bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type S Non Ribosomal Peptide Synthetases for the rapid generation of tailor-made peptide libraries
Authors: Abbood Nadya , Vo Tien Duy , Watzel Jonas , Bozhueyuek Kenan A. J. , Bode Helge B. 
Published: October 2021

AbstractBacterial natural products in general, and non-ribosomally synthesized peptides in particular, are structurally diverse and provide us with a broad range of pharmaceutically relevant bioactivities. Yet, traditional natural product research suffers from rediscovering the same scaffolds and has been stigmatized as inefficient, time-, labour- and cost-intensive. Combinatorial chemistry, on the other hand, can produce new molecules in greater numbers, cheaper and in less time than traditional natural product discovery, but also fails to meet current medical needs due to the limited biologically relevant chemical space that can be addressed. Consequently, methods for the high throughput generation of new-to-nature natural products would offer a new approach to identifying novel bioactive chemical entities for the hit to lead phase of drug discovery programms. As a follow-up to our previously published proof-of-principle study on generating bipartite type S non-ribosomal peptide synthetases (NRPSs), we now envisaged the de novo generation of non-ribosomal peptides (NRPs) on an unreached scale. Using synthetic zippers, we split NRPS in up to three subunits and rapidly generated different bi- and tripartite NRPS libraries to produce 49 peptides, peptide derivatives, and de novo peptides at good titres up to 145 mgL-1. A further advantage of type S NRPSs not only is the possibility to easily expand the created libraries by re-using previously created type S NRPS, but that functions of individual domains as well as domain-domain interactions can be studied and assigned rapidly.
Zn2+ triggered two-step mechanism of CLIC1 membrane insertion and activation into chloride channels
Authors: Varela Lorena , Hendry Alex C. , Cassar Joseph , Martin-Escolano Ruben , Cantoni Diego , Edwards John C , Abdul-Salam Vahitha , Ortega-Roldan Jose L. 
Published: October 2021

ABSTRACTThe CLIC protein family displays the unique feature of altering its structure from a soluble form to a membrane-bound chloride channel. CLIC1, a member of this family, is found in the cytoplasm or in internal and the plasma membranes, with membrane relocalisation linked to endothelial disfunction, tumour proliferation and metastasis. The molecular switch promoting CLIC1 activation remains unclear. Here, cellular chloride efflux assays and immunofluorescence microscopy studies have identified Zn2+ intracellular release as the trigger for CLIC1 activation and membrane relocalisation. Biophysical assays confirmed specific binding to Zn2+, inducing membrane association and enhancing chloride efflux in a pH dependent manner. Together, our results identify a two-step mechanism with Zn2+ binding as the molecular switch promoting CLIC1 membrane insertion, followed by pH activation of chloride efflux.
MACA: Marker-based automatic cell-type annotation for single cell expression data
Authors: Xu Yang , Baumgart Simon J. , Stegmann Christian , Hayat Sikander 
Published: October 2021

AbstractSummaryAccurately identifying cell-types is a critical step in single-cell sequencing analyses. Here, we present marker-based automatic cell-type annotation (MACA), a new tool for annotating single-cell transcriptomics datasets. We developed MACA by testing 4 cell-type scoring methods with 2 public cell-marker databases as reference in 6 single-cell studies. MACA compares favorably to 4 existing marker-based cell-type annotation methods in terms of accuracy and speed. We show that MACA can annotate a large single-nuclei RNA-seq study in minutes on human hearts with ~290k cells. MACA scales easily to large datasets and can broadly help experts to annotate cell types in single-cell transcriptomics datasets, and we envision MACA provides a new opportunity for integration and standardization of cell-type annotation across multiple datasets.Availability and implementationMACA is written in python and released under GNU General Public License v3.0. The source code is available at https://github.com/ImXman/MACA.ContactYang Xu (yxu71@vols.utk.edu), Sikander Hayat (hayat221@gmail.com)
Desire and Craving ratings vary significantly for healthy alcohol consumers: Differences in semantic interpretation?
Authors: Peterson H , Veach LJ , Simpson SL , Fanning J , Laurienti PJ , Gauvin L 
Published: October 2021

ABSTRACTCraving is a central concept in alcohol, and other substance, research. Beginning in 1955 the World Health Organization outlined a working definition of the term to be used in research and clinical settings. However, the semantic interpretation of “craving” as a concept is not widely agreed upon. Since the publication of this first craving definition, a handful of studies have been conducted to investigate differences in operational definitions of “craving”, and have demonstrated a lack of agreement between studies and across research subjects. With this background as evidence, our research group investigated, when left to their own semantic understanding of the terms, if regular alcohol consumers would rate craving for alcohol and desire for alcohol in similar ways using related descriptors. Thirty-nine healthy, non-binging regular alcohol consumers were studied across periods of their typical alcohol consumption and imposed alcohol abstinence, collecting ratings of desire and craving for alcohol approximately every two hours across the two experimental periods, and during neutral and alcohol related imagery viewing. Among these non-binging regular drinkers, ratings of desire and craving for alcohol are consistently different while drinking according to a person’s typical routine or abstaining, throughout the day, and when viewing alcohol cue imagery.
A basement membrane discovery pipeline uncovers network complexity, new regulators, and human disease associations
Authors: Jayadev Ranjay , Morais Mychel RPT , Ellingford Jamie M , Srinivasan Sandhya , Naylor Richard W , Lawless Craig , Li Anna S , Ingham Jack F , Hastie Eric , Chi Qiuyi , Fresquet Maryline , Koudis Nikki-Maria , Thomas Huw B , T O’Keefe Raymond , Williams Emily , Adamson Antony , Stuart Helen M , Banka Siddharth , Smedley Damian ,   Genomics England Research Consortium, Sherwood David R , Lennon Rachel 
Published: October 2021

SummaryBasement membranes (BMs) are ubiquitous extracellular matrices whose composition remains elusive, limiting our understanding of BM regulation and function. By developing a bioinformatic and in vivo discovery pipeline, we define a network of 222 human proteins localized to BMs. Network analysis and screening in C. elegans and zebrafish identified new BM regulators, including ADAMTS, ROBO, and TGFβ. More than 100 BM-network genes associate with human phenotypes and by screening 63,039 genomes from families with rare disorders, we discovered loss-of-function variants in LAMA5, MPZL2, and MATN2, and show they regulate BM composition and function. This cross-disciplinary study establishes the immense complexity and role of BMs in human health.
Psychological stress disrupts intestinal epithelial cell function and mucosal integrity through microbe and host-directed processes
Authors: Allen Jacob M. , Mackos Amy R. , Jaggers Robert M. , Brewster Patricia C. , Webb Mikaela , Lin Chia-Hao , Ladaika Chris , Davies Ronald , White Peter , Loman Brett R. , Bailey Michael T. 
Published: October 2021

AbstractPsychological stress alters the gut microbiota and predisposes individuals to increased risk for enteric infections and chronic bowel conditions. Intestinal epithelial cells (IECs) are responsible for maintaining homeostatic interactions between the gut microbiota and its host. In this study, we hypothesized that disruption to colonic IECs is a key factor underlying stress-induced disturbances to intestinal homeostasis. Conventionally raised (CONV-R) and germ-free (GF) mice were exposed to a social disruption stressor (Str) to ascertain how stress modifies colonic IECs, the mucosal layer, and the gut microbiota. RNA sequencing of IECs isolated from CONV-R mice revealed a robust pro-inflammatory (Saa1, Il18), pro-oxidative (Duox2, Nos2), and antimicrobial (Reg3b/g) transcriptional profile as a result of Str. This response occurred concomitant to mucus layer thinning and signs of microbial translocation. In contrast to their CONV-R counterparts, IECs from GF mice or mice treated with broad spectrum antibiotics exhibited no detectable transcriptional changes in response to Str. Nevertheless, IECs from Str-exposed GF mice exhibited an altered response to ex vivo bacterial challenge (increased dual Oxidase-2 [Duox2] and nitric oxide synthase-2 (Nos2)), indicating that STR primes host IEC pro-oxidative responses. In CONV-R mice stress-induced increases in colonic Duox2 and Nos2 (ROS generating enzymes) strongly paralleled changes to microbiome composition and function, evidencing Str-mediated ROS production as a primary factor mediating gut-microbiota dysbiosis. In conclusion, a mouse model of social stress disrupts colonic epithelial and mucosal integrity, a response dependent on an intact microbiota and host stress signals. Together these preclinical findings may provide new insight into mechanisms of stress-associated bowel pathologies in humans.
Transposable elements continuously remodel the regulatory landscape, transcriptome, and function of decidual stromal cells
Authors: Mika Katelyn , Lynch Vincent J. 
Published: October 2021

AbstractGene expression evolution underlies the origin, divergence, and conservation of biological characters including cell-types, tissues, and organ systems. Previously we showed that large-scale gene expression changes in decidual stromal cells contributed to the origins of pregnancy in eutherians and the divergence of pregnancy traits in primates, and that transposable elements likely contributed to these gene expression changes. Here we show that two large waves of TEs remodeled the transcriptome and regulatory landscape of decidual stromal cells, including a major wave in primates. Genes nearby TE-derived regulatory elements are among the most progesterone responsive in the genome and play essential roles in orchestrating progesterone responsiveness and the core function of decidual cells by donating progesterone receptor binding sites to the genome. We tested the regulatory abilities of 89 TE consensus sequences and found nearly all acted as repressors in mammalian cells, but treatment with a histone deacetylase inhibitor unmasked latent enhancer functions. These data indicate TEs have played an important role in the development, evolution, and function of primate decidual stromal cells and suggest a two-step model in which latent enhancer functions of TEs are unmasked after they lose primary repressors functions.Significance statementGene expression patterns evolved very rapidly during the evolutionary origins of pregnancy in early mammals and in primates. These episodes of gene expression evolution and linked with important processes that establish and maintain pregnancy, and appear to be driven by domestication of transposable elements.
The toll-like receptor 7 agonist imiquimod increases ethanol self-administration and induces expression of toll-like receptor related genes
Authors: Lovelock Dennis F. , Liu Wen , Langston Sarah E. , Liu Jiaqi , Van Voorhies Kalynn , Giffin Kaitlin A. , Vetreno Ryan P. , Crews Fulton T. , Besheer Joyce 
Published: October 2021

AbstractBackgroundThere is growing evidence that immune signaling may be involved in both the causes and consequences of alcohol abuse. Toll-like receptor (TLR) expression is increased by alcohol consumption and is implicated in AUD, and specifically TLR7 may play an important role in ethanol consumption.MethodsWe administered the TLR7-specific agonist imiquimod in male and female Long-Evans rats to determine 1) gene expression changes in brain regions involved in alcohol reinforcement, the nucleus accumbens core and anterior insular cortex, in rats with and without an alcohol history, and 2) whether TLR7 activation could modulate operant alcohol self-administration.ResultsInterferon regulatory factor 7 (IRF7) was dramatically increased in both sexes at both 2 and 24 h post-injection regardless of alcohol history, while TLR3 and 7 gene expression changes were region- and sex-specific. The pro-inflammatory cytokine TNFα was increased 24h post-injection in rats with an alcohol self-administration history but this effect did not persist after four injections, suggesting molecular tolerance. In both males and females, ethanol consumption was increased 24 h after imiquimod injections with sex-specific differences: in females this effect emerged following the first injection but in males this increase did not occur until the third injection, suggesting sex differences in adaptation to repeated TLR7 activation. Notably, imiquimod reliably induced weight loss, indicating that sickness behavior persisted across repeated injections.ConclusionThese findings show that TLR7 activation can modulate alcohol drinking in an operant self-administration paradigm, and suggest that TLR7 and IRF7 signaling pathways may be a viable druggable target for treatment of AUD.
Mouse lemur, a new animal model to investigate cardiac pacemaker activity in primates
Authors: DiFrancesco Mattia L. , Davaze Romain , Torre Eleonora , Mesirca Pietro , Marrot Manon , Lautier Corinne , Fontes Pascaline , Cuoq Joёl , Fernandez Anne , Lamb Ned , Pifferi Fabien , Mestre-Francés Nadine , Mangoni Matteo E. , Torrente Angelo G. 
Published: October 2021

AbstractBackgroundGray mouse lemurs (Microcebus murinus) are the smallest and most ancestral primates known. Their size falls in between that of mice and rats, and their genetic proximity to humans makes them an emerging model to study age-related neurodegeneration. Since mouse lemurs replicate similar senescence processes of humans, they constitute a useful model for studying cardiovascular dysfunctions. However, their cardiac physiology is unknown. Thus, we investigated the cardiac pacemaker activity generated by the sinoatrial node (SAN) of mouse lemurs, presenting the first characterization of heart automaticity in nonhuman primates.Methods and ResultsWe recorded cardiac automaticity in mouse lemurs and in their SAN tissues and pacemaker myocytes. Mouse lemurs have a heart rate (HR) in between those of mice and rats and a similar generation of the SAN electrical impulse. Their SAN myocytes express the main pacemaker currents at densities similar to mice: the hyperpolarization-activated current (If) and the L-type (Ica,L) and T-type (Ica,T) calcium currents. Conversely, their ventricular depolarization resembles that of large mammals and despite the small size of mouse lemurs, the total number of heartbeats in their life corresponds to what can be attained by humans.Using muscle-derived stem cells (MDSCs) from mouse lemurs, we also differentiated pacemaker-like (PML) cells showing spontaneous automaticity and expressing markers of native SAN myocytes (HCN4 and connexin-45).ConclusionsOur characterization of heart automaticity in Microcebus murinus provides new opportunities for comparative cardio-physiology studies in primates and with humans and for testing molecules that could modulate age-related dysfunctions of heart rate.
Statistics of antibody binding to the spike protein explain the dependence of COVID 19 infection risk on antibody concentration and affinity
Authors: Williams David E 
Published: October 2021

AbstractThe increase of COVID-19 breakthrough infection risk with time since vaccination has a clear relationship to the decrease of antibody concentration with time. The empirically-observed dependence on blood IgG anti-receptor binding domain antibody concentration of SARS-CoV-2 vaccine efficacy against infection has a rational explanation in the statistics of binding of antibody to spike proteins on the virus surface, leading to blocking of binding to the receptor: namely that the probability of infection is the probability that a critical number of the spike proteins protruding from the virus are unblocked. The model is consistent with the observed antibody concentrations required to induce immunity and with the observed dependence of vaccine efficacy on antibody concentration and thus is a useful tool in the development of models to relate, for an individual person, risk of infection given measured antibody concentration. It can be used to relate population breakthrough infection risk to the distribution across the population of antibody concentration, and its variation with time.
Nelfinavir induces cytotoxicity towards high-grade serous ovarian cancer cells, involving induction of the unfolded protein response, modulation of protein synthesis, DNA damage, lysosomal impairment, and potentiation of toxicity caused by proteasome inhibition
Authors: Subeha Mahbuba R , Goyeneche Alicia A , Bustamante Prisca , Lisio Michael A. , Burnier Julia V. , Telleria Carlos M. 
Published: October 2021

AbstractHigh-grade serous ovarian cancer (HGSOC) is a significant cause of mortality among women worldwide. Traditional treatment consists of platinum-based therapy; however, rapid development of platinum resistance contributes to lower life expectancy, warranting newer therapies to supplement the current platinum-based protocol. Repurposing market-available drugs as cancer therapeutics is a cost- and time-effective way to avail new therapies to drug-resistant patients. The anti-HIV agent nelfinavir (NFV) has shown promising toxicity against various cancers; however, its role against HGSOC is unknown. Here, we studied the effect of NFV against HGSOC cells obtained from patients along disease progression and carrying different sensitivities to platinum. NFV triggered, independently of platinum sensitivity, a dose-dependent reduction of HGSOC cell number and viability, and a parallel increase in hypo-diploid DNA content. Moreover, a dose-dependent reduction of clonogenic survival of cells escaping the acute toxicity was indicative of long-term residual damage. In addition, dose- and time-dependent phosphorylation of H2AX indicated NFV-mediated DNA damage, which was associated with decreased survival and proliferation signals driven by the AKT and ERK pathways. NFV also mediated a dose-dependent increase in endoplasmic reticulum stress-related molecules associated with long-term inhibition of protein synthesis and concurrent cell death; such events were accompanied by a proapoptotic environment, signaled by increased phospho- eIF2α, ATF4, and CHOP, increased Bax/Bcl-2 ratio, and cleaved executer caspase-7. Finally, we show that NFV potentiates the short-term cell cycle arrest and long-term toxicity caused by the proteasome inhibitor bortezomib. Overall, ourin vitrostudy demonstrates that NFV can therapeutically target HGSOC cells of differential platinum sensitivities via several mechanisms, suggesting its prospective repurposing benefit considering its good safety profile.
SERCA function is impaired in skeletal and cardiac muscles from young DBA/2J mdx mice
Authors: Cleverdon Riley EG , Whitley Kennedy C , Marko Daniel M , Hamstra Sophie I , Braun Jessica L , Roy Brian D , MacPherson Rebecca EK , Fajardo Val A 
Published: October 2021

SummaryThe DBA/2J (D2) mdx mouse has emerged as a more severe model of Duchenne muscular dystrophy when compared to the traditional C57BL/10 (C57) mdx mouse. Here, we questioned whether sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) function would differ in muscles from young D2 and C57 mdx mice. In gastrocnemius muscles, both D2- and C57 mdx mice exhibited signs of impaired Ca2+ uptake, however, this was more severe in D2 mdx mice. Maximal SERCA activity was lowered only in D2 mdx gastrocnemius muscles and not C57 mdx muscles. Furthermore, in the left ventricle and diaphragm, Ca2+ uptake was impaired in C57 mdx muscles with lowered rates of Ca2+ uptake compared with C57 WT mice, whereas in muscles from D2 mdx mice, rates of Ca2+ uptake were unattainable due to the severe impairments in their ability to transport Ca2+. Overall, our study demonstrates that SERCA function is drastically impaired in young D2 mdx mice.
Transmission ofKlebsiellastrains and plasmids within and between Grey-headed flying fox colonies
Authors: Vezina Ben , Judd Louise M. , McDougall Fiona K. , Boardman Wayne S.J. , Power Michelle L. , Hawkey Jane , Brisse Sylvain , Monk Jonathan M. , Holt Kathryn E. , Wyres Kelly L. 
Published: October 2021

AbstractThe Grey-headed flying fox (Pteropus poliocephalus) is an endemic Australian fruit bat, known to carry pathogens with zoonotic potential. We recently showed these bats harbour the bacterial pathogensKlebsiella pneumoniaeand closely related species in theK. pneumoniaespecies complex (KpSC). However, the dynamics ofKlebsiellatransmission and gene flow within flying fox colonies were not explored and remain poorly understood.Here we report a high-resolution genomic comparison of 39KpSC isolates from Greyheaded flying foxes. Illumina whole genome sequences (n=39) were assembledde novoand the Kleborate genotyping tool was used to infer sequence types (STs). Oxford Nanopore sequences were generated for 13 isolates (one for each distinct ST) in order to generate high-quality completed reference genomes. Read mapping and variant calling was used to identify single nucleotide variants (SNVs) within each ST, using the relevant reference genome.In silicogenome-scale metabolic models were generated to predict and compare substrate usage to 59 previously publishedKpSC models for isolates from human and environmental sources, which indicated no distinction on the basis of metabolic capabilities.High-resolution genome comparisons identified five putative strain transmission clusters (four intra- and one inter-colony, n=2-15 isolates each, ≤25 pairwise SNVs). Inter-colony transmission ofKlebsiella africanawas found between two flying fox populations located within flying distance. The 13 completed genomes harboured 11 plasmids, all of which showed 37-98% coverage (mean 73%) and ≥95% identity to those previously reported from human-associatedKpSC. Comparison of plasmids from different flying fox associatedKpSC indicated an interspecies horizontal plasmid transmission betweenK. pneumoniaeandK. africanafor a 98 kbp plasmid, pFF1003.These data indicate thatKpSC are able to transmit directly via flying fox populations or indirectly via a common source, and that these isolates can harbour plasmids with similarity to those found in human derivedKpSC, indicating gene flow is occurring between isolates from Grey-headed flying foxKpSC and human clinical isolates.
Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation from mouse embryonic stem cells
Authors: Komoto Tetsushi , Fujii Masashi , Awazu Akinori 
Published: October 2021

AbstractX chromosome inactivation center (Xic) pairing is robustly observed during the differentiation of embryonic stem (ES) cells from female mouse embryos, and this process is related to X chromosome inactivation, the circadian clock, intra-nucleus architecture, and metabolism. However, the mechanisms underlying the identification and approach of X chromosome pairs in the crowded nucleus are unclear. To elucidate the driving force of Xic pairing, we developed a coarse-grained molecular dynamics model of intranuclear chromosomes in ES cells and in cells 2 days after the onset of differentiation (2-days cells) by considering intrachromosome epigenetic-structural feature-dependent mechanics. The analysis of the experimental data showed X-chromosomes change to specifically softer than autosomes during the cell differentiation by the rearrangement of their distributions of open-close chromatin regions, and the simulations of these models exhibited such softening promoted the mutual approach of the Xic pair. These findings suggested that local intrachromosomal epigenetic features may contribute to the regulation of cell species-dependent differences in intranuclear architecture.