bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Association ofSLC47A1Gene Variant (17:19571562C >T) and Bioinformatics Analyses of MATE1 Protein in Chronic Kidney Disease Patients of Pakistani Origin
Authors: Hussain Mehnaz Ghulam , Saif Rashid , Younus Amna , Zahid Mehmoona , Jabeen Sadia , Younas Hooria 
Published: August 2023

AbstractChronic Kidney Disease (CKD) is a serious human threat worldwide which is associated with a number of environmental, clinical and genetic factors that affect serum creatinine (SCr) and glomerular filtration rate (eGFR). One of the best biochemical and genetic markers to study renal functioning isSLC47A1which encodes MATE1 protein and can be a promising target to study its genetic causes, subject protein is a cationic transporter involved in the regulation of creatinine and urea levels in the blood which may cause toxicity and renal disorders. Hence, the current study focused to interrogate the putative association ofSLC47A1gene variant (17:19571562C>T) in 75 individuals (cases=50, controls=25) of Pakistani origin using ARMS-PCR genotyping, out of which 10 were found heterozygous, 57 homozygous wild-type and 08 homozygous mutants. PLINK data analysis toolset was used which manifested that sampled population complies the Hardy-Weinberg Equilibrium by χ2(2,N= 75) =,p= 4.756 × 10-005, similarly the Chi-square statisticsp= 0.03274 along with odds-ratio of 3.244 showing a significant genotypic association with the subject phenotype indicating that mutant allele is almost 3-times more prevalent in cases vs control cohorts with an alternative allele frequency of 0.22 and 0.08 in CKD patients and healthy controls respectively. Besides, few of the bioinformatics tools i.e., ProtParam, PsiPred, PDB-RCSB, Motif Scan, CTU-TMHMM-2.0, ScanProsite, PRmePRed, GPS PAIL2.0, NetOGlyc4.0, NetPhos3, SIFT, Polyphen-2 and STRING were also used for the prediction of different parameters of both the wild-type and mutant MATE1 proteins such as physiochemical properties, secondary structure prediction, 3-D structure, protein conserved domains, transmembrane structures, posttranslational modifications, SNP prediction/amino acid substitution, pathogenicity and protein-protein interaction networks. Current preliminary genotyping provided an insight into the association of the aforementioned genetic variant with CKD to estimate the genetic risks along with prediction of its functional effects in the system biology context which may be considered for developing new targeted drugs along with genetic counselling initiatives to evade this peril in the population.
PARG inhibition induces nuclear aggregation of PARylated PARP1
Authors: Paradkar Sateja , Purcell Julia , Cui Annie , Friedman Sam , Sundaram Ranjini , Jensen Ryan , Bindra Ranjit 
Published: August 2023

AbstractPARG inhibitors are currently under clinical development for the treatment of DNA repair-deficient cancers, however, their precise mechanism of action is still unclear. Here we report that PARG inhibition causes increased nuclear PARylated PARP1 that limits PARP1 chromatin binding in response to DNA damage. This PARylated PARP1 accumulates as aggregates at sites distinct from the site of DNA damage, leading to the mis-localization of PARP1. Additionally, these aggregates are formed through PAR chains as abrogating PARP1 catalytic activity prevents their formation. Finally, these PARP1 nuclear aggregates persist long-term and are associated with cleaved cytoplasmic PARP1, a cell death hallmark, which ultimately leads to a non-apoptotic form of cell death. Overall, our data uncovers a novel mechanism of PARG inhibitor cytotoxicity, which will inform ongoing clinical studies.
MidRISH: Unbiased harmonization of rotationally invariant harmonics of the diffusion signal
Authors: Newlin Nancy R. , Kim Michael E. , Kanakaraj Praitayini , Yao Tianyuan , Hohman Timothy , Pechman Kimberly R. , Beason-Held Lori L. , Resnick Susan M. , Archer Derek , Jefferson Angela , Landman Bennett A. , Moyer Daniel 
Published: August 2023

AbstractObjectiveData harmonization is necessary for removing confounding effects in multi-site diffusion image analysis. One such harmonization method, LinearRISH, scales rotationally invariant spherical harmonic (RISH) features from one site (“target”) to the second (“reference”) to reduce confounding scanner effects. However, reference and target site designations are not arbitrary and resultant diffusion metrics (fractional anisotropy, mean diffusivity) are biased by this choice. In this work we propose MidRISH: rather than scaling reference RISH features to target RISH features, we project both sites to a mid-space.MethodsWe validate MidRISH with the following experiments: harmonizing scanner differences from 37 matched patients free of cognitive impairment, and harmonizing acquisition and study differences on 117 matched patients free of cognitive impairment.ConclusionMidRISH reduces bias of reference selection while preserving harmonization efficacy of LinearRISH.SignificanceUsers should be cautious when performing LinearRISH harmonization. To select a reference site is to choose diffusion metric effect-size. Our proposed method eliminates the bias-inducing site selection step.
Water migration through enzyme tunnels is sensitive to choice of explicit water model
Authors: Thirunavukarasu Aravind Selvaram , Szleper Katarzyna , Tanriver Gamze , Mitusinska Karolina , Gora Artur , Brezovsky Jan 
Published: August 2023

AbstractUnderstanding the utilization of tunnels and water transport within enzymes is crucial for the catalytic function of enzymes, as water molecules can stabilize bound substrates and help with unbinding processes of products and inhibitors. Since the choice of water models for molecular dynamics simulations was shown to determine the accuracy of various calculated properties of the bulk solvent and solvated proteins, we have investigated if and to what extent the water transport through the enzyme tunnels depends on the selection of the water model. Here, we have focused on simulating enzymes with various well-defined tunnel geometries. In a systematic investigation using haloalkane dehalogenase as a model system, we focused on the well-established TIP3P, OPC, and TIP4P-Ew water models to explore their impact on using tunnels for water molecules transport. The TIP3P water model showed significantly faster migration, resulting in the transport of approximately 2.5 times more water molecules in comparison to OPC and 2.0 times greater than the TIP4P-Ew. The increase in migration of TIP3P water molecules was mainly due to faster transit times, and in the case of narrower tunnels, greater concurrent transport was evident as well. We have observed similar behavior in two different enzymes with buried active sites and different tunnel network topologies, indicating that our findings are likely not restricted to a particular enzyme family. Our study emphasizes the critical importance of water models in comprehending the use of enzyme tunnels for small molecule transport. Given the significant role of water availability in various stages of the catalytic cycle and solvation of substrates, products, and drugs, choosing an appropriate water model might be crucial for accurate simulations of complex enzymatic reactions, rational enzyme design, and predicting drug residence times.
PROTAC-mediated Degradation of HIV-1 Nef Efficiently Restores Cell-surface CD4 and MHC-I Expression and Blocks HIV-1 Replication
Authors: Emert-Sedlak Lori A. , Tice Colin M. , Shi Haibin , Alvarado John J. , Shu Sherry T. , Reitz Allen B. , Smithgall Thomas E. 
Published: August 2023

SUMMARYThe HIV-1 Nef accessory factor is critical to the viral life cyclein vivowhere it promotes immune escape of HIV-infected cells and viral persistence. While these features identify Nef as an attractive antiretroviral drug target, Nef lacks enzymatic activity and an active site, complicating development of occupancy-based drugs. Here we describe the development of proteolysis targeting chimeras (PROTACs) for the targeted degradation of Nef. Nef-binding compounds, based on a previously reported hydroxypyrazole core, were coupled to ligands for ubiquitin E3 ligases via flexible linkers. The resulting bivalent PROTACs induced formation of a ternary complex between Nef and the Cereblon E3 ubiquitin ligase, resulting in ubiquitylation of Nef and proteolytic degradation. Nef-directed PROTACs efficiently rescued Nef-mediated MHC-I and CD4 downregulation in T cells and suppressed HIV-1 replication in donor PBMCs. Targeted degradation of Nef is anticipated to reverse all HIV-1 Nef functions and may help restore adaptive immune responses against HIV-1 reservoir cellsin vivo.
Apparent RNA bridging between PRC2 and chromatin is an artefact of non-specific chromatin precipitation upon RNA degradation
Authors: Hickman Alex Hall , Jenner Richard G. 
Published: August 2023

ABSTRACTPolycomb repressive complex 2 (PRC2) modifies chromatin to maintain repression of genes specific for other cell lineages and is essential for development. In vitro, RNA inhibits PRC2 catalytic activity and interaction with nucleosomes but the effect of RNA on PRC2 in cells has been unclear, with studies concluding that RNA either antagonises or promotes the association of PRC2 with chromatin. The addition of RNase A to chromatin immunoprecipitation reactions has been reported to reduce detection of PRC2 target sites, suggesting the existence of an RNA bridge that connects PRC2 to chromatin. Here, we show that this apparent loss of PRC2 chromatin association after RNase A treatment is due to non-specific chromatin precipitation. RNA degradation causes chromatin to precipitate out of solution, thereby reducing the enrichment of specific DNA sequences in chromatin immunoprecipitation reactions. Maintaining chromatin solubility by the addition of poly-L-glutamic acid (PGA) rescues detection of PRC2 chromatin association upon RNA degradation. These findings undermine support for the model that RNA bridges PRC2 and chromatin in cells.
Pure wild forest reindeer (Rangifer tarandus fennicus) or hybrids? A whole-genome sequencing approach to solve the taxonomical status
Authors: Weldenegodguad Melak , Niemi Milla , Mykrä-Pohja Sakari , Pokharel Kisun , Hamama Tuula-Marjatta , Paasivaara Antti , Kantanen Juha 
Published: August 2023

AbstractIn Finland, the geographic distribution of semi-domestic reindeer (Rangifer tarandus tarandus) and wild forest reindeer (Rangifer tarandus fennicus) partly overlap in the vicinity of the southern border of the reindeer herding area. Hybridisation of these two subspecies is one of the major threats for the wild forest reindeer population, and the implemented conservation program targets preventing the crossbreeding of these reindeer. In this paper, we resequenced genomes of fourRangifer tarandusindividuals with unknown taxonomical status and investigated their ancestries by comparing the genomic data with the existing resequenced data of the Finnish semi-domestic reindeer and Finnish wild forest reindeer. The genetic relationship investigations suggest that the four individuals were pure forest reindeer animals. Our study provides critical knowledge for practical conservation actions of wild forest reindeer in the reintroduction project, for which it is essential to recognise each individual’s origin. In the future, it will also offer novel insights into the spread of native wild forest reindeer to new geographic regions in Finland. For subsequent studies, additional resequenced genomic data ofRangiferindividuals will be needed to develop an ancestry information marker panel of single nucleotide polymorphisms for rapid and cost-effective identification of hybrid individuals of semi-domestic reindeer and wild forest reindeer.
Shocker - a molecular dynamics protocol and tool for accelerating and analyzing the effects of osmotic shocks
Authors: van Tilburg Marco P. A. , Marrink Siewert J. , König Melanie , Grünewald Fabian 
Published: August 2023

AbstractThe process of osmosis, a fundamental phenomenon in life, drives water through a semi-permeable membrane in response to a solute concentration gradient across this membrane. In vitro, osmotic shocks are often used to drive shape changes in lipid vesicles, for instance, to study fission events in the context of artificial cells. While experimental techniques provide a macroscopic picture of large-scale membrane remodeling processes, molecular dynamics (MD) simulations are a powerful tool to study membrane deformations at the molecular level. However, simulating an osmotic shock is a time-consuming process due to the slow water diffusion across the membrane, making it practically impossible to examine its effects in classic MD simulations. In this paper, we present Shocker, a Python-based MD tool for simulating the effects of an osmotic shock by selecting and relocating water particles across a membrane over the course of several pumping cycles. Although this method is primarily aimed at efficiently simulating volume changes of vesicles it can handle membrane tubes and double bilayer systems as well. Additionally, Shocker is force field independent and compatible with both coarse-grained and all-atom systems. We demonstrate that our tool is applicable to simulate both hypertonic and hypotonic osmotic shocks for a range of vesicular and bilamellar setups, including complex multi-component systems containing membrane proteins or crowded internal solutions.
Automated, high-throughput quantification of EGFP-expressing neutrophils in zebrafish by machine learning and a highly-parallelized microscope
Authors: Efromson John , Ferrero Giuliano , Bègue Aurélien , Doman Thomas Jedidiah Jenks , Dugo Clay , Barker Andi , Saliu Veton , Reamey Paul , Kim Kanghyun , Harfouche Mark , Yoder Jeffrey A. 
Published: August 2023

AbstractNormal development of the immune system is essential for overall health and disease resistance. Bony fish, such as the zebrafish (Danio rerio), possess all the major immune cell lineages as mammals and can be employed to model human host response to immune challenge. Zebrafish neutrophils, for example, are present in the transparent larvae as early as 48 hours post fertilization and have been examined in numerous infection and immunotoxicology reports. One significant advantage of the zebrafish model is the ability to affordably generate high numbers of individual larvae that can be arrayed in multi-well plates for high throughput genetic and chemical exposure screens. However, traditional workflows for imaging individual larvae have been limited to low-throughput studies using traditional microscopes and manual analyses. Using a newly developed, parallelized microscope, the Multi-Camera Array Microscope (MCAM™), we have optimized a rapid, high-resolution algorithmic method to count fluorescently labeled cells in zebrafish larvaein vivo. Using transgenic zebrafish larvae, in which neutrophils express EGFP, we captured 18 gigapixels of images across a full 96-well plate, in 75 seconds, and processed the resulting datastream, counting individual fluorescent neutrophils in all individual larvae in 5 minutes. This automation is facilitated by a machine learning segmentation algorithm that defines the most in-focus view of each larva in each well after which pixel intensity thresholding and blob detection are employed to locate and count fluorescent cells. We validated this method by comparing algorithmic neutrophil counts to manual counts in larvae subjected to changes in neutrophil numbers, demonstrating the utility of this approach for high-throughput genetic and chemical screens where a change in neutrophil number is an endpoint metric. Using the MCAM™ we have been able to, within minutes, acquire both enough data to create an automated algorithm and execute a biological experiment with statistical significance. Finally, we present this open-source software package which allows the user to train and evaluate a custom machine learning segmentation model and use it to localize zebrafish and analyze cell counts within the segmented region of interest. This software can be modified as needed for studies involving other zebrafish cell lineages using different transgenic reporter lines and can also be adapted for studies using other amenable model species.
Molecular evolution and adaptation of SARS-CoV-2 omicron XBB sub-lineage Spike protein under African selection pressure
Authors: Kambarami Milton S , Godwins Ngorima , Moyo Praise K , Lucy Mabaya , Tawanda Mushiri , Justen Manasa 
Published: August 2023

AbstractThe SARS-CoV-2 Omicron variant of concern (VOC) has multiple mutations in the spike (S) protein, which mediates viral infection and immunity. We analysed a sub-lineage of Omicron, designated XBB, that showed structural and functional changes in the S protein in response to the African selection pressures. We used molecular modelling to compare the S protein structures of Omicron and XBB and found that XBB had a reduced receptor-binding domain (RBD) due to the loss of some β-sheets, which may increase its affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. We also used Fast Unconstrained Bayesian AppRoximation (FUBAR) and Recombination Detection Program 4 (RDP 4) to perform selection and recombination analysis of the S protein sequences of Omicron and XBB and detected signals of positive selection and recombination in the N-terminal domain (NTD) of the S1 subunit, which contains antibody-binding epitopes, and the RBD, which is involved in viral entry. Our results reveal the structural and functional adaptation of the Omicron XBB variant in Africa and its potential implications for viral pathogenesis and immunity.
GSK3α/β restrains IFNγ-inducible costimulatory molecule expression in alveolar macrophages, limiting CD4+T cell activation
Authors: Ankley Laurisa M. , Conner Kayla N. , Vielma Taryn E. , Thapa Mahima , Olive Andrew J 
Published: August 2023

ABSTRACTMacrophages play a crucial role in eliminating respiratory pathogens. Both pulmonary resident alveolar macrophages (AMs) and recruited macrophages contribute to detecting, responding to, and resolving infections in the lungs. Despite their distinct functions, it remains unclear how these macrophage subsets regulate their responses to infection, including how activation by the cytokine IFNγ is regulated. This shortcoming prevents the development of therapeutics that effectively target distinct lung macrophage populations without exacerbating inflammation. We aimed to better understand the transcriptional regulation of resting and IFNγ-activated cells using a newex vivomodel of AMs from mice, fetal liver-derived alveolar-like macrophages (FLAMs), and immortalized bone marrow-derived macrophages (iBMDMs). Our findings reveal that IFNγ robustly activates both macrophage types; however, the profile of activated IFNγ-stimulated genes varies greatly between these cell types. Notably, FLAMs show limited expression of costimulatory markers essential for T cell activation upon stimulation with only IFNγ. To understand cell type-specific differences, we examined how the inhibition of the regulatory kinases GSK3α/β alters the IFNγ response. GSK3α/β controlled distinct IFNγ responses, and in AM-like cells, we found GSK3α/β restrained the induction of type I IFN and TNF, thus preventing the robust expression of costimulatory molecules and limiting CD4+T cell activation. Together, these data suggest that the capacity of AMs to respond to IFNγ is restricted in a GSK3α/β-dependent manner and that IFNγ responses differ across distinct macrophage populations. These findings lay the groundwork to identify new therapeutic targets that activate protective pulmonary responses without driving deleterious inflammation.
Iron regulatory proteins 1 and 2 have opposing roles in regulating inflammation in bacterial orchitis
Authors: Ghatpande N. , Harrer A. , Azouly B. , Guttmann-Raviv N. , Bhushan S. , Meinhardt A. , Meyron-Holtz E.G. 
Published: August 2023

AbstractAcute bacterial orchitis (AO) is a prevalent cause of intra-scrotal inflammation, often resulting in sub-or infertility. A frequent cause eliciting AO is uropathogenicEscherichia coli(UPEC), a gram negative pathovar, characterized by the expression of various iron acquisition systems to survive in a low-iron environment. On the host side, iron is tightly regulated by iron regulatory proteins (IRP) 1 and 2 and these factors have been reported to play a role in testicular and immune cell function, however, their precise role remains unclear. Here, we show in a mouse model of UPEC-induced orchitis that the absence of IRP1 results in reduced immune response and testicular damage. Compared to infected wild-type (WT)-mice, testis of UPEC-infectedIrp1-/-mice showed impaired ERK signalling. Conversely, IRP2 deletion led to a stronger inflammatory response. Notably, differences in immune cell infiltrations were observed among the different genotypes. In contrast to WT andIrp2-/-mice, no increase in monocytes and neutrophils was detected in testis ofIrp1-/-mice upon UPEC-infection. Interestingly, inIrp1-/-UPEC-infected testis, we observed an increase in a subpopulation of macrophages (F4/80+ CD206+) associated with anti-inflammatory and wound-healing activities compared to WT. These findings suggest that IRP1 deletion may protect against UPEC-induced inflammation by modulating ERK signalling and dampening the immune response.
Assembly of SARS-CoV-2 ribonucleosomes by truncated N* variant of the nucleocapsid protein
Authors: Adly Armin N. , Bi Maxine , Carlson Christopher R. , Syed Abdullah M. , Ciling Alison , Doudna Jennifer A. , Cheng Yifan , Morgan David O. 
Published: August 2023

AbstractThe Nucleocapsid (N) protein of SARS-CoV-2 compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein SR region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N* or Δ(1–209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we show that Δ(1–209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of Δ(1–209) vRNPs requires the leucine-rich helix (LH) of the central disordered region, and that the LH promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to Δ(1–209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by SR phosphorylation.