Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuroligin 2 Induced Allosteric Transition of Collybistin Underlies Inhibitory Postsynaptic Differentiation

Synaptic inhibition is vital to brain function. GABAergic and glycinergic synapses, mediating fast inhibition in the mammalian central nervous system (CNS), balance the activity of neural circuits. At the inhibitory postsynapse, GABA and glycine receptors accumulate around a scaffold composed of the protein Gephyrin, which is recruited to sites apposed to GABA or glycine releasing terminals through interaction with Neuroligin 2 (NL2), a member of the Neuroligin family of synaptic adhesion molecules that function as powerful synapse organizers. Another Gephyrin-binding molecule, Collybistin, regulates this recruitment process, functioning as a switch that is activated at sites of NL2 accumulation, leading to tethering of Gephyrin scaffold to the postsynaptic membrane and allowing the subsequent clustering of receptors at sites of transmitter release. Despite the well-documented studies about the critical role of Collybistin in the development of synaptic inhibition, the mechanism of Collybistin function has not yet been clearly identified. In the present study, a structure-function analysis on Collybistin, which was followed by protein-lipid interaction assays, led to the identification of two crucial molecular mechanisms: a conformational switch in Collybistin induced by NL2 binding and subsequent membrane tethering of Gephyrin-Collybistin complex via protein-lipid interactions. These data allow formulation of a coherent molecular model of the assembly of inhibitory synapses and covers a gap in our understanding of the development of synaptic inhibition in the mammalian CNS.
Modelling the growth of Northern Cod

We develop a body size growth model of Northern cod (Gadus morhua) in Northwest Atlantic Fisheries Organization (NAFO) Divisions 2J3KL during 2009-2013. We use individual length-at-age data from the bottom trawl survey in these divisions during 2009–2013. We use the Von Bertalanffy (VonB) model extended to account for between-individual variations in growth, and variations that may be caused by the methods which fish are caught and sampled for length and age measurements. We assume between-individual variation in growth appears because individuals grow at a different rate (k), and they achieve different maximum sizes (l∞). We also included measurement error in length and age in our model since ignoring these errors can lead to biased estimates of the growth parameters. We use the structural errors-invariables (SEV) approach to estimate individual variation in growth, ageing error variation, and the true age distribution of the fish. Our results shows the existence of individual variation in growth and ME in age. According to the negative log likelihood ratio (NLLR) test, the best model indicated: 1) different growth patterns across divisions and years. 2) Between individual variation in growth is the same for the same division across years. 3) The ME in age and true age distribution are different for each year and division.
MOVEMENTS OF RADIOSODIUM (Na$sup 24$) WITHIN AN ICE-COVERED LAKE

Sodium-24 was transported horizontally a maximum distance of 15 to 20 m during the first 24 hr of replicated experiments conducted during January of 1960 and 1961 in a small ice-covered lake in northwestern Wisconsin. Subsequent horizontal displacement was somewhat slower but reached a maximum distance of almost 30 m from the release point in 3 days. The dispersal pattern was asymmetrical and different in each of the two experiments. Results indicated that some vertical movement occurred during the experimental periods but was of very low velocity. A crushing device was described for releasing the radioactive solution in deep water. In addition a portable scintillation counting system was developed for measuring radioactivity within the lake. (auth)
Within-individual physiology constrains carnivorous investment in the rainbow plant Byblis guehoi more than does environmental light intensity

Abstract The cost–benefit model of plant carnivory posits that benefits of carnivory exceed its costs only in environments where light and moisture levels are high, while soil nutrient levels are low. Carnivorous investment is a plastic trait that can be regulated by individual plants. The literature provides strong support for nutrient-dependent plasticity in carnivorous investment, but is less conclusive regarding light-dependent responses, while nothing is known of the effect of within-individual physiological constraints on carnivorous investments in carnivorous plants. We examined the relative importance of light availability and within-individual factors on the carnivorous investment of Byblis guehoi Lowrie & Conran, a recently described flypaper-type carnivorous plant from Western Australia. Twelve pots of B. guehoi plants were cultivated under four different fluorescent light setups with 12-h, light–dark cycles under controlled laboratory conditions. Mucilage production after six weeks was quantified and modelled against light intensity and other within-individual factors. Total leaves borne per stem had a strong, hump-shaped relationship with mucilage production. Other within-individual factors were weak predictors as well, but light intensity was not a good predictor. Our results suggest that, contrary to the expectation of the cost–benefit model of plant carnivory, individual plant investment in carnivory may be more dependent upon within-individual physiological constraints than environmental light availability, although the latter is likely to affect carnivorous investment in more indirect ways through individual plants’ physiological conditions. These results thus do not contradict the cost–benefit model, but identify an important caveat to it, which may have been overlooked previously.
Role of plant growth promoting microbial consortium as bioprotectant for controlling Fusarium wilt in chickpea (Cicer arietinum L.)

The present investigation was undertaken to develop a plant growth promoting microbial bioinoculant as biofertilizer and bioprotectant to reduce the Fusarium wilt in chickpea (Cicer arietinum L.) for improving crop productivity in sustainable manner. Mesorhizobium (15) and endophytic bacterial (5) isolates were assessed for antagonism against wilt causing Fusarium oxysporum sp. ciceris. Mesorhizobium (6) and endophytic bacterial (5) isolates were selected as potential antagonists on the basis of fungal growth inhibition ranged from 50-93.7%. Compatible consortium of Mesorhizobium sp. and endophytic bacteria was developed by plate assay and broth studies, further screened for multifarious PGP traits viz. IAA, Phosphatesolubilization, siderophore, ACC-deaminase and seed germination in single and dual treatments. Maximum IAA (50.13μg/ml) and siderophore production (4.0cm) was recorded with LGR33+RB-1. Highest P-solubilization (13.93mg/100ml) and ACCdeaminase (OD600nm 1.492) was observed with LGR2+NE8. Mesorhizobium (LGR33 and LGR2) and all endophytic isolates were able to grow on recommended dose of captan in disc plate method. Synergistic effect of Mesorhizobium sp. and endophytic bacteria was evaluated for biocontrol, growth, symbiotic parameters and grain yield in chickpea (desi PBG-7 and PBG-1) under wilt sick field. Significant improvement in growth and symbiotic parameters was observed with LGR2+NE8 (69NN/plant, 104.24mg nodule dry weight, leghaemoglobin content of 5.13μg/g nodules) as compared to control. An enhanced antioxidant enzymes viz. catalase (15.04U/min/g FW), peroxidase (2.404U/min/g FW) and total phenols (109.54 tannic acid equivalents/g FW) were observed with the appearance of disease in chickpea roots. On pooled mean basis dual inoculant LGR2+LCNE8 improved the grain yield by 6.5% over control. It thus appears that the consortium of Mesorhizobium sp. and endophytic bacteria can be explored as potential bioinoculant for control of wilt incidence in chickpea.
In vitro drought effects on morphological and physiological indices of two fig (Ficus carica L.) cultivars

In vitro responses of two fig cultivars, ‘Sabz’ and ‘Siah’, were evaluated in MS media containing four levels of polyethylene glycol (PEG) (0, 2, 4, 6%) as a simulation of water stress. The results showed that in Sabz cultivar, shoot length, shoot fresh and dry weights were 43, 36 and 25%, respectively, lower than control in drought treatments caused by 4% PEG, while the leaf area and specific leaf area were not significantly (P>0.05) affected. In Siah cultivar, shoot length, fresh and dry weights were 57, 58 and 40%, respectively, lower in stressed media in comparison to control. In contrast to Sabz cultivar, leaf area and specific leaf area of Siah cultivar were significantly reduced by addition of 6% PEG (56 and 21.5%, respectively). Naturally, the amount of proline in ‘Sabz’ was higher than in ‘Siah’ (81.8 µmole g-1 versus 16.7 µmole g-1). However, in both cultivars, with the addition of PEG in culture media, leaf proline content was increased, in comparison to control. With increasing PEG% in culture media, the amount of leaf soluble sugars content increased and the amount of starch decreased. The results show that ‘Siah’ is more sensitive to drought than ‘Sabz’ and that in vitro culture can be used to evaluate drought tolerance of cultivars.
Effects of wilting and lactic acid bacteria inoculation on fermentation and microbial community of elephant grass silage produced in Vietnam

Direct-cut (dry matter [DM] 165 g kg (cid:1) 1 ) and wilted (DM 250 g kg (cid:1) 1 ) elephant grass silages were prepared in Hue, Vietnam, with and without a mixture of Lactobacillus paracasei and Lactococcus lactis (LP + LC) or Lactobacillus buchneri (LB). The silages were stored for 4 months, and fermentation products and aerobic stability were determined. The microbial community was assessed using denaturing gradient gel electrophoresis and quantitative polymerase chain reaction. Acetate was predominantly produced during the fermentation of control and LB-inoculated silages, whereas the content was not sufﬁcient to inhibit aerobic spoilage for 7 days in control silage. The LP + LC inoculation greatly enhanced lactate content, suppressed the alcohol content, and did not improve aerobic stability or decrease the total fungal population. The bacterial community and L. buchneri populations were similar between control and LB-inocu-lated silages; however, Kluyveromyces delphensis was undetectable and the total fungal population was lowered in LB-inoculated
Spatial and temporal PCP protein dynamics coordinate cell intercalation during neural tube closure

Planar cell polarity (PCP) controls the convergent extension cell movements that drive axis elongation in all vertebrates. Though asymmetric localization of core PCP proteins is central to their function, we currently understand little about PCP protein localization as it relates to the subcellular behaviors that drive convergent extension. Here, we have used high magnification time-lapse imaging to simultaneously monitor cell intercalation behaviors and the localization of the PCP proteins Prickle2 and Vangl2. We observed the expected asymmetric enrichment of PCP proteins, but more interestingly, we also observed tight temporal and spatial correlation of PCP protein enrichment with contractile behavior in cell-cell junctions. These patterns of localization were associated with similar pattern of protein turnover at junctions as assessed by FRAP. In fact, dynamic enrichment of PCP proteins was linked more strongly to junction behavior than to spatial orientation. Finally, recruitment of Prickle2 and Vangl2 to cell-cell junctions was temporally and spatially coordinated with planar polarized oscillations of actomyosin enrichment, and all of these dynamic relationships were disrupted when PCP signaling was manipulated. Together, these results provide a dynamic and quantitative view of PCP protein localization during convergent extension and suggest a complex and intimate link between the dynamic localization of core PCP proteins, actomyosin assembly, and polarized junction shrinking during cell intercalation of the closing vertebrate neural tube.
Correlations and path analysis between fruit characteristics and seeds of Pachira aquatica Aubl.

Pachira aquatica Aubl. is an important fruit-ornamental tree of Sinu valley at risk of genetic erosion. The objective was to estimate correlations between fruit characteristics, seeds, and path analyses for fresh fruit weight, for the purpose of genetic improvement. The treatments corresponded to 10 trees; 10 random fruits of each tree were taken. Analysis of variance were performed for fixed effects models, correlations and path analysis among the variables: fresh fruit weight, fruit length, fruit peel weight, number of seed per fruit, weight of seed per fruit and weight and volume and density of a seed. Statistical differences between trees were presented for all the characteristics, except for volume of one seed. Genetic correlations were greater in magnitude (32.8%) and statistical significance than phenotypic ones (29.7%). Seed weight showed high genetic correlation with seven characteristics (rG>0.53). The fresh fruit weight showed significant and direct genetic correlations with five variables, with correlation coefficients between 0.65* and 1.00**. The indirect effects explained the level of association between fruit length, seed/fruit weight, and percentage of seed/fruit with fresh fruit weight. The weight of peel/fruit exhibited greater direct and indirect effects on the fresh fruit weight in the two path analysis. It is possible to increase the weight of seed/fruit, weight and volume of a seed indirectly through the selection of trees with higher fresh fruit weight and/or peel/fruit weight, to improve yield and physiological quality of the seed.
Artemisinin and Total Flavonoid Content in In Vitro Cultivted Artemisia Annua L. "Hairy" Root Culture

In this paper artemisinin and total flavonoid content in in vitro cultivated non-transformed Artemisia annua L. plants and “hairy” root culture were compared. The amount of total flavonoids was determined using modified Aluminium chloride colorimetric method. Determination of artemisinin in Artemisia annua extracts was carried out using HPLC analysis. Transgenic roots of Artemisia annua accumulated flavonoids in more degree than the roots (1.8 times higher) and leaves (1.6 times higher) of in vitro cultivated control plants. At the same time the control roots synthesized artemisinin four times more (up to 6.5 mg/g dry weight) than “hairy” roots. Owing to the higher growth rate (almost 40 times higher in 3 weeks of cultivation) transgenic roots may be suitable for artemisinin production. The data obtained suggest the possibility of using of Artemisia annua “hairy” root culture as a potential source of flavonoids and artemisinin.
GWAS for genotype by lactation stage interaction in dairy cattle.

Most Genome Wide Association Studies (GWAS) identified quantitative traits locus (QTLs) based on their average effect over the lactation. However, it is known that additive genetic variance changes during lactation and genetic correlations among milk production traits during different lactation stages deviates from unity. We conducted a GWAS specifically for SNPs whose effects on milk protein content change during lactation, i.e. those that show significant SNP by lactation stage interaction. Significance thresholds for SNP by lactation stage interaction cannot be based on standard distributions but requires permutation of the data. We detected regions on BTA 10 and 14 with significant SNP effects as well as significant SNP by lactation stage effects. Regions on BTA 3 and 27 only showed significant SNP by lactation stage effects. Regions on BTA 6, 15, 16, 20 and 26 only showed significant effects in a traditional GWAS. These results show that a GWAS accounting for a SNP by lactation stage interaction effect can help elucidate the genetic background of milk protein content. Keywords: GWAS, genotype by lactation stage interaction, permutation, milk protein content.
Canine and Feline Differences in the Cytochrome P450 Transcriptome and Drug Metabolism

ii Acknowledgments. v List of Tables . ix List of Figures . x List of Equations . xi Supplemental Data . xii List of Abbreviations . xiii Chapter 1: Literature Review . 1 Cytochrome P450 Overview . 1 Cytochrome P450 Structure . 2 Cytochrome genomics . 4 Identification of CYP . 5 Phenotyping CYP Function . 7 Current Knowledge of Canine and Feline Metabolizing Cytochromes . 10 Aim . 18 Chapter 2: Use of RNA-seq to determine variation in canine cytochrome P450 mRNA expression between blood, liver, lung, kidney and duodenum in healthy beagles. 25 Abstract . 25. 25 Introduction . 25 Methods: . 27
A local risk map using field observations of the Asian longhorned beetle to optimize monitoring activities

The Asian longhorned beetle Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae) is one of the most dangerous xylophagous pests affecting broadleaf trees in the world. Eradication programmes are undertaken in non‐native regions, requiring extensive resources and involving high costs. An adapted strategy must be set up to optimize the ratio cost/probability of success. We developed a method to generate a risk index of A. glabripennis presence at a local scale, in the surrounding area of an infestation, using field observations (counts of adult insects, exit holes and infested trees). The method, mathematically based on the bivariate symmetric Laplace distribution, has thus reasonable input requirements. The output risk map is easy to interpret and can be directly used by decision‐makers. We used our approach in three infestations in Switzerland. The risk map represented well the insect pressure (beetle population density). We highlighted the fact that survey boundaries, commonly chosen using constant distances from the infestation, should be selected regarding the spatial distribution of the insect pressure, to prioritize monitoring activities. The risk map provides a helpful instrument for advanced survey planning after a first overview, for example to decide which area and which host trees should be inspected for infestations.
Epidemiology of White spot syndrome virus in the daggerblade grass shrimp (Palaemonetes pugio) and the Gulf sand-fiddler crab (Uca panacea)

ii ACKNOWLEDGMENTS . iv LIST OF TABLES . x LIST OF ILLUSTRATIONS . xii CHAPTER I – INTRODUCTION . 1 General Background . 1 Research Objectives . 4 Dissertation Organization . 4 White Spot Syndrome Virus Review . 5 Infectious Disease Modeling. 10 CHAPTER II PREVALENCE OF WHITE SPOT SYNDROME VIRUS IN THE DAGGERBLADE GRASS SHRIMP (PALAEMONETES PUGIO) AND THE GULF SAND FIDDLER CRAB (UCA PANACEA) . 14 Introduction . 14 Materials and Methods . 16 Sample Collection . 16 Genomic DNA Extraction. 17 Standard Curve. 17 Detection and Quantification of WSSV using TaqMan Real-Time PCR . 18
Seed Dispersal Limitation in a Neotropical Nutmeg, Virola flexuosa (Myristicaceae): an Ecological and Genetic Approach

A seed disperser’s effectiveness, measured as its contribution to plant fitness, has both qualitative and quantitative components. Quantitatively-restricted seed dispersal occurs when the quantity of seeds dispersed is limited by disperser abundances or behavior. To understand how different avian frugivores impact dispersal, we studied the assemblage of frugivores that feed on Virola flexuosa (Myristicaceae) over a two-year period at two sites differing in hunting pressure in Amazonia Ecuador. Here, we focus on the effectiveness of toucans (Ramphastidae) as dispersers and test the hypothesis that removal of V. flexuosa seeds, influenced by differential visits of large-bodied frugivores, will differ between hunted and non-hunted sites. All visiting frugivores were identified and fruit handling behavior, fruit removal rates and time spent foraging were quantified. Seventeen bird and three primate species were recorded foraging in V. flexuosa trees. Toucans and primates were the most important avian dispersers comprising nearly 85% of visits with six toucan species recorded in 74% of visits. For all visiting frugivores, mean visit length was 7.1 ± 9.1 minutes and mean number of seeds consumed per visit Holbrook, Kimberly M. , 2006, UMSL, p. 76 was 2.4 ± 3.1. Ramphastos toucans and Pteroglossus pluricinctus were responsible for 38.2% and 11.9% of all seeds removed, respectively. A proportionately larger number of seeds were removed from fruiting trees at the non-hunted site (TBS, 89.4%) than at the hunted site (YRS, 66.8%). In addition, there were more frugivore visits at TBS than YRS. We found that species more likely to swallow seeds, and, thus more likely to disperse seeds away from parent trees made significantly more visits to trees at TBS than did species that drop seeds. Moreover, species more likely to be hunted had higher visitation rates at TBS than YRS. Examining the dispersers of the Neotropical tree V. flexuosa, we found differences in the frugivore assemblage and the overall number of seeds dispersed from individual trees between two structurally similar forest sites. We suggest a quantitative effect on dispersal of seeds at the Yasuní Research Station, potentially resulting from a reduction in seed dispersers.
Single-cell transcriptomic profiling of progenitors of the oligodendrocyte lineage reveals transcriptional convergence during development

Pdgfra+ oligodendrocyte precursor cells (OPCs) arise in distinct specification waves during embryogenesis in the central nervous system (CNS). It is unclear whether there is a correlation between these waves and different transcriptional oligodendrocyte (OL) states at adult stages. Here we present a bulk and single-cell transcriptomics resource providing insights on how transitions between these states occur. We show that E13.5 Pdgfra+ populations are not OPCs, exhibiting instead hallmarks of neural progenitors. A subset of these progenitors, which we refer as pre-OPCs, rewires their transcriptional landscape, converging into indistinguishable OPC states at E17.5 and post-natal stages. P7 brain and spinal cord OPCs present similar transcriptional profiles at the single-cell level, indicating that OPC states are not region-specific. Postnatal OPC progeny of E13.5 Pdgfra+ have electrophysiological and transcriptional profiles similar to OPCs derived from subsequent specification waves. In addition, lineage tracing indicates that a subset of E13.5 Pdgfra+ cells also originate cells of the pericyte lineage. In summary, our results indicate that embryonic Pdgfra+ cells are diverse and give rise at post-natal stages to distinct cell lineages, including OPCs with convergent transcriptional profiles in different CNS regions.