bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Inducible Cre Mouse with Preferential Activity in Vascular Smooth Muscle Evades a Previously Lethal Intestinal Phenotype
Authors: Warthi Ganesh D. , Faulkner Jessica L. , Doja Jaser , Ghanam Amr R. , Gao Pan , Yang Allison C. , Slivano Orazio J. , Barris Candee T. , Kress Taylor C. , Zawieja Scott D. , Griffin Susan H. , Xie Xiaoling , Ashworth Alan , Christie Christine K. , Bryant William B. , Kumar Ajay , Davis Michael J. , Long Xiaochun , Gan Lin , Belin de Chantemèle Eric J. , Lyu Qing , Miano Joseph M. 
Published: February 2022

AbstractAll smooth muscle cell (SMC) restricted Cre mice recombine floxed alleles in vascular and visceral SMCs. We generated a new tamoxifen-inducible CreERT2 mouse, Itga8-CreERT2, and compared its activity to the widely used Myh11-CreERT2 mouse. Both CreERT2 mice showed similar activity in vascular SMCs; however, Itga8-CreERT2 displayed limited activity in visceral SMC-containing tissues (e.g., intestine). Myh11-CreERT2 (but not Itga8-CreERT2) mice displayed high levels of CreERT2 protein, tamoxifen-independent activity, and an altered transcriptome. Whereas Myh11-CreERT2-mediated knockout of Srf resulted in a lethal intestinal phenotype, loss of Srf with Itga8-CreERT2 (SrfItga8) revealed viable mice with attenuated vascular SMC contractile gene expression, but no evidence of intestinal pathology. Male and female SrfItga8 mice presented with vascular contractile incompetence; however, only male SrfItga8 mice showed systemic changes in blood pressure. These results establish the Itga8-CreERT2 mouse as an alternative to existing SMC Cre strains, including Myh11-CreERT2, where SMC gene loss results in visceral myopathies that obfuscate accurate phenotyping in vascular SMCs.
In vitrophenotypic and transcriptomic variation inNeisseria musculimorphotypes correlate with colonization variability and persistencein vivo
Authors: Thapa Eliza , Lauderback Leah , Simmons Cassandra , Holzschu Donald L. , D’Mello Adonis , Ma Mancheong , So Magdalene , Tettelin Hervé , Weyand Nathan J. 
Published: February 2022

ABSTRACTAsymptomatic colonization of the upper respiratory tract is a common trait of the two human restricted pathogens,Neisseria gonorrhoeaeandNeisseria meningitidis. In vivomodels of pathogenic neisserial infections are heterologous systems that permit short-term colonization but do not fully recapitulate infections in humans. StudyingNeisseria musculi(Nmus), an oral commensal, in laboratory mice allows investigation ofNeisseria-host interactions that avoids host restriction barriers. Nmus produces smooth and rough morphotypes on solid media. We compared thein vitrophenotypes, biofilm transcriptomes,in vivocolonization patterns and burdens of the two Nmus morphotypes. We observed that the two morphotypes differ in biofilm formation, pilin production, transformation frequency, and aggregationin vitro. These phenotypes strongly correlated with differential expression of a set of genes in the Nmus biofilms including those that encoded factors for bacterial attachment.In vivo, the smooth morphotype stably colonized the oral cavities of all inoculated A/J and C57BL/6J mice at higher burdens relative to the rough. Interestingly, both morphotypes colonized the oral cavities of A/Js at higher magnitudes than in C57BL/6Js. Gut colonization by the smooth morphotype was qualitatively higher than the rough. Nasal colonization in the A/Js were transient following nasal inoculations. Collectively, our results demonstrate that colonization by Nmus can be affected by various factors including Nmus morphotypes, inoculation routes, anatomical niches, and host backgrounds. The Nmus-mouse model can use variable morphotype-host combinations to study the dynamics of neisserial asymptomatic colonization and persistence in multiple extragenital niches.IMPORTANCEAnimal models for human adapted pathogenicNeisseriaspp. do not fully mimic human infections and are complicated by host restriction barriers that can hinder long-term persistence. Such barriers can be avoided by studyingNeisseriaspp. native to the animal host used for disease models.Neisseria musculi(Nmus) isolated from wild mice colonizes the oral cavity and gut of laboratory mice for extended periods. Nmus shares host interaction factors with species pathogenic to humans and thus provides a native system to study orthologs of factors that may facilitate asymptomatic colonization and persistence in the human upper respiratory tract. We investigated the Nmus-mouse system to comparein vitroandin vivophenotypes of two Nmus morphotypes. Our results support the hypothesis that the two morphotypes vary in different aspects ofNeisseria-host interactions. Future use of the Nmus-host system will help identify molecular mechanisms required for neisserial asymptomatic colonization, dissemination, and persistence.
In vitro effect of a non-immunosuppressive FKBP ligand, FK1706, on SARS-CoV-2 replication in combination with antivirals
Authors: Fitzsimmons William E. , Hartman Tracy L. , Mendenhall Michelle , Chen Catherine Z. 
Published: February 2022

AbstractFKBP, a naturally occurring ubiquitous intracellular protein, has been proposed as a potential target for coronavirus replication. A non-immunosuppressive FKBP ligand, FK1706, was studied in vitro in a Vero cell model to assess potential activity alone and in combination with antivirals against SARS-CoV-2 replication. When combined with remdesivir, synergistic activity was seen (summary synergy score 24.7+9.56). FK1706 warrants in vivo testing as a potential new combination therapeutic for the treatment of COVID-19 infections.
The relationship of maternal gestational mass spectrometry-derived metabolites with offspring congenital heart disease: results from multivariable and Mendelian randomization analyses
Authors: Taylor Kurt , McBride Nancy , Zhao Jian , Oddie Sam , Azad Rafaq , Wright John , Andreassen Ole A. , Stewart Isobel D , Langenberg Claudia , Magnus Maria , Borges Maria Carolina , Caputo Massimo , Lawlor Deborah A 
Published: February 2022

AbstractBackgroundIt is plausible that maternal pregnancy metabolism influences risk of offspring congenital heart disease (CHD). We sought to explore this through a systematic approach using different methods and data.MethodsWe undertook multivariable logistic regression of the odds of CHD for 923 Mass Spectrometry (MS)-derived metabolites in a sub-sample of a UK birth cohort (Born in Bradford (BiB); N = 2,605, 46 CHD cases). We considered metabolites reaching a p-value threshold <0.05 to be suggestively associated with CHD. We sought validation of our findings, by repeating the multivariable regression analysis within the BiB cohort for any metabolite that was measured by nuclear magnetic resonance (NMR) or clinical chemistry (N = 7,296, 87 CHD cases), and by using genetic risk scores (GRS: weighted genetic risk scores of single nucleotide polymorphisms (SNPs) that were associated with each metabolite) in Mendelian randomization (MR) analyses. MR analyses were performed in BiB and two additional European birth cohorts (N = 38,662, 319 CHD cases).ResultsIn the main multivariable analyses, we identified 44 metabolites suggestively associated with CHD, including those from the following super pathways: amino acids, lipids, co-factors and vitamins, xenobiotics, nucleotides, energy, and several unknown molecules. Of these 44, isoleucine and leucine were available in the larger BiB cohort (NMR), and for these the results were validated. MR analyses were possible for 27/44 metabolites and for 11 there was consistency with multivariable regression results.ConclusionsIn summary, we have used complimentary data sources and statistical techniques to construct layers of evidence. We found that amino acid metabolism during pregnancy, several lipids (more specifically androgenic steroids), and levels of succinylcarnitine could be important contributing factors for CHD.
Single cell transcriptomic and spatial landscapes of the developing human pancreas
Authors: Olaniru Oladapo E. , Kadolsky Ulrich , Kannambath Shichina , Vaikkinen Heli , Fung Kathy , Dhami Pawan , Persaud Shanta J. 
Published: February 2022

ABSTRACTThe progress made in directed differentiation of stem cells has shown that understanding human pancreas development can provide cues for generating unlimited amounts of insulin-producing beta cells for transplantation therapy in diabetes. However, current differentiation protocols have not been successful in reproducibly generating functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single cell RNA sequencing with spatial transcriptomics at multiple developmental timepoints and revealed distinct temporal-spatial gene cascades in the developing human pancreas. Cell trajectory inference identified endocrine progenitor populations and novel branch-specific genes as the progenitors differentiate towards alpha or beta cells, indicating that transcriptional maturation occurred over this developmental timeframe. Spatial differentiation trajectories indicated that immature Schwann cells are spatially co-located with endocrine progenitors and contribute to beta cell maturation via the L1CAM-EPHB2 pathway. Our integrated approach enabled us to identify heterogeneity and multiple lineage dynamics within the mesenchyme, showing that it contributed to the exocrine acinar cell state. Finally, we have generated an interactive web resource for interrogating human pancreas development for the research community.
Candidate undecaprenyl phosphate translocases enable conditional microbial fitness and pathogenesis
Authors: Sit Brandon , Srisuknimit Veerasak , Hullahalli Karthik , Bueno Emilio , Cava Felipe , Waldor Matthew K. 
Published: February 2022

AbstractThe mechanisms that enable adaptation of peptidoglycan, the structural unit of the bacterial cell wall, to shifting extracellular conditions such as pH remain largely unknown. Here, we identify a DUF368-containing membrane protein in the cholera pathogen Vibrio cholerae that is critical for pathogenesis and alkaline fitness. V. cholerae and Staphylococcus aureus lacking their cognate DUF368-containing protein have pH-dependent cell wall defects consistent with surface accumulation of undecaprenyl phosphate (C55-P), an essential lipid carrier for the biogenesis of peptidoglycan and other key bacterial cell surface polymers. In both species, DUF368-containing proteins exhibit synthetic genetic interactions with putative transporters from the DedA family, suggesting these proteins represent complementary long-sought C55-P translocases that enable envelope maintenance functions critical for microbial fitness within and outside the host.One-Sentence SummaryDUF368-containing and DedA-family proteins are undecaprenyl phosphate transporter candidates and are required for bacterial alkaline fitness and pathogenesis.
Evaluation of Nutritional Potential and Effect of Processing on Improving Nutrient Content of Cassava (Mannihot esculenta crantz) Root and Leaves
Authors: Lambebo Tagesse , Deme Tesfaye 
Published: February 2022

AbstractCassava (Manihot esculenta crantz) is a major food crop in Sub-Saharan Africa, Asia, the Pacific, and South America, where it feeds around 800 million people. Its roots are an excellent source of energy, and its leaves are rich in minerals, vitamins, and protein, which could substantially supplement the current starchy diets if properly detoxified since they contain some toxic anti-nutritional factors. The objective of this study was to provide information on the nutritional profile of cassava root and leaves and role of processing in enhancing and stabilizing their valuable nutrients. Two cassava varieties, kello and qulle, obtained from Areca Agricultural Research Center were used in this study. Roots and leaves were processed (fermented, boiled, and fluid bed dried), and nutritional, anti-nutritional, and functional properties were assessed using AOAC (Association of Official Analytical Chemists) standard procedures. As compared to leaves, roots had higher carbohydrate contents, ranging from 81.0 to 87.1 g/100g, whereas leaves had higher protein (21.2 to 28.4g/100g), total carotenoid (234.1 to 987.9 μg/g), fiber (16.1 to 22.9 g/100g), Ca (499.8 to 545.4 mg/100g), K (1193.4 to 1211.0 mg/100g), Mg (274.5 to 340.5 mg/100g) and Fe (129.1 to 146.1 mg/kg) contents. Anti-nutritional factors were slightly higher in the leaves than in the roots, with toxic cyanides ranging from 10.1 to 61.0 mg/kg in the leaves and from 1.8 to 47.5 mg/kg in the roots. However, the processing of leaves decreased cyanide content from 61.0 mg/kg to 10.1 mg/kg. Similarly, other anti-nutritional factors, such as condensed tannins, oxalates, and phytate were reduced from 52.0 to 21.0 mg/100g, 156.5 to 25.9 mg/100g, and 35.9 to 4.0 mg/100g), respectively. Hence, the fermentation of leaves and roots followed by boiling and drying is an interesting approach to reduce anti-nutritional factors significantly and ensure their nutritional quality. This study revealed that variety kello had a relatively better nutritional profile than variety qulle, for both root and leaves, except for total carotenoid content, which was higher in the latter. Genetic background and processing methods can greatly affect the nutritional profile of cassava varieties, so it is critical to analyze diverse cassava germplasm and refine the processing method to identify highly nutritious and healthy varieties.
Monitoring conservation effectiveness in tropical forests: bushmeat offtake parameters vary more quickly compared to parameters related to the living wildlife community
Authors: Kuenbou Jacques Keumo , Tagg Nikki , Khan Donald Mbohli , Speelman Stjin , Willie Jacob 
Published: February 2022

AbstractEvaluating the effectiveness of conservation actions in tropical forests is essential. Generally based on the monitoring of living wildlife communities, combination with bushmeat extraction indicators is seldom used. It is therefore interesting to carry out a monitoring of indices related to these two categories of indicators in order to identify indices presenting more temporal variation and allowing for a rapid detection of real changes. Between 2017 and 2020, data on bushmeat offtake were recorded and surveys of wildlife and human activity signs were conducted in a conservation zone in Dja Biosphere Reserve in Cameroon. Data were collected around villages where human pressure is high. Our results show a decline in total biomass and number of animals killed. An increase in numbers of traps set was observed, but there was no notable difference in the mean biomass of a carcass and mean number of hunting trips. Overall, wildlife abundance decreased slightly in 2020, mainly reflecting changes for three species—bay duiker (Cephalophus dorsalis), yellow-backed duiker (Cephalophus sylvicultor) and red river hog (Potamocherus porcus)—which were more abundant in 2018. Regarding keystone species, we noted a slight increase in the abundance of chimpanzees. Patterns of species richness in both study years were similar. These results suggest that bushmeat offtake data may be more informative for early evaluations of the effectiveness of wildlife conservation efforts. This underlines the importance of monitoring bushmeat for the evaluation of wildlife conservation projects in contexts where hunting occurs.
AAA+ protease-adaptor structures reveal altered conformations and ring specialization
Authors: Kim Sora , Fei Xue , Sauer Robert T. , Baker Tania A. 
Published: February 2022

SummaryClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here, we present high-resolution cryo-EM structures of ClpAPS complexes showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two structural classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated and tucked away from the channel, and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies demonstrate new structures and functions for key AAA+ elements. In addition to ClpAPS delivery, pore-loop tucking may be used broadly by AAA+ unfoldases, for example during enzyme pausing/unloading.
Changes in DNA double-strand break repair during aging correlate with an increase in genomic mutations
Authors: Mojumdar Aditya , Mair Nicola , Adam Nancy , Cobb Jennifer A. 
Published: February 2022

AbstractA double -strand break (DSB) is one of the most deleterious forms of DNA damage. In eukaryotic cells, two main repair pathways have evolved to repair DSBs, homologous recombination (HR) and non-homologous end-joining (NHEJ). HR is the predominant pathway of repair in the unicellular eukaryotic organism, S. cerevisiae. However, during replicative aging the relative use of HR and NHEJ shifts in favor of end-joining repair. By monitoring repair events in the HO-DSB system, we find that early in replicative aging there is a decrease in the association of long-range resection factors, Dna2-Sgs1 and Exo1 at the break site and a decrease in DNA resection. Subsequently, as aging progressed, the recovery of Ku70 at DSBs decreased and the break site associated with the nuclear pore complex at the nuclear periphery, which is the location where DSB repair occurs through alternative pathways that are more mutagenic. End-bridging remained intact as HR and NHEJ declined, but eventually it too became disrupted in cells at advanced replicative age. In all, our work provides insight into the molecular changes in DSB repair pathway during replicative aging. HR first declined, resulting in a transient increase in the NHEJ. However, with increased cellular divisions, Ku70 recovery at DSBs and NHEJ subsequently declined. In wild type cells of advanced replicative age, there was a high frequency of repair products with genomic deletions and microhomologies at the break junction, events not observed in young cells which repaired primarily by HR.HighlightsDecreased DNA resection at DSBs is an early event of replicative agingEnd-joining repair increases as resection decreases at DSBs in older cellsIn older cells the products of DSB repair contain deletions and microhomologiesDSBs associate with the NPC at the nuclear periphery more in older cellsOld Cell Enrichment method suitable for molecular biology approaches in budding yeast
Membrane-catalyzed aggregation of islet amyloid polypeptide is dominated by secondary nucleation
Authors: Elenbaas Barend O.W. , Khemtemourian Lucie , Killian J. Antoinette , Sinnige Tessa 
Published: February 2022

AbstractType II diabetes is characterized by the loss of pancreatic β-cells. This loss is thought to be a consequence of membrane disruption, caused by the aggregation of islet amyloid polypeptide (IAPP) into amyloid fibrils. However, the molecular mechanisms of IAPP aggregation in the presence of membranes have remained unclear. Here, we use kinetic analysis to elucidate the aggregation mechanism of IAPP in the presence of mixed zwitterionic and anionic lipid membranes. The results converge to a model in which aggregation on the membrane is strongly dominated by secondary nucleation, i.e. the formation of new nuclei on the surface of existing fibrils. The critical nucleus consists of a single IAPP molecule, and anionic lipids catalyze both primary and secondary nucleation, but not elongation. The fact that anionic lipids promote secondary nucleation implies that these events take place at the interface between the membrane and existing fibrils, demonstrating that fibril growth occurs at least to some extent on the membrane surface. These new insights into the mechanism of IAPP aggregation on membranes may help to understand IAPP toxicity and will be important for the development of therapeutics to prevent β-cell death in type II diabetes.
IgD+ Age-Associated B cells are the progenitors of the main T-independent B cell response to infection that generates protective Ab and can be induced by an inactivated vaccine in the aged
Authors: Kugler-Umana Olivia , Zhang Wenliang , Kuang Yi , Liang Jialing , Castonguay Catherine H. , Tonkonogy Susan L. , Marshak-Rothstein Ann , Devarajan Priyadharshini , Swain Susan L. 
Published: February 2022

AbstractAge-associated B cells (ABC) accumulate with age and are associated with autoimmunity and chronic infection. However, their contributions to acute infection in the aged and their developmental pathways are unclear. We find that the response against influenza A virus infection in aged mice is dominated by a Fas+GL7- effector B cell population we call infection-induced-ABC (iABC). Most iABC express IgM and include antibody-secreting cells in the spleen, lung and bone marrow. We find that in response to influenza, IgD+CD21-CD23-ABC are the precursors of iABC. These IgD+ABC develop in germ free mice, so are independent of foreign antigen recognition, suggesting they arise from an intrinsic age-associated developmental program. The response of ABC to influenza infection, resulting in iABC, is T cell independent and requires both extrinsic TLR7 and TLR9 signals. In response to influenza infection, IgD+ABC can induce a faster recovery of weight and higher total anti-influenza IgG and IgM titers that can neutralize virus. Immunization with whole inactivated virus also generates iABC in aged mice. Thus, in unimmunized aged mice, whose other B and T cell responses have waned, IgD+ABC are likely the naïve B cells with the potential to become Ab-secreting cells and to provide protection from infection in the aged.
Cryo-EM structures reveal that RFC recognizes both the 3’- and 5’-DNA ends to load PCNA onto gaps for DNA repair
Authors: Zheng Fengwei , Georgescu Roxana E. , Yao Nina Y. , Li Huilin , O’Donnell Michael E. 
Published: February 2022

AbstractRFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases δ and ε. The RFC pentamer forms a central chamber that binds 3’ ss/ds DNA junctions to load PCNA onto DNA during replication. We show here five structures that identify a 2nd DNA binding site in RFC that binds a 5’ duplex. This 5’ DNA site is located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. Our structures reveal ideal binding to a 7-nt gap, which includes 2 bp unwound by the clamp loader. Biochemical studies show enhanced binding to 5 and 10 nt gaps, consistent with the structural results. Because both 3’ and 5’ ends are present at a ssDNA gap, we propose that the 5’ site facilitates RFC’s PCNA loading activity at a DNA damage-induced gap to recruit gap-filling polymerases. These findings are consistent with genetic studies showing that base excision repair of gaps greater than 1 base requires PCNA and involves the 5’ DNA binding domain of Rfc1. We further observe that a 5’ end facilitates PCNA loading at an RPA coated 30-nt gap, suggesting a potential role of the RFC 5’-DNA site in lagging strand DNA synthesis