bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence and associated factors of khat chewing among pregnant women: A Systematic Review and Meta-analysis
Authors: Basa Muluken , Comiskey Catherine
Published: May 2022

Background

Khat (Catha edulis) is a stimulant plant, broadly cultivated and consumed in the Horn of Africa and the Arabian Peninsula. It contains Cathinone, which is an amphetamines-like chemical and causes various adverse outcomes for pregnant women and babies when it is consumed during pregnancy. Decisive estimates of the prevalence of khat chewing and related risk factors which may increase this practice have not been determined.

Aim

To determine the pooled prevalence and associated factors of khat chewing among pregnant women in the Horn Africa and the Arabian Peninsula countries with a view to informing targeted interventions for the region.

Method

The study protocol was prepared and registered on PROSPERO, ID CRD42021190837. A database search including Gray literature and Google scholar was explored to identify 667 studies. Finally, 14 studies were considered relevant for meta-analysis, after removing 259 duplicates, 388 unrelated topics and 6 studies with full text examination. The Newcastle-Ottawa Scale quality assessment tool was used to assess the quality of the studies. The pooled prevalence was determined by using the random-effect model and the p- values of ≤ 0.05 were considered stastically significant to examine associations. Statistical heterogeneity amongst the studies was assessed by Cochrane chi-square and the I2statistical test.

Main Findings

From the meta-analysis of 14 studies with 15,343 study participants, the pooled prevalence of khat chewing among pregnant women was 21.42%, 95% CI (14.49 - 29.29); (I2=99.05% (p<0.0001). The results of the meta-analysis demonstrated that pregnant women who had a khat chewing partner [OR 6.50 (95% CI 5.01, 8.43)]; low educational status [OR 2.53 (95% CI 2.24 - 2.85)], lived in rural area [OR 1.69 (95% CI 1.52 – 1.88)] or had a low level of income [OR 1.70 (95% CI 1.55 – 1.87)] were significantly more likely to chew khat during pregnancy.

Conclusion

The prevalence of khat chewing amongst pregnant women in the Horn of Africa and the Arabian Peninsula has never been measured before and was found to be high. Partners khat chewing status, maternal low educational and economic status were the main factors associated with the problem. Designing intervention strategies to specifically target these risk factors and reduce the burden of the problem for women and their babies is urgently needed.
Disentangling the lipid divide: Identification of key enzymes for the biosynthesis of unusual Membrane-spanning and Ether lipids in Bacteria
Authors: Sahonero-Canavesi Diana X. , Siliakus Melvin , Abdala Asbun Alejandro , Koenen Michel , von Meijenfeldt F. A. Bastiaan , Boeren Sjef , Bale Nicole J. , Engelman Julia C. , Fiege Kerstin , Strack van Schijndel Lora , Sinninghe Damsté Jaap S. , Villanueva Laura
Published: May 2022

Bacterial membranes are composed of fatty acids (FAs) ester-linked to glycerol-3-phosphate, while archaea possess membranes made of isoprenoid chains ether-linked to glycerol-1-phosphate. Many archaeal species organize their membrane as a monolayer of membrane-spanning lipids (MSLs). Exceptions to this ‘lipid divide’ are the production by some bacterial species of (ether-bound) MSLs, formed by tail-tail condensation of fatty acids resulting in the formation of (iso) diabolic acids (DAs), which are the likely precursors of paleoclimatological relevant branched glycerol dialkyl glycerol tetraether molecules. However, the enzymes responsible for their production are unknown. Here, we report the discovery of bacterial enzymes responsible for the condensation reaction of fatty acids and for ether bond formation, and confirm that the building blocks of iso-DA are branched iso-FAs. Phylogenomic analyses of the key biosynthetic genes reveal a much wider diversity of potential MSL (ether)-producing bacteria than previously thought, with significant implications for our understanding of the evolution of lipid membranes.
Ubiquitination occurs in the mitochondrial matrix by eclipsed targeted components of the ubiquitin machinery
Authors: Zhang Yu , Karmon Ofri , Koyeli Das , Mark Maayan , Lehming Norbert , Pines Ophry
Published: May 2022

Ubiquitination is a critical type of post translational modification in eukaryotic cells. It is involved in regulating nearly all cellular processes in the cytosol and nucleus. Mitochondria, known as the metabolism heart of the cell, are organelles that evolved from bacteria. Using the subcellular compartment-dependent α-complementation, we detect multiple components of ubiquitination machinery as being eclipsed distributed to yeast mitochondria. Subsequently, the results with respect to MTS (mitochondrial targeting sequence) targeted HA-tagged ubiquitin demonstrate that certain ubiquitination events specifically occur in yeast mitochondria and are independent of proteasome activity in the cytosol/nucleus. Importantly, we show that the E2 Rad6 affects the pattern of protein ubiquitination in mitochondria and provides an in vivo assay for its activity in the matrix of the organelle. This study shows that ubiquitination occurs in the mitochondrial matrix by eclipsed targeted components of the ubiquitin machinery, providing a new perspective of mitochondrial and ubiquitination research.
Computational modeling of deep tissue heating by an automatic thermal massage bed: predicting the effects on circulation
Authors: Dmochowski Jacek P. , Khadka Niranjan , Cardoso Luis , Meneses Edson , Jin Youngsoo , Bikson Marom
Published: May 2022

Automatic thermal and mechanical massage beds support selfmanaged treatment, including reduction of pain and stress, enhanced circulation, and improved mobility. As the devices become more sophisticated (increasing the degrees of freedom), it is essential to identify the settings that best target the desired tissue. To that end, we developed an MRI-derived model of the lower back and simulated the physiological effects of a commercial thermal-mechanical massage bed. Here we specifically estimated the tissue temperature and increased circulation under steady-state conditions for typical thermal actuator settings (i.e., 45-65°C). Energy transfer across nine tissues was simulated with finite element modeling (FEM) and the resulting heating was coupled to blood flow with an empirically-guided model of temperature-dependent circulation. Our findings indicate that thermal massage increases tissue temperature by 3-8°C and 1-3°C at depths of 2 and 3 cm, respectively. Importantly, due to the rapid (non-linear) increase of circulation with local temperature, this is expected to increase blood flow four-fold (4x) at depths occupied by deep tissue and muscle. These predictions are consistent with prior clinical observations of therapeutic benefits derived from spinal thermal massage.
CAPG: Comprehensive Allopolyploid Genotyper
Authors: Kulkarni Roshan , Zhang Yudi , Cannon Steven B. , Dorman Karin S.
Published: May 2022

Motivation

Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heterozygosity, parental cross or other information to resolve read assignment, but good subgenomic references offer the most direct information. The typical strategy aligns reads to the joint reference, performs diploid genotyping within each subgenome, and filters the results, but persistent read misassignment results in an excess of false heterozygous calls.

Results

We introduce the Comprehensive Allopolyploid Genotyper (CAPG), which formulates an explicit likelihood to weight read alignments against both subgenomic references and genotype individual allopolyploids from whole genome resequencing (WGS) data. We demonstrate CAPG in allotetraploids, where it performs better than GATK’s HaplotypeCaller applied to reads aligned to the combined subgenomic references.

Availability

Code and tutorials are available athttps://github.com/Kkulkarni1/CAPG.git.
DiffBrainNet: differential analyses add new insights into the response to glucocorticoids at the level of genes, networks and brain regions
Authors: Gerstner Nathalie , Krontira Anthi C. , Cruceanu Cristiana , Roeh Simone , Pütz Benno , Sauer Susann , Rex-Haffner Monika , Schmidt Mathias V. , Binder Elisabeth B. , Knauer-Arloth Janine
Published: May 2022

Genome-wide gene expression analyses are invaluable tools for increasing our knowledge of biological and disease processes, allowing a hypothesis-free comparison of gene expression profiles across experimental groups, tissues and cell types. Traditionally, transcriptomic data analysis has focused on gene-level effects found by differential expression. In recent years, network analysis has emerged as an important additional level of investigation, providing information on molecular connectivity, especially for diseases associated with a large number of linked effects of smaller magnitude, like neuropsychiatric disorders and their risk factors, including stress. In this manuscript, we describe how combined differential expression and prior-knowledge-based differential network analysis can be used to explore complex datasets. As an example, we analyze the transcriptional responses following administration of the glucocorticoid/stress hormone receptor agonist dexamethasone in C57Bl/6 mice, in 8 brain regions important for stress processing: the prefrontal cortex, the amygdala, the paraventricular nucleus of the hypothalamus, the cerebellar cortex, and sub regions of the hippocampus: the dorsal and ventral Cornu Ammonis 1, the dorsal and ventral dentate gyrus. By applying a combination of differential network- and differential expression-analyses, we find that these explain distinct but complementary aspects and biological mechanisms of the responses to the stimulus. In addition, network analysis identifies new differentially connected partners of important genes and can be used to generate hypotheses on specific molecular pathways affected. With this work, we provide an analysis framework and a publicly available resource for the study of the transcriptional landscape of the mouse brain: DiffBrainNet (http://diffbrainnet.psych.mpg.de), which can identify molecular pathways important for basic functioning and response to glucocorticoids in a brain-region specific manner.
UMINT: Unsupervised Neural Network For Single Cell Multi-Omics Integration
Authors: Maitra Chayan , Seal Dibyendu Bikash , Das Vivek , De Rajat K.
Published: May 2022

Abstract

Multi-omics studies have enabled us to understand the mechanistic drivers behind complex disease states and progressions, thereby providing novel and actionable biological insights into health status. However, integrating data from multiple modalities is challenging due to the high dimensionality of data and noise associated with each platform. Non-overlapping features and technical batch effects in the data make the task of learning more complicated. Conventional machine learning (ML) tools are not quite effective against such data integration hazards. In addition, existing methods for single cell multi-omics integration are computationally expensive. This has encouraged the development of a novel architecture that produces a robust model for integration of high-dimensional multi-omics data, which would be capable of learning meaningful features for further downstream analysis. In this work, we have introduced a novel Unsupervised neural network for single cell Multi-omics INTegration (UMINT). UMINT serves as a promising model for integrating variable number of single cell omics layers with high dimensions, and provides substantial reduction in the number of parameters. It is capable of learning a latent low-dimensional embedding that can capture useful data characteristics. The effectiveness of UMINT has been evaluated on benchmark CITE-seq (paired RNA and surface proteins) datasets. It has outperformed existing state-of-the-art methods for multi-omics integration.
GABAergic regulation of cell proliferation within the adult mouse spinal cord
Authors: New Lauryn E , Yanagawa Yuchio , McConkey Glenn A , Deuchars Jim , Deuchars Susan A
Published: May 2022

Manipulation of neural stem cell proliferation and differentiation in the postnatal CNS is receiving significant attention due to therapeutic potential. In the spinal cord, such manipulations may promote repair in conditions such as multiple sclerosis or spinal cord injury, but may also limit excessive cell proliferation contributing to tumours such as ependymomas. Here we show that when ambient GABA is increased in vigabatrin-treated or decreased in glutamic acid decarboxylase67-green fluorescent protein (GAD67-GFP) mice, the numbers of proliferating cells respectively decreased or increased. Thus, intrinsic spinal cord GABA levels are correlated with the extent of cell proliferation, providing important evidence for the possibility of manipulating these levels. Diazepam binding inhibitor, an endogenous protein that interacts with GABA receptors and its breakdown product, octadecaneuropeptide, which preferentially activates central benzodiazepine (CBR) sites, were highly expressed in the spinal cord, especially in ependymal cells surrounding the central canal. Furthermore, animals with reduced CBR activation via treatment with flumazenil or Ro15-4513, or with a G2F77I mutation in the CBR binding site had greater numbers of Ethynyl-2’-deoxyuridine positive cells compared to control, which maintained their stem cell status since the proportion of newly proliferated cells becoming oligodendrocytes or astrocytes was significantly lower. Altering endogenous GABA levels or modulating GABAergic signaling through specific sites on the GABA receptors therefore influences NSC proliferation in the adult spinal cord. These findings provide a basis for further study into how GABAergic signaling could be manipulated to enable spinal cord self-regeneration and recovery or limit pathological proliferative activity.
Evaluating risk-taking behaviors in Lycosidae: are the nutritional benefits of sugar water worth the risk of predation?
Authors: Woyak Lauren , McCullagh Elizabeth , Wiggins Will
Published: May 2022

The risk-taking tendencies and addiction in small vertebrates are often used to understand the processes of larger vertebrates, such as humans. We set out to find whether certain risk-taking behaviors characteristic of addiction remain consistent between vertebrates and invertebrates. Different animals will gorge on sugar water, and addiction-like tendencies are often associated with the overconsumption of sucrose. The goal of my study was to evaluate those risk-taking behaviors and compare invertebrate risk-taking behaviors to vertebrate risk-taking behaviors. The risk-taking behavior we observed was the process of relieving cravings while the risk of predation was present. Through this study we document evidence of wolf spiders feeding on a 25% sucrose solution and explain the wolf spiders’ preference to a sugar water solution over filtered tap water. To evaluate if wolf spiders exhibit addiction like behaviors associated with sucrose, we placed a green-colored, sugar water-soaked cotton ball on the silk of a large, predatory Tigrosa helluo wolf spider and a regular, filtered water-soaked cotton ball on the “safe” side of a plastic trial arena and then evaluated the behaviors of the prey spiders. We used a mixture of Pardosa milvina and Rabidosa rabida as test spiders, with one group given a sugar-water treatment beforehand and the other group was given a green colored control cotton ball with filtered tap water (n=14 for both the sugar water treatment and control groups). The wolf spiders who were predisposed to the sugar water treatment were more likely to cross through their predator’s silk in order to gain access to the sugar water cotton ball than their counterparts who were not given a sugar water treatment prior. These results suggest the risk for predation of the wolf spider is not worth the benefits of the sugar water, unless a wolf spider has been allowed unlimited access to sugar water in advance. When a wolf spider who was allowed unlimited access to sugar water beforehand is presented with a risky situation, they will increase their risk-taking behaviors via crossing through a predator’s silk in order indulge in the sugar water. These results suggest the addictive properties of sugar spans across vertebrates and invertebrates, and potentially opens the door for a cost-efficient and ethically acceptable invertebrate model-organism for examining the risk-taking behaviors associated with addiction.
Divergent acute versus prolonged pharmacological GLP-1R responses in adult beta cell-selective β-arrestin 2 knockout mice
Authors: Bitsi Stavroula , Manchanda Yusman , ElEid Liliane , Mohamed Nimco , Hansen Ben , Suba Kinga , Rutter Guy A. , Salem Victoria , Jones Ben , Tomas Alejandra
Published: May 2022

The glucagon-like peptide-1 receptor (GLP-1R) is a major therapeutic target in type 2 diabetes (T2D) and obesity. Following activation, GLP-1Rs are rapidly desensitised by β-arrestins, scaffolding proteins that terminate G protein interactions but also act as independent signalling mediators. While GLP-1R interacts with β-arrestins 1 and 2, expression of the latter is greatly enhanced in beta cells, making this the most relevant isoform. Here, we have assessed in vivo glycaemic responses to the pharmacological GLP-1R agonist exendin-4 in adult beta cell-selective β-arrestin 2 knockout (KO) mice. Lean female and high-fat, high-sucrose-fed KO mice of both sexes displayed worse acute responses versus control littermates, an effect that was inverted 6 hours post-agonist injection, resulting in prolonged in vivo cell-cell connectivity in KO islets implanted in mouse eyes. Similar effects were observed for the clinically relevant semaglutide and tirzepatide but not with exendin-phe1, an agonist biased away from β-arrestin recruitment. Ex vivo acute cAMP was impaired, but overnight desensitisation was reduced in KO islets. The acute signalling defect was attributed to enhanced β-arrestin 1 and phosphodiesterase (PDE) 4 activity in the absence of β-arrestin 2, while the reduced desensitisation correlated with altered GLP-1R trafficking, involving impaired recycling and lysosomal targeting and increased trans-Golgi network (TGN) localisation and signalling, as well as reduced GLP-1R ubiquitination by the E3 ubiquitin ligase NEDD4. This study has unveiled fundamental aspects of the role of β-arrestin 2 in regulating pharmacological GLP-1R responses with direct application to the rational design of improved GLP-1R-targeting therapeutics.
Secondary reversion to sexual monomorphism associated with tissue-specific loss of doublesex expression
Authors: Gao Jian-jun , Barmina Olga , Thompson Ammon , Kim Bernard , Suvorov Anton , Tanaka Kohtaro , Watabe Hideaki , Toda Masanori J. , Chen Ji-Min , Katoh Takehiro K. , Kopp Artyom
Published: May 2022

Animal evolution is characterized by frequent turnover of sexually dimorphic traits – new sex- specific characters are gained, and some ancestral sex-specific characters are lost, in many lineages. In insects, sexual differentiation is predominantly cell-autonomous and depends on the expression of the doublesex (dsx) transcription factor. In most cases, cells that transcribe dsx have the potential to undergo sex-specific differentiation, while those that lack dsx expression do not. Consistent with this mode of development, comparative research has shown that the origin of new sex-specific traits can be associated with the origin of new spatial domains of dsx expression. In this report, we examine the opposite situation – a secondary loss of the sex comb, a male-specific grasping structure that develops on the front legs of some drosophilid species. We show that, while the origin of the sex comb is linked to an evolutionary gain of dsx expression in the leg, sex comb loss in a newly identified species of Lordiphosa (Drosophilidae) is associated with a secondary loss of dsx expression. We discuss how the developmental control of sexual dimorphism affects the mechanisms by which sex-specific traits can evolve.
enclone: precision clonotyping and analysis of immune receptors
Authors: Jaffe David B. , Shahi Payam , Adams Bruce A. , Chrisman Ashley M. , Finnegan Peter M. , Raman Nandhini , Royall Ariel E. , Tsai FuNien , Vollbrecht Thomas , Reyes Daniel S. , McDonnell Wyatt J.
Published: May 2022

Half a billion years of evolutionary battle forged the vertebrate adaptive immune system, an astonishingly versatile factory for molecules that can adapt to arbitrary attacks. The history of an individual encounter is chronicled within a clonotype: the descendants of a single fully rearranged adaptive immune cell. For B cells, reading this immune history for an individual remains a fundamental challenge of modern immunology. Identification of such clonotypes is a magnificently challenging problem for three reasons:

The cell history is inferred rather than directly observed: the only available data are the sequences of V(D)J molecules occurring in a sample of cells.

Each immune receptor is a pair of V(D)J molecules. Identifying these pairs at scale is a technological challenge and cannot be done with perfect accuracy—real samples are mixtures of cells and fragments thereof.

These molecules can be intensely mutatedduring the optimization of the response to particular antigens, blurring distinctions between kindred molecules.

It is thus impossible to determine clonotypes exactly. All solutions to this problem make a trade-off between sensitivity and specificity; useful solutions must address actual artifacts found in real data.

We presentenclone1, a system for computing approximate clonotypes from single cell data, and demonstrate its use and value with the 10x Genomics Immune Profiling Solution. To test it, we generate data for 1.6 million individual B cells, from four humans, including deliberately enriched memory cells, to tax the algorithm and provide a resource for the community. We analytically determine the specificity ofenclone’s clonotyping algorithm, showing that on this dataset the probability of co-clonotyping two unrelated B cells is around 10−9. We prove that using only heavy chains increases the error rate by two orders of magnitude.

enclonecomprises a comprehensive toolkit for the analysis and display of immune receptor data. It is ultra-fast, easy to install, has public source code, comes with public data, and is documented atbit.ly/enclone. It has three “flavors” of use: (1) as a command-line tool run from a terminal window, that yields visual output; (2) as a command-line tool that yields parseable output that can be fed to other programs; and (3) as a graphical version (GUI).
Why the architecture of environmental fluctuation matters for fitness
Authors: Park John S. , Felmy Anja
Published: May 2022

The physical environment provides the very stage upon which the eco-evolutionary play unfolds. How fluctuations in the environment affect demographic fitness is thus central to selection predictions, life history analyses, and viability of populations. Treatment of fluctuating environments typically leverages the mathematics of random variability. However, environmental fluctuations in nature are almost always combinations of random and non-random components. For example, some fluctuations contain feedbacks which generate autocorrelation (e.g.disturbances such as floods, fires, and hurricanes), while others are driven by geophysical forces that create fixed cyclicality (e.g.seasonal, tidal, and diel). Despite theoretical developments, the consideration of non-random characteristics of fluctuations is still rare in empirical work on natural populations, mostly due to convention and partially due to difficulties in measuring and analyzing timeseries of environmental fluctuations. We show why non-randomness matters for fitness. Using a simple demographic model, we systematically compare four major categories of fluctuating environments: stochastic, positively autoregressive, negatively autoregressive, and periodic with error (“Noisy Clock”). The architectures of fluctuations influence the fitness of structured populations even when the modelled environments only differ in the timing of fluctuations, and not in their overall frequency. Importantly, we highlight two quantitative mechanisms through which fitness depends on fluctuation architecture—the consecutiveness of deviations from the environmental mean, and Jensen’s Inequality acting on nonlinear biological parameters—both relevant features in virtually all populations inhabiting variable environments. Our goal is to argue that non-random structures of environmental variability should be more seriously considered in empirical work. Such an endeavor would tap into the rich diversity of variable environments in nature to expand our understanding of the commensurate diversity of population dynamics.
Pharmacological intervention of the FGF-PTH axis as a potential therapeutic for craniofacial ciliopathies
Authors: Bonatto Paese Christian Louis , Chang Ching-Fang , Kristeková Daniela , Brugmann Samantha A.
Published: May 2022

Ciliopathies represent a disease class characterized by a broad range of phenotypes including polycystic kidneys and skeletal anomalies. Ciliopathic skeletal phenotypes are among the most common and most difficult to treat due to a poor understanding of the pathological mechanisms leading to disease. Using an avian model (talpid2) for a human ciliopathy with skeletal anomalies (Orofaciodigital syndrome 14), we identified disruptions in the FGF23-PTH axis that resulted in reduced calcium uptake in the developing mandible and subsequent micrognathia. While pharmacological intervention with the FDA-approved pan-FGFR inhibitor AZD4547 alone rescued expression of the FGF target Sprouty2, it did not significantly rescue micrognathia. In contrast, treatment with a cocktail of AZD4547 and Teriparatide acetate, a PTH agonist and FDA-approved treatment for osteoporosis, resulted in a molecular, cellular, and phenotypic rescue of ciliopathic micrognathia in talpid2 mutants. Together, these data provide novel insight into pathological molecular mechanisms associated with ciliopathic skeletal phenotypes and a potential therapeutic strategy for a pleiotropic disease class with limited to no treatment options.

Summary Statement

Treatment options for ciliopathic phenotypes are very limited. Using an avian model, we report a novel molecular mechanism and potential therapeutic treatment for ciliopathic micrognathia.
Deceptive learning in histopathology
Authors: Shahamatdar Sahar , Saeed-Vafa Daryoush , Linsley Drew , Khalil Farah , Lovinger Katherine , Li Lester , McLeod Howard , Ramachandran Sohini , Serre Thomas
Published: May 2022

Deep learning holds immense potential for histopathology, automating tasks that are simple for expert pathologists, and revealing novel biology for tasks that were previously considered difficult or impossible to solve by eye alone. However, the extent to which the visual strategies learned by deep learning models in histopathological analysis are trustworthy or not has yet to be systematically analyzed. In this work, we address this problem and discover new limits on the histopathological tasks for which deep learning models learn trustworthy versus deceptive solutions. While tasks that have been extensively studied in the field like tumor detection are reliable and trustworthy, recent advances demonstrating the ability to learn molecular profiling from hematoxylin and eosin (H&E) stained slides do not hold up to closer scrutiny. Our analysis framework represents a new approach in understanding the capabilities of deep learning models, which should be incorporated into the computational pathologists toolkit.
Formation of multiple flagella caused by a mutation of the flagellar rotor protein FliM inVibrio alginolyticus
Authors: Homma Michio , Takekawa Norihiro , Fujiwara Kazushi , Hao Yuxi , Onoue Yasuhiro , Kojima Seiji
Published: May 2022

The marine bacteriumVibrio alginolyticusforms only a single flagellum at the cell pole. InVibrio, two proteins (GTPase FlhF and ATPase FlhG) regulate flagellar number at the cell pole. We previously isolated a mutant strain characterized as NMB155 that forms multiple flagella despite the absence of mutations inflhFandflhG. NMB155 also exhibited straight swimming without a directional change in flagellar rotation. Whole-genome sequencing of NMB155 identified an E9K mutation in FliM that is a component of the C-ring in the flagellar rotor. Mutations in FliM result in defects in flagellar formation (fla) and flagellar rotation (cheormot); however, there are few reports indicating that FliM mutations increase the number of flagella. Here, we determined that the E9K mutation confers the multi-flagellar phenotype and also thechephenotype. The co-expression of wild-type FliM and FliM-E9K indicated that they were competitive in regard to determining the flagellar number. It had been shown that the ATPase activity of FlhG corresponds to the flagellar number. We observed that the ATPase activity of FlhG was increased by the addition of FliM but not by the addition of FliM-E9K. This indicates that the N-terminal region of FliM that includes the E9 residue interacts with FlhG to increase its ATPase activity, and the E9K mutation may inhibit this interaction. We concluded that FliM downregulate FlhG activity to inhibit the formation of additional flagella.

Importance

The flagellar rotor generates a driving force to rotate the flagellum and is not involved in controlling the number of flagella inVibrio. However, we observed that the E9K mutation in the rotor protein FliM confers multiple flagella. Our findings reveal a novel regulatory mechanism controlling flagellar number.
The Free Fatty Acid-Binding Pocket is a Conserved Hallmark in Pathogenic β-Coronavirus Spike Proteins from SARS-CoV to Omicron
Authors: Toelzer Christine , Gupta Kapil , Yadav Sathish K.N. , Hodgson Lorna , Williamson Maia Kavanagh , Buzas Dora , Borucu Ufuk , Powers Kyle , Stenner Richard , Vasileiou Kate , Garzoni Frederic , Fitzgerald Daniel , Payré Christine , Lambeau Gérard , Davidson Andrew D. , Verkade Paul , Frank Martin , Berger Imre , Schaffitzel Christiane
Published: May 2022

As COVID-19 persists, severe acquired respiratory syndrome coronavirus-2 (SARS-CoV-2) Variants of Concern (VOCs) emerge, accumulating spike (S) glycoprotein mutations. S receptor-binding domain (RBD) comprises a free fatty acid (FFA)-binding pocket. FFA-binding stabilizes a locked S conformation, interfering with virus infectivity. We provide evidence that the pocket is conserved in pathogenic β-coronaviruses (β-CoVs) infecting humans. SARS-CoV, MERS-CoV, SARS-CoV-2 and VOCs bind the essential FFA linoleic acid (LA), while binding is abolished by one mutation in common cold-causing HCoV-HKU1. In the SARS-CoV S structure, LA stabilizes the locked conformation while the open, infectious conformation is LA-free. Electron tomography of SARS-CoV-2 infected cells reveals that LA-treatment inhibits viral replication, resulting in fewer, deformed virions. Our results establish FFA-binding as a hallmark of pathogenic β-CoV infection and replication, highlighting potential antiviral strategies.

One-Sentence Summary

Free fatty acid-binding is conserved in pathogenic β-coronavirus S proteins and suppresses viral infection and replication.
Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral
Authors: Ide Keigo , Nishikawa Yohei , Maruyama Toru , Tsukada Yuko , Kogawa Masato , Takeda Hiroki , Ito Haruka , Wagatsuma Ryota , Miyaoka Rimi , Nakano Yoshikatsu , Kinjo Koji , Ito Michihiro , Hosokawa Masahito , Yura Kei , Suda Shoichiro , Takeyama Haruko
Published: May 2022

Endozoicomonas bacteria symbiose with various marine organisms and are known to be beneficial for coral health. However, genome analysis of coral-associated Endozoicomonas has been limited owing to the difficulty in cultivation and metagenomic approach by contamination of host-derived sequences. In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genome (SAGs) for coral-associated Endozoicomonas spp. genome. We obtained seven novel Endozoicomonas genomes from Acropora tenuis coral. These genomes revealed that Endozoicomonas bacteria played host-associated functions in host corals and had undergone independent host-adaptive evolution in different clades. These adaptive evolutions were mediated by host-derived eukaryotic-like genes, some of which were speculated to influence host immune mechanisms. These genes are speculated to enhance coral tolerance to environmental stresses. This study suggests the possibility of host adaptation of Endozoicomonas spp. in symbiosis with corals and their contribution to coral bleaching tolerance.
An intrinsic oscillator underlies visual navigation in ants
Authors: Clement Leo , Schwarz Sebastian , Wystrach Antoine
Published: May 2022

Controlling behavior implies a constant balance between exploration – to gather information – and exploitation – to use this information to reach one’s goal. However, how this tradeoff is achieved in navigating animals is unclear. Here we recorded the paths of two phylogenetically distant visually navigating ant species (Myrmecia croslandi and Iridomyrmex purpureus) using a trackball-treadmill directly in their habitat. We show that both species continuously produce regular lateral oscillations with bursts of forward movement when facing the general direction of travel, providing a remarkable tradeoff between visual exploration across directions and movement areas. This dynamical signature is conserved across navigational contexts but requires certain visual cues to be fully expressed. Rotational feedback regulates the extent of turns, but is not required to produce them, indicating that oscillations are generated intrinsically. Learnt visual information modulates the oscillation’s amplitudes to fit the task at hand in a continuous manner: an unfamiliar panorama enhances the amplitude of oscillations in both naïve and experienced ants, favoring visual exploration; while a learnt familiar panorama reduces them, favoring exploitation through. The observed dynamical signature readily emerges from a simple neural-circuit model of the insect’s conserved pre-motor area known as the lateral accessory lobe, endorsing oscillations as a core, ancestral way of moving in insects. We discuss the importance and evolution of self-generated behaviors and how such an oscillator has been exapted to various modalities, behaviors and way of moving.
Metabolic size scaling reflects growth performance effects on age-size relationships in mussels (Mytilus galloprovincialis)
Authors: Ibarrola Irrintzi , Arranz Kristina , Markaide Pablo , Navarro Enrique
Published: May 2022

Body-size scaling of metabolic rate in animals is typically allometric, with mass exponents that vary to reflect differences in the physiological status of organisms of both endogenous and environmental origin. Regarding the intraspecific analysis of this relationship in bivalve molluscs, one important source of metabolic variation comes from the large inter-individual differences in growth performance characteristic of this group. In the present study, we aimed to address the association of growth rate differences recorded among individual mussels (Mytilus galloprovincialis) with variable levels of the standard metabolic rate (SMR) resulting in growth-dependent shift in size scaling relationships. SMR was measured in mussels of different sizes and allometric functions fitting SMR vs. body-mass relationships were compared both inter- and intra-individually. The results revealed a metabolic component (the overhead of growth) attributable to the differential costs of maintenance of feeding and digestion structures between fast and slow growers; these costs were estimated to amount to a 3% increase in SMR per unit of increment in the weight specific growth rate. Scaling exponents computed for intraindividual SMR vs body-mass relationships had a common value b = 0.79 (~ ¾); however, when metabolic effects caused by differential growth were discounted, this value declined to 0.67 (= ⅔), characteristic of surface dependent processes. This last value of the scaling exponent was also recorded for the interindividual relationships of both SMR and RMR after long-lasting maintenance of mussels under optimal uniform conditions in the laboratory. The above results were interpreted based on the metabolic level boundary (MLB) hypothesis.
Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species “L. swaminathanii”
Authors: Hudson Lauren K. , Chaggar Harleen K. , Schamp Claire N. , Claxton Michelle L. , Bryan Daniel W. , Peters Tracey L. , Song Yaxiong , Carlin Catharine R. , den Bakker Henk C. , Denes Thomas G.
Published: May 2022

Recently, a newListeriaspecies, “Listeria swaminathanii”, was proposed. Here, we phenotypically and genotypically characterize two additional strains that were previously obtained from soil samples and compare the results to the type strain. Complete genomes for both strains were assembled from hybrid Illumina and Nanopore sequencing reads and annotated. Further genomic analysis including average nucleotide identity (ANI) and detection of mobile genetic elements and genes of interest (e.g., virulence-associated) were conducted. The strains showed 98.7-98.8% ANI with the type strain. The UTK C1-0015 genome contained a partial monocin locus and a plasmid while the UTK C1-0024 genome contained a full monocin locus and a prophage. Phenotypic characterization consistent with those performed on the proposed type strain was conducted to assess consistency of phenotypes across a greater diversity of the proposed species (n=3 instead of n=1). Only a few findings were notably different from those of the type strain, such as catalase activity, glycerol metabolism, starch metabolism, and growth at 41°C. This study further expands our understanding of this newly proposedsensu stricto Listeriaspecies.
Designing multiphase biomolecular condensates by coevolution of protein mixtures
Authors: Chew Pin Yu , Joseph Jerelle A. , Collepardo-Guevara Rosana , Reinhardt Aleks
Published: May 2022

Control of biomolecular condensates may hold considerable therapeutic potential. Intracellular condensates are highly multi-component systems in which complex phase behaviour can ensue, including the formation of architectures comprising multiple immiscible condensed phases. Conceivable avenues for manipulating condensates to bypass pathologies thus extend beyond merely controlling their stability and material properties, and relying solely on physical intuition to manipulate them is difficult because of the complexity of their composition. We address this challenge by developing an efficient computational approach to design pairs of protein sequences that result in well-separated multilayered condensates. Our method couples a genetic algorithm to a residue-resolution coarse-grained protein model. We demonstrate that we can design protein partners to form multiphase condensates containing naturally occurring proteins, such as the low-complexity domain of hnRNPA1 and its mutants, and show how homo- and heterotypic interactions must differ between proteins to result in multiphasicity.
Active mechanics of sea star oocytes
Authors: Foster Peter J. , Fürthauer Sebastian , Fakhri Nikta
Published: May 2022

Actomyosin is a canonical example of an active material, driven out of equilibrium in part through the injection of energy by myosin motors. This influx of energy allows actomyosin networks to generate cellular-scale contractility, which underlies cellular processes ranging from division to migration. While the molecular players underlying actomyosin contractility have been well characterized, how cellular-scale deformation in disordered actomyosin networks emerges from filament-scale interactions is not well understood. Here, we address this question in vivo using the meiotic surface contraction wave of Patiria miniata oocytes. Using pharmacological treatments targeting actin polymerization, we find that the cellular deformation rate is a nonmonotonic function of cortical actin density peaked near the wild type density. To understand this, we develop an active fluid model coarse-grained from filament-scale interactions and find quantitative agreement with the measured data. This model further predicts the dependence of the deformation rate on the concentration of passive actin crosslinkers and motor proteins, including the surprising prediction that deformation rate decreases with increasing motor concentration. We test these predictions through protein overexpression and find quantitative agreement. Taken together, this work is an important step for bridging the molecular and cellular length scales for cytoskeletal networks in vivo.
Statistical analysis of spatially resolved transcriptomic data by incorporating multi-omics auxiliary information
Authors: Li Yan , Zhou Xiang , Cao Hongyuan
Published: May 2022

Effective control of false discovery rate is key for multiplicity problems. Here, we consider incorporating informative covariates from external datasets in the multiple testing procedure to boost statistical power while maintaining false discovery rate control. In particular, we focus on the statistical analysis of innovative high-dimensional spatial transcriptomic data while incorporating external multi-omics data that provide distinct but complementary information to the detection of spatial expression patterns. We extend OrderShapeEM, an efficient covariate-assisted multiple testing procedure that incorporates one auxiliary study, to make it permissible to incorporate multiple external omics studies, to boost statistical power of spatial expression pattern detection. Specifically, we first use a recently proposed computationally efficient statistical analysis method, spatial pattern recognition via kernels, to produce the primary test statistics for spatial transcriptomic data. Afterwards, we construct the auxiliary covariate by combining information from multiple external omics studies, such as bulk or single-cell RNA-seq data and genome wise association study data, using the Cauchy combination rule. Finally, we extend and implement the integrative analysis method OrderShapeEM on the primary p-values along with auxiliary data incorporating multi-omics information for efficient covariate-assisted spatial expression analysis. We conduct a series of realistic simulations to evaluate the performance of our method with known ground truth. Four case studies in mouse olfactory bulb, mouse cerebellum, human breast cancer and human heart tissues further demonstrate the substantial power gain of our method in detecting genes with spatial expression patterns compared to existing classic approaches that do not utilize any external information.
A highly sensitive strand-specific multiplex RT-qPCR assay for quantitation of Zika virus replication
Authors: Barnard Trisha R. , Wang Alex B. , Sagan Selena M.
Published: May 2022

Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is widely used to quantify viral RNA genomes for diagnostics and research, yet conventional RT-qPCR protocols are unable to accurately distinguish between the different viral RNA species that exist during infection. Here we show that false-priming and self-priming occur during reverse transcription with several published Zika virus (ZIKV) primer sets. We developed a RT-qPCR assay using tagged primers and thermostable reverse transcriptase, which greatly reduced the occurrence of nonspecific cDNA products. Furthermore, we optimized the assay for use in multiplex qPCR which allows for simultaneous quantitative detection of positive-strand and negative-strand ZIKV RNA along with an internal control from both human and mosquito cells. Importantly, this assay is sensitive enough to study early stages of virus infection in vitro. Strikingly, using this assay, we detected ZIKV negative-strand RNA as early as 3 h post-infection in mammalian cell culture, at a time point prior to the onset of positive-strand RNA synthesis. Overall, the strand-specific RT-qPCR assay developed herein is a valuable tool to quantify ZIKV RNA and to study viral replication dynamics during infection. The application of these findings has the potential to increase accuracy of RNA detection methods for a variety of viral pathogens.

Highlights

Self-primed cDNA is amplified by widely-used ZIKV qPCR primer sets

Use of tagged primers and thermostable RT increases strand-specificity for RT-qPCR

Multiplexed qPCR allows for simultaneous quantitation of (+) and (-) strand viral RNAs, and an internal control

Strand-specific RT-qPCR can detect fewer than one copy of viral RNA per cell in human and mosquito cells
cMYC protein interactions and chromatin association in NUT carcinoma
Authors: Zee Barry M. , Alekseyenko Artyom A. , Smolko Anne E. , Kang Hyuckjoon , Kuroda Mitzi I.
Published: May 2022

The oncogene cMYC (HGNC:7553) is a critical genomic target of the BRD4-NUT (B4N) protein that defines many of the NUTM1-rearrangement cancer subtypes in NUT carcinoma (NC). Previously, we reported that B4N interacts with the EP300 lysine acetyltransferase (KAT3B) and creates hyperacetylated “megadomains” that activate downstream genes such as cMYC. Here we ask how misregulated cMYC in turn interacts with protein partners and target genes in patient-derived NC797 cells, and whether these interactions change in response to B4N inactivation. We used CRISPR-Cas9 mediated knock-in of a BioTAP affinity tag to analyze cMYC protein expressed from its normal chromosomal context. This allowed us to implement a crosslinking purification method termed BioTAP-XL to preserve cMYC integrity and chromatin association for genomic and mass spectrometry-based proteomic analyses. We found that in the NC797 cell line, cMYC interacts primarily with the NuA4 KAT5 lysine acetyltransferase complex, with interactions that are maintained despite a decrease in cMYC levels after JQ1 treatment. We propose that a cascade of aberrant acetyltransferase activities in NC797 cells, first via EP300 recruitment by B4N to mis-regulate cMYC, and then by KAT5 interaction with the resulting overexpressed cMYC protein, drive NC cell proliferation and blockade to differentiation.

Graphical Abstract

Simple Summary

A longstanding goal in biology is to understand how protein interactions influence and reflect cellular disease states. MYC is a critical regulator of cellular proliferation that is mis-regulated in many cancers, including those with NUTM1-rearrangements featured in this issue. NUT carcinoma cells are dependent on MYC expression, which blocks differentiation. Using a crosslinking approach to identify MYC protein interactions in a NUTM1-rearranged patient cell line, we found that MYC interacts primarily with subunits of the NuA4 lysine acetyltransferase (KAT5), one of two KAT complexes previously discovered as MYC interactors in non-NUTM1 cell lines.