Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of collagen synthesis by a growth factor and by the extracellular matrix: comparison of cellular response to two different stimuli

Cultured bovine corneal endothelial cells can be grown in three ways: on plastic, on plastic with fibroblast growth factor present in the media, and on their own preformed extracellular matrix. On plastic alone, cells grow in a disorderly fashion and secrete matrix on all cell surfaces. Cells grown on plastic with growth factor or on a matrix, at confluence, have matrix deposition only on the basal surface of the cells and an orderly contact-inhibited pattern of growth. This correlates with the polarity they demonstrate histologically. This cell- matrix pattern resembles the pattern observed in vivo. Both the soluble growth factor and the extracellular matrix are able to modulate the pattern of collagen synthesis and deposition by cells, but they do so in two entirely different ways. In cells grown on the extracellular matrix, total collagen synthesis is lower but more efficient. Collagen is deposited primarily into the cell layer even at the early sparse stage of culture. In cells grown on plastic with growth factor in the media, collagen is initially secreted into the media and does not become incorporated into the matrix. The deposition of collagen on the basal surface of cell occurs only late in the culture, and is achieved by increments in a stepwise manner. The in vivo-like pattern is not manifest until confluence has been reached. Thus, the extracellular matrix functions not only as a structural support, but is also instructional to the cells plated on it. In this case, the matrix regulates the level of collagen synthesis in the cells and modulates the pattern of collagen deposition. Soluble growth factors may act in part by enhancing a cell's ability to elaborate an appropriate matrix pattern necessary for the cell's own growth and accurate function.
Single-cell protein production through microbial conversion of lignocellulosic residue (wheat bran) for animal feed

Agricultural residue (wheat bran) rich in carbohydrates was utilized in the fermentation process to produce microbial biomass. Single-cell biomass consists of the dried cells of microorganisms, which are used as protein supplements in human food and in animal feed. In the present study, two different microorganisms ( Candida utilis and Rhizopus oligosporus ) were studied for biomass production. To enhance the nutritional contents of wheat bran, a number of different fermentation parameters (effect of inoculum size, age of inoculum, incubation period, moisture to substrate ratio and incubation temperature) were optimized. Maximum yield was obtained at an inoculum size of 10% (v/w), with the age of the inoculum being a 48h old culture. A fermentation period of 48h was found to give the maximum protein yield and viable counts of yeast cells and mould hyphae. The micro- organisms showed good growth at 30°C. After complete optimization of the fermentation parameters, a batch of wheat bran was fermented with C . utilis and R . oligosporus under the optimized conditions, resulting in a maximum crude protein yield of 41.02% compared with the 4.21% crude protein of the non-fermented wheat bran. Copyright © 2015 The Institute of Brewing & Distilling biomass. In present study, by the function of certain strains of microorganisms in the agricultural waste medium under optimum cultural and nutritional conditions, the protein content of the SCP increases, making it an ideal supplement for animal and poul-try feeds. The output of microbial protein, which in turn can be applied to upgrade animal feeds and agricultural composts, can occur by using agricultural residues (wheat bran) rich in carbohydrates through fermentation processes. Two types of microorganisms, mainly yeast and moulds, are used for biomass production.
Evolution of insect pheromones and their role in reproductive isolation and speciation

Abstract The importance for reproductive isolation of a change in the pheromone biosynthetic pathway, resulting in a different pheromone blend, is discussed in Lepidoptera and Diptera. The different sites of pheromone production and the biosynthetic enzymes are briefly reviewed. Two examples of a modification in the pheromone blend leading to reproductive isolation in Lepidoptera are taken as examples: the first, in Ostrinia nubilalis, is involved in the formation of two different populations showing reproductive isolation; the second, in the genus Ostrinia, might be at the origin of the formation of two different species. In both examples, a modification in the function of a desaturase involved in pheromone biosynthesis brings about change in the pheromone blend. In the fruitfly, Drosophila melanogaster, a mutation at a desaturase locus leads to the formation of two populations which differ in their pheromone mixtures and have developed premating isolation. The closely related species, D. melanogaster and D. simulans, differ in their female pheromonal cuticular hydrocarbons. This pheromonal difference is due to two species- and female-specific genes, desatF and eloF. The activity of desatF could account for an effective barrier between these species. All these examples show that a birth and death process of desaturases is at the origin of major shifts in the pheromone blend leading to sexual isolation and speciation.
Response of soil microbial community and diversity to increasing water salinity and nitrogen fertilization rate in an arid soil

ABSTRACT The scarcity of fresh water has forced farmers to use saline water (SW) for irrigation. It is important to understand the response of the soil microbial community and diversity to saline irrigation water. The objective of this study was to determine the effects of irrigation water salinity and nitrogen fertilization rates on soil physicochemical properties, microbial activity, microbial biomass, and microbial functional diversity. The field experiment consisted of a factorial design with three levels of irrigation water salinity (electrical conductivities (ECs) of 0.35, 4.61 or 8.04 dS m−1) and two nitrogen rates (0 and 360 kg N ha−1). The results showed that the 4.61 and 8.04 dS m−1 treatments both reduced soil microbial biomass C (MBC), microbial biomass N (MBN), basal respiration, total phospholipid fatty acid (PLFA), bacterial PLFA, fungal PLFA, and fungal:bacterial ratios. In contrast, the SW treatments increased the MBC:MBN ratio. Nitrogen fertilization increased soil MBC, MBN, basal respiration, total PLFA, bacterial PLFA, and gram-negative bacterial PLFA. In contrast, N fertilization decreased gram-positive bacterial PLFA, fungal PLFA, and fungal:bacterial ratios. Average well color development, Richness, and Shannon's Index were always lowest in the 8.04 dS m−1 treatment. Carbon utilization patterns in the 8.04 dS m−1 treatment were different from those in the 0.35 dS m−1 treatment. In conclusion, five years of irrigation with brackish or SW reduced the soil microbial biomass, activity, and functional diversity, which may cause the deterioration of soil quality. Thus, the high-salinity water (EC > 4.61 dS m−1) is not appropriate as a single irrigation water resource. Proper N fertilizer input may overcome some of the negative effects of salinity on soil microbial.
Inbreeding and Extinction in Island Populations: a Cautionary Note

Extinction rates may appear generally higher on island than mainland populations, but the reason for this difference is controversial (e.g., Pimm 1991). Characteristically, small island populations are susceptible to demographic and environmental stochasticity (e.g., Pimm 1991), but genetic factors such as inbreeding and lack of genetic variation may also decrease their viability (e.g., Frankham 1995). For example, there is compelling evidence that inbreeding depresses individual reproductive success in typically out-breeding domestic plants and animals (e.g., Wright 1977; Falconer 1989; Frankham 1999) and captive populations of vertebrate wildlife (e.g., Ralls et al. 1988). But drawing general conclusions from individual species requires quantitative comparative analyses, rather than appeals to particular studies. Frankham (1998) addresses this issue by using interspecific comparative data to test several hypotheses derived from theoretical population genetics. In particular, Frankham (1998) claims that inbreeding coefficients are significantly higher in endemic than nonendemic island populations and that many island populations show levels of inbreeding associated with elevated extinction rates in domestic and laboratory species. Such interspecific comparative studies and meta-analyses of different populations are useful techniques to address apparently inconsistent empirical evidence (e.g., Harvey 1996; Frankham 1999). However, phylogenetic information should be taken into account in such analyses (Harvey & Pagel 1991), because closely related species share many traits as a result of common ancestory (Harvey 1996). Unfortunately, Frankham (1998) did not incorporate phylogenetic data into his analyses; hence, his conclusions may be misleading. We reanalyzed the data presented by Frankham (1998), correcting for taxonomic relationships. In particular, we explored the relationship between inbreeding and population viability and compared the inbreeding coeffi-
Adaptation of wheat, barley, canola, field pea and chickpea to the thermal environments of Australia

Abstract. Warming trends involve two agronomically relevant aspects: a gradual increase in long-term mean temperature with the primary effect of shifting phenological patterns, and an increasing incidence of heat waves. Depending on timing, intensity and duration, heat can reduce crop growth and disrupt reproduction. Agronomic and breeding adaptations to elevated temperature have been listed but there is an overall lack of frameworks for systematic analysis. This paper provides agronomic and physiological background for the quantitative assessment of spatial patterns of the thermal regimes for wheat, barley, canola, field pea and chickpea. First, we revise the notion that Australian agriculture is ‘European’ and ill-adapted to the local environments. By showing that Australian agriculture in the southern and western regions is rather Levantine, we advance a more accurate and relevant framework to the thermal regimes of winter crops. Second, we outline the direct and indirect effects of temperature on crop traits and highlight the limitations of different approaches to investigate crop responses to temperature. This is important to make explicit the assumptions of studies dealing with crop responses to temperature; for example, indirect effects of temperature on crops mediated by effects on weeds, pathogens or herbivores could be important. Third, we compare the cardinal temperatures (including base, optimal, and critical thresholds) of our target crops. Cardinal temperatures respond to both natural and agronomic selection and are relevant for crop adaptation. Fourth, we develop a conceptual framework to assess thermal effects on crop yield and adaptive practices and traits, based on the notions of yield being a primary function of seed number, the species-specific critical window for the determination of seed number, and two complementary perspectives involving the photothermal quotient and crop growth rate in the critical window. The framework accounts for both aspects of warming: non-stressful elevated temperature and heat stress. Testable propositions are advanced that inform future research on crop adaptation to elevated temperature.
Climate change facilitated range expansion of the non-native angular crab Goneplax rhomboides into the North Sea

The angular crab Goneplax rhomboides is native to the north-eastern Atlantic and Mediterranean Sea. It has rarely been reported from the North Sea, with no evidence of sustain- able populations. Compiled survey data, however, revealed an increasing abundance of this spe- cies in the North Sea since 2000. The data were used to (1) describe the range expansion of the angular crab into the North Sea; and (2) to apply species distribution modeling (maximum entropy approach-MAXENT) to predict the potential habitats of this species. Habitats of species with a similar ecology were modeled to analyse habitat overlap and potential competition. The spatial and temporal patterns of records revealed that the expansion of the angular crab into the North Sea is due to natural larval dispersal rather than anthropogenic vectors. Modeled habitats of the angular crab showed a core distribution area along the Scottish coastline and in the southern North Sea. Sea bottom temperatures in February had the highest influence on the model results. We concluded that the angular crab has extended its distribution range from the north-eastern Atlantic to the North Sea, which was facilitated by an increase in water temperature and the pre- vailing hydrodynamics over the last decade. This was the first time that a benthic range expansion was observed in quasi real time for the North Sea. Habitats of the angular crab overlapped those of possible competitors to a large extent. However, co-existence of the species is expected rather than any negative effects resulting from the range expansion of the angular crab.
Adeno-associated virus type 2 as vector for human gene therapy: Characterization of virus-host interactions

Vectors based on adeno-associated virus type 2 (AAV) offer considerable promise for somatic gene therapy of various diseases (e.g. cystic fibrosis, hemophilia B, cancer). Limitations, however, still exist and require further improvement. The study presented here addresses two major problems that hamper a widespread use of AAV in human gene therapy: First, the loss of site-specific integration of recombinant AAV vectors (rAAV) due to the deletion of the rep gene, and secondly, the potential neutralization of AAV gene therapy vectors by preexisting antibodies. It could be demonstrated that site-specific integration of a transgene encoding rAAV vector can be efficiently restored by providing rep as plasmid DNA in trans. Based on these findings, a rAAV vector was developed where a plasmid coding for Rep was coupled as polylysine/DNA complex (PLL/DNA) directly to the capsid of the virion and co-transduction of such a PLL/DNA coupled to AAV was shown. Thus, providing rep-DNA as PLL/DNA should allow rAAV vectors to integrate specifically at chromosome 19. To characterize immunogenic domains of the AAV capsid and to develop strategies to circumvent neutralization by antibodies, AAV capsid mutants carrying peptide insertions in surface exposed loop regions were investigated in binding and neutralization assays. Three positions could be identified in the AAV capsid (at aa 534, 573, and 578 of the VP1 protein) where binding and neutralization of the virus by human serum samples was markedly reduced. These result suggest that capsid modifications could help to overcome binding and neutralization by human antisera in clinical gene therapy applications.
Lipids and fatty acids in wild and pond‐reared mud crab Scylla serrata (Forsskål) during ovarian maturation and spawning

Wild-caught and pond-reared female mud crab Scylla serrata at different stages of ovarian maturation were collected from Samar and Capiz, Philippines. Crabs were categorized into five stages according to the external morphological and microscopic appearance of the most advanced oocytes. The ovaries, hepatopancreas, muscle and newly spawned eggs (NSE) were analysed for lipid class components and fatty acids. Total lipid was higher in pond-reared than in wild-caught crabs but increased with ovarian maturation in both groups. Ovarian lipid peaked at the fully mature stage, coinciding with a decline in hepatopancreatic and muscle lipids. Lipid levels declined significantly in spent females. The tissues contained elevated highly unsaturated fatty acids such as arachidonic (20:4n-6), eicosapentaenoic (20:5n-3) and docosahexaenoic (22:6n-3) acids, but at higher levels in late maturing and fully mature ovaries and in NSE. The type of lipid class and fatty acid components in mature ovaries as well as in NSE are generally considered to be indicative of their importance in reproductive physiology and embryonic and larval development.
Mesocorticolimbic adaptations in synaptic plasticity underlie the development of alcohol dependence

33 Introduction 34 Materials and Methods 37 Brain slice preparation 37 Patch clamp electrophysiology 37 Data acquisition and analysis 38 Chronic intermittent ethanol exposure 40 Results 42 NMDAR-mediated LTD in the NAc shell of ethanol-naive mice 42 Non-specific or subunit-specific NMDA receptor inhibition blocks NAc LTD 43 Acute in vitro ethanol exposure of increasing concentrations differentially inhibits NAc LTD 43 Activation of dopamine D1 receptors restores LTD expression in the presence of ethanol 44 NAc LTD is completely occluded in the presence of ethanol (60mM) when D1 receptors are inhibited 45 Chronic intermittent ethanol exposure increases voluntary ethanol consumption in C57BL/6J mice 45
A GABAA Receptor α1 Subunit Tagged with Green Fluorescent Protein Requires a β Subunit for Functional Surface Expression*

γ-Aminobutyric acid, type A (GABAA) receptors, the major inhibitory neurotransmitter receptors in the central nervous system, are heteropentameric proteins assembled from distinct subunit classes with multiple subtypes, α(1–6), β(1–4), γ(1–3), δ(1), and ε(1). To examine the process of receptor assembly and targeting, we tagged the carboxyl terminus of the GABAA receptor α1 subunit with red-shifted enhanced green fluorescent protein (EGFP). Xenopus oocytes were injected with cRNA of this fusion protein, α1-EGFP, alone or in combination with cRNA of GABAA receptor β2, γ2, or β2+γ2 subunits. Within 72 h after injection, EGFP fluorescence was visible in all fusion protein-injected cells. The fluorescence was associated with the plasmalemma only when the β2 subunit was co-injected with α1-EGFP. Texas Red-conjugated immunolabeling of EGFP on nonpermeabilized cells demonstrated that EGFP was localized extracellularly. Hence, the COOH terminus of the α1subunit is extracellular. Two-electrode voltage clamp of α1-EGFPβ2- and α1-EGFPβ2γ2-injected oocytes demonstrates that these cells express functional receptors, with EC50 values for GABA and diazepam similar to wild-type receptors. Thus, a COOH-terminal tag of the α1 subunit appears to be functionally silent, providing a useful marker for studies of GABAA receptor expression, assembly, transport, targeting, and clustering. Moreover, the β2 subunit is required for receptor assembly and surface expression.
CORRECTION OF TEMPERATURE AND MOISTURE DISTRIBUTIONS IN WOOD DRYING

A procedure is proposed to improve the numerical solutions of the Luikov equations of heat and mass transfer in capillary-porous bodies based on the measured temperature and moisture data. The main idea of the procedure can be summarized as a modeling technique with online correction ability. The procedure is demonstrated by a one-dimensional problem of heat and mass transfer in spruce sample. Numerical simulation shows that the accuracy of the solutions for the heat and mass transfer can be improved significantly by using the proposed method.
Resin-coated Fertilizers Affect Postproduction Growth, but Not Flowering, of Potted Alstroemeria

Seven resin-coated fertilizers (RCF) (Osmocote 19-6-12, 18-6-12, 14-14-14, 13-13-13, and 19-6-12, and Polyon 19-6-12, 17-17-17, and 13.5-13.5-13.5) were applied to marketable potted Alstroemeria hybrid FL101 plants to determine their effects on postproduction flowering and growth. The nonfertilized control produced the greatest number of floral stems, total florets, and mean number of florets per stem, but these plants were extremely chlorotic and spindly, and had the lowest fresh weight and number of vegetative stems. In a subsequent experiment, plants were fertilized with low, medium, and high concentrations of either Osmocote 19-6-12 or Sierra HighN 24-4-8. Nonfertilized controls were again chlorotic and spindly, but produced as many florets as fertilized plants. Plants fertilized with Osmocote 19-6-12 had greater fresh weight and more vegetative stems, but fewer total florets than those fertilized with Sierra HighN 24-4-8. We concluded that potted Alstroemeria do not need fertilizer for continued flowering, and fertilization favors production of vegetative stems relative to flowering stems. However, application of RCF to marketable plants prevents chlorosis, increases fresh weight, and, if low to moderate rates of formulations with N-P ratios of at least 6:1 are applied, does not inhibit flowering.
Terrestrial Liming As a Restoration Technique for Acidified Forest Ecosystems

We studied the effects of liming on soils and forest songbirds as well as vegetation and calcium-rich invertebrate prey variables that were predicted to link birds to changes in soil conditions. We observed increases in soil pH, calcium, and magnesium, as well as in songbird abundances in response to lime application, with continuing increases through five years after liming. We observed an overall increase in snail abundance on limed sites, but an initial peak of a 23 fold increase three years after liming was reduced to an 11 fold increase five years after liming. We observed an increase in forb ground cover on limed sites, but liming had no effect on millipede abundance or other vegetation measures. Of the variables we measured, snail abundance was the most likely mechanism for the response in bird abundances. Because we observed continued benefits of liming up to five years post treatment, we concluded that liming is a very promising technique for restoring forest ecosystems impacted by acidic deposition.
New species records for butterflies (Lepidoptera) on Herschel Island, Yukon, Canada, with notes on natural history

Abstract Comparisons of past and current butterfly species distributions are being used to gauge the effects of climatic change in various parts of the world. Historic butterfly records from Herschel Island, Yukon, Canada, presented an opportunity to do such a comparison in an Arctic tundra region known to have a diverse butterfly fauna. We compared historic species records (1916–1983) with newly collected ones (2007–2009) to assess possible changes in species distributions. Of the 21 species documented for Herschel Island, six were newly found and two were not reconfirmed. We postulate that warmer temperatures facilitated the apparent northerly range expansions of several species by making butterfly flight and dispersal possible. This is supported by interannual comparisons on a smaller time scale, 2007–2009. During this period, we observed accelerated butterfly phenology and higher relative abundance of butterflies associated with earlier snowmelt and with earlier and more intense early summer heating. Résumé Des comparaisons des distributions antérieures et actuelles d'espèces de papillons sont utilisées afin d’évaluer les effets des changements climatiques dans différentes parties du monde. Des inventaires historiques de papillons de l’île Herschel au Yukon (Canada) offrent une opportunité de faire une telle comparaison dans une région arctique de toundra connue pour la diversité de sa faune de papillons. Nous avons comparé les inventaires historiques (1916–1983) avec des inventaires récents (2007–2009) afin d’évaluer de possibles changements de distribution des espèces. Parmi les 21 espèces documentées pour l’île Herschel, il y avait six nouvelles espèces et deux qui n'ont pas été reconfirmées. Nous suggérons que les températures plus chaudes facilitent l'expansion nordique apparente de plusieurs espèces en permettant le vol et la dispersion des papillons. Ceci est supporté par les comparaisons interannuelles sur une plus petite échelle de temps, de 2007 à 2009. Durant cette période, nous avons observé une phénologie accélérée chez les papillons et une plus grande abondance relative des papillons associés avec une fonte des neiges hâtive et avec des chaleurs de début d’été plus hâtives et plus intenses.