bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exome re-analysis driven by deep phenotyping increases diagnostic yield
Authors: Dutta Atanu Kumar , Bhunia Niladri Sekhar , Bhowmik Rohit , Mishra Nihar Ranjan , Sonowal Rimjhim , Goswami Kalyan , C Anbu Kayalvizhi 
Published: September 2022

ObjectiveTo explore if clinician driven systematic reanalysis of “negative” exome sequencing data of patients with a strong suspicion of a Mendelian disease by a Clinical Geneticist using deep phenotyping can increase the diagnostic yield.MethodsTen patients were deep phenotyped using Gestalt matching (Face2Gene) and OMIM database searching (Phenomizer) to build a list of candidate genes of interest. The Variant Call Format (vcf) files for individual patients were obtained from the sequencing laboratory and reanalyzed in the wANNOVAR server. The annotated list of variants was queried for the genes of interest. Copy number variant analysis was performed using ExomeDepth (v1.1.10) R package.ResultsA homozygous pathogenic mutation in the NPHP3 gene (c.2805C>T) was identified in one child with Renal-Hepatic-Pancreatic Dysplasia and a multiexon deletion in the CUL7 gene was identified in another child with 3M syndrome.ConclusionsSystematic re-analysis of exome sequencing data by a Clinical Geneticist can increase the diagnostic yield with minimal additional cost.
Reserpine maintains photoreceptor survival in retinal ciliopathy by resolving proteostasis imbalance and ciliogenesis defects
Authors: Chen Holly Y. , Swaroop Manju , Papal Samantha , Mondal Anupam K. , Tawa Gregory J. , Regent Florian , Shimada Hiroko , Nagashima Kunio , de Val Natalia , Jacobson Samuel G. , Zheng Wei , Swaroop Anand 
Published: September 2022

AbstractCiliopathies manifest from sensory abnormalities to syndromic disorders with multiorgan pathologies, with retinal degeneration a highly penetrant phenotype. Photoreceptor cell death is a major cause of incurable blindness in retinal ciliopathies. To identify drug candidates to maintain photoreceptor survival, we performed an unbiased, high-throughput screening of over 6,000 bioactive small molecules using retinal organoids differentiated from induced pluripotent stem cells (iPSC) of rd16 mouse, which is a model of Leber congenital amaurosis (LCA)10 caused by mutations in the cilia-centrosomal gene CEP290. We identified five non-toxic positive hits, including the lead molecule reserpine, which improved photoreceptor survival in rd16 organoids. Reserpine also maintained photoreceptors in retinal organoids derived from induced pluripotent stem cells of LCA10 patients and in rd16 mouse retina in vivo. Reserpine-treated patient organoids revealed modulation of signaling pathways related to cell survival/death, metabolism, and proteostasis. Further investigation uncovered misregulation of autophagy associated with compromised primary cilium biogenesis in patient organoids and rd16 mouse retina. Reserpine partially restored the balance between autophagy and the ubiquitin-proteasome system, at least in part by increasing the cargo adaptor p62 and improving primary cilium assembly. Our study identifies effective drug candidates in preclinical studies of CEP290 retinal ciliopathies through cross-species drug discovery using iPSC-derived organoids, highlights the impact of proteostasis in the pathogenesis of ciliopathies, and provides new insights for treatments of retinal neurodegeneration.
Intraoperative phrenic stimulation offsets diaphragm fiber weakness during cardiothoracic surgery
Authors: Bresciani Guilherme , Beaver Thomas , Martin A. Daniel , van der Pijl Robbert , Mankowski Robert , Leeuwenburgh Christiaan , Ottenheijm Coen A.C. , Martin Tomas , Arnaoutakis George , Ahmed Shakeel , Mariani Vinicius , Xue Wei , Smith Barbara K. , Ferreira Leonardo F. 
Published: September 2022

ABSTRACTRationaleMechanical ventilation rapidly induces slow and fast fiber contractile dysfunction in the human diaphragm, which could be attenuated by phrenic nerve stimulation. Here, we present data from a controlled trial of intraoperative phrenic stimulation to offset slow and fast fiber contractile dysfunction and myofilament protein derangements.ObjectivesIn this study, we tested the hypothesis that intraoperative hemidiaphragm stimulation would mitigate slow and fast fiber loss of contractile function in the human diaphragm.MethodsNineteen adults (9 females, age 59 ±12 years) consented to participate. Unilateral phrenic twitch stimulation was applied for one minute, every 30 minutes during cardiothoracic surgery. Thirty minutes following the last stimulation bout, biopsies were obtained from the hemidiaphragms for single fiber force mechanics and quantitation of thin filament protein abundance. Effects of stimulation and fiber type on force mechanics were evaluated with linear mixed models with the subject treated as a random intercept effect.Measurements and Main ResultsSubjects underwent 6 ±2 hemidiaphragm stimulations at 17 ±6 mA, during 278 ±68 minutes of mechanical ventilation. In slow-twitch fibers, cross-sectional area (p<0.0001) and specific force (p<0.0005) were significantly greater on the stimulated side. Longer-duration surgeries were associated with lower slow-twitch specific force (p<0.001). Stimulation did not alter contractile function of fast-twitch fibers or calcium-sensitivity in either fiber type. There were no differences in abundance or phosphorylation of myofilament proteins.ConclusionUnilateral phrenic stimulation during open chest surgery preserved contractile function of slow-twitch diaphragm fibers, but had no effect on relative abundance of sarcomeric proteins.
Schistosoma mansonicercarial invadolysin cleaves complement C3 and suppresses proinflammatory cytokine production
Authors: Hambrook Jacob R. , Hanington Patrick C. 
Published: September 2022

AbstractSchistosoma mansoniemploys immune evasion and immunosuppression to overcome immune responses mounted by its snail and human hosts. Myriad immunomodulating factors underlie this process, some of which are proteases. Here, we demonstrate that one protease, an invadolysin we have termed SmCI-1, is released from the acetabular glands ofS. mansonicercaria and is involved in creating an immunological milieu favorable for survival of the parasite. We confirm the presence of SmCI-1 in the cercarial stage ofS. mansoniand demonstrate that it is released during transformation into the schistosomula. We confirm SmCI-1 functions as a metalloprotease with the capacity to cleave collagen type IV, gelatin and fibrinogen. We also show that complement component C3b is cleaved by this protease, resulting in inhibition of the classical and alternative complement pathways. Finally, we assess the effect of SmCI-1 on cytokine release from human peripheral blood mononuclear cells, providing compelling evidence that SmCI-1 promotes an anti-inflammatory microenvironment by enhancing production of IL-10 and suppressing the production of inflammatory cytokines like IL-1B and IL-12p70 and those involved in eosinophil recruitment and activation, like eotaxin-1 and IL-5.
ZnO nanoparticles and SWCNT induced general stress response pathway in HepG2 cells at non-cytotoxic doses revealed by RNA sequencing
Authors: Mittal Deepti , Ali Syed Azmal , Kaul Gautam 
Published: September 2022

AbstractNanoparticles (NPs) are important in a variety of sectors, including disease diagnostics, medicine, nutrition, and many other industries. The risk of human exposure demands an early evaluation of both the basic dynamics of NPs’ interaction with biological systems and their potential consequences. Deciphering these occurrences will provide critical information regarding the health hazards and safety advantages associated with next-generation nanoformulations in clinical practice. We examined the HepG2 cell line in a systematic manner to determine the cellular response to single-walled carbon nanotubes (SWCNTs) and zinc oxide (ZnO) NPs. With the use of high-throughput transcriptomic methods, we found that both NPs induce comparable dysregulation of the endocytic and proteasomal complex genes in liver hepatocellular carcinoma cells, at levels (> 80 percent cell viability) that do not cause over-toxicity at early incubation period (6 h). SWCNT and ZnO NPs were shown to enter cells through clathrin-mediated pathways, affecting cytoskeleton gene expression, DNA damage and repair, protein ubiquitination, and cell transcriptional machinery. Our findings indicate that early response strategies activate stress-related mechanisms. Finally, this method for studying nanomaterial–cell interactions demonstrates how changes in the transcriptome profile may predict downstream consequences even at doses that do not cause acute toxicity.
A second generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives
Authors: Zhang Junli , Debernardi Juan M. , Burguener German , Choulet Frédéric , Paux Etienne , O’Connor Lauren , Enk Jacob , Dubcovsky Jorge 
Published: September 2022

ABSTRACTAs genome resources for wheat expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here, we developed an updated regulatory region enrichment capture for wheat (TriticumL.) and otherTriticeaespecies. The core target space includes sequences from two Kbp upstream of each gene predicted in the Chinese Spring wheat genome (IWGSC RefSeq Annotation v1.1) and regions of open chromatin identified with ATAC-seq from wheat leaf and root samples. To improve specificity, we aggressively filtered candidate repetitive sequences using a combination of BLASTN searches to the Triticeae Repetitive Sequence Database (TREP), identification of regions with read over-coverage from previous target enrichment experiments, and k-mer frequency analyses. The final design comprises 216 Mbp of predicted hybridization space in hexaploid wheat and showed increased specificity and coverage of targeted sequences relative to previous protocols. Test captures on hexaploid and tetraploid wheat and other diploid cereals show that the assay has broad potential utility for cost-effective promoter and open chromatin resequencing and general-purpose genotyping of variousTriticeaespecies.
Metagenomic analysis of concrete bridge reveals a microbial community dominated by halophilic Bacteria and Archaea
Authors: Kiledal E. Anders , Shaw Mark , Polson Shawn W. , Maresca Julia A. 
Published: September 2022

AbstractConcrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both diversity and function of the microbial community in concrete, but because the biomass in concrete is so low, this analysis is highly affected by laboratory contamination. Here, we demonstrate improved DNA extraction from concrete, and show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing. DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with Illumina MiSeq. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Prior work found that halophilic bacteria were relatively rare in younger concrete samples, which had abundant oligotrophic taxa. These results suggest that as concrete ages and weathers, salt and osmotic stresses become more important selective pressures, and suggest that long-term persistence and performance of microbes for biorepair or biosensing applications might improve if halophilic strains were used.
Splicing-dependent transcriptional activation
Authors: Uriostegui-Arcos Maritere , Mick Steven T. , Shi Zhuo , Rahman Rufuto , Fiszbein Ana 
Published: September 2022

SummaryTranscription and splicing are intrinsically coupled. Transcription dynamics regulate splicing, and splicing feeds back to transcription initiation to jointly determine gene expression profiles. A recently described phenomenon called exon-mediated activation of transcription starts (EMATS) shows that splicing of internal exons can regulate transcription initiation and activate cryptic promoters. Here, we present the first complete catalog of human EMATS genes that have a weak alternative promoter located upstream and proximate to an efficiently spliced internal skipped exon. We found that EMATS genes are associated with Mendelian genetic diseases —specifically intellectual development disorders, cardiomyopathy, and immunodeficiency— and provide a list of EMATS genes with pathological variants. EMATS was originally described as a natural mechanism used during evolution to fine-tune gene expression through punctual genomic mutations that affect splicing. Here, we show that EMATS can be used to manipulate gene expression with therapeutic purposes. We constructed stable cell lines expressing a splicing reporter based on the alternative splicing of exon 7 of SMN2 gene under the regulation of different promoters. Using a small molecule (Risdiplam) and an antisense oligonucleotide (ASO) modeled after Spinraza, we promoted the inclusion of SMN2 exon 7 which triggered an increase in gene expression up to 40-folds by activating transcription initiation. We observed the strongest effects in reporters under the regulation of weak human promoters, where the highest drug doses dramatically increased exon inclusion. Overall, our findings present evidence to develop the first therapeutic strategy to use EMATS to activate gene expression using small molecules and ASOs that affect splicing.
Supervised Machine Learning Enables Geospatial Microbial Provenance
Authors: Bhattacharya Chandrima , Tierney Braden T. , Ryon Krista A. , Bhattacharyya Malay , Hastings Jaden J. A. , Basu Srijani , Bhattacharya Bodhisatwa , Bagchi Debneel , Mukherjee Somsubhro , Wang Lu , Henaff Elizabeth M. , Mason Christopher E. 
Published: September 2022

AbstractThe recent increase in publicly available metagenomic datasets with geospatial metadata has made it possible to determine location-specific, microbial fingerprints from around the world. Such fingerprints can be useful for comparing microbial niches for environmental research, as well as for applications within forensic science and public health. To determine the regional specificity for environmental metagenomes, we examined 4305 shotgun-sequenced samples from the MetaSUB Consortium dataset – the most extensive public collection of urban microbiomes, spanning 60 different cities, 30 countries, and 6 continents. We were able to identify city-specific microbial fingerprints using supervised machine learning (SML) on the taxonomic classifications, and we also compared the performance of ten SML classifiers. We then further evaluated the five algorithms with the highest accuracy, with the city and continental accuracy ranging from 85-89% to 90-94%, respectively. We then used these results to develop Cassandra, a random-forest-based classifier that identifies indicator species to aid in fingerprinting and can infer higher-order microbial interactions at each site. We further tested the Cassandra algorithm on the Tara Oceans dataset, the largest collection of marine-based microbial genomes, where it classified the oceanic sample locations with 83% accuracy. These results and code show the utility of SML methods and Cassandra to identify bioindicator species across both oceanic and urban environments, which can help guide ongoing efforts in biotracing, environmental monitoring, and microbial forensics (MF).
In-vitro activity of Cefiderocol against clinical isolates of meropenem-resistant Klebsiella pneumoniae from India
Authors: Borde Kalyani , Kareem M A , Sharma Ratna Mani , Dass S Manick , Ravi Vedantham , Mathai Dilip 
Published: September 2022

AbstractBackgroundCefiderocol (FDC), a novel siderophore drug, is active against gram negative bacteria producing carbapenemases, including metallo-beta-lactamases.ObjectiveTo compare the in-vitro activity of FDC with ceftazidime-avibactam (CZA), CZA/ aztreonam (AT) combination and colistin (CST), in clinical isolates of meropenem-resistant (MER-R) Klebsiella pneumoniae.MethodsFrom 2052 clinical specimens submitted for culture testing, 245 K. pneumoniae isolates were recovered within a six month period in 2021. 103 non-duplicate, non-outbreak, MER-R (MIC >4 μg/ml) strains were included in the study. Identification and susceptibility was performed using VITEK-2 (bioMérieux). 10 meropenem-susceptible isolates served as controls. For FDC, BMD was performed after in-house standardisation. Disc diffusion (Liofilchem, Italy) and broth microdilution (BMD; ComASP, STC, Liofilchem, Italy) were used for susceptibility testing of CZA and CST respectively. Synergy testing for CZA and aztreonam (AT) was performed using disk approximation method. CLSI breakpoints were used for interpretation of results.ResultsFor FDC, MIC50 and MIC90 was 2 μg/ml and 8 μg/ml, respectively. 80% isolates were susceptible to FDC. 26.2% isolates were susceptible to CZA, synergy testing with CZA/ AT was positive for 74 (72%) of the isolates. 89.3% had intermediate susceptibility to CST. Nine (8.7%) were susceptible only to FDC.ConclusionFDC is active in-vitro against MER-R K. pneumoniae > CZA/AT> CZA > CST, as observed in this study, applying CLSI criteria. Clinico-microbiological studies should be performed for assessing clinical efficacy of this novel drug in this region with high prevalence of carbapenem resistance among gram-negative organisms.
STAT1 is required to establish but not maintain IFNγ-induced transcriptional memory
Authors: Tehrani Sahar S.H. , Mikulski Pawel , Abdul-Zani Izma , Mata João F. , Siwek Wojciech , Jansen Lars E.T. 
Published: September 2022

AbstractExposure of human cells to interferon-γ (IFNγ) results in a mitotically heritable yet reversible state called long-term transcriptional memory. We previously identified the clustered GBP genes as strongly primed by IFNγ. Here we discovered that in primed cells, both interferon-responsive transcription factors STAT1 and IRF1 target chromatin with accelerated kinetics upon re-exposure to IFNγ, specifically at promotors of primed genes. Priming does not alter the degree of IFNγ-induced STAT1 activation or nuclear import, indicating that memory does not alter upstream JAK-STAT signalling. We found STAT1 to be critical to establish transcriptional memory but in a manner that is independent of mere transcription activation. Interestingly, while Serine 727 phosphorylation of STAT1 was maintained during the primed state, STAT1 is not required for the heritability of GBP gene memory. Our results suggest that memory of interferon exposure constitutes a STAT1-mediated, heritable state that is established during priming. This renders GBP genes poised for subsequent STAT1 and IRF1 binding and accelerated gene activation upon a secondary interferon exposure.
CD73 generated extracellular adenosine promotes resolution of neutrophil-mediated tissue injury and restrains metaplasia in pancreatitis
Authors: O’Brien Baylee J. , Faraoni Erika Y. , Strickland Lincoln N. , Ma Zhibo , Mota Victoria , Mota Samantha , Chen Xuebo , Mills Tingting , Eltzschig Holger K. , DelGiorno Kathleen E. , Bailey-Lundberg Jennifer M. 
Published: September 2022

ABSTRACTBackground and AimsPancreatitis is currently the leading cause of gastrointestinal hospitalizations in the US. This condition occurs in response to abdominal injury, gallstones, chronic alcohol consumption or, less frequently, the cause remains idiopathic. CD73 is a cell surface ecto-5’-nucleotidase that generates extracellular adenosine, which can contribute to resolution of inflammation by binding adenosine receptors on infiltrating immune cells. We hypothesized genetic deletion of CD73 would result in more severe pancreatitis due to decreased generation of extracellular adenosine.MethodsCD73 knockout (CD73-/-) and C57BL/6 (wild type, WT) mice were used to evaluate the progression and response of caerulein-induced acute and chronic pancreatitis.ResultsIn response to caerulein-mediated chronic or acute pancreatitis, WT mice display resolution of pancreatitis at earlier timepoints than CD73-/- mice. Using immunohistochemistry and analysis of single cell RNA-seq (scRNA-seq) data, we determined CD73 localization in chronic pancreatitis is primarily observed in mucin/ductal cell populations and immune cells. In murine pancreata challenged with caerulein to induce acute pancreatitis, we compared CD73-/- to WT mice and observed a significant infiltration of Ly6G+, MPO+, and Granzyme B+ cells in CD73-/- compared to WT pancreata and we quantified a significant increase in acinar-to-ductal metaplasia demonstrating sustained metaplasia and inflammation in CD73-/- mice. Using neutrophil depletion in CD73-/- mice, we show neutrophil depletion significantly reduces metaplasia defined by CK19+ cells per field and significantly reduces acute pancreatitis.ConclusionsThese data identify CD73 agonists as a potential therapeutic strategy for patients with acute and chronic pancreatitis as adenosine generation and activation of adenosine receptors is critical to resolve persistent inflammation in the pancreas.Graphical Abstract
Heterotypic electrostatic interactions control complex phase separation of tau and prion into multiphasic condensates and co-aggregates
Authors: Rai Sandeep K. , Khanna Roopali , Avni Anamika , Mukhopadhyay Samrat 
Published: September 2022

AbstractBiomolecular condensates formed via phase separation of proteins and nucleic acids are thought to perform a wide range of critical cellular functions by maintaining spatiotemporal regulation and organizing intracellular biochemistry. However, aberrant phase transitions are implicated in a multitude of human diseases. Here, we demonstrate that two neuronal proteins namely, tau and prion undergo complex coacervation driven by domain-specific electrostatic interactions to yield highly dynamic, mesoscopic liquid-like droplets. The acidic N-terminal segment of tau interacts electrostatically with the polybasic N-terminal intrinsically disordered segment of the prion protein (PrP). We employed a unique combination of time-resolved tools that encompass several orders of magnitude of timescales ranging from nanoseconds to seconds. These studies unveil an intriguing orchestra of molecular events associated with the formation of heterotypic condensates comprising ephemeral, domain-specific, short-range electrostatic nanoclusters. Our results reveal that these heterotypic condensates can be tuned by RNA in a stoichiometry-dependent manner resulting in reversible, multiphasic, immiscible, ternary condensates of different morphologies ranging from core-shell to nested droplets. This ternary system exhibits a typical three-regime phase behavior reminiscent of other membraneless organelles including nucleolar condensates. We also show that upon aging, tau-PrP droplets gradually convert into solid-like co-assemblies by sequestration of persistent intermolecular interactions. Our vibrational Raman spectroscopic data in conjunction with atomic force microscopy and multi-color fluorescence imaging results reveal the presence of amorphous and amyloid-like co-aggregates upon maturation. Our findings provide mechanistic underpinnings of overlapping neuropathology involving tau and PrP and highlight a broader role of complex phase transitions in physiology and disease.