, life experiences, and housing and husbandry protocols. It is important to recognise this and evaluate what is preferable from animal welfare and ethical perspectives in each case.
Thu, 17 January 2019
ARTICLE Download: 131| View: 738| Comments: 0 | doi:10.20944/preprints201901.0176.v1
Subject: Biology, Physiology Keywords: homeostasis, energy, neuronal networks, behavior, emergent properties
Online: 17 January 2019 (11:58:15 CET)
A major goal of neuroscience is understanding how neurons arrange themselves into neural networks that result in behavior. Most theoretical and experimental efforts have focused on a top-down approach which seeks to identify neuronal correlates of behaviors. This has been accomplished by effectively mapping specific behaviors to distinct neural patterns, or by creating computational models that produce a desired behavioral outcome. Nonetheless, these approaches have only implicitly considered the fact that neural tissue, like any other physical system, is subjected to several restrictions and boundaries of operations.Here, we propose a new, bottom-up conceptual paradigm: The Energy Homeostasis Principle, where the balance between energy income, expenditure, and availability are the key parameters in determining the dynamics of the found neuronal phenomena from molecular to behavioral levels. Neurons display high energy consumption relative to other cells, with metabolic consumption of the brain representing 20% of the whole-body oxygen uptake, contrasting with this organ representing only 2% of the body weight. Also, neurons have specialized surrounding tissue providing the necessary energy which, in the case of the brain, is provided by astrocytes. Moreover, and unlike other cell types with high energy demands such as muscle cells, neurons have strict aerobic metabolism. These facts indicate that neurons are highly sensitive to energy limitations, with Gibb’s free energy dictating the direction of all cellular metabolic processes. From this activity, the largest energy, by far, is expended by action potentials and post-synaptic potentials; therefore, plasticity can be reinterpreted in terms of their energy context. Consequently, neurons, through their synapses, impose energy demands over post-synaptic neurons in a close loop-manner, modulating the dynamics of local circuits. Subsequently, the energy dynamics end up impacting the homeostatic mechanisms of neuronal networks. Furthermore, local energy management also emerges as a neural population property, where most of the energy expenses are triggered by sensory or other modulatory inputs. Local energy management in neurons may be sufficient to explain the emergence of behavior, enabling the assessment of which properties arise in neural circuits and how. Essentially, the proposal of the Energy Homeostasis Principle is also readily testable for simple neuronal networks.
Mon, 15 May 2017
ARTICLE Download: 872| View: 737| Comments: 0 | doi:10.20944/preprints201705.0113.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Solanum nigrum; anthocyanins purification; HPLC-MS/MS; antioxidant capacity; SnMYB
Online: 15 May 2017 (17:31:53 CEST)
Solanum nigrum fruits have been conventionally available as a material of beverage due to its nutritional substances such as minerals, vitamins, amino acids, proteins, sugars, polyphenols and anthocyanins. Here has rarely reported on the characterizaton of the components and the regulatory mechanism of Anthocyanins in S. nigrum. In this study, we determined that the peel and flesh of S. nigrum fruits shared the similar HPLC profiles, but the different contents and total antioxidant activities for Anthocyanins. After an efficient purification method mainly including extraction with pH 1.0 distilled water and then desorption with pH 1.0 95% ethanol after a DM-130 resin adsorption step to obtain more pure anthocyanins extracts, the purity of anthocyanins extract from S. nigrum fruits reached to 56.1%. Moreover, eight anthocyanins from S. nigrum fruit were identified with HPLC-MS/MS for the first time. A typical R2R3-MYB transcription factor gene, SnMYB, was also cloned for the first time by RACE-PCR from S. nigrum. Moreover, the contents of anthocyanins was shown a good correlation (r = 0.93) with the expression levels of SnMYB during the fruits developmental stages. Most significantly, SnMYB successfully produced high anthocyanins contents (1.03 mg/g) when SnMYB was transiently expressed in tobacco leaves. Taken together, S. nigrum fruits are a promising resource for anthocyanins extraction and SnMYB is an activator that positively regulates anthocyanins biosynthesis in S. nigrum.
Tue, 22 August 2017
REVIEW Download: 1072| View: 736| Comments: 0 | doi:10.20944/preprints201708.0076.v1
Subject: Biology, Ecology Keywords: Acanthaster; coral reefs, disturbance; management; population outbreaks; research priorities
Online: 22 August 2017 (10:20:00 CEST)
Research on the coral-eating crown-of-thorns starfish (CoTS) has waxed and waned over the last few decades, mostly in accordance with the occurrence of population outbreaks at key locations, such as Australia’s Great Barrier Reef. This review considers advances in our understanding of the biology and ecology of CoTS based on the latest resurgence of research interest, which culminated in this current special issue on the Biology, Ecology and Management of Crown-of-Thorns Starfish. More specifically, this review considers progress against 41 specific research questions posed in the seminal review by P. Moran 30 years ago, as well as exploring new directions for CoTS research. Despite the plethora of research on CoTS (>1,200 research articles), there are persistent knowledge gaps that constrain effective management of outbreaks. Although directly addressing some of these questions will be extremely difficult, there have been considerable advances in understanding the biology of CoTS, if not the proximal and ultimate cause(s) of outbreaks. Moving forward, researchers need to embrace new technologies and opportunities to advance understanding of CoTS biology and behaviour, with focus given to key questions that will improve effectiveness of management to reduce the frequency and likelihood of future outbreaks, if not preventing them altogether.
Fri, 18 January 2019
ARTICLE Download: 83| View: 730| Comments: 0 | doi:10.20944/preprints201901.0136.v2