bluuebunny/crossref_metadata_2025 huggingface dataset:
Bloodstream infection by Saccharomyces cerevisiae in a COVID-19 patient receiving probiotic supplementation in the ICU in Brazil
Authors: Pinto Gabryela , Lima Lorena , Pedra Thaís , Assumpção Adriana , Morgado Sergio , Mascarenhas Luiz
Published: August 2021

Care-related infections (CRIs) have a negative impact on the morbidity and mortality of patients in intensive care. Among them, fungal infections (e.g. Candida spp. and Aspergillus spp.) have high mortality in critically ill patients, particularly those with acute respiratory distress syndrome (ARDS) and immunosuppression. Coronavirus disease 2019 (COVID-19) causes severe respiratory changes and deregulation of the immune system. Here, we describe a case of fungal infection in an intensive care unit (ICU) patient with COVID-19 caused by Saccharomyces cerevisiae, a yeast widely used in the baking and wine production industries. It is also used as a probiotic, both for prevention and as adjunctive therapy in patients with diarrhoea. The patient was admitted to the ICU with a diagnosis of COVID-19, respiratory failure, complications of ARDS and renal failure, and was being treated with antibiotics and vasoactive amines. Later, the patient had diarrhoea and, after supplementation with Saccharomyces, he developed a bloodstream infection with Saccharomyces. The patient died after 61 days of hospitalization due to thrombocytopenia and bleeding. This case report suggests avoiding the use of probiotics in intensive care patients under the administration of antibiotics and amines, and with damage to the intestinal mucosa and immunodeficiency caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), since these factors could favour the translocation of fungi.
ICTV Virus Taxonomy Profile: Arteriviridae 2021
Authors: Brinton Margo A. , Gulyaeva Anastasia A. , Balasuriya Udeni B. R. , Dunowska Magda , Faaberg Kay S. , Goldberg Tony , Leung Frederick C. C. , Nauwynck Hans J. , Snijder Eric J. , Stadejek Tomasz , Gorbalenya Alexander E.
Published: August 2021

The family Arteriviridae comprises enveloped RNA viruses with a linear, positive-sense genome of approximately 12.7 to 15.7 kb. The spherical, pleomorphic virions have a median diameter of 50–74 nm and include eight to eleven viral proteins. Arteriviruses infect non-human mammals in a vector-independent manner. Infections are often persistent and can either be asymptomatic or produce overt disease. Some arteriviruses are important veterinary pathogens while others infect particular species of wild rodents or African non-human primates. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Arteriviridae, which is available at ictv.global/report/arteriviridae.
ICTV Virus Taxonomy Profile: Marnaviridae 2021
Authors: Lang Andrew S. , Vlok Marli , Culley Alexander I. , Suttle Curtis A. , Takao Yoshitake , Tomaru Yuji ,   ICTV Report Consortium
Published: August 2021

The family Marnaviridae comprises small non-enveloped viruses with positive-sense RNA genomes of 8.6–9.6 kb. Isolates infect marine single-celled eukaryotes (protists) that come from diverse lineages. Some members are known from metagenomic studies of ocean virioplankton, with additional unclassified viruses described from metagenomic datasets derived from marine and freshwater environments. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Marnaviridae, which is available at ictv.global/report/marnaviridae.
Association Between Ultrasonography Fetal Anomalies and Autism Spectrum Disorder
Authors: Regev Ohad , Hadar Amnon , Meiri Gal , Flusser Hagit , Michaelovski Analya , Dinstein Ilan , Hershkovitz Reli , Menashe Idan
Published: August 2021

Abstracts

Background

Prenatal ultrasound is frequently used to monitor fetal growth and identify fetal anomalies that may suggest genetic or developmental abnormalities which may develop into congenital anomalies and diseases. Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, associated with a wide range of congenital anomalies. Nevertheless, very little has been done to investigate organ development using prenatal ultrasound as a means to identify fetuses with ASD susceptibility.

Methods

A retrospective matched case-sibling-control study. ASD cases were matched to two control groups: typically developing sibling (TDS) closest in age to ASD child; and typically developing population (TDP), matched for age, sex, and ethnicity. The study comprised 659 children: 229 ASD, 201 TDS, and 229 TDP; 471 (71.5%) males.

Results

Ultrasonography fetal anomalies (UFAs) were found in 29.3% of ASD cases vs. only 15.9% and 9.6% in the TDS and TDP groups (aOR=2.23, 95%CI=1.32-3.78, and OR=3.50, 95%CI=2.07-5.91, respectively). Also, multiple co-occurring UFAs were significantly more prevalent among ASD cases. UFAs in the urinary system, heart, and head&brain were the most significantly associated with ASD diagnosis (aORUrinary =2.08, 95%CI=0.96-4.50 and aORUrinary=2.90, 95%CI=1.41-5.95; aORHeart=3.72, 95%CI=1.50-9.24 and aORHeart=8.67, 95%CI=2.62-28.63; and aORHead&Brain=1.96, 95%CI=0.72-5.30 and aORHead&Brain=4.67, 95%CI=1.34-16.24; vs. TDS and TDP, respectively). ASD females had significantly more UFAs than ASD males (43.1% vs. 25.3%, p=0.013) as well as higher prevalence of multiple co-occurring UFAs (15.7% vs. 4.5%, p=0.011), while no sex differences were seen among TDS and TDP controls. ASD fetuses were characterized by a narrower head and a relatively wider ocular-distance vs. TDP fetuses (aORBPD=0.81, 95%CI=0.70-0.94, and aOROcular-Distance=1.29, 95%CI=1.06-1.57). Finally, UFAs were associated with more severe ASD symptoms.

Conclusions

Our findings shed important light on the abnormal multiorgan embryonic development of ASD and suggest fetal ultrasonography biomarkers for ASD.
Spatially localized fMRI metrics as predictive and highly distinct state-independent fingerprints
Authors: Larabi Daouia I. , Gell Martin , Amico Enrico , Eickhoff Simon B. , Patil Kaustubh R.
Published: August 2021

Precision medicine and the investigation of brain-behavior associations require biomarkers that are stable (low intraindividual variability) and unique (high interindividual variability) at the same time, hence calling them “fingerprints”. The functional connectome (FC) has good “fingerprint properties”, as individuals can be accurately identified in a database based on their FC. Importantly, research has shown lower intraindividual variability of more localized measures of brain function such as regional homogeneity (ReHo) and (fractional) amplitude of low-frequency fluctuations ((f)ALFF), compared to the FC. Here, with fMRI data from two publicly available datasets we demonstrate that individuals can be identified with near-perfect accuracies using local functional fingerprints, and especially the regional homogeneity (ReHo) fingerprint. Further analyses reveal that the dorsal attention network contributes most to the individual “uniqueness” of the ReHo fingerprint. Moreover, using a machine-learning setup, we show that the small intraindividual ReHo fingerprint variability across sessions is meaningful for explaining individual-level intelligence. Last, using two other publicly available datasets, clinical applicability is shown with high fingerprint accuracies and a significant correlation between fingerprint stability and intelligence in individuals with schizophrenia. Altogether, our findings suggest that the ReHo fingerprint is a good candidate for further exploration of applicability in precision medicine.
Deficits in seizure threshold and other behaviors in adult mice without gross neuroanatomic injury after late gestation transient prenatal hypoxia
Authors: Cristancho Ana G. , Gadra Elyse C. , Samba Ima M. , Zhao Chenying , Ouyang Minhui , Magnitsky Sergey , Huang Hao , Viaene Angela N. , Anderson Stewart A. , Marsh Eric D.
Published: August 2021

Intrauterine hypoxia is a common cause of brain injury in children resulting in a broad spectrum of long-term neurodevelopmental sequela, including life-long disabilities that can occur even in the absence of severe neuroanatomic damage. Postnatal hypoxia-ischemia rodent models are commonly used to understand the effects of ischemia and transient hypoxia on the developing brain. Postnatal models, however, have some limitations. First, they do not test the impact of placental pathologies on outcomes from hypoxia. Second, they primarily recapitulate severe injury because they provoke substantial cell death, which is not seen in children with mild hypoxic injury. Lastly, they do not model preterm hypoxic injury. Prenatal models of hypoxia in mice may allow us to address some of these limitations to expand our understanding of developmental brain injury. The published rodent models of prenatal hypoxia employ multiple days of hypoxic exposure or complicated surgical procedures, making these models challenging to perform consistently in mice. Furthermore, large animal models suggest that transient prenatal hypoxia without ischemia is sufficient to lead to significant functional impairment to the developing brain. However, these large animal studies are resource-intensive and not readily amenable to mechanistic molecular studies. Therefore, here we characterized the effect of late gestation (embryonic day 17.5) transient prenatal hypoxia (5% inspired oxygen) on long-term anatomical and neurodevelopmental outcomes in mice. Late gestation transient prenatal hypoxia increased hypoxia-inducible factor 1 alpha protein levels (a marker of hypoxic exposure) in the fetal brain. Hypoxia exposure predisposed animals to decreased weight at postnatal day 2, which normalized by day 8. However, hypoxia did not affect gestational age at birth, litter size at birth, or pup survival. No differences in fetal brain cell death or long-term gray or white matter changes resulted from hypoxia. Animals exposed to prenatal hypoxia did have several long-term functional consequences, including sex-dichotomous changes. Hypoxia exposure was associated with a decreased seizure threshold and abnormalities in hindlimb strength and repetitive behaviors in males and females. Males exposed to hypoxia had increased anxiety-related deficits, whereas females had deficits in social interaction. Neither sex developed any motor or visual learning deficits. This study demonstrates that late gestation transient prenatal hypoxia in mice is a simple, clinically relevant paradigm for studying putative environmental and genetic modulators of the long-term effects of hypoxia on the developing brain.
Integrated transcriptomic meta-analysis provides novel insights into breast cancer molecular subtypes
Authors: Bajpai Akhilesh Kumar , Davuluri Sravanthi , Thirumurugan Kavitha , Acharya Kshitish K.
Published: August 2021

Breast cancer is the most common cancer in women worldwide. There are four major breast cancer subtypes (luminal A, luminal B, HER2-enriched and triple-negative/TNBC). TNBC is the most aggressive form with the worst prognosis. However, the differences among the subtypes have not been completely established at the molecular level, thereby limiting therapeutic and diagnostic options for TNBC. We performed a meta-analysis of microarray and RNA-sequencing data to identify candidate genes with an expression-based association in each molecular subtype of breast cancer. The protein interaction network of the candidate genes was analyzed to discover functionally significant gene clusters and hub genes. Potential therapeutic candidates for TNBC were explored through gene-miRNA interactions. We identified 316, 347, 382, and 442 candidate genes in luminal A, luminal B, HER2 and TNBC subtypes, respectively. A total of 135 (26 up- and 109 down-regulated) candidate genes were shared by all four subtypes. Functional analysis of the candidate genes indicated up-regulation of ‘cell cycle’ and ‘p53 signaling’ pathways and down-regulation of multiple signaling pathways. COL10A1 was found to be highly up-regulated in all subtypes. It may be a good target for research towards multiple types of applications, including therapeutics. KIF4A, a commonly up-regulated X-chromosome gene was significantly associated with the survival of breast cancer patients. Protein interaction network and centrality analysis revealed that low-moderately differentially regulated genes play an important role in functional cascades across proteins in breast cancer subtypes and may be potential candidates for therapeutics. Targeting FN1 (fibronectin 1), the key up-regulated hub gene by miR-1271 5p may be an important molecular event to be targeted for potential therapeutic application in TNBC.
Robust bacterial co-occurence community structures are independent of r- and K-selection history
Authors: Pettersen Jakob Peder , Gundersen Madeleine S. , Almaas Eivind
Published: August 2021

Selection for bacteria which are K-strategists instead of r-strategists has been shown to improve fish health and survival in aquaculture. We considered an experiment where microcosms were inoculated with natural seawater and the selection regime was switched from K-selection (by continuous feeding) to r-selection (by pulse feeding) and vice versa. We found the networks of significant co-occurrences to contain clusters of taxonomically related bacteria having positive associations. Comparing this with the time dynamics, we found that the clusters most likely were results of similar niche preferences of the involved bacteria. In particular, the distinction between r- or K-strategists was evident. Each selection regime seemed to give rise to a specific pattern, to which the community converges regardless of its prehistory. Furthermore, the results proved robust to parameter choices in the analysis, such as the filtering threshold, level of random noise, replacing absolute abundances with relative abundances, and the choice of similarity measure. Even though our data and approaches cannot directly predict ecological interactions, our approach provides insights on how the selection regime affects the composition and workings of the microbial community, providing a basis for aquaculture experiments targeted at eliminating opportunistic fish pathogens.
High glucose enhances antigen-independent CTL killing via TRAIL
Authors: Yang Wenjuan , Denger Andreas , Diener Caroline , Küppers Frederic , Soriano-Baguet Leticia , Schäfer Gertrud , Yanamandra Archana K. , Zhao Renping , Knörck Arne , Schwarz Eva C. , Hart Martin , Lammert Frank , Roma Leticia Prates , Brenner Dirk , Christidis Grigorios , Helms Volkhard , Meese Eckart , Hoth Markus , Qu Bin
Published: August 2021

Cytotoxic T lymphocytes (CTLs) are involved in development of diabetes. However, the impact of excessive glucose on CTL-mediated antigen-independent killing remains elusive. Here, we report that TNF-related apoptosis inducing ligand (TRAIL) is substantially up- regulated in CTLs in environments with high glucose (HG) both in vitro and in vivo. The PI3K- Akt-NFκB axis and non-mitochondrial reactive oxygen species are essential in HG-induced TRAIL upregulation in CTLs. TRAILhigh CTLs induce apoptosis of pancreatic beta cell line 1.4E7. Metformin and Vitamin D synergistically reduce HG-enhanced expression of TRAIL in CTLs and coherently protect 1.4E7 cells from TRAIL-mediated apoptosis. Notably, in patients with diabetes, correlation between Vitamin D concentrations in plasma and glucose levels is linked to HG-enhanced TRAIL expression on CTLs. Microarray data reveal that OXCT2, an important enzyme in ketone body catabolism, is a promising target in response to vitamin D. Our work not only reveals a novel mechanism of CTL involvement in progression of diabetes, but also establishes CTLs as a target for combined metformin and vitamin D therapy to protect pancreatic beta cells of diabetic patients.
Molecular Evolution across Mouse Spermatogenesis
Authors: Kopania Emily E. K. , Larson Erica L. , Callahan Colin , Keeble Sara , Good Jeffrey M.
Published: August 2021

Genes involved in spermatogenesis tend to evolve rapidly, but we still lack a clear understanding of how different components of molecular evolution vary across this complex developmental process. We used fluorescence activated cell sorting (FACS) to generate expression data for both early (meiotic) and late (postmeiotic) cell types across thirteen inbred strains of mice (Mus) spanning ~7 million years of evolution. We used these comparative developmental data to investigate the evolution of lineage-specific expression, protein-coding sequences, and expression levels. We found increased lineage specificity and more rapid protein-coding and expression divergence during late spermatogenesis, suggesting that signatures of rapid testis molecular evolution are punctuated across sperm development. Despite strong overall developmental parallels in these components of molecular evolution, protein and expression divergences were only weakly correlated across genes. We detected more rapid protein evolution on the X chromosome relative to the autosomes, while X-linked gene expression tended to be relatively more conserved likely reflecting chromosome-wide regulatory constraints. Using allele-specific FACS expression data from crosses between four strains, we found that the relative contributions of different regulatory mechanisms also differed between cell-types. Genes showingcis-regulatory changes were more common late in spermatogenesis, and tended to be associated with larger differences in expression levels and greater expression divergence between species. In contrast, genes withtrans-acting changes were more common early and tended to be more conserved across species. Our findings advance understanding of gene evolution across spermatogenesis and underscore the fundamental importance of developmental context in molecular evolutionary studies.
Using adopted individuals to partition maternal genetic effects into prenatal and postnatal effects on offspring phenotypes
Authors: Hwang Liang-Dar , Moen Gunn-Helen , Evans David M.
Published: August 2021

Maternal genetic effects can be defined as the effect of a mother’s genotype on the phenotype of her offspring, independent of the offspring’s genotype. Maternal genetic effects can act via the intrauterine environment during pregnancy and/or via the postnatal environment. In this manuscript, we present a simple extension to the basic adoption design that uses structural equation modelling (SEM) to partition maternal genetic effects into prenatal and postnatal effects. We assume that in biological families, offspring phenotypes are influenced prenatally by their mother’s genotype and postnatally by both parents’ genotypes, whereas adopted individuals’ phenotypes are influenced prenatally by their biological mother’s genotype and postnatally by their adoptive parents’ genotypes. Our SEM framework allows us to model the (potentially) unobserved genotypes of biological and adoptive parents as latent variables, permitting us in principle to leverage the thousands of adopted singleton individuals in the UK Biobank. We examine the power, utility and type I error rate of our model using simulations and asymptotic power calculations. We apply our model to polygenic scores of educational attainment and birth weight associated variants, in up to 5178 adopted singletons, 983 trios, 3650 mother-offspring pairs, 1665 father-offspring pairs and 350330 singletons from the UK Biobank. Our results show the expected pattern of maternal genetic effects on offspring birth weight, but unexpectedly large prenatal maternal genetic effects on offspring educational attainment. Sensitivity and simulation analyses suggest this result may be at least partially due to adopted individuals in the UK Biobank being raised by their biological relatives. We show that accurate modelling of these sorts of cryptic relationships is sufficient to bring type I error rate under control and produce unbiased estimates of prenatal and postnatal maternal genetic effects. We conclude that there would be considerable value in following up adopted individuals in the UK Biobank to determine whether they were raised by their biological relatives, and if so, to precisely ascertain the nature of these relationships. These adopted individuals could then be incorporated into informative statistical genetics models like the one described in our manuscript to further elucidate the genetic architecture of complex traits and diseases.
PixR, a novel activator of conjugative transfer of IncX4 resistance plasmids, mitigates the fitness cost of mcr-1 carriage in Escherichia coli
Authors: Yi Lingxian , Durand Romain , Grenier Frédéric , Yang Jun , Yu Kaiyang , Burrus Vincent , Liu Jian-Hua
Published: August 2021

The emergence of the plasmid-borne colistin resistance gene mcr-1 threats public health. IncX4-type plasmids are one of the most epidemiologically successful vehicles for spreading mcr-1 worldwide. Since MCR-1 is known for imposing a fitness cost to its host bacterium, the successful spread of mcr-1-bearing plasmids might be linked to high conjugation frequency, which would enhance the maintenance of the plasmid in the host without antibiotic selection. However, the mechanism of IncX4 plasmids conjugation remains unclear. In this study, we used high-density transposon mutagenesis to identify factors required for IncX4 plasmid transfer and 18 genes were identified, including five with annotations unrelated to conjugation. The Cappable-seq and RNA-seq analysis confirmed that a novel transcriptional regulator gene, pixR, directly regulates the transfer of IncX4 plasmids by binding the promoter of 13 essential transfer genes to increase their transcription. Plasmid invasion and co-culture competition assays revealed that pixR is essential for the spread and persistence of mcr-1-bearing IncX4 plasmids in bacterial populations, and effective conjugation is crucial for alleviating the fitness cost exerted by mcr-1 carriage. The existence of the IncX4-specific pixR gene increases plasmid transmissibility while promoting the invasion and persistence of mcr-1-bearing plasmids in bacterial populations, which helps explain their global prevalence.

IMPORTANCE

The spread of clinical important antibiotic resistance genes is frequently related to some epidemic plasmids. However, the underlying molecular mechanisms contributing to the successful spread of these epidemic plasmids remains unclear. The significant of our research indicated that efficient conjugation could promote the invasion and persistence of plasmids within a bacterial population, resulting in the successful dissemination of epidemic plasmids in nature. Our data also highlight the importance of developing plasmid conjugation inhibitors to solve the antibiotic resistance crisis.
Energetics of a protein disorder-order transition in small molecule recognition
Authors: Mendoza-Martinez Cesar , Papadourakis Michail , Llabrés Salomé , Gupta Arun A. , Barlow Paul N. , Michel Julien
Published: August 2021

Many proteins recognise other proteins via mechanisms that involve the folding of intrinsically disordered regions upon complex formation. Here we investigate how the selectivity of a drug-like small molecule arises from its modulation of a protein disorder-to-order transition. Binding of the compound AM-7209 has been reported to confer order upon an intrinsically disordered ‘lid’ region of the oncoprotein MDM2. Calorimetric measurements revealed that truncation of the lid region of MDM2 increases the apparent dissociation constant of AM-7209 250-fold. By contrast, lid truncation has little effect on the binding of the ligand Nutlin-3a. Insights into these differential binding energetics were obtained via a complete thermodynamic analysis that featured adaptive absolute alchemical free energy of binding calculations with enhanced-sampling molecular dynamics simulations. The simulations reveal that in apo MDM2 the ordered lid state is energetically disfavoured. AM-7209, but not Nutlin-3a, shows a significant energetic preference for ordered lid conformations, thus shifting the balance towards ordering of the lid in the AM-7209/MDM2 complex. The methodology reported herein should facilitate broader targeting of intrinsically disordered regions in medicinal chemistry.
Genes for tRNA recycling are upregulated in response to infection with Theiler’s mouse encephalitis virus
Authors: Seki Mineaki , Komuro Akihiko , Ishikawa Tatsuya , Takahashi Masayuki , Nashimoto Masayuki
Published: August 2021

The concept of tRNA recycling has recently emerged from the studies of ribosome-associated quality control. Therein tRNase ZS removes the 2′, 3′>p from the ANKZF1-cleaved tRNA and the subsequent TRNT1 action re-generates the intact tRNA. To know the roles of the tRNA recycling in vivo, we investigated how viral infection affects the tRNA recycling system by analyzing the mRNA levels of tRNase ZS and TRNT1. We found that both genes in HeLa cells are upregulated in response to infection of Theiler’s mouse encephalitis virus but not to that of an influenza A virus. Upregulation was also observed in cells infected with encephalomyocarditis virus with reduced efficiency. The levels of the IFN-β mRNA appeared to positively correlate with those of the tRNase ZS and TRNT1 mRNAs. The tRNase ZS gene may be regulated post-transcriptionally in the cells infected with Theiler’s mouse encephalitis virus.
Cellular heterogeneity and molecular reprogramming of host response during influenza acute lung injury
Authors: Guo Kai , Kalenda Yombo Dan Justin , Schmit Taylor , Wang Zhihan , Ghosh Sumit , Sathish Venkatachelem , Mathur Ramkumar , Wu Min , Hur Junguk , Khan M. Nadeem
Published: August 2021

Acute lung injury (ALI) caused by influenza A virus (IAV or influenza) manifests from dysregulated cellular interactions between hematopoietic and non-hematopoietic cells that develop into a pathologic host response. However, the lung’s diverse cellular framework that dictates the pathologic host response and acute lung injury remains incompletely understood. We performed a single-cell RNA-seq (scRNA-seq) analysis of total lung cells in mice from severe influenza to examine the cellular heterogeneity and cell-specific regulation of host response. We observed that IAV infection resulted in significant myelopoiesis, predominantly monocyte, and macrophage subsets, which constituted over 50% of total immune cells. IAV infection resulted in the significant loss of endothelial and fibroblast cells, representing the most predominant non-hematopoietic cells and crucial to regulating inflammatory response and barrier integrity. We also show the cell-cell communication dynamics of interferon and chemokine signaling and global regulation of these responses in transition from homeostatic to IAV infection state. These data highlight a robust application of scRNA-seq technology in establishing the atlas of cellular heterogeneity from its homeostatic transition to infection state and the host response regulation in IAV-mediated lung pathology.
Evolution-Inspired Engineering of Anthracycline Methyltransferases
Authors: Dinis Pedro , Tirkkonen Heli , Wandi Benjamin Nji , Siitonen Vilja , Niemi Jarmo , Grocholski Thadée , Metsä-Ketelä Mikko
Published: August 2021

Streptomyces soil bacteria produce hundreds of anthracycline anticancer agents with a relatively conserved set of genes. This diversity depends on the rapid evolution of biosynthetic enzymes to acquire novel functionalities. Previous work has identified S-adenosyl-L-methionine-dependent methyltransferase-like proteins that catalyze either 4-O-methylation, 10-decarboxylation or 10-hydroxylation, with additional differences in substrate specificities. Here we focused on four protein regions to generate chimeric enzymes using sequences from four distinct subfamilies to elucidate their influence in catalysis. Combined with structural studies we managed to depict factors that influence gain-of-hydroxylation, loss-of-methylation and substrate selection. The engineering expanded the catalytic repertoire to include novel 9,10-elimination activity, and 4-O-methylation and 10-decarboxylation of unnatural substrates. The work provides an instructive account on how the rise of diversity of microbial natural products may occur through subtle changes in biosynthetic enzymes.
Direct reprogramming of human fibroblasts into insulin-producing cells by transcription factors
Authors: Fontcuberta-PiSunyer Marta , García-Alamán Ainhoa , Prades Èlia , Téllez Noèlia , Figueiredo Hugo , Fernandez-Ruiz Rebeca , Cervantes Sara , Enrich Carlos , Clua Laura , Ramón-Azcón Javier , Broca Christophe , Wojtusciszyn Anne , Novials Anna , Montserrat Nuria , Vidal Josep , Gomis Ramon , Gasa Rosa
Published: August 2021

Direct lineage reprogramming of one somatic cell into another bypassing an intermediate pluripotent state has emerged as an alternative to embryonic or induced pluripotent stem cell differentiation to generate clinically relevant cell types. One cell type of clinical interest is the pancreatic β cell that secretes insulin and whose loss and/or dysfunction leads to diabetes. Generation of functional β-like cells from developmentally related somatic cell types (pancreas, liver, gut) has been achieved via enforced expression of defined sets of transcription factors. However, clinical applicability of these findings is challenging because the starting cell types are not easily obtainable. Skin fibroblasts are accessible and easily manipulated cells that could be a better option, but available studies indicate that their competence to give rise to β cells through similar direct reprogramming approaches is limited. Here, using human skin fibroblasts and a protocol that ensures high and consistent expression of adenovirus-encoded reprogramming factors, we show that the transcription factor cocktail consisting of Pdx1, Ngn3, MafA, Pax4 and Nkx2-2 activates key β cell genes and down-regulates the fibroblast transcriptional program. The converted cells produce insulin and exhibit intracellular calcium responses to glucose and/or membrane depolarization. Furthermore, they secrete insulin in response to glucose in vitro and after transplantation in vivo. These findings demonstrate that transcription factor-mediated direct reprogramming of human fibroblasts is a feasible strategy to generate insulin-producing cells.
Cancer Cells Viscoelasticity Measurement by Quantitative Phase and Flow Stress Induction
Authors: Vicar Tomas , Gumulec Jaromir , Chmelik Jiri , Navratil Jiri , Kolar Radim , Chmelikova Larisa , Cmiel Vratislav , Provaznik Ivo , Masarik Michal
Published: August 2021

Cell viscoelastic properties are affected by the cell cycle, differentiation, pathological processes such as malignant transformation. Therefore, evaluation of the mechanical properties of the cells proved to be an approach to obtaining information on the functional state of the cells. Most of the currently used methods for cell mechanophenotypisation are limited by low robustness or the need for highly expert operation. In this paper, the system and method for viscoelasticity measurement using shear stress induction by fluid flow is described and tested. Quantitative Phase Imaging (QPI) is used for image acquisition because this technique enables to quantify optical path length delays introduced by the sample, thus providing a label-free objective measure of morphology and dynamics. Viscosity and elasticity determination were refined using a new approach based on the linear system model and parametric deconvolution. The proposed method allows high-throughput measurements during live cell experiments and even through a time-lapse, where we demonstrated the possibility of simultaneous extraction of shear modulus, viscosity, cell morphology, and QPI-derived cell parameters like circularity or cell mass. Additionally, the proposed method provides a simple approach to measure cell refractive index with the same setup, which is required for reliable cell height measurement with QPI, an essential parameter for viscoelasticity calculation. Reliability of the proposed viscoelasticity measurement system was tested in several experiments including cell types of different Young/shear modulus and treatment with cytochalasin D or docetaxel, and an agreement with atomic force microscopy was observed. The applicability of the proposed approach was also confirmed by a time-lapse experiment with cytochalasin D washout, where an increase of stiffness corresponded to actin repolymerisation in time.

SIGNIFICANCE

We present an approach for viscoelasticity measurement using QPI and shear stress induction by fluid flow. Our system builds and extends a recently published approach by parametric deconvolution, which allows us to eliminate the influence of the fluidic system and reliably measure both the shear modulus and viscosity of the cells in high throughput. Additionally, the proposed method enables to simultaneously determine cell refractive index map, cell dry mass map, and morphology, thereby enabling a multimodal cellular characterisation in a single measurement.
EnGRNT: Inference of gene regulatory networks using ensemble methods and topological feature extraction
Authors: Khojasteh Hakimeh , Olyaee Mohammad Hossein , Khanteymoori Alireza
Published: August 2021

The development of computational methods to predict gene regulatory networks (GRNs) from gene expression data is a challenging task. Many machine learning methods have been developed, including supervised, unsupervised, and semi-supervised to infer gene regulatory networks. Most of these methods ignore the class imbalance problem which can lead to decreasing the accuracy of predicting regulatory interactions in the network. Therefore, developing an effective method considering imbalanced data is a challenging task. In this paper, we propose EnGRNT approach to infer GRNs with high accuracy that uses ensemble-based methods. The proposed approach, as well as the gene expression data, considers the topological features of GRN. We applied our approach to the simulated Escherichia coli dataset. Experimental results demonstrate that the appropriateness of the inference method relies on the size and type of expression profiles in microarray data. Except for multifactorial experimental conditions, the proposed approach outperforms unsupervised methods. The obtained results recommend the application of EnGRNT on the imbalanced datasets.
Co-translational biogenesis of lipid droplet integral membrane proteins
Authors: Leznicki Pawel , Schneider Hayden O. , Harvey Jada V. , Shi Wei Q. , High Stephen
Published: August 2021

Membrane proteins destined for lipid droplets (LDs), a major intracellular storage site for neutral lipids, are inserted into the endoplasmic reticulum (ER) and then trafficked to LDs where they reside in a hairpin loop conformation. Here, we show that LD membrane proteins can be delivered to the ER either co- or post-translationally and that their membrane-embedded region specifies pathway selection. The co-translational route for LD membrane protein biogenesis is insensitive to a small molecule inhibitor of the Sec61 translocon, Ipomoeassin F, and instead relies on the ER membrane protein complex (EMC) for membrane insertion. Strikingly, this route can also result in a transient exposure of the short N-termini of LD membrane proteins to the ER lumen, followed by topological rearrangements that enable their transmembrane segment to form a hairpin loop and N-termini to face the cytosol. Our study reveals an unexpected complexity to LD membrane protein biogenesis and identifies a role for the EMC during their co-translational insertion into the ER.

SUMMARY STATEMENT

Insertion of many lipid droplet membrane proteins into the endoplasmic reticulum (ER) is co-translational, mediated by the ER membrane protein complex (EMC) and involves topology reorientation.
Genetic load and extinction in peripheral populations: the roles of migration, drift and demographic stochasticity
Authors: Sachdeva Himani , Olusanya Oluwafunmilola , Barton Nick
Published: August 2021

We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic vs. demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients.
Pancreatic Brsk2 amplifies parasympathetic signals to promote type 2 diabetes
Authors: Xu Rufeng , Wang Kaiyuan , Yao Zhengjian , Jin Li , Pang Jing , Zhou Yuncai , Wang Kai , Liu Dechen , Zhang Yaqin , Sun Peng , Wang Fuqiang , Chang Xiaoai , Li Yating , Wang Shusen , Zhang Yalin , Lin Shuyong , Hu Cheng , Zhu Yunxia , Han Xiao
Published: August 2021

The parasympathetic nervous system (PNS) modulates postprandial glucose metabolism via innervating pancreas; however, its significance in the pathogenesis of type 2 diabetes (T2DM) remains unclear. Here we show that brain-specific serine/threonine-protein kinase 2 (Brsk2), accumulated in obese mouse islets, responds to PNS activation and initiates pre-absorptive insulin release. In inducible mouse models, excessive Brsk2 amplifies parasympathetic signaling to β cells and increases their secretion, ensuing insulin resistance and T2DM. Conversely, Brsk2 inhibition prevents and treats HFD-induced metabolic abnormities via avoiding β-cell oversecretion. Mechanistically, parasympathetic acetylcholine activates cholinergic receptor M3 (Chrm3), then Chrm3 recruits and stabilizes Brsk2, which in turn phosphorylates phospholipase A2 activating protein (Plaa). A Chrm3-Brsk2-Plaa axis stimulates β-cell hypersecretion during both pre-absorptive and absorptive stages in HFD-feeding mice, thus imposing insulin resistance and β-cell dysfunction. Blocking parasympathetic signaling to β cells by Brsk2 protein restoration, autonomic mediation drugs, or vagotomy restricted diabetes development. Moreover, three human BRSK2 variants are associated with hyperinsulinemia, insulin resistance, and T2DM in the Chinese population. These findings reveal that Brsk2 links parasympathetic nervous system to nutrition-overload induced T2DM.
A Network-centric Framework for the Evaluation of Mutual Exclusivity Tests on Cancer Drivers
Authors: Ahmed Rafsan , Erten Cesim , Houdjedj Aissa , Kazan Hilal , Yalcin Cansu
Published: August 2021

One of the key concepts employed in cancer driver gene identification is that of mutual exclusivity (ME); a driver mutation is less likely to occur in case of an earlier mutation that has common functionality in the same molecular pathway. Several ME tests have been proposed recently, however the current protocols to evaluate ME tests have two main limitations. Firstly the evaluations are mostly with respect to simulated data and secondly the evaluation metrics lack a network-centric view. The latter is especially crucial as the notion of common functionality can be achieved through searching for interaction patterns in relevant networks. We propose a network-centric framework to evaluate the pairwise significances found by statistical ME tests. It has three main components. The first component consists of metrics employed in the network-centric ME evaluations. Such metrics are designed so that network knowledge and the reference set of known cancer genes are incorporated in ME evaluations under a careful definition of proper control groups. The other two components are designed as further mechanisms to avoid confounders inherent in ME detection on top of the network-centric view. To this end, our second objective is to dissect the side effects caused by mutation load artifacts where mutations driving tumor subtypes with low mutation load might be incorrectly diagnosed as mutually exclusive. Finally, as part of the third main component, the confounding issue stemming from the use of nonspecific interaction networks generated as combinations of interactions from different tissues is resolved through the creation and use of tissue-specific networks in the proposed framework. The data, the source code and useful scripts are available at: https://github.com/abu-compbio/NetCentric.
Spatial organisation and homeostasis of epithelial lineages at the gastroesophageal junction is regulated by the divergent Wnt mucosal microenvironment
Authors: Kumar Naveen , Gurumurthy Rajendra Kumar , Prakash Pon Ganish , Kurian Shilpa Mary , Wentland Christian , Brinkmann Volker , Mollenkopf Hans-Joachim , Krammer Tobias , Toussaint Christophe , Saliba Antoine-Emmanuel , Biebl Matthias , Juergensen Christian , Wiedenmann Bertram , Meyer Thomas F , Chumduri Cindrilla
Published: August 2021

The gastroesophageal junction (GEJ), where squamous and columnar epithelia meet, is a hotspot for Barrett’s metaplasia development, dysbiosis and carcinogenesis. However, the mechanisms regulating GEJ homeostasis remain unclear. Here, by employing organoids, bulk and single-cell transcriptomics, single-molecule RNA in situ hybridisations and lineage tracing, we identified the spatial organisation of the epithelial, stromal compartment and the regulators that maintain the normal GEJ homeostasis. During development, common KRT8 progenitors generate committed unilineage p63/KRT5-squamous and KRT8-columnar stem cells responsible for the regeneration of postnatal esophagus and gastric epithelium that meet at GEJ. A unique spatial distribution of Wnt regulators in the underlying stromal compartment of these stem cells creates diverging Wnt microenvironments at GEJ and supports their differential regeneration. Further, we show that these tissue-resident stem cells do not possess the plasticity to transdifferentiate to the other lineage with the altered Wnt signals. Our study provides invaluable insights into the fundamental process of GEJ homeostasis and is crucial for understanding disease development.
A computational modeling approach for predicting multicell patterns based on signaling-induced differential adhesion
Authors: Sivakumar Nikita , Warner Helen V. , Peirce Shayn M. , Lazzara Matthew J.
Published: August 2021

Differential adhesion within cell populations enables the emergence of unique patterns in heterogeneous multicellular systems. This process has been previously explored using synthetically engineered heterogenous multicell spheroid systems, in which cell subpopulations engage in bidirectional intercellular signaling to regulate the expression of different cadherins. While engineered cell systems provide excellent experimental tools to observe pattern formation in cell populations, computational models may be leveraged to more systematically explore the key parameters that drive the emergence of different patterns. We developed and validated two- and three-dimensional agent-based models (ABMs) of spheroid patterning for cells engineered with a bidirectional signaling circuit that regulates N- and P-cadherin expression. The model was used to predict how varying initial cell seedings, cadherin induction probabilities, or homotypic adhesion strengths between cells impact spheroid patterning, and unsupervised machine learning techniques were used to map system parameters to unique spheroid patterns. The model was then deployed to design new synthetic cell signaling circuits based on a desired final multicell pattern.
Dynamically unstable ESS in matrix games under time constraints
Authors: Varga Tamás , Garay József
Published: August 2021

Matrix games under time constraints are natural extensions of matrix games. They consider the fact that, in addition to the payoff, a pairwise interaction has a further consequence for the contestants. Namely, both players have to wait for some time before becoming fit to participate in a subsequent interaction. Every matrix game can be assigned a continuous dynamical system (the replicator equation) which describes how the frequencies of different phenotypes evolve in the population. One of the fundamental theorems of evolutionary matrix games asserts that the state corresponding to an evolutionarily stable strategy is an asymptotically stable rest point of the replicator equation (Taylor and Yonker 1978, Hofbauer et al. 1979, Zeeman 1980). Garay et al. (2018) and Varga et al. (2020) generalized the statement to two-strategy and, in some particular cases, three- or more strategy matrix games under time constraints. However, the question of whether the implication holds in general remained open. Here examples are provided demonstrating that the answer is no. Moreover, we point out through the rock-scissor-paper game that arbitrary small differences between waiting times can destabilize the rest point corresponding to an ESS. It is also shown that a stable limit cycle can arise around the unstable rest point in a supercritical Hopf bifurcation.

Mathematics Subject Classification

91A22, 92D15, 92D25, 91A80, 91A05, 91A10, 91A40, 92D40