Miracle-dz/UniFAR-FTUs huggingface dataset:
Chloride-dependent conformational changes in the GlyT1 glycine transporter

Significance The NSS (neurotransmitter sodium symporter) or SLC6 family comprises a group of plasma membrane transport proteins that includes transporters for amino acid and amine neurotransmitters. Transporters in this family use transmembrane ion gradients as driving forces for intracellular accumulation of their substrates. Although all NSS transporters use Na+ ions for transport, a large subset also requires Cl− ions. Na+ is known to act at two sites on these proteins to stabilize an outward-open conformation and to interact with substrate to facilitate transition to an inward-open conformation, but the role of Cl− has not previously been established. We show here how Cl− acts independently from substrate to facilitate the conversion of an NSS transporter for glycine from outward- to inward-open states. The human GlyT1 glycine transporter requires chloride for its function. However, the mechanism by which Cl− exerts its influence is unknown. To examine the role that Cl− plays in the transport cycle, we measured the effect of Cl− on both glycine binding and conformational changes. The ability of glycine to displace the high-affinity radioligand [3H]CHIBA-3007 required Na+ and was potentiated over 1,000-fold by Cl−. We generated GlyT1b mutants containing reactive cysteine residues in either the extracellular or cytoplasmic permeation pathways and measured changes in the reactivity of those cysteine residues as indicators of conformational changes in response to ions and substrate. Na+ increased accessibility in the extracellular pathway and decreased it in the cytoplasmic pathway, consistent with stabilizing an outward-open conformation as observed in other members of this transporter family. In the presence of Na+, both glycine and Cl− independently shifted the conformation of GlyT1b toward an outward-closed conformation. Together, Na+, glycine, and Cl− stabilized an inward-open conformation of GlyT1b. We then examined whether Cl− acts by interacting with a conserved glutamine to allow formation of an ion pair that stabilizes the closed state of the extracellular pathway. Molecular dynamics simulations of a GlyT1 homolog indicated that this ion pair is formed more frequently as that pathway closes. Mutation of the glutamine blocked the effect of Cl−, and substituting it with glutamate or lysine resulted in outward- or inward-facing transporter conformations, respectively. These results provide an unexpected insight into the role of Cl− in this family of transporters.
Protein interaction probability landscapes for yeast replicative aging

We proposed a novel probability landscape approach to map the systems-level profile changes of gene networks during replicative aging in Saccharomyces cerevisiae. This approach enabled us to apply quasi-potentials, the negative logarithm of the probabilities, to calibrate the elevation of the landscapes with young cells as a reference state. Our approach detected opposite landscape changes based on protein abundances from transcript levels, especially for intra-essential gene interactions. We showed that essential proteins play different roles from hub proteins on the age-dependent landscapes. We verified that hub proteins tend to avoid other hub proteins, but essential proteins are attractive to other essential proteins. Overall, we showed that the probability landscape is promising for inferring network profile change during aging and that the essential hub proteins may play an important role in the uncoupling between protein and transcript levels during replicative aging.
Molecular tracking devices quantify antigen distribution and archiving in the lymph node

Live, attenuated vaccines generate humoral and cellular immune memory, increasing the duration of protective immune memory. We previously found that antigens derived from vaccination or viral infection persist within lymphatic endothelial cells (LECs) beyond the clearance of the infection, a process we termed “antigen archiving”. Technical limitations of fluorescent labeling have precluded a complete picture of antigen archiving across cell types in the lymph node. We developed a “molecular tracking device” to follow the distribution, acquisition, and retention of antigen in the lymph node. We immunized mice with an antigen conjugated to a nuclease-resistant DNA tag and used single-cell mRNA sequencing to quantify its abundance in lymph node hematopoietic and non-hematopoietic cell types. At early and late time points after vaccination we found antigen acquisition by dendritic cell populations (DCs), associated expression of genes involved in DC activation and antigen processing, and antigen acquisition and archiving by LECs as well as unexpected stromal cell types. Variable antigen levels in LECs enabled the identification of caveolar endocytosis as a mechanism of antigen acquisition or retention. Molecular tracking devices enable new approaches to study dynamic tissue dissemination of antigens and identify new mechanisms of antigen acquisition and retention at cellular resolution in vivo.
Naphthalene monoimide derivative ameliorates amyloid burden and cognitive decline in a transgenic mouse model of Alzheimer’s disease

Alzheimer’s disease (AD) is a major neurodegenerative disorder and the leading cause of dementia worldwide. Predominantly, misfolding and aggregation of amyloid-β (Aβ) peptides associated with multifaceted toxicity is the neuropathological hallmark of AD pathogenesis and thus, primary therapeutic target to ameliorate neuronal toxicity and cognitive deficits. Herein, we report the design, synthesis and evaluation of small molecule inhibitors with naphthalene monoimide scaffold to ameliorate in vitro and in vivo amyloid induced neurotoxicity. The detailed studies established TGR63 as the lead candidate to rescue neuronal cells from amyloid toxicity. The in silico studies showed disruption of salt bridges and intermolecular hydrogen bonding interactions within Aβ42 fibrils by the interaction of TGR63, causing destabilization of Aβ42 assembly. Remarkably, TGR63 treatment showed a significant reduction in cortical and hippocampal amyloid burden in the progressive stages of APP/PS1 AD mice brain. Various behavioral tests demonstrated rescued cognitive deficits. The excellent biocompatibility, BBB permeability and therapeutic efficacy to reduce amyloid burden make TGR63 a promising candidate for the treatment of AD.
Mechanism of negative membrane curvature generation by the IRSP53 I-BAR domain

The membrane sculpting ability of BAR domains has been attributed to the intrinsic curvature of their banana-shaped dimeric structure. However, there is often a mismatch between this intrinsic curvature and the diameter of the membrane tubules generated. For example, I-BAR domains are almost flat but generate much higher membrane curvature. Furthermore, F-BAR and I-BAR domains are quite similar, but the former generates positive curvature and the latter negative curvature. Here, we use implicit-solvent computer modeling to show that the membrane bending of the IRSP53 I-BAR domain is dictated by its oligomeric structure, whose curvature is completely unrelated to the intrinsic curvature of the dimer. We find that I-BAR dimers undergo lateral and end-to-end interactions to form higher oligomers. The lateral interactions, which can occur with varying register, are stronger and give a curved shape that has the membrane binding interface on its convex surface. Two other I-BARs (MIM and I-BARa) gave similar results, whereas a flat F-BAR sheet curved to make its membrane binding interface concave, consistent with positive membrane curvature generation. Individual dimers orient parallel to the tube axis when the tube radius is small, whereas perpendicular orientation is preferred for larger diameter tubes. This orientational preference exists even in the higher oligomeric form. Helical spirals on tube interiors are stable at a density comparable to experimental measurements. The sorting ratio computed from our membrane binding energies is also consistent with experimental measurements. Significance Statement Changes in membrane shape are required in numerous biological processes, such as endocytosis/exocytosis, viral budding, filopodia formation, etc. The BAR domains are one protein family that mediates these changes, but their mechanism of action is not entirely clear. The BAR domains possess an intrinsic curvature but this curvature often does not match the curvature of the membranes generated.This is especially true of the I-BAR domains which are known to generate negative curvature. Here, we show that a well-studied I-BAR domain forms oligomers that possess a curvature unrelated to the intrinsic curvature of individual dimers and matches the membrane curvatures generated. This resolves a long-standing mystery about the mechanism of negative membrane curvature generation.
Design of in silico Trifunctional Antibody (hIgG1-FC: mouse-antiHER2?human-B7.1) Gene Cassettes and Expression Vectors: The Stage Prior toProduction

The specific gene cassettes and expression vectors for tri-functional antibody (hIgG1-FC: mouse-antiHER2× human-B7.1) were designed in silico. The in silico tri-functional antibody has been derived from human IgG1, human B7.1, and mouse antiHER2 antibody. The variable domains of IgG1 framework were substituted by Cha21 (mouseantiHER2 scFV) VH-VL, and B7.1 IgV-like domains. The domain data of human IgG1 heavy and light chain-constant regions, human B7.1 IgV-like, and cha21 variable regions were obtained from UniprtoKB and PDB databases. The 3D structure of domains was trimmed and modeled by pyMol software. To ensure the presence of antigen binding residues, complementarity determining regions, and framework regions in variable domain structure, the researchers analyzed the cha21-VH and VL nucleotide sequences using Paratome and IMGT softwares, respectively. In this study, two in silico expression vectors were designed. The vector forms were ready in silico to be synthesized and transfected into CHO cells in order to be developed; the cells expressing the chimeric tri-functional antibody which enables the eradication of HER2-expressing cancer cells using apoptotic induction, T-cell activation and accessory cell activation by antiHER2, B7.1, and Fc domains, respectively.
Global population genomic analysis of Mycoplasma bovis isolates reveals transcontinental variations and potential virulence genes

Among more than twenty species belonging to the class Mollecutes, Mycoplasma bovis is the most common cause of bovine mycoplasmosis in North America and Europe. Bovine mycoplasmosis causes significant economic loss in the cattle industry. The number of M. bovis positive herds has recently increased in North America and Europe. Since antibiotic treatment is ineffective and no efficient vaccine is available, M. bovis-induced mycoplasmosis is primarily controlled by herd management measures such as the restriction of moving infected animals out of the herds and culling of infected animals or shedders. To better understand the population structure and genomic factors that may contribute to its transmission, we sequenced 147 M. bovis strains isolated from four different countries and hosts, primarily cattle. We performed a large-scale comparative analysis of M. bovis genomes by integrating 104 publicly available genomes and our dataset (251 total genomes). A whole genome-single nucleotide polymorphism (SNP)-based phylogeny revealed that M. bovis population structure is composed of five clades with one of the isolates clustering with the outgroup M. agalactiae. These isolates were found to cluster with those from Canada, Israel, Lithuania, and Switzerland, suggesting trans-continental transmission of the strains. We also validated a previous report suggesting minimum divergence in isolates of Australian origin, which grouped within a single clade along with strains from China and Israel. However, no observable pattern of host association in M. bovis genomes was found in this study. Our comparative genome analysis also revealed that M. bovis has an open pangenome with a large breadth of unexplored diversity of genes. Analysis of vsp gene-host association revealed a single vsp significantly associated with bovine isolates that may be targeted for diagnostics or vaccine development. Our study also found that M. bovis genome harbors a large number of IS elements, including a novel 1624 bp IS element, and ISMbov9. Collectively, the genome data and the whole genome-based population analysis in this study may help to develop control measures to reduce the incidence of M. bovis-induced mycoplasmosis in cattle and/or to identify candidate genes for vaccine development.
Effects of Fall Hunting on Wild Turkey Populations in Virginia and West Virginia

The effect of fall either-sex hunting on eastern wild turkey (Meleagris gallopavo silvestris) populations is a common concern of wildlife agencies. We examined the effect of fall either-sex hunting on survival of radiotagged female wild turkeys from 1989 to 1994 in Virginia and West Virginia. We tested the hypothesis that survival of female wild turkeys did not differ among areas closed to fall hunting, open to a 4-week fall season, or open to an. 8- or 9-week fall hunting season. Mean annual survival rates were higher in the area closed to fall hunting than in regions where fall hunting occurred (P = 0.05). Mean annual survival rates varied within years (P ≤ 0.05). Differences in annual survival rate among areas were attributed to legal hunting (P ≤ 0.01). Poaching was a major mortality factor. Juvenile, yearling, and adult hens had similar survival rates in the areas closed to fall hunting and with 4 weeks of fall hunting (P = 0.39), but survival rates of juveniles were lower (P = 0.03) than those of yearling and adult females in the area with an 8-9-week fall hunting season. Harvest rates of female turkeys averaged 4.3% in the 4-week fall hunted area and 12.3% on the 8-9-week fall hunted area. Higher harvests were achieved on the study area opened only to spring hunting than the combined fall-spring harvests on the other study areas. Total harvest was negatively associated with survival (r s =- 0.90, P = 0.04) on the 8-9-week fall hunted area and positively associated with survival (r s = 0.90, P = 0.04) in the area closed to fall hunting. Spring gobbler-only hunting is suggested for maximum growth in a wild turkey population. Guidelines are presented for fall harvest programs.
Collaboration of multiple pathways in making a compound leaf

The variability in leaf form in nature is immense. Leaf patterning occurs by differential growth that occurs during a limited window of morphogenetic activity at the leaf marginal meristem. While many regulators have been implicated in the designation of the morphogenetic window and in leaf patterning, how these effectors interact to generate a particular form is still not well understood. We addressed the interaction among different effectors of tomato compound leaf development, using genetic and molecular analyses. Mutations in the tomato auxin response factor SlARF5/SlMP, which promotes leaflet formation, suppressed the increased leaf complexity of mutants with extended morphogenetic window. Impaired activity of the NAC/CUC transcription factor GOBLET (GOB), which specifies leaflet boundaries, also reduced leaf complexity in these backgrounds. Analysis of genetic interactions showed that the patterning factors SlMP, GOB and the MYB transcription factor LYRATE (LYR) act in parallel to promote leaflet formation. This work places an array of developmental regulators in a morphogenetic context. It reveals how organ-level differentiation rate and local growth are coordinated to sculpture an organ. These concepts and findings are applicable to other plant species and developmental processes that are regulated by patterning and differentiation.
Arabidopsis myosin XIK interacts with the exocyst complex to facilitate vesicle tethering during exocytosis

Myosin motors are essential players in secretory vesicle trafficking and exocytosis in yeast and mammalian cells; however, similar roles in plants remain a matter for debate, at least for diffusely-growing cells. Here, we demonstrate that Arabidopsis (Arabidopsis thaliana) myosin XIK, via its globular tail domain (GTD), participates in the vesicle tethering step of exocytosis through direct interactions with the exocyst complex. Specifically, myosin XIK GTD bound directly to the SEC5B subunit of exocyst in vitro and functional fluorescently-tagged XIK colocalized with multiple exocyst subunits at plasma membrane (PM)-associated stationary foci. Moreover, genetic and pharmacological inhibition of myosin XI activity reduced the frequency and lifetime of stationary exocyst complexes at the PM. By tracking single exocytosis events of cellulose synthase (CESA) complexes (CSCs) with high spatiotemporal resolution imaging and pair-wise colocalization analysis of myosin XIK, exocyst subunits and CESA6, we demonstrated that XIK associates with secretory vesicles earlier than exocyst and is required for the recruitment of exocyst to the PM tethering site. This study reveals an important functional role for myosin XI in secretion and provides new insights about the dynamic regulation of exocytosis in plants.
Mass Spectrometry Imaging of N-Glycans Reveals Racial Discrepancies in Low Grade Prostate Tumors

Prostate cancer is the most common cancer in men worldwide. Despite its prevalence, there is a critical knowledge gap regarding the underlining molecular events that result in higher incidence and mortality rate in Black men. Identifying molecular features that separate racial disparities is a critical step in prostate cancer research that could lead to predictive biomarkers and personalized therapy. N-linked glycosylation is a co-translational event during protein folding that modulates a myriad of cellular processes. Recently, aberrant N-linked glycosylation has been reported in prostate cancers. However, the full clinical implications of dysregulated glycosylation in prostate cancer has yet to be explored. Herein, we performed high-throughput matrix-assisted laser desorption ionization mass spectrometry analysis to characterize the N-glycan profile from tissue microarrays of over 100 patient tumors with over 10 years of follow up data. We identified several species of N-glycans that were profoundly different between low grade prostate tumors resected from White and Black patients. Further, these glycans predict opposing overall survival between White and Black patients with prostate cancer. These data suggest differential N-linked glycosylation underline the racial disparity of prostate cancer prognosis. Our study highlights the potential applications of MALDI-MSI for digital pathology and biomarker to study racial disparity of prostate cancer patients. Graphical Abstract
In Silico Modeling of Virus Particle Propagation and Infectivity along the Respiratory Tract: A Case Study for SARS-COV-2

Respiratory viruses including Respiratory syncytial virus (RSV), influenza virus and cornaviruses such as Middle Eastern respiratory virus (MERS) and SARS-CoV-2 infect and cause serious and sometimes fatal disease in thousands of people annually. It is critical to understand virus propagation dynamics within the respiratory system because new insights will increase our understanding of virus pathogenesis and enable infection patterns to be more predictable in vivo, which will enhance targeting of vaccines and drug delivery. This study presents a computational model of virus propagation within the respiratory tract network. The model includes the generation network branch structure of the respiratory tract, biophysical and infectivity properties of the virus, as well as air flow models that aid the circulation of the virus particles. The model can also consider the impact of the immune response aim to inhibit virus replication and spread. The model was applied to the SARS-CoV-2 virus by integrating data on its life-cycle, as well as density of Angiotensin Converting Enzyme (ACE2) expressing cells along the respiratory tract network. Using physiological data associated with the respiratory rate and virus load that is inhaled, the model can improve our understanding of the concentration and spatiotemporal dynamics of virus.
Links between mouse and vole social networks and their gut microbiomes support predictions from metacommunity theory

Metacommunity theory predicts that strongly connected individuals will harbour similar gut microbiomes (GMs) and affiliating with more individuals should increase GM diversity. Additionally, cross-species bacterial transmission may play a role in how interspecific interactions affect host community dynamics. We tracked sympatric mice (Peromyscus maniculatus) and voles (Myodes gapperi) and constructed social networks for each species and both species together. We tested whether: 1) similarity in GM composition between individuals correlates with their social proximity within and across species; 2) GM diversity correlates with a host’s number of conspecific or heterospecific neighbours. We could not differentiate associations between GM composition and mouse social proximity or habitat. In voles, social proximity explained part of the GM composition. GM composition associated with interspecific social proximity, and mouse GM diversity correlated with number of vole neighbours. Contributions of host-host bacterial transmission to the GM partly follow metacommunity theory but depend on host species.
Cooperative Multi-Agent Reinforcement Learning for Spectrum Management in IoT Cognitive Networks

The paper investigates the applications of cooperative Multi-Agent Reinforcement Learning (MARL) schemes to Cognitive Radio Networking (CRN), which in turn can facilitate spectrum utilization for wireless (ad hoc) networks within the Internet of Things (IoT). These schemes provide the ability of wireless transceivers to learn the optimal control and configuration in unknown environmental and application conditions, exploiting potential for cooperation among spectrum secondary users. An overview of the existing MARL approaches to the CRN is provided, with an analysis of their advantages and weaknesses compared to the rest of CRN approaches. We argue that in typical CRN practical scenarios including IoT systems, it is of essential importance that the cooperative algorithms are completely decentralized and distributed, having also a capability that the agents/nodes together can successfully calculate the optimal strategy even if the individual agents cannot. Hence, we propose a new scheme for cooperative spectrum sensing and selection within CRN, based on an adaptation of a recently proposed cooperative MARL scheme, provide detailed analysis of its properties and potential performance, indicating its superiority compared to the existing schemes.
A Framework for Intrusion Detection Targeted at Non-Expert Users

The wide spreading of the Internet leads to the born of a whole interconnected world. Among all these devices, smart voice assistants are gaining particular attention thanks to their ease of use, allowing users to comfortably deploy commands for controlling other devices. The simplicity of use of voice assistants allowed non-expert to interact with complex systems, leading to that category of users with limited knowledge, to interact with s without being perfectly aware of the risks they are exposed to. For example, common network monitoring systems are so useful as they are complex to use for non-expert users. This paper presents a framework for intrusion detection speciﬁcally designed to be used by any category of users, using visual interfaces for simplifying the user interaction with the framework, allowing him/her to properly conﬁgure and run an Intrusion Detection System (IDS). The implementation of voice assistants as a communication channel will further improve the overall user experience.