Miracle-dz/UniFAR-FTUs huggingface dataset:
A Taxonomic Review of Tan-Brown Glassfrogs (Anura: Centrolenidae), with the Description of a New Species from Southwestern Colombia

Abstract. Thirty species of the glassfrogs genus Nymphargus, including a new species, are known to inhabit the cloud forest of the Andes of Colombia and Ecuador. Four of these species (Nymphargus anomalus, N. ignotus, N. rosada, and the new species) are unusual by having a tan-brown dorsal coloration instead of the widespread green coloration commonly found in glassfrogs. Herein, we review tan-brown glassfrogs species, providing information on their external morphology, color ontogeny, ecology, and distribution. The new taxon inhabits the Andes of southwestern Colombia, Departamento del Cauca, and it is distinguished from other centrolenids by having a tan-brown dorsum with dark spots lacking ocelli, reduced (basal) webbing between outermost fingers, and lacking iridophores on the digestive tract and hepatic peritonea. We also find that Nymphargus ignotus is a polymorphic species distributed along the western flank of the Cordillera Occidental in Colombia. The egg masses of N. ignotus are similar to those known in others Nymphargus species, except for the presence of supplementary empty capsules. The distribution, abundance and function of empty capsules and the nature of the tan-brown color pattern in glassfrogs are discussed.
Nitrogen availability and early corn growth on plowed and no-till soils amended with different types of cover crops

Heavy application of nitrogen (N) fertilizers to agroecosystems contributes to water pollution and emission of nitrous oxide (N2O), an atmospheric constituent implicated in the greenhouse effect and stratospheric ozone depletion. The incorporation of cover crops biomass into agricultural soil is a practice that could provide a portion of the N needed by growing crops, and thereby could help reduce N fertilizer input and N loss from agroecosystems. Although the cover crop composition and the tillage management history of receiving soils could affect the pattern of mineral N release and its fates, these questions have not been addressed in previous research. A greenhouse experiment (85 d) was conducted to investigate the effects of two cover crops, hairy vetch (Vicia villosa, C/N: 11) and rye (Secale cereale, C/N: 82) on mineral N flux, N2O emission, and corn growth in soils under no-till (NT, 11 years) and plow-till (PT). Overall, tillage practice had only a marginal influence on N dynamics. Although NO3 flux was enhanced by both cover crops, the NO3 released was more efficiently utilized in the rye treatment. Corn growth and N uptake were significantly greater (P<0.02; 1.5 times) with rye compared to the vetch treatment. Conversely, N2O emission was significantly (P<0.03) higher with vetch than rye addition, with cumulative emission (across PT and NT) averaging 2.45 kg N ha-1 with vetch and 1.28 kg N ha-1 with rye addition. Positive relationships were found between NO3 flux and N2O emission, with the slopes of the regression lines suggesting a greater propensity of NO3 released from vetch to be converted into N2O. By leading to less N2O emission and better corn N uptake, the study results indicate that rye is a better cover crop option than vetch, regardless of tillage practice.
Comparing Provisional Seed Transfer Zone Strategies for a Commonly Seeded Grass, Pseudoroegneria spicata

ABSTRACT: Restoration practitioners balance the desire to use locally adapted plant materials with the uncertainty of what constitutes “local. ” Provisional seed transfer zones are intended to guide managers on how far plant materials can be moved during revegetation with the assumption that all populations within a zone will show similarly adapted traits. There are multiple approaches to developing provisional transfer zones, including limiting transfer to specific populations, within ecoregions, within climatic zones, or within climatic zones within ecoregion; there is little information about which of these approaches is best or whether the best approach could vary by region. We used Pseudoroegneria spicata as a test species to assess (1) whether EPA Level III Ecoregion or population explained more variation in traits, and (2) which of four common provisional seed transfer zones (Ecoregion-only, Climate-only, USFS seed transfer zone, and Climate in Ecoregion) best explains trait variation. Plants from 14 populations and three ecoregions were grown in a common garden for two years; growth traits, final biomass, seed set, and mortality were measured. Ecoregion explained more variation than population for most growth traits and mortality; population explained more variation only for seed set. Only one of the three ecoregions showed strong trait differentiation. Out of the four provisional seed transfer zone models compared, we found the most support for models containing climate (Climate-only and Climate in Ecoregion). Findings suggest that Level III Ecoregions may be too broad for seed transfer and that managers should consider climate within ecoregion when making seed transfer decisions.
Incipient establishment of human adipose-derived mesenchymal stem cells bank

Objective To explore the possibility of establishing the human adipose-derived mesenchymal stem cells (hADSCs ) bank as to provide an alternative source for the seed cells of tissue engineering. Methods The cell surface antigens of the purified, expanded hADSCs and the ones following cryopreservation were detected by flow cytometry, cultured in an induced culture medium to induce the osteogenic and adipogenic differentiation. The specific marker alkaline phosphatase (ALP) in osteogenic special medium was also detected by immunohistochemistry. Results The phenotype and expansion possibility of hADSCs after cryopreservation were remained. It could expand for 10 generations. The doubling time was 48 hours. The 2nd, 6th and 10th generation of hADSCs kept stronger ability of osteogenic and adipogenic differentiation. Conclusion The bank of hADSCs has been incipiently established and can provide eligible seed cells for tissue engineering. DOI: 10.11855/j.issn. 0577-7402.2016. 12.05
Deficiency In Stress Response Gadd45a and Gadd45b Alters MAPK Kinase Signaling Leading to Functional Defects In Innate Immune Responses of Neutrophils and Macrophages In Vitro and In Vivo

Abstract 927 Stress sensor GADD45 proteins modulate p38-NF-Kb and JNK signaling; which play major roles in leukocyte activation and innate immunity. We have previously documented that GADD45a-deficient and GADD45b-deficient mice exhibit impaired responses to hematological stress, including acute stimulation with inflammatory cytokines (Gupta et. al, Oncogene. 25:5537, 2006). Whether GADD45 genes modulate myeloid compartment function, notably the response of macrophages & granulocytes to inflammatory stress, remains largely unexplored. Data obtained thus far indicate that bone marrow (BM) derived neutrophils and macrophages lacking GADD45 family members exhibit defects in chemotaxis towards inflammatory stimuli. BM derived neutrophils and macrophages lacking GADD45 family members were also observed to exhibit defects in the production of reactive oxygen species (ROS) upon treatment with LPS (500ng/mL) in vitro. Furthermore, BM derived macrophages from mice lacking GADD45a and GADD45b were found to be defective in phagocytosis and cellular adhesion upon stimulation with LPS (500ng/mL) in vitro. Additionally, it was observed that BM derived neutrophils and macrophages lacking GADD45 family members exhibit defects in inflammatory cytokine secretion in response to activation with LPS. Notably, GADD45a, GADD45b & GADD45g null mice injected intraperitoneally with sublethal doses of LPS were significantly more susceptible to septic shock compared to wt mice, showing significantly increased morbidity. Moreover at 18 hrs. post-injection, the spleens of KO mice harbored apoptotic foci in the white pulp, identified as tingible body macrophages ingesting dying cells. To dissect the signaling pathways involved, MAPK specific chemical inhibitors were used to correlate MAPK signaling alteration to defects in innate immune responses of neutrophils and macrophages lacking GADD45a or GADD45b. LPS stimulated wt neutrophils treated with MAPK inhibitors exhibited defects in signaling and innate immune responses mimicking neutrophils and macrophages lacking GADD45a or GADD45b. Collectively, these novel data provide evidence to show that deficiency in GADD45a and GADD45b leads to functional defects in the myeloid innate immune responses of neutrophils and macrophages in vitro and in vivo. These findings increase our understanding of innate immunity and have the potential to contribute towards development of novel approaches to clinical treatment of sepsis. Disclosures: No relevant conflicts of interest to declare.
COMPUTATIONAL METHODS FOR THE FUNCTIONAL ANALYSIS OF DNA SEQUENCE VARIANTS

Complex diseases, such as cancer and inflammatory bowel disease, are caused by a combination of genetic and environmental factors. The advent of next-generation sequencing (NGS) technology allowed the genome-wide investigation of the underlying genetic causes of complex disorders. Analysis of the large amount of data generated by NGS is computationally intensive and require new computational methods. One of the current problems in genomic data analysis is the lack of computational methods for functional annotation of DNA sequence variants (DSVs), especially regulatory DNA sequence variants (rDSVs). In recent years, rDSVs have been shown to be the primary cause of complex diseases, supported by the fact that functional regulatory sites are more polymorphic than coding regions, and that rDSVs vastly outnumber coding variants. Also, GWAS studies of complex traits have shown that SNPs with the strongest association signals lie outside known genes in non-coding regions of the genome. This dissertation contributes to a solution to the lack of computational methods for the analysis of DNA sequence variants. Two novel computational methods for the analysis of DSVs are proposed here: 1) an algorithm, called is-miRSNP, DSVs on miRNA binding, 2) a pipeline for the functional annotation of DSVs using NGS. The is-miRSNP algorithm uses a binding-energy approach for the prediction of DSVs effects on miRNA binding. The algorithm is flexible enough to process large amounts of data and can be easily integrated into existing pipelines. Experiments using a manually curated set of experimentally validated DSVs-miRNA showed that is-miRSNP outperforms all most popular existing methods. The pipeline for functional annotation of functional DSVs utilizes state-of-the- art existing computational methods. The pipeline has been applied to an effector memory T cell RNA-Seq dataset that is related to inflammatory bowel disease and has identified biologically relevant genes and isoforms that are differentially expressed upon treatment with Prostaglandin E2. Important pathways and biologically relevant DSVs were also identified and recovered. These methods have the potential to help clinicians and researchers analyze and interpret genomic datasets, and might in the future help the development of new diagnostics methods and treatments.
Matrix-assisted protein refolding

Overexpression of hetereologous proteins in E. coli often leads to the formation of large insoluble aggregates, the so called inclusion bodies (IBs). In this work, IMAC (immobilized metal affinity chromatography) was applied to identify optimal buffer conditions for the refolding of his-tagged IBs protein. To minimize the number of buffer conditions in the screening procedure a stepwise approach was introduced. The optimization of the refolding buffer was successful for six test proteins Furthermore matrix-assisted refolding could be efficiently carried out at 1000 fold higher protein concentrations was faster, compared to refolding in solution. Special attention was paid to the analysis of the re-association of a large tetrameric protein s-galactosidase in the matrix-assisted refolding process.
Genotype by environment interaction for yearling weight in Nellore cattle applying reaction norms models

In the present study, a possible existence of genotype × environment interaction was verified for yearling weight in Nellore cattle, utilising a reaction norms model. Therefore, possible changes in the breeding value were evaluated for 46 032 animals, from three distinct herds, according to the environmental gradient variation of the different contemporary groups. Under a Bayesian approach, analyses were carried out utilising INTERGEN software resulting in solutions of contemporary groups dispersed in the environmental gradient from –90 to +100 kg. The estimates of heritability coefficients ranged from 0.19 to 0.63 through the environmental gradient and the genetic correlation between intercept and slope of the reaction norms was 0.76. The genetic correlation considering all animals of the herds in the environmental gradient ranged from 0.83 to 1.0, and the correlation between breeding values of bulls in different environments ranged from 0.79 to 1.0. The results showed no effect of genotype × environment interaction on yearling weight in the herds of this study. However, it is important to verify a possible influence of the genotype × environment in the genetic evaluation of beef cattle, as different environments might cause interference in gene expression and consequently difference in phenotypic response.
A Molecular Odorant Transduction Model and the Complexity of Combinatorial Encoding in the Drosophila Antenna

In the past two decades, a substantial amount of work characterized the odorant receptors, neuroanatomy and odorant response properties of the early olfactory system of Drosophila melanogaster. Yet many odorant receptors remain only partially characterized and, the odorant transduction process and the axon hillock spiking mechanism of the olfactory sensory neurons (OSNs) have yet to be fully determined. Identity and concentration, two key aspects of olfactory coding, originate in the odorant transduction process. Detailed molecular models of the odorant transduction process are, however, scarce for fruit flies. To address these challenges we advance a comprehensive model of fruit fly OSNs as a cascade consisting of an odorant transduction process (OTP) and a biophysical spike generator (BSG). We model identity and concentration in OTP using an odorant-receptor binding rate tensor, modulated by the odorant concentration profile, and an odorant-receptor dissociation rate tensor, and quantitatively describe the ligand binding/dissociation process. We model the BSG as a Connor-Stevens point neuron. The resulting combinatorial encoding model of the Drosophila antenna provides a theoretical foundation for understanding the neural code of both odorant identity and odorant concentration and advances the state-of-the-art in a number of ways. First, it quantifies on the molecular level the combinatorial complexity of the transformation taking place in the antennae. The concentration-dependent combinatorial code determines the complexity of the input space driving olfactory processing in the downstream neuropils, such as odorant recognition and olfactory associative learning. Second, the model is biologically validated using multiple electrophysiology recordings. Third, the model demonstrates that the currently available data for odorant-receptor responses only enable the estimation of the affinity of the odorant-receptor pairs. The odorant-dissociation rate is only available for a few odorant-receptor pairs. Finally, our model calls for new experiments for massively identifying the odorant-receptor dissociation rates of relevance to flies.
The effect of the thawing temperature on the integrity of canine cryopreserved sperm

Aiming to evaluate the influence of the thawing temperature on the viability of canine cryopreserved sperm, Basset Hound (n=3) and Rottweiler (n=3) dogs were used, submitted to semen collected through manual manipulation. Semen samples were thawed at 37oC during 1min (G1) or at 70oC during 6s (G2), and evaluated for progressive motility, vigor and acrosome integrity, after 0, 30 e 60 minutes of incubation (37oC), and sperm ultrastructure immediately after thawing. In all incubation times, the average of progressive motility was higher (P 0.05) between groups, and the percentage of gametes with intact acrosome was higher (P<0.05) on sperm cells from G1 than from G2. Ultrastructural changes were identified on dog sperm from both groups, and were observed in higher quantity in gametes from G2 Group. It can be concluded that samples of frozen dog sperm must be thawed at 37°C for 1min.
Developmental dynamics of cross-modality in mouse visual cortex

Maturation of GABAergic circuits in primary visual cortex (V1) opens a critical period (CP), a developmental window of enhanced plasticity for visual functions. However, how inhibition promotes the plasticity remains unclear. Here, we investigated the developmental dynamics of auditory responses and audiovisual interactions in mouse V1. Modulation of V1 spiking activity by a transient sound was temporally dynamic with alternating enhancement and suppression phases. When paired with grating visual stimuli, sound-driven spike enhancement and suppression were weaker and stronger with preferred orientation than with non-preferred orientations, respectively, leading to impaired net orientation selectivity in V1 neurons. Strikingly, the net orientation selectivity was impervious to sound specifically during the CP due to equal total amounts of sound-driven spike enhancements and suppressions. This balance of spike modulations at the CP was achieved by the preferential maturation of sound-driven spike suppression. However, further maturation of sound-driven spike enhancement broke the balance after the CP. Spectral analysis of field potentials revealed the enhancement of a GABA-mediated sound-driven power suppression specifically at CP. Reduction of inhibition by 10-day dark-exposure or genetic deletion of GAD65 gene dampened sound-driven spike suppression in V1. Furthermore, acute suppression of either parvalbumin-expressing (PV) or somatostatinexpressing (SST) neurons suggested their early or late recruitments by sound, respectively. Our results point to the dampened net non-visual sensory influence as one of the functional roles of GABA circuit maturation during a developmental CP. The insensitivity of visual selectivity to sound during the CP may promote functional maturation of V1 as visual cortex.
Safety evaluation of the food enzyme pullulanase from Pullulanibacillus naganoensis strain AE‐PL

Abstract The food enzyme considered in this opinion is a pullulanase (pullulan 6‐α‐glucanohydrolase; EC 3.2.1.41) produced with a non‐genetically modified Pullulanibacillus naganoensis (strain AE‐PL) by Amano Enzyme Inc. (Japan). The pullulanase food enzyme is intended to be used in starch processing for the production of glucose syrups. Since residual amounts of total organic solid (TOS) in glucose syrups are removed by filtration and purification during starch processing, dietary exposure assessment was not performed. Genotoxicity tests made with the food enzyme indicated no genotoxic potential. A repeated dose 90‐day oral toxicity study in rodents, carried out with the food enzyme, showed minor effects that were considered to be of no biological relevance. The allergenicity was evaluated by comparing the amino acid sequence to those of known allergens and no match was found. The Panel considered that there are no indications for food allergic reactions to dietary intake of this food enzyme. Based on the removal of residual amounts of TOS from glucose syrups, consumer exposure is not expected. In addition, the safety of the manufacturing process, the compositional and biochemical data lead the Panel to conclude that the food enzyme pullulanase from P. naganoensis (strain AE‐PL) does not give rise to safety concerns under the intended conditions of use.
Adventitious root formation in Arabidopsis : underlying mechanisms and applications

Adventitious root (AR) formation is indispensable in vegetative propagation and is widely used. A better understanding of the underlying mechanisms is needed to improve rooting treatments. We first established a system to study rooting in Arabidopsis, the model organism in plant biology but only occasionally used to study adventitious rooting. Inhibition of polar auxin transport reduced AR formation. The role of auxin transporter proteins (several PIN-proteins) was found to be tissue-specific. Maturation (the transition from juvenile to adult) negatively influenced AR formation. Maturation was associated with increased DNA methylation and decreased miR156 level. 5-Azacytidine, a drug that reduces DNA methylation, increased rooting. We also examined the effect of two donor plant pre-treatments, etiolation and flooding, on rooting. Both increased AR formation.
The activation loop residue serine 173 of S.pombe Chk1 kinase is critical for the response to DNA replication stress

Why the DNA damage checkpoint kinase Chk1 protects the genome of lower and higher eukaryotic cells differentially is still unclear. Mammalian Chk1 regulates replication origins, safeguards DNA replication forks and promotes fork progression. Conversely, yeast Chk1 acts only in G1 and G2. We report here that the mutation of serine 173 (S173A) in the activation loop of fission yeast Chk1 abolishes the G1-M and S-M checkpoints without affecting the G2-M arrest. Although Chk1-S173A is fully phosphorylated at serine 345 by the DNA damage sensor Rad3 (ATR) when DNA replication forks break, cells fail to stop the cell cycle. Mutant cells are uniquely sensitive to the DNA alkylation agent methyl- methanesulfate (MMS). This MMS sensitivity is genetically linked with the lagging strand DNA polymerase delta. Chk1-S173A is also unable to block mitosis when the G1 transcription factor Cdc10 is impaired. Serine 173 is equivalent to lysine 166 in human Chk1, an amino acid important for substrate specificity. We conclude that the removal of serine 173 impairs the phosphorylation of a Chk1 target that is important to protect cells from DNA replication stress. Summary statement Mutation of serine-173 in the activation loop of Chk1 kinase may promote cancer as it abolishes the response to genetic alterations that arise while chromosomes are being copied.