bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France
Authors: Hamame Afaf , Davoust Bernard , Rolain Jean-Marc , Diene Seydina M. 
Published: September 2021

ABSTRACTThe current study is about genomic characterisation of an atypical multidrug-resistant Escherichia coli harbouring two mobilised colistin resistance (mcr) genes isolated from pigs in France. Stool samples taken from a pig farm in Avignon in the department of the Vaucluse were subjected to a molecular screening for the detection of mcr gene variants. These samples were cultured on selective LBJMR medium. Growing bacteria were identified using MALDI-TOF, followed by antibiotic susceptibility testing (AST). Whole genome sequencing (WGS) and bioinformatic genome analysis was performed. The selective culture of stools revealed the presence of an E. coli strain named Q4552 which was simultaneously positive for the mcr-1.1 and mcr-3.5 genes. This strain exhibited resistance phenotype to fourteen antibiotics, including colistin. Genome sequencing revealed a circular chromosome and eight plasmids. Genomic analysis revealed a chromosomic integration of a mobile genetic element (MGE) harbouring the mcr-1.1 gene, while the mcr-3.5 gene was plasmidic (i.e., an IncFII plasmid). Its resistome exhibited twenty-two resistance genes, explaining its multidrug resistance phenotype. The Q4552 strain is an ST-843 clone belonging to the clonal complex Cplx-568 and is the only ST type of this cplx-568 which has been isolated from animals, humans, and the environment. Here, we report the first co-occurrence of the mcr-1 and mcr-3 genes in France from a pathogenic E. coli strain isolated from a pig farm. Since this clone (ST-843) has been reported in zoonotic transmissions, programs to monitor such colistin resistant bacterium are urgently required to avoid its spread and zoonotic transmission to humans.
A large-volume sputum dry storage and transportation device for molecular and culture-based diagnosis of tuberculosis
Authors: Dsouza Andrea , Jangam Saylee , Naik Vishwanath , Manjula J. , Nair Chandrasekhar B. , Toley Bhushan J. 
Published: September 2021

AbstractTechnologies for preservation of specimens in the absence of cold chains are essential for optimum utilization of existing laboratory services in the developing world. We present a prototype called specimen transportation tube (SPECTRA-tube) for the collection, exposure-free drying, ambient transportation, and liquid state recovery of large-volume (>1 mL) specimens. Specimens introduced into SPECTRA-tube are dried in glass fiber membranes, which are critical for efficient liquid-state sample recovery by rehydration and centrifugation. Mycobacterium smegmatis (Msm)-spiked mock sputum dried in native Standard 17 glass fiber was stable for molecular testing after 10-day storage at 45°C, and for culture testing after 10- and 5-day storage at 37°C and 45°C, respectively. Compatibility with human sputum storage was demonstrated by dry storing Mycobacterium bovis-spiked pooled human sputum in SPECTRA-tube for 5 days at room temperature followed by successful qPCR detection. By significantly increasing the volume of samples that can be transported in the dry state and enabling recovery of the entire sample in liquid state, SPECTRA-tube presents a potential universal solution for the preservation and transportation of liquid specimens.
Numb is required for optimal contraction of skeletal muscle
Authors: De Gasperi Rita , Mo Chenglin , Azulai Daniella , Wang Zhiying , Harlow Lauren M. , Du Yating , Graham Zachary , Pan Jiangping , Liu Xin-hua , Guo Lei , Zhang Bin , Ko Fred , Raczkowski Ashleigh M , Bauman William A. , Goulbourne Chris N , Zhao Wei , Brotto Marco , Cardozo Christopher P. 
Published: September 2021

ABSTRACTBackgroundThe role of Numb, a protein that is important for cell fate and development was investigated in adult skeletal muscle in mice using a conditional, inducible knockout (cKO) model.MethodsNumb expression was evaluated by Western blot. Numb localization was determined by confocal microscopy. The effects of cKO of Numb and the closely-related gene Numb-like in skeletal muscle fibers was evaluated by in-situ physiology; transmission and focused ion beam scanning electron microscopy; 3-dimensional reconstruction of mitochondrial; lipidomics; and bulk RNA-sequencing. Additional studies using primary mouse myotubes investigated the effects the effects of Numb knockdown on cell fusion, mitochondrial function and calcium transients.ResultsNumb protein expression was reduced by ∼70% (p < 0.01) at 24 as compared to 3 months of age. Numb was localized within muscle fibers as bands traversing fibers at regularly spaced intervals in close proximity to dihydropyridine receptors.The cKO of Numb and Numb-like reduced specific tetanic force by 36%, p < 0.01), altered mitochondrial spatial relationships to sarcomeric structures, increased Z-line spacing by 30% (p < 0.0001), perturbed sarcoplasmic reticulum organization and reduced mitochondrial volume by over 80% (p < 0.01). Only six genes were differentially expressed in cKO mice: Itga4, Sema7a, Irgm2, Vezf1, Mib1 and Tmem132a. Several lipid mediators derived from polyunsaturated fatty acid (PUFAs) through lipoxygenases were upregulated in Numb cKO skeletal muscle; 12-HEPE was increased by ∼250% (p < 0.05) and 17,18-EpETE by ∼240% (p < 0.05). In mouse primary myotubes, Numb knock-down reduced cell fusion (∼20%, p < 0.01) and mitochondrial function and delayed the caffeine-induced rise in cytosolic calcium concentrations by more than 100% (p < 0.01).ConclusionsThese findings implicate Numb as a critical factor in skeletal muscle structure and function which appear to be critical for calcium release; we therefore speculate Numb plays critical roles in excitation-contraction coupling, one of the putative targets of aged skeletal muscles. These findings provide new insights into the molecular underpinnings of the loss of muscle function observed with sarcopenia.
GLS1 is a protective factor rather than a molecular target in ARID1A-mutated ovarian clear cell carcinoma
Authors: Clemente Valentino , Nelson Andrew , Erickson Britt , Baker Ruth , Rubin Nathan , Khalifa Mahmoud , Hoshino Asumi , Shetty Mihir , Lou Emil , Bazzaro Martina 
Published: September 2021

AbstractTargeting glutamine metabolism has emerged as a novel therapeutic strategy for several human cancers, including ovarian cancer. The primary target of this approach is the kidney isoform of glutaminase, glutaminase 1 (GLS1), a key enzyme in glutamine metabolism that is overexpressed in several human cancers. A first-in-class inhibitor of GLS1, called CB839 (Telaglenastat), has been investigated in several clinical trials, with promising results. The first clinical trial of CB839 in platinum-resistant ovarian cancer patients is forthcoming. ARID1A-mutated ovarian clear cell carcinoma (OCCC) is a relatively indolent and chemoresistant ovarian cancer histotype. In OCCC-derived cells in vitro and mouse models, loss of ARID1A leads to upregulation of GLS1. Thus, targeting of GLS1 with CB839 has been suggested as a targeted approach for OCCC patients with tumors harboring ARID1A-mutations. Here, we investigated whether GLS1 is differentially expressed between OCCC patients whose tumors are ARID1A positive and patients whose tumors are ARID1A negative. In clinical specimens of OCCC, we found that GLS1 overexpression was not correlated with ARID1A loss. In addition, GLS1 overexpression was associated with better clinical outcomes. Our findings suggest that GLS1 expression in OCCC may be a protective factor and that caution should be taken when considering the use of CB839 to treat OCCC patients.
A separation-of-functionZIP4wheat mutant allows crossover between related chromosomes and is meiotically stable
Authors: Martín Azahara C. , Alabdullah Abdul Kader , Moore Graham 
Published: September 2021

ABSTRACTMany species, including most flowering plants, are polyploid, possessing multiple genomes. During polyploidisation, fertility is preserved via the evolution of mechanisms to control the behaviour of these multiple genomes during meiosis. On the polyploidisation of wheat, the major meiotic geneZIP4duplicated and diverged, with the resulting new geneTaZIP4-B2being inserted into chromosome 5B. Previous studies showed that thisTaZIP4-B2promotes pairing and synapsis between wheat homologous chromosomes, whilst suppressing crossover between related (homoeologous) chromosomes. Moreover, in wheat, the presence ofTaZIP4-B2preserves up to 50% of grain number. The present study exploits a ‘separation-of-function’ wheatTazip4-B2mutant namedzip4-ph1d, in which theTazip4-B2copy still promotes correct pairing and synapsis between homologues (resulting in the same pollen profile and fertility normally found in wild type wheat), but which also allows crossover between the related chromosomes in wheat haploids of this mutant. This suggests an improved utility for the newzip4-ph1dmutant line during wheat breeding exploitation, compared to the previously described CRISPRTazip4-B2andph1mutant lines. The results also reveal that loss of suppression of homoeologous crossover between wheat chromosomes does not in itself reduce wheat fertility when promotion of homologous pairing and synapsis byTaZIP4-B2is preserved.
Metabolic modeling of the International Space Station microbiome reveals key microbial interactions
Authors: Kumar Rachita K. , Singh Nitin K. , Balakrishnan Sanjaay , Parker Ceth W. , Raman Karthik , Venkateswaran Kasthuri 
Published: September 2021

AbstractBackgroundRecent studies have provided insights into the persistence and succession of microbes aboard the International Space Station (ISS), notably the dominance of Klebsiella pneumoniae. However, the interactions between the various microbes aboard the ISS, and how it shapes the microbiome remain to be clearly understood. In this study, we apply a computational approach to predict possible metabolic interactions in the ISS microbiome and shed further light on its organization.ResultsThrough a combination of a systems-based graph-theoretical approach, and a constraint-based community metabolic modelling approach, we demonstrated several key interactions in the ISS microbiome. These complementary approaches provided insights into the metabolic interactions and dependencies present amongst various microbes in a community, highlighting key interactions and keystone species. Our results showed that the presence of K. pneumoniae is beneficial to many other microorganisms it coexists with, notably those from the Pantoea genus. Species belonging to the Enterobacteriaceae family were often found to be the most beneficial for the survival of other microorganisms in the ISS microbiome. However, K. pneumoniae was found to exhibit parasitic and amensalistic interactions with Aspergillus and Penicillium species, respectively. To prove this metabolic prediction, K. pneumoniae and Aspergillus fumigatus were co-cultured under normal and simulated microgravity, where K. pneumoniae cells showed parasitic characteristics to the fungus. The electron micrography revealed that the presence of K. pneumoniae compromised the morphology of fungal conidia and its biofilm biofilm-forming structures.ConclusionsOur study underscores the importance of K. pneumoniae in the ISS, and its potential contribution to the survival (mutualism) and eradication (parasitism) of other microbes, including potential pathogens. This integrated modelling approach, combined with experiments, demonstrates immense potential for understanding the organization of other such microbiomes, unravelling key organisms and their interdependencies.
Allosteric mechanism of signal transduction in the two-component system histidine kinase PhoQ
Authors: Mensa Bruk , Polizzi Nicholas F. , Molnar Kathleen , Natale Andrew , Lemmin Thomas , DeGrado William F. 
Published: September 2021

AbstractTransmembrane signaling proteins couple extracytosolic sensors to cytosolic effectors. Here, we examine how binding of Mg2+ to the sensor domain of an E. coli two component histidine kinase (HK), PhoQ, modulates its cytoplasmic kinase domain. We use cysteine-crosslinking and reporter-gene assays to simultaneously and independently probe the signaling state of PhoQ’s sensor and autokinase domains in a set of over 30 mutants. Strikingly, conservative single-site mutants distant from the sensor or catalytic site strongly influence PhoQ’s ligand-sensitivity as well as the magnitude and direction of the signal, endowing diverse signaling characteristics without need for epistasis. Data from 35 mutants are explained by a semi-empirical 3-domain model in which the sensor, intervening HAMP, and catalytic domains can adopt kinase-promoting or inhibiting conformations, that are in allosteric communication. The catalytic and sensor domains intrinsically favor a constitutively ‘kinase-on’ conformation, while the HAMP favors the ‘off’ state; when coupled, they create a bistable system responsive to physiological [Mg2+]. Mutants alter signaling by locally modulating these intrinsic equilibrium constants and couplings. Our model suggests signals transmit via interdomain allostery rather than propagation of a single concerted conformational change, explaining the diversity of signaling structural transitions observed in individual HK domains.
Plasma derived cell-free mitochondrial DNA originates mainly from circulating cell-free mitochondria
Authors: Roch Benoit , Pisareva Ekaterina , Sanchez Cynthia , Pastor Brice , Tanos Rita , Mirandola Alexia , Mazard Thibault , Amir Dache Zahra Al , Thierry Alain R. 
Published: September 2021

ABSTRACTCirculating mitochondrial DNA (cir-mtDNA) could have a potential comparable to circulating nuclear DNA (cir-nDNA), with numerous applications. However, research and development in this area have fallen behind, particularly considering its origin and structural features. To tackle this, we initially combined Q-PCR and low-pass whole genome sequencing in the same analytical strategy previously and successfully used for cir-nDNA. This revealed unexplained structural patterns and led us to correlate these data with observations made during physical examinations such as filtration, and differential centrifugation in various plasma preparations. Both the integrity index and number of reads revealed a very minor proportion of low size-ranged fragments (<1000 bp) in plasma obtained with a standard preparation (0.06%). Filtration and high speed second step centrifugation revealed that 98.7 and 99.4% corresponded to extracellular mitochondria either free or in large extracellular vesicles. When avoiding platelet activation during plasma preparation, the proportion of both types of entities was still preponderant (76-80%), but the amount of detected mitochondrial DNA decreased 67-fold. In correlation with our previous study on the presence of circulating cell-free mitochondria in blood, our differential centrifugation procedure suggested that cir-mtDNA is also associated with approximately 18% small extracellular vesicles, 1.7% exosomes and 4% protein complexes.
Protein Structure Prediction Using a Maximum Likelihood Formulation of a Recurrent Geometric Network
Authors: Qi Guowei , Tollefson Mallory R. , Gogal Rose A. , Smith Richard J. H. , AlQuraishi Mohammed , Schnieders Michael J. 
Published: September 2021

AbstractOnly ∼40% of the human proteome has structural coordinates available from experiment (i.e., X-ray crystallography, NMR spectroscopy, or cryo-EM) or homology modeling with quality templates (i.e., 30% sequence identity or greater), leaving most of the proteome structurally unsolved. Deep learning (DL) methods for predicting protein structure can help close knowledge gaps where experimental and homology models are difficult to obtain. Recent advances in these DL methods have shown promising results in expanding structural coverage to the scale of the entire human proteome, providing researchers with more complete protein structural information. Here, we improve upon an existing DL algorithm for protein structure prediction, the Recurrent Geometric Network (RGN). We first expand the training dataset to include experimental uncertainty data in the form of atomic displacement parameters, then derive a maximum likelihood loss function that incorporates this uncertainty data into model training. Compared to the original RGN, our novel maximum likelihood model improves the rate of convergence of initial model training and ultimately results in more accurate structure prediction according to the root mean square deviation (RMSD) of backbone atoms, the Global Distance Test (GDT), the Global Distance Test High Accuracy (GDT-HA), and the Template-Modeling Score (TM-Score). Our model also predicts structures with more favorable backbone torsions, which provide more accurate starting coordinates for downstream physics-based simulations. Based on these results, our maximum likelihood reformulation provides a framework for improving existing or future machine learning algorithms for protein structure prediction. The augmented dataset, data collection scripts, reformulated RGN source code, and a series of trained models are publicly available at https://github.com/SchniedersLab/likelihood-rgn.
Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors
Authors: Reher Raphael , Aron Allegra T , Fajtová Pavla , Stincone Paolo , Liu Chenxi , Ben Shalom Ido Y , Bittremieux Wout , Wang Mingxun , Matos-Hernandez Marie L , Alexander Kelsey L , Caro-Diaz Eduardo J , Naman C Benjamin , Hughes Chambers C. , Dorrestein Pieter C , O’Donoghue Anthony J , Gerwick William H , Petras Daniel 
Published: September 2021

AbstractThe identity and biological activity of most metabolites still remain unknown. A key bottleneck in the full exploration of this tremendous source of new structures and pharmaceutical activities is the compound purification needed for bioactivity assignments of individual compounds and downstream structure elucidation. To enable bioactivity-focused compound identification from complex mixtures, we developed a scalable native metabolomics approach that integrates non-targeted liquid chromatography tandem mass spectrometry, and simultaneous detection of protein binding via native mass spectrometry. While screening for new protease inhibitors from an environmental cyanobacteria community, native metabolomics revealed 30 cyclodepsipeptides as chymotrypsin binders. Mass spectrometry-guided purification then allowed for the full structure elucidation of four new specialized metabolites via tandem mass spectrometry, chemical derivatization, and nuclear magnetic resonance spectroscopy. Together with the evaluation of biological activities, our results identified the rivulariapeptolides as a family of serine protease inhibitors with nanomolar potency, highlighting native metabolomics as promising approach for drug discovery, chemical ecology, and chemical biology studies.
Aberrant localization of CDC42 C-terminal variants to the Golgi apparatus drives pyrin inflammasome-dependent autoinflammation
Authors: Nishitani-Isa Masahiko , Mukai Kojiro , Honda Yoshitaka , Nihira Hiroshi , Tanaka Takayuki , Shibata Hirofumi , Kodama Kumi , Hiejima Eitaro , Izawa Kazushi , Kawasaki Yuri , Osawa Mitsujiro , Katata Yu , Onodera Sachiko , Watanabe Tatsuya , Kure Shigeo , Takita Junko , Ohara Osamu , Saito Megumu K. , Nishikomori Ryuta , Taguchi Tomohiko , Sasahara Yoji , Yasumi Takahiro 
Published: September 2021

AbstractMutations in the C-terminal region of the CDC42 gene cause severe neonatal-onset autoinflammation. Elevated levels of serum IL-18 in patients and effectiveness of IL-1β-blocking therapy indicate that the pathology involves abnormal inflammasome activation; however, the mechanism underlying autoinflammation remains to be elucidated. Using induced-pluripotent stem cells established from patients carrying CDC42R186C, we found that patient-derived cells secreted larger amounts of IL-1β in response to pyrin-activating stimuli. Aberrant palmitoylation and localization of CDC42R186C protein to the Golgi apparatus promoted pyrin inflammasome assembly downstream of pyrin dephosphorylation. Aberrant subcellular localization was the common pathological feature shared by CDC42 C-terminal variants with inflammatory phenotypes, including CDC42*192C*24 that also localizes to the Golgi apparatus. Furthermore, the level of pyrin inflammasome overactivation paralleled that of mutant protein accumulation in the Golgi apparatus, but no that of the mutant GTPase activity. These results reveal an unexpected association between CDC42 subcellular localization and pyrin inflammasome activation that could pave way for elucidating the mechanism of pyrin inflammasome formation.
Chromosomal-level genome assembly of the bioluminescent cardinalfishSiphamia tubifer, an emerging model for symbiosis research
Authors: Gould AL , Henderson JB , Lam AW 
Published: September 2021

AbstractThe bioluminescent symbiosis between the sea urchin cardinalfishSiphamia tubifer(Kurtiformes: Apogonidae) and the luminous bacteriumPhotobacterium mandapamensisis an emerging vertebrate-bacteria model for the study of microbial symbiosis. However, there is little genetic data available for the host fish, limiting the scope of potential research that can be carried out with this association. In this study, we present a chromosomal-level genome assembly ofS. tubiferusing a combination of PacBio HiFi sequencing and Hi-C technologies. The final genome assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO completeness score of 99%. A comparison of theS. tubifergenome to that of another non-luminous cardinalfish revealed a high degree of synteny, whereas a similar comparison to a more distant relative in the Gobiiformes order revealed a fusion of two chromosomes in the cardinalfish genomes. An additional comparison of orthologous clusters among these three genomes revealed a set of 710 clusters that were unique toS. tubiferin which 23 GO pathways were significantly enriched, including several relating to host-microbe interactions and one involved in visceral muscle development, which could be related to the musculature involved in the gut-associated light organ ofS. tubifer. We also assembled the complete mitogenome ofS. tubiferand discovered both an inversion in the WANCY tRNA gene region resulting in a WACNY gene order as well as heteroplasmy in the length of the control region for this individual. A phylogenetic analysis based on the whole mitochondrial genome indicated thatS. tubiferis divergent from the rest of the cardinalfish family, bringing up questions of the involvement of the bioluminescent symbiosis in the initial divergence of the ancestralSiphamiaspecies. This draft genome assembly ofS. tubiferwill enable future studies investigating the evolution of bioluminescence in fishes as well as candidate genes involved in the symbiosis and will provide novel opportunities to use this system as a vertebrate-bacteria model for symbiosis research.