Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidation of the viral disassembly switch of tobacco mosaic virus

Stable capsid structures of viruses protect viral RNA while they also require controlled disassembly for releasing the viral genome in the host cell. A detailed understanding of viral disassembly processes and the involved structural switches is still lacking. Biochemically, this process has been extensively studied using the tobacco mosaic virus model system and carboxylate interactions have been proposed to play a critical part in this process. Here, we present two cryo-EM structures of the helical TMV assembly at 2.1 and 2.0 Å resolution in conditions of high Ca2+ concentration at low pH and in water. Based on our atomic models, we identified the conformational details of the disassembly switch mechanism: in high Ca2+/acidic pH environment the virion is stabilized between neighboring subunits through carboxyl groups E95 and E97 in close proximity to a Ca2+ binding site. Upon increase in pH and lower Ca2+ levels, mutual repulsion of the E95/E97 pair and Ca2+ removal destabilize the network of interactions at lower radius and release the switch of virus disassembly. Our TMV structures revealed the conformational details for one of the reference systems of viral assembly/disassembly and provide the mechanistic explanation of a plethora of experimental results that were acquired over decades. Significance Statement Tobacco mosaic virus presents the text-book example of virus structure and RNA release from a viral capsid through disassembly. Despite the wealth of structural and biochemical data on the assembly/disassembly properties generated from more than 80 years of research, the atomic-resolution structural details of the proposed conformational changes have not been resolved to date. The here determined high-resolution cryo-EM structures reveal the conformational details of the molecular disassembly switch. When the virus enters the cell, carboxylate repulsion and loss of calcium-ion coordination destabilize the switch region and can trigger RNA release through virus disassembly. The two determined structural states resolve a long-standing question on environment-driven virus disassembly switches.
Reduced-representation bisulfite sequencing finds epigenome-wide response to oil pollution in the foundation plant Spartina alterniflora

The application of genomics technology in ecological contexts allows for examination of how rapid environmental change may shape standing molecular level variation and organismal response. We previously demonstrated an effect of oil pollution on gene expression patterns and genetic variation, but not methylation variation, in oil-exposed populations of the foundation salt marsh grass, Spartina alterniflora. Here, we used a reduced representation bisulfite sequencing approach, epigenotyping by sequencing (epiGBS), to examine relationships among DNA sequence, DNA methylation, gene expression, and exposure to oil pollution. With the increased resolution of epiGBS, we document genetic and methylation differentiation between oil-exposed and unexposed populations, and a correlation of genome-wide methylation patterns and gene expression, independent of population genetic structure. Overall, these findings demonstrate that variation in DNA methylation is abundant, responsive, and correlated to gene expression in natural populations, and may represent an important component of the response to environmental stress.
Amino acid efficiency with dietary glycine supplementation: Part 2

Glycine is a multi-tasking amino acid involved in multiple metabolic and functional systems, including sulphur amino acids, proteins and immunoglobulins syntheses, blood haem and bile production. Glycine is also capable of eliciting responses at whole animal level, such as those promoting gut and immune health, animal welfare as well as feed/food safety. Empirical evidence shows that glycine supplementation can arrest systemic inflammation via deletion of cytokine production. Some investigators have corrected gut wall damage in challenge studies via gastric infusion of glycine. Efficacy data further document that glycine aids bone accretion in broilers fed reduced protein diets. Given these glycine bioefficacies, particularly in broilers, its nutrition needs to be critically assessed in the light of modern paradigms of animal welfare, feed-food safety, efficiency, reduced antibiotic application, and eco-sustainability. Such efforts should concentrate on precise estimation of inevitable ileal flow of glycine so as to generate a database on the digestible glycine levels in feedstuffs. Only this can provide for proper control of feed glycine density. Controversies on dietary glycine optimum for broilers also need to be addressed, as this has significant ramifications for raw materials selection and eco-sustainability. Based on a meta-analysis of published reports a range of 1.91-2.27% of total glycine+serine is recommended in young broilers diets, depending on production goals. But clarity is still needed on how this may be modified by practical stress conditions. The efficacy of copious supplementation of crystalline glycine to promote key parameters of poultry health and zootechnical performance under different rearing conditions still needs to be resolved.
Dynamics of Neuronal Interactions in the Visual Cortex of Macaca Mulatta

This work is dedicated to studying the effects of attention which result in measurable changes in the functioning of single neurons and neuronal populations. A special emphasis lies on establishing a suitable method of recording from multiple neuronal populations in the visual cortex of a behaving monkey, as well as on analyzing the acquired signals. A chronically implanted large-area electrode array was used for epidural recording of brain potentials. Additionally, two electrode arrays for large-area chronic intracortical recording were designed, manufactured, and successfully implemented on a macaque monkey. By this means, local field potentials were recorded from different neuronal populations in two visual areas of a macaque monkey, as he performed a shape-tracking task presented in front of him on a screen. Two kinds of stimulus-driven neuronal response in areas V1 and V4 were acquired: with the stimulus being behaviorally relevant and hence lying within the locus of the monkey’s attention, and with the stimulus being ignored and hence lying outside the locus of the monkey’s attention. Comparing the two response types provided a clue to the differences in neuronal processing of attended and non-attended stimuli. According to the working hypothesis, oscillatory responses generated in different neuronal populations by an attended stimulus would be synchronized in the gamma frequency band. To test this hypothesis, the acquired brain potentials were wavelet transformed and oscillatory power of different neuronal populations as well as phase coherence between them was computed. The results revealed a high degree of phase coherence in the gamma frequency band between oscillatory responses of neuronal populations in areas V1 and V4 representing the attended stimulus. A non-attended stimulus, however, produced non-phase-locked oscillatory responses in areas V1 and V4. The results presented here supported the working hypothesis, and the gamma-band synchronization was suggested to provide the mechanism of attention which enhances the processing of behaviorally relevant stimuli.
WEED CONTROL IN WHEAT WITH POST-EMERGENCE HERBICIDES

Mehmeti, A. , Z. Pacanoski, R. Fetahaj, A. Kika and B. Kabashi, 2018. Weed control in wheat with post-emergence herbicides. Bulg. J. Agric. Sci., 24 (1): 74–79 A fi eld study was carried out during the 2011-12 to identify weed species and to investigate the effi cacy of post-emergence herbicides on weeds and their effect on wheat grain yield in the region of Podujeva (north-east part of Kosovo). Four different herbicides were applied at the post-emergence stage of wheat, namely Lintur 70 WG (a.i. triasulfuron + dicamba), Granstar 75 WG (a.i. tribenuron-methyl), Mustang (a.i. fl orasulam + 2,4-D-EHE-ethyl-hepthyl ester) and herbicide combination Sekator OD (a.i. iodosulfuron-methyl Na + amidosulfuron + safener mefenpyr-diethyl) + Furore Super (a.i. fenoxaprop-p-ethyl) in the wheat cultivar Evropa. A total number of 16 weed species was documented in the wheat crop. The highest number of individuals was recorded for Convolvulus arvensis (24.0 plants/m2), Consolida regalis (15.5 plants/m2), Polygonum aviculare (11.5 plants/m2), and Galium aparine (9.8 plants/m2). The most effi cient herbicides proved to be combination iodosulfuron-methyl Na + amidosulfuron + safener mefenpyr-diethyl + fenoxaprop-p-ethyl (83.0%), triasulfuron + dicamba (75.4%), tribenuron methyl (65.6 %), and fl orasulam + 2,4-D-EHE-ethyl-hepthyl ester (64.6%) was markedly lower. Based on the results presented, it is recommended the use of triasulfuron + dicamba or herbicide combination iodosulfuron-methyl Na + amidosulfuron + safener mefenpyr-diethyl + fenoxaprop-p-ethyl in the study region for successful weed control and high wheat grain yields.
Efficacy of Different Coloured Sticky Traps Against Thrips of Chilli

The field experiment was conducted at Spices Research Centre, Shibganj, Bogura, Bangladesh during Rabi season of 2017-18 to study the color preference of Scirtothrips dorsalis in chilli. The treatments were T1= Blue trap @40 trap/ha; T2= Yellow trap @40 trap/ha; T3= White trap @40 trap/ha; T4= Green trap @40 trap/ha and T5= Pink trap @40 trap/ha. Among the color traps used, at 35 days after installation (DAI) of trap blue color attracted highest (8.44 thrips/ sq. inch area of trap) number of S. dorsalis adults followed by white (5.43 thrips/ sq. inch area of trap), yellow (4.30 thrips/ sq. inch area of trap), green (3.52 thrips/ sq. inch area of trap) and pink (3.40 thrips/ sq. inch area of trap) color. Blue coloured sticky trap also attracted comparatively less number of beneficial insects and can be used for relative estimate of S. dorsalis population and also for monitoring and mass trapping as a component of IPM program.
Antidiabetic and Antioxidant Effects of Acteoside from Jacaranda mimosifolia Family Biognoniaceae in Streptozotocin–Nicotinamide Induced Diabetes in Rats

BACKGROUND: Acteoside is a phenylethanoid compound isolated from Jacaranda mimosifolia D. Don leaves with a potential antidiabetic effect. OBJECTIVES: This study was designed to investigate the antidiabetic and antioxidant effects of acteoside in streptozotocin-nicotinamide (STZ-NA)-induced Type 2 diabetes in rats. METHODS: Diabetes was induced by intraperitoneal (i.p.) injection of a single dose of STZ (52.5 mg/kg), 15 min following i.p. administration of NA (25 mg/kg). Rats were divided into six groups; Group I: Normal rat group received the vehicle, Group II: Diabetic control group, and Groups III-IV: Diabetic rat groups were treated by either oral acteoside (10, 20, and 40 mg/kg) or pioglitazone (30 mg/kg) for 21 consecutive days. Biochemical parameters were assessed in the serum and liver homogenates. Examination of liver sections for histopathology was also carried out. RESULTS: Acteoside treated rats showed significant lower levels of blood glucose, glycosylated hemoglobin, total cholesterol, triglycerides, and increased serum insulin compared to control diabetic rats. Furthermore, acteoside treated rats, in comparison to the diabetic control, demonstrated significantly reduced malondialdehyde, increased reduced glutathione liver contents, and attenuated pathological alterations in the liver. These effects were comparable to those caused by the standard antidiabetic drug, pioglitazone. In vitro, acteoside scavenged stable free radical 1,1-diphenyl-2-picrylhydrazyl. CONCLUSION: Acteoside could be considered as a potential therapeutic agent for type 2 diabetes mellitus. However, studying further mechanisms underlying its antidiabetic effect is recommended.
Ballots Instead of Bullets? The Effect of the Voting Rights Act on Political Violence

The extension of voting rights epitomizes the construction of modern democracies. This paper empirically investigates the effect of such an enfranchisement on political violence in the context of the US Voting Rights Act (VRA) of 1965, which forbade discrimination in voting. The formula the VRA used to determine the counties it applied to generated both geographic and temporal local discontinuities in enfranchisement. This paper’s empirical strategy takes advantage of these features by comparing the evolution of political violence in geographically close covered and non-covered counties. Difference-in-differences estimates indicate that VRA coverage halved the incidence and the onset of political violence. Additional empirical evidence implies that voting became the new institutionalized way to state political preferences. Indeed, VRA coverage mostly decreased electoral and small-scale strategic violence. This result is not explained by disaggrievement. Extensions suggest that new strategies of political action may explain a decrease in violence after enfranchisement.
MECHANISTIC ROLE OF VARUNA (CRATAEVA NURVALA) EXTRACT ON THYROID GLAND AND ITS HISTOLOGY THROUGH IODOTHYRONINE DEIODINASES

Objective: Crataeva nurvala (CN) is used for its therapeutic effects, but its effect on the thyroid gland in euthyroid conditions and mechanism behind its thyrotropic activity in hypothyroidism is still not explored. This study screened the pharmacological effect of the ethanolic extract of the bark of CN on thyroid hormones, free and total thyroxine (FT4 and T4), triiodothyronine (T3), thyroid-stimulating hormone (TSH) levels, and thyroid histology in normal Swiss albino female mice.Methods: Eighteen animals of 28–33 g were segregated into three groups: Group I treated with vehicle (NOR+VEH), Group II administered CN 400 mg/kg (NOR+CN 400), and Group III given CN 600 mg/kg (NOR+CN 600), for 15 days, per os (p.o.). The variation in the T4, FT4, T3, and TSH levels was recorded using ELISA, 24 h after the last dose, and T3/T4 ratio thus calculated along with the histopathological studies of the thyroid gland.Results: The findings were presented as mean ± standard error of the mean, using one-way ANOVA, followed by Dunnett’s post-tests to compare all columns with the control. NOR+CN 600 has shown thyroid protective effect through retaining euthyroid profile, normal T3/T4 ratio, and near-normal histology. However, NOR+CN 400 had shown the significant decline in T3/T4 ratio and pathological changes in thyroid histology, in comparison with the control and NOR+VEH group.Conclusion: The higher dose of CN was found to sustain the euthyroid levels through retention of iodothyronine deiodinases activity, facilitating the peripheral conversion of T4 to T3, and in retaining normal histoarchitecture of the thyroid gland in contrary to a lower dose.
Genetic Evaluation For Some Economically Importance Variables In Friesian Cows

A total of 1018 standard lactating of Friesian cows, progeny of 54 sires and 432 dams kept at Sakka Experimental farm, during 2012 to 2017 are used to calculate phenotypic and genetic effects for milk production in tenth months (MP), lactation length (LL) and fat percent (F%). Four selection indexes are calculated using relative economic weights (REW), method 1: standard deviation (REW1) and method 2: Lamont method (REW2). The overall means of MP, LL and Fat % are 3879 kg, 301 d and 3.69%, respectively. Month, year of parturition and lactation order had significant (P<0.01) effects on all studied traits, except month of parturition and lactation order effects (P>0.05) on F%. Bulls and cow within bulls had significant (P<0.01) effects on all traits studied. Heritability estimates are 0.32, 0.10 and 0.55 for MP, LL and Fat %, respectively. Genetic correlations among three variables are significant and ranged from 0.21 to 1.00. The basic index (Index1), which includes the three variables MY, LL and Fat % was the best (had the highest accuracy (RIH) and relative efficiency values (RIH was 0.87 and 0.88 for REW1 and REW2, respectively).
Correlation of occludin protein mobility with paracellular leak pathway permeability in renal epithelia

Studies have demonstrated regulation of the epithelial paracellular permeability barrier, the tight junction, by a variety of stimuli. Recent studies have reported a correlation between changes in paracellular permeability, particularly paracellular permeability to large solutes (leak pathway), and mobility of the tight junction protein, occludin, in the plane of the plasma membrane. This had led to the hypothesis that changes in occludin protein mobility are causative for changes in paracellular permeability. Using a renal epithelial cell model system, MDCK, we examined the effect of various manipulations on both leak pathway permeability, monitored as the paracellular movement of a fluorescent molecule (calcein), and occludin protein mobility, monitored through fluorescence recovery after photobleaching. Our results indicate that knockdown of the associated tight junction protein, ZO-1, increases baseline leak pathway permeability, whereas, knockdown of the related tight junction protein, ZO-2, does not alter baseline leak pathway permeability. Knockdown of either ZO-1 or ZO-2 decreases the rate of movement of occludin protein but only knockdown of ZO-2 protein alters the percent of occludin protein that is mobile. Further, treatment with hydrogen peroxide increases leak pathway permeability in wild type MDCK cells and in ZO-2 knockdown MDCK cells but not in ZO-1 knockdown MDCK cells. This treatment decreases the rate of occludin movement in all three cell lines but only alters the mobile fraction of occludin protein in ZO-1 knockdown MDCK cells. Finally, we examined the effect of renal ischemia/reperfusion injury on occludin protein mobility in vivo. Ischemia/reperfusion injury both increased the rate of occludin mobility and increased the fraction of occludin protein that is mobile. These results indicate that, at least in our cell culture and in vivo model systems, there is no consistent correlation between paracellular leak pathway permeability and occludin protein mobility.
Stability of working memory in continuous attractor networks under the control of short-term plasticity

Continuous attractor models of working-memory store continuous-valued information in continuous state-spaces, but are sensitive to noise processes that degrade memory retention. Short-term synaptic plasticity of recurrent synapses has previously been shown to affect continuous attractor systems: short-term facilitation can stabilize memory retention, while short-term depression possibly increases continuous attractor volatility. However, it currently remains unclear to which degree these two short-term plasticity mechanisms interact, what their combined quantitative effect on working memory stability is, and whether these effects persist in neuronal networks with spike-based transmission. Here, we present a comprehensive description of the effects of short-term plasticity on noise-induced memory degradation in one-dimensional continuous attractor models. Our theoretical description, applicable to spiking and rate-based models alike, accurately describes the slow dynamics of stored memory positions in separate processes of diffusion due to spiking variability and drift due to sparse connectivity and neuronal heterogeneity. We find that facilitation decreases both diffusion and directed drifts, while short-term depression tends to increase both. Using mutual information, we evaluate the combined impact of short-term facilitation and depression on the ability of networks to retain stable working memory. Finally, our theory establishes links to experiments: we are able to predict the sensitivity of continuous working memory to distractor inputs and place constraints on network and synapse properties necessary to implement stable working memory. Author summary The ability to transiently memorize positions in the visual field is crucial for behavior. Models and experiments have shown that such memories can be maintained in networks of cortical neurons with a continuum of possible activity states, that reflects the continuum of positions in the environment. However, the accuracy of positions stored in such networks will degrade over time due to the noisiness of neuronal signaling and imperfections of the biological substrate. Previous work in simplified models has shown that synaptic short-term plasticity could stabilize this degradation by dynamically up- or down-regulating the strength of synaptic connections, thereby ”pinning down” memorized positions. Here, we present a general theory that accurately predicts the extent of this ”pinning down” by short-term plasticity in a broad class of biologically plausible models, thereby untangling the interplay of varying biological sources of noise with short-term plasticity. Importantly, our work provides a direct and novel theoretical link from the microscopic substrate of working memory – neurons and synaptic connections – to observable behavioral correlates. This allows us to constrain properties of cortical networks that are currently hard to assess experimentally, which we hope will help guide future theoretical and experimental work.
The structural evolution of host-pathogen protein interactions: an integrative approach

The evolution of protein-protein interactions (PPIs) is directly influenced by the evolutionary histories of the genes and the species encoding the interacting proteins. When it comes to PPIs of host-pathogen systems, the complexity of their evolution is much higher, as two independent, but biologically associated entities, are involved. In this work, an integrative approach combining phylogenetics, tree reconciliations, ancestral sequence reconstructions, and homology modelling is proposed for studying the evolution of host-pathogen PPIs. As a case study, we analysed the evolution of interactions between herpesviral glycoproteins gD/gG and the cell membrane proteins nectins. By modelling the structures of more than 12,000 ancestral states of these virus-host complexes it was found that in early times of their evolution, these proteins were unable to interact, most probably due to electrostatic incompatibilities between their interfaces. After the event of gene duplication that gave rise to a paralog of gD (known as gG), both protein lineages evolved following distinct functional constraints, with most gD reaching high binding affinities towards nectins, while gG lost such ability, most probably due to a process of neofunctionalization. Based on their favourable interaction energies (negative ΔG), it is possible to hypothesize that apart from nectins 1 and 2, some alphaherpesviruses might also use nectins 3 and 4 as cell receptors. These findings show that the proposed integrative method is suitable for modelling the evolution of host-pathogen protein interactions, and useful for raising new hypotheses that broaden our understanding about the evolutionary history of PPIs, and their molecular functioning.
Mismatch repair impedes meiotic crossover interference

Sequence divergence, mediated by the anti-recombinogenic activity of mismatch repair (MMR), forms a potent barrier to meiotic recombination and in turn the formation of viable gametes1–5. However, exactly how MMR jeopardizes meiotic success is unclear. Here we utilize a combination of S. cerevisiae genetics, genome-wide mapping of recombination and computational modelling to demonstrate that MMR unexpectedly influences the global distribution of recombination through preferential suppression of interfering crossovers (COs) at regions of greater sequence divergence. As a result, inactivation of MMR not only increases the rate of recombination, as previously observed, but also, paradoxically, the strength of CO interference. Our observations reveal a new mechanism by which MMR spatially sculpts the meiotic landscape—linking CO control to the mechanisms that can reproductively isolate a population, and highlighting how genomes may become meiotically incompatible at the molecular level, dependent upon interactions of the primary DNA sequence.