bluuebunny/crossref_metadata_2025 huggingface dataset:
Landscape of semi-extractable RNAs across five human cell lines
Authors: Zeng Chao , Chujo Takeshi , Hirose Tetsuro , Hamada Michiaki
Published: October 2022

Phase-separated membraneless organelles often contain RNAs that exhibit unusual semi-extractability upon the conventional RNA extraction method, and can be efficiently retrieved by needle shearing or heating during RNA extraction. Semi-extractable RNAs are promising resources for understanding RNA-centric phase separation. However, limited assessments have been performed to systematically identify and characterize semi-extractable RNAs. In this study, 1,074 semi-extractable RNAs were identified across five human cell lines, including ASAP1, DANT2, EXT1, FTX, IGF1R, LIMS1, NEAT1, PHF21A, PVT1, SCMH1, STRG.3024.1, TBL1X, TCF7L2, TVP23C-CDRT4, UBE2E2, ZCCHC7, ZFAND3, and ZSWIM6, which exhibited consistent semi-extractability. By integrating publicly available datasets, we found that semi-extractable RNAs tend to be distributed in the nuclear compartments but are dissociated from the chromatin. Long and repeat-containing semi-extractable RNAs act as hubs to provide global RNA-RNA interactions. Semi-extractable RNAs were divided into four groups based on their k-mer content. The NEAT1 group preferred to interact with paraspeckle proteins, such as FUS and NONO, implying that RNAs in this group are potential candidates of architectural RNAs that constitute nuclear bodies.
Mining novel cis-regulatory elements from the emergent host Rhodosporidium toruloides using transcriptomic data
Authors: Nora Luísa Czamanski , Anzolini Cassiano Murilo Henrique , Santana Ítalo Paulino , Guazzaroni María-Eugenia , Silva-Rocha Rafael , da Silva Ricardo Roberto
Published: October 2022

The demand for robust microbial cell factories that can produce valuable biomaterials while being resistant to stresses imposed by current bioprocesses is rapidly growing. R. toruloides is an emerging host that presents desirable features for bioproduction, since it can grow in a wide range of substrates and tolerate a variety of toxic compounds. In order to explore R. toruloides suitability for application as a cell factory in biorefineries, we sought to understand the transcriptional responses of this yeast when growing under experimental settings that simulated those used in biofuels-related industries. Thus, we performed RNA sequencing of the oleaginous, carotenogenic yeast in different contexts. The first ones were stress-related: two conditions of high temperature (37 °C and 42 °C) and two ethanol concentrations (2% and 4%), while the other was using the inexpensive and abundant sugarcane juice as substrate. Using transcriptomic data, differential expression and functional analysis were implemented to select differentially expressed genes and enriched pathways from each set-up. A reproducible bioinformatics workflow was developed for mining new regulatory elements. We then predicted, for the first time in this yeast, binding motifs for several transcription factors, including HAC1, ARG80, RPN4, ADR1, and DAL81. Most of the putative transcription factors uncovered here were involved in stress responses and found in the yeast genome. Our method for motif discovery provides a new realm of possibilities in the study of gene regulatory networks, not only for the emerging host R. toruloides, but for other organisms of biotechnological importance.
Differential expression of RSK4 transcript isoforms in cancer and its clinical relevance
Authors: Chen Sisi , Seckl Michael J , Lorentzen Marc PG , Pardo Olivier E.
Published: October 2022

RSK4 belongs to the p90 Ribosomal S6 Kinase family which lies downstream of the MAPK pathway. While we previously revealed this kinase to be a therapeutic target in lung and bladder cancers, there is conflicting evidence for its wider role in other cancer types. Indeed, RSK4 was instead suggested to be a tumour suppressor in colorectal and gastric cancers, and reports of its role in breast malignancies are contradictory. One possible explanation for these discrepancies may be the expression of different RSK4 isoforms across cancers. Four RNAs are produced from the RSK4 gene with two being protein-coding. Here, we analysed the expression of the two RSK4 protein-coding mRNAs across 30 normal and 33 cancer tissue types from the combined GTEx/TCGA dataset and correlated it with associated clinical features. This analysis revealed the mRNA expression of RSK4 isoform 1 and 2 to be independent prognostic factors for patient survival, pathological stage, cancer metastasis, recurrence, and immune infiltration in brain, stomach, cervical, and kidney cancers. However, we found that the upregulation of either RSK4 isoform can equally be associated with good or bad prognosis depending on the cancer type considered, and changes in the expression ratio of isoforms fail to predict clinical outcome. Taken together, we show that differential isoform expression alone cannot explain the contradictory roles of RSK4 in cancers and that further research is needed to highlight the underlying mechanisms for the context-dependent function of this kinase.
Phosphoproteomic analysis of the AKT signalling axis in cutaneous squamous carcinoma progression reveals novel therapeutic targets
Authors: Button R , Harwood C , O’Shaughnessy RFL
Published: October 2022

Cutaneous Squamous Cell Carcinoma (cSCC) represents about 20% of all non-melanoma skin cancers. Whilst generally low risk to patients, metastases are associated with a poor prognosis. cSCC incidence is increasing, owing to an ageing population, greater exposure to UV radiation, and more patients receiving immunosuppressive treatments associated with organ transplants. Therefore, there is interest in identifying new biomarkers that may be to track progression of the disease and to exploit as therapeutic vulnerabilities. We show dynamic changes in AKT expression in precursor lesions and in SCC tumour tissue, with initial loss of AKT activity followed by progressive and widespread increase in AKT activity in SCC.

Phosphoproteomic analysis and kinase substrate enrichment analysis on a panel of isogenic cSCC cell lines representing different stages of the disease from premalignancy to metastasis revealed several up-regulated kinases and AKT-targets. From this analysis we chose DNA dependent protein kinase (DNA-PK), a key kinase upstream of AKT phoshorlyation, and N-Myc downstream-regulated gene 2 (NDRG2) a downstream AKT phosphorylation target, to investigate in further detail. Both proteins were up-regulated and mis-expressed in a panel of SCC tissue from different patients. We therefore explored the potential of inhibiting DNA-PK and NDRG2 as cSCC treatments. Treatment with the iron chelator Dp44mT decreased levels of phosphorylated NDRG2 and led to significant losses to viability and reduced migration in our cSCC cell lines, while DNA-PK inhibition promoted the differentiation of premalignant and early-stage SCC cell lines. Our results suggest that NDRG2 and DNA-PK may be viable targets in cSCC treatment, with effectiveness at different stages of SCC progression.
Body size, not species identity, drives body heating in alpineErebiabutterflies
Authors: Kleckova Irena , Okrouhlik Jan , Svozil Tomas , Matos-Maraví Pável , Klecka Jan
Published: October 2022

Efficient thermoregulation is crucial for animals living under fluctuating climatic and weather conditions. We studied the body heating of six butterfly species of the genusErebia(Lepidoptera: Nymphalidae) that co-occur in the European Alps. We tested whether butterfly physical characteristics (body size, wing loading) are responsible for the inter-specific differences in body temperatures recorded previously under natural conditions. We used a thermal camera to measure body heating of wild butterfly individuals in a laboratory experiment with artificial light and heating sources. We revealed that physical characteristics had a small effect on explaining inter-specific differences in mean body temperatures recorded in the field. Our results show that larger butterflies, with higher weight and wing loading, heated up more slowly but reached the same asymptotic body temperature as smaller butterflies. Altogether, our results suggest that differences in body temperatures amongErebiaspecies observed in the field might be caused mainly by species-specific microhabitat use and point towards an important role of active behavioural thermoregulation in adult butterflies. We speculate that microclimate heterogeneity in mountain habitats facilitates behavioural thermoregulation of adults. Similarly, microclimate structuring might also increase survival of less mobile butterfly life stages, i.e., eggs, larvae and pupae. Thus, landscape heterogeneity in management practices may facilitate long term survival of montane invertebrates under increased anthropogenic pressures.
Computational investigation of mechanisms for pH modulation of human chloride channels
Authors: Elverson Kathleen , Freeman Sally , Manson Forbes , Warwicker Jim
Published: October 2022

Many transmembrane proteins are modulated by intracellular or extracellular pH. Investigation of pH-dependence generally proceeds by mutagenesis of a wide set of amino acids, guided by properties such as amino acid conservation and structure. This study shows how web-based calculation of pKas allows rapid and effective identification of amino acids of interest with respect to pH-dependence. Commencing with the calcium-activated chloride channel bestrophin 1, the carboxylate ligand structure around calcium sites relaxes in the absence of calcium, consistent with a measured lack of pH-dependence. By contrast, less relaxation in the absence of calcium in TMEM16A, and maintenance of elevated carboxylate sidechain pKas, is suggested to give rise to pH-dependent chloride channel activity. This hypothesis, modulation of calcium/proton coupling and pH-dependent activity through extent of structural relaxation, is shown to apply to the well-characterised cytosolic proteins calmodulin (pH-independent) and calbindin D9k (pH-dependent). Further application of destabilised ionisable charge sites, or electrostatic frustration, is made to other human chloride channels (that are not calcium-activated), ClC-2, GABAA, and GlyR. Experimentally-determined sites of pH modulation are readily identified. The structure-based tool is freely available, allowing users to focus mutagenesis studies, construct hypothetical proton pathways, and derive hypotheses such as the model for control of pH-dependent calcium activation through structural flexibility. Predicting altered pH-dependence for mutations in ion channel disorders can support experimentation and, ultimately, clinical intervention.
Apolipoprotein E2 Promotes Melanoma Growth, Metastasis, and Protein Synthesis via the LRP1 Receptor
Authors: Adaku Nneoma , Ostendorf Benjamin N. , Tavazoie Sohail F.
Published: October 2022

The secreted lipid transporter apolipoprotein E (APOE) plays important roles in atherosclerosis and Alzheimer’s disease and has been implicated as a suppressor of melanoma progression. APOE germline genotype predicts human melanoma outcomes, as APOE4 and APOE2 allele carriers exhibit increased versus reduced melanoma survival, respectively, relative to APOE3 homozygotes. While the APOE4 variant was recently shown to suppress melanoma progression by enhancing anti-tumor immunity, the melanoma cell-intrinsic effects of APOE variants on cancer progression remain poorly characterized. By using a genetically engineered mouse model, we show that human germline APOE genetic variants differentially modulate melanoma growth and metastasis in a melanoma LRP1 receptor-dependent manner. We identify protein synthesis as a tumor cell-intrinsic process differentially modulated by APOE variants, with APOE2 surprisingly promoting translation via LRP1. Our findings reveal a gain-of-function role for the APOE2 variant in melanoma progression, raising important implications for other diseases impacted by APOE genetics.

Significance

Our work reveals that germline APOE variants differentially impact genetically initiated melanoma progression, with APOE2 acting as a promoter of tumor growth, metastasis, and a cell-intrinsic process—protein synthesis. These findings may aid in predicting patient outcomes and may partly explain the protective effect of APOE2 in Alzheimer’s disease.
EMC holdase:CaV1.2/CaVβ3 complex and CaV1.2 channel structures reveal CaV assembly and drug binding mechanisms
Authors: Chen Zhou , Mondal Abhisek , Abderemane-Ali Fayal , Montano José , Zaro Balyn , Minor Daniel L.
Published: October 2022

Voltage-gated ion channels (VGICs) comprise multiple structural units whose assembly is required for function1,2. There is scant structural understanding of how VGIC subunits assemble and whether chaperone proteins are required. High-voltage activated calcium channels (CaVs)3,4 are paradigmatic multi-subunit VGICs from electrically excitable tissues whose function and trafficking is powerfully shaped by interactions between pore-forming CaV1 or CaV2 CaVα13 and auxiliary CaVβ5, and CaVα2δ subunits6,7. Here, we present cryo-EM structures of human brain and cardiac CaV1.2 bound with CaVβ3 to a chaperone, the endoplasmic reticulum membrane protein complex (EMC)8,9, and of the isolated CaV1.2/CaVβ3/CaVα2δ-1 channel. These provide an unprecedented view of an EMC holdase:client complex and define EMC sites, the TM and Cyto docks, whose interaction with the client channel cause partial extraction of a pore subunit and splay open the CaVα2δ interaction site. The structures further identify the CaVα2δ binding site for gabapentinoid anti-pain and anti-anxiety drugs6, show that EMC and CaVα2δ channel interactions are mutually exclusive, and indicate that EMC to CaVα2δ handoff involves a Ca2+-dependent step and ordering of multiple CaV1.2 elements. Together, the structures unveil a CaV assembly intermediate and previously unknown EMC client binding sites that have broad implications for biogenesis of VGICs and other membrane proteins.
Integrative multispecies omics reveals a hierarchy of cold-responsive regulatory network launched by circadian components in rosids
Authors: Guo Liangyu , Xu Zhiming , Wang Shuo , Nie Yuqi , Ye Xiaoxue , Jin Xuejiao , Zhu Jianhua , Wu Wenwu
Published: October 2022

Elucidating regulators and molecular mechanisms underlying gene transcriptional and post-transcriptional co-regulatory network is key to understand plant cold-stress responses. Previous studies were mainly conducted on single species and whether the regulators and mechanisms are conserved across different species remains elusive. Here, we selected three species that diverged at early evolution of rosids (93–115 million years ago) and integrated phylotranscriptome and ChIP/DAP-seq datasets to identify cold-responsive regulators and their regulatory networks. First, we found over ten thousand cold-responsive genes including differentially expressed genes (DEGs) and alternative splicing genes (DASGs) in each species. Among the DEGs, genes encoding a set of transcription factors (TFs) (AP2/ERF, MYB, WRKY, NAC, etc.) and RNA binding proteins (RBPs) (Ribosomal, RRM, DEAD, Helicase_C, etc.) are conserved in cold responses in rosids. Compared to TFs, RBPs show a delayed cold-responsive pattern, likely suggesting a hierarchical regulation of DEGs and DASGs. Between DEGs and DASGs, we identified 259 overlapping DE-DASG orthogroups and interestingly, pathway analysis on each dataset of DEGs, DASGs, and DE-DASGs coincidently shows an enrichment of circadian rhythm. Evidentially, many circadian components are cold-regulated at both transcriptional and post-transcriptional levels. Moreover, we reasoned 226 cold-responsive genes regulated by at least two of five circadian components (CCA1, LHY, RV4, RVE8, and RVE7) in rosids. Finally, we unveiled a conserved hierarchical network in dynamic transcriptional and post-transcriptional regulation of cold-responsive genes launched by circadian components in rosids. Together, our results provide insights into core regulators and mechanisms underlying cold-responsive regulatory network across rosids, despite a long evolutionary history.
Evaluating sickness-induced anxiety versus lethargy at the behavioral and neuronal activity level
Authors: Lanovoi Hunter T. , Oyama Rumi , Carcea Ioana
Published: October 2022

In mammals, inflammatory responses to infections trigger adaptive behavioral changes collectively known as ‘sickness behavior’. Among these, lethargy protects the sick individual by conserving energy, and increased anxiety is believed to prevent exposure to threats. However, the characterization of these conflicting behavioral states in sickness could be an artifact of behavioral assessment, particularly in rodents. We adjusted existing behavioral testing and designed a new paradigm to disambiguate between increased lethargy versus increased anxiety. Our data indicate that in mice sickness induces a significant increase in lethargy but not in anxiety. Further supporting our behavioral results, at the neuronal level we found evidence that sickness activates anxiolytic rather than anxiogenic regions of the amygdala, including oxytocin receptor expressing neurons. Putative mechanisms by which sickness could activate CeA-OTR+ neurons were investigated.
Photosynthetically active radiation is required for seedling growth promotion by volcanic dacitic tuff breccia (Azomite)
Authors: McCue Kent F. , Mehlferber Elijah , Reed Robert , Ortiz Alexis , Ferrel Jon , Khanna Rajnish
Published: October 2022

A plant’s growth and development are shaped by its genome and the capacity to negotiate its environment for access to light, water, and nutrients. There is a vital need to understand the interactions between the plant, its physical environment, and the fertilizers used in agriculture. In this study, a commercially available volcanic ash fertilizer, Azomite®, characterized as dacitic (rhyolitic) tuff breccia (DTB), was tested for its effect on promoting early seedling vigor. Early growth and photomorphogenesis processes are well studied in Arabidopsis. Seedling assays under different light conditions were used to dissect the underlying mechanisms involved. These assays are well established and can be translated to agriculturally important crop plants. The volcanic ash fertilizer was tested at different concentrations on seedlings grown on basic media lacking sucrose either in continuous darkness (Dc), continuous Red (Rc), Far-Red (FRc), or White Light (WLc). Micronutrients in the volcanic ash significantly increased seedling growth under Rc and WLc, but not under Dc and FRc, indicating that photosynthetically active radiation (PAR) was required for the observed growth increase. Furthermore, red-light photoreceptor mutant, phyB-9 lacked the growth response, and higher amount of fertilizer reduced growth in all conditions tested. These data suggest that light triggers the ability of the seedling to utilize micronutrients in volcanic ash in a dose-dependent manner. The methods described here can be used to establish mechanisms of activity of various nutrient inputs, and coupled with whole-genome expression profiling, can lead to better insights into optimizing nutrient field applications to improve crop production.
Irx1 and Irx2 play dose-dependent cooperative functions in mammalian development
Authors: Sheybani-Deloui Sepideh , Xu Leo , Hu Lijuan , Yuan Qiongjing , Son Joe Eun , Kim Kyoung-Han , Liu Weifan , Mo Rong , Zhang Xiaoyun , Chi Lijun , Olguin Paul Delgado , Hui Chi-Chung
Published: October 2022

Irx1 and Irx2 (Irx1/2) are two closely linked and widely expressed members of the conserved Iroquois homeobox family of transcription factors. Despite mounting evidence suggesting the importance of homologs of these genes in many aspects of vertebrate development and function, the role of Irx1/2 in mammals has remained largely unknown. Here, we used mice carrying our newly generated Irx1flox and Irx1floxIrx2del mutant alleles to perform a stepwise genetic ablation of Irx1 and Irx2 levels. Our analysis revealed reduced postnatal growth and viability of Irx1KO mice with gross histological defects in the lung and gut and demonstrated that ablation of one copy of Irx2 in these mice results in neonatal lethality with exacerbated phenotypic defects. Conversely, while Irx2KO mice appear normal, ablation of one copy of Irx1 in these mutants leads to lethality at weaning. Furthermore, we found that homozygous deletion of both Irx1 and Irx2 results in embryonic lethality by mid-gestation with defective extraembryonic vasculature. Our results illustrate that Irx1 and Irx2 play distinct dose-dependent cooperative functions during both the early and late stages of mouse development.
Modelling the gastrointestinal carriage of Klebsiella pneumoniae infections
Authors: Calderon-Gonzalez Ricardo , Lee Alix , Lopez-Campos Guillermo , Hancock Steven J. , Sa-Pessoa Joana , Dumigan Amy , McMullan Ronan , Campbell Eric L. , Bengoechea Jose A.
Published: October 2022

Klebsiella pneumoniae is a leading cause of nosocomial and community acquired infections, making K. pneumoniae the second pathogen associated with the most deaths attributed to any antibiotic resistant infection. K. pneumoniae colonises the nasopharynx and the gastrointestinal tract in an asymptomatic manner without dissemination to other tissues; importantly gastrointestinal colonisation is a requisite for infection. Our understanding of K. pneumoniae colonisation is still based on interrogating mouse models in which animals are pre-treated with antibiotics to disturb the colonisation resistance imposed by the gut microbiome. In these models, infection disseminates to other tissues. Here, we report a murine model to allow for the study of the gastrointestinal colonisation of K. pneumoniae without tissue dissemination. Hypervirulent and antibiotic resistant strains stably colonise the gastrointestinal tract of in an inbred mouse population without antibiotic treatment. The small intestine is the primary site of colonisation followed by a transition to the colon over time without dissemination to other tissues. Our model also mimics the disease dynamics of metastatic K. pneumoniae strains able to disseminate from the gastrointestinal tract to other sterile sites. Colonisation is associated with mild to moderate histopathology, no significant inflammation, and no effect on the richness of the microbiome. Our model recapitulates the clinical scenario in which antibiotic treatment disturbs the colonisation of K. pneumoniae resulting in dissemination to other tissues. Finally, we establish that the capsule polysaccharide is necessary for the colonisation of the large intestine whereas the type VI secretion system contributes to colonisation across the gastrointestinal tract.

IMPORTANCE

Klebsiella pneumoniae is one of the pathogens sweeping the World in the antibiotic resistance pandemic. Klebsiella colonises the nasopharynx and the gut of healthy subjects in an asymptomatic manner, being gut colonisation a requisite for infection. This makes essential to understand the gastrointestinal carriage to prevent Klebsiella infections. Current research models rely on the perturbation of the gut microbiome by antibiotics, resulting in an invasive infection. Here, we report a new model of K. pneumoniae gut colonisation that recapitulates key features of the asymptomatic human gastrointestinal tract colonisation. In our model, there is no need to disturb the microbiota to achieve stable colonization without dissemination to other tissues. Our model recapitulates the clinical scenario in which antibiotic treatment triggers invasive infection. We envision our model will be an excellent platform to test therapeutics to eliminate Klebsiella asymptomatic colonisation, and to investigate factors enhancing colonisation and invasive infections.
Population-level relative effectiveness of the COVID-19 vaccines and the contribution of naturally acquired immunity
Authors: Shioda Kayoko , Chen Yangping , Collins Matthew H , Lopman Benjamin A
Published: October 2022

Background

Immune protection against SARS-CoV-2 can be induced by natural infection or vaccination or both. The interaction between vaccine-induced immunity and naturally acquired immunity at the population level has been understudied.

Methods

We used regression models to evaluate whether the impact of COVID-19 vaccines differed across states with different levels of naturally acquired immunity from March 2021 to April 2022 in the United States. Analysis was conducted for three evaluation periods separately (Alpha, Delta, and Omicron waves). As a proxy of the proportion of the population with naturally acquired immunity, we used either the reported seroprevalence or the estimated proportion of the population ever infected in each state.

Results

COVID-19 mortality decreased as the coverage of ≥1 dose increased among people ≥65 years of age, and this effect did not vary by seroprevalence or the proportion of the total population ever infected. Seroprevalence and the proportion ever infected were not associated with COVID-19 mortality, after controlling for vaccine coverage. These findings were consistent in all evaluation periods.

Conclusions

COVID-19 vaccination was associated with a sustained reduction in mortality at the state level during the Alpha, Delta, and Omicron periods. The effect did not vary by naturally acquired immunity.
Adaptation to spindle assembly checkpoint inhibition through the selection of specific aneuploidies
Authors: Adell Manuel Alonso Y , Klockner Tamara C. , Höfler Rudolf , Wallner Lea , Schmid Julia , Markovic Ana , Martyniak Anastasiia , Campbell Christopher S.
Published: October 2022

Both the presence of an abnormal complement of chromosomes (aneuploidy) and an increased frequency of chromosome missegregation (chromosomal instability) are hallmarks of cancer. Analyses of cancer genome data have identified certain aneuploidy patterns in tumors; however, the bases behind their selection are largely unexplored. By establishing time-resolved long-term adaptation protocols, we found that human cells adapt to persistent spindle assembly checkpoint (SAC) inhibition by acquiring specific chromosome arm gains and losses. Independently adapted populations converge on complex karyotypes, which over time are refined to contain ever smaller chromosomal changes. Of note, the frequencies of chromosome arm gains in adapted cells correlate very well with those detected in cancers, suggesting that our cellular adaptation approach recapitulates selective traits that dictate pan-cancer aneuploidy patterns. We further engineered specific aneuploidies to determine the genetic basis behind the observed karyotype patterns. These experiments demonstrated that the adapted and engineered aneuploid cell lines limit CIN by extending mitotic duration. Heterozygous deletions of key SAC and APC/C genes recapitulated the rescue phenotypes of the monosomic chromosomes. We conclude that aneuploidy-induced gene dosage imbalances of individual mitotic regulators are sufficient for altering mitotic timing to reduce CIN.
AnIn VivoAnalysis of the Functional Motifs of DEAD-box RNA Helicase Me31B inDrosophilaFertility and Germline Development
Authors: Kara Evan , McCambridge Aidan , Proffer Megan , Dilts Carol , Pumnea Brooke , Eshak John , Smith Korey A. , Fielder Isaac , Doyle Dominique A. , Ortega Bianca M. , Mukatash Yousif , Malik Noor , Mohammed Ammaar R. , Govani Deep , Niepielko Matthew G. , Gao Ming
Published: October 2022

InDrosophilagermline, Me31B is a putative ATP-dependent, RNA helicase that plays role in post-transcriptional RNA regulation to ensure the correct spatial and temporal expression of the mRNAs, a process crucial for proper germline development and fertility. However, Me31B’sin vivoworking mechanism remains unclear. In this study, we aim to analyze the functions of Me31B’s key domains/motifs to understand how these domains/motifs operate to fulfill the protein’s overall activities. We generatedDrosophilastrains mutant for six important motifs including three ATPase/helicase motifs (DEAD-box, DVLARAK, and HRIGR), the N-terminal domain (N-ter), the C-terminal domain (C-ter), and a protein-binding motif (FDF motif-binding motif). In characterizing these mutants, we observed that the three ATPase/helicase motif mutations cause dominant female sterility which is associated with developmental defects in oogenesis and embryogenesis. Follow-up examination of the DVLARAK motif mutant revealed its abnormalities in germline mRNA localization and transcript level. The Me31B N-ter domain (deletion of C-ter), C-ter domain (deletion of N-ter), and mutation of FDF motif-binding motif led to a decrease in female fertility and abnormal subcellular Me31B localizations in the egg chambers. Moreover, deletion of Me31B N-ter or C-ter motif results in a decrease of Me31B protein levels in the ovaries. This study indicates that these six motifs of Me31B play different roles to contribute to Me31B’s whole-protein functions like ATPase, RNA helicase, protein stability, protein localization, and partner protein binding, which are crucial for germline development and fertility. Considering Me31B protein family’s conserved presence in bothDrosophilagermline and soma (for example, neurons) and in other organisms such as yeast, worm, mouse, and human, the results from this study could expand our understanding of Me31B helicase family’s general working mechanisms in different cell types and species.
Fission-independent compartmentalization of mitochondria during budding yeast cell division
Authors: Yoshii Saori R. , Barral Yves
Published: October 2022

Lateral diffusion barriers compartmentalize membranes to generate polarity or asymmetrically partition membrane-associated macromolecules. Budding yeasts assemble such barriers in the endoplasmic reticulum (ER) and the outer nuclear envelope at the bud neck to retain aging factors in the mother cell and generate naïve and rejuvenated daughter cells. However, little is known about whether other organelles are similarly compartmentalized. Here, we show that the membranes of mitochondria are laterally compartmentalized at the bud neck and near the cell poles. The barriers in the inner mitochondrial membrane are constitutive, whereas those in the outer membrane form in response to stresses. The strength of mitochondrial diffusion barriers is regulated positively by spatial cues from the septin axis, and negatively by retrograde (RTG) signaling. These data indicate that mitochondria are compartmentalized in a fission-independent manner. We propose that these diffusion barriers may promote mitochondrial polarity and contribute to mitochondrial quality control.
Comparative genomics and transcriptomic response to root exudates of six rice root-associatedBurkholderia sensu latospecies
Authors: Wallner Adrian , Klonowska Agnieszka , Guigard Ludivine , King Eoghan , Rimbault Isabelle , Ngonkeu Eddy , Nguyen Phuong , Béna Gilles , Moulin Lionel
Published: October 2022

Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of theBurkholderiaandParaburkholderiagenera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species,Burkholderiaare often studied for their human opportunistic traits. Here, we used root exudate stimulation on threeBurkholderiaand threeParaburkholderiastrains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling.
Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps
Authors: Eyring Luca Vincent , Klein Dominik , Palla Giovanni , Becker Soeren , Weiler Philipp , Kilbertus Niki , Theis Fabian J.
Published: October 2022

Optimal Transport (OT) has proven useful to infer single-cell trajectories of developing biological systems by aligning distributions across time points. Recently, Parameterized Monge Maps (PMM) were introduced to learn the optimal map between two distributions. Here, we apply PMM to model single-cell dynamics and show that PMM fails to account for asymmetric shifts in cell state distributions. To alleviate this limitation, we propose Unbalanced Parameterised Monge Maps (UPMM). We first describe the novel formulation and show on synthetic data how our method extends discrete unbalanced OT to the continuous domain. Then, we demonstrate that UPMM outperforms well-established trajectory inference methods on real-world developmental single-cell data.
Structure of human phagocyte NADPH oxidase in the resting state
Authors: Liu Rui , Song Kangcheng , Wu Jing-Xiang , Geng Xiao-Peng , Zheng Liming , Gao Xiaoyin , Peng Hailin , Chen Lei
Published: October 2022

Phagocyte oxidase plays an essential role in the first line of host defense against pathogens. It oxidizes intracellular NADPH to reduce extracellular oxygen to produce superoxide anions for pathogen killing. The resting phagocyte oxidase is a heterodimeric complex formed by two transmembrane proteins NOX2 and p22. Despite the functional importance of this complex, its structure remains elusive. Here we reported the cryo-EM structure of the human NOX2-p22 complex in nanodisc in the resting state. The structure shows that p22 is formed by four transmembrane helices and interacts with NOX2 through its M1 and M4 helices. Hydrophobic residues on M3, M4, and M5 of NOX2 contribute to the complex formation. Structural analysis suggests that the cytosolic factors activate the NOX2-p22 complex by stabilizing the dehydrogenase domain (DH) in a productive docked conformation which is efficient for electron transfer between DH and the transmembrane domain.
Pervasive mRNA uridylation in fission yeast catalysed by both Cid1 and Cid16 terminal uridyltransferases
Authors: Lipińska-Zubrycka L , Grochowski M , Bähler J , Małecki M
Published: October 2022

Messenger RNA uridylation is pervasive and conserved among eukaryotes, but the consequences of this modification for mRNA fate are still under debate. Utilising a simple model organism to study uridylation may facilitate efforts to understand the cellular function of this process. Here we demonstrate that uridylation can be detected using simple bioinformatics approach. We utilise it to unravel widespread transcript uridylation in fission yeast and demonstrate the contribution of both Cid1 and Cid16, the only two annotated terminal uridyltransferases (TUT-ases) in this yeast.

To detect uridylation in transcriptome data, we used a RNA-sequencing (RNA-seq) library preparation protocol involving initial linker ligation to fragmented RNA. We next explored the data to detect uridylation marks. Our analysis shows that uridylation in yeast is pervasive, similarly to the ones in multicellular organisms. Importantly, our results confirm the role of the cytoplasmic uridyltransferase Cid1 as the primary uridylation catalyst. However, we also observed an auxiliary role of the second uridyltransferase, Cid16. Thus both fission yeast uridyltransferases are involved in mRNA uridylation. Intriguingly, we found no physiological phenotype of the single and double deletion mutants of cid1 and cid16 and only limited impact of uridylation on steady-state mRNA levels.

Our work establishes fission yeast as a potent model to study uridylation in a simple eukaryote, and we demonstrate that it is possible to detect uridylation marks in RNA-seq data without the need for specific methodologies.
MTCH2 cooperates with MFN2 and lysophosphatidic acid synthesis to sustain mitochondrial fusion
Authors: Goldman Andres , Mullokandov Michael , Zaltsman Yehudit , Regev Limor , Zaidman Smadar , Gross Atan
Published: October 2022

Mitochondrial dynamics is critical to sustain normal mitochondrial function and is linked to the response of cells to stressful conditions. Fusion of the outer mitochondrial membrane (OMM) is regulated by mitofusin 1 (MFN1) and 2 (MFN2), yet the differential contribution of each of these proteins to this process is less understood. Mitochondrial carrier homolog 2 (MTCH2) was shown to compensate for MFN2’s loss, however its exact function in mitochondrial fusion remains poorly understood. Here we determined the mitochondrial fusion-interplay between MFN1, MFN2 and MTCH2 and demonstrate that MFN2 and MTCH2 play separate, but redundant, roles required for mitochondrial fusion. Loss of either MFN2 or MTCH2 elicits mitochondrial fragmentation that retains mitochondrial plasticity, while loss of both proteins completely impairs mitochondrial fusion. We also show that expression of an MFN2 mutant targeted to the endoplasmic reticulum (ER) is sufficient to restore mitochondrial elongation in MTCH2 KO cells and that this restoration depends on the synthesis of the pro-mitochondrial fusion lipid lysophosphatidic acid (LPA). Moreover, silencing of MFN2 or inhibition of de novo LPA synthesis, revealed the requirement of MTCH2 to sustain mitochondrial plasticity in response to stress. Thus, we unmask two cooperative mechanisms that sustain mitochondrial fusion: one in the OMM, dependent on MTCH2 and MFN1, and independent of MFN2; and a second mechanism in the ER that relies on MFN2 and LPA synthesis.
A corset of adhesions during development establishes individual neural stem cell niches and controls adult behaviour
Authors: Banach-Latapy Agata , Rincheval Vincent , Briand David , Guénal Isabelle , Spéder Pauline
Published: October 2022

Neural stem cells (NSCs) reside in a defined cellular microenvironment, the niche, which supports the generation and integration of neuronal lineages. The mechanisms building a sophisticated niche structure around NSCs, and their functional relevance for neurogenesis are yet to be understood. In the Drosophila larval brain, the cortex glia (CG) encase individual NSC lineages, organizing the stem cell population and newborn neurons into a stereotypic structure. We first found that lineage information is dominant over stem cell fate. We then discovered that, in addition to timing, the balance between multiple adhesion complexes supports the individual encasing of NSC lineages. An intra-lineage adhesion through homophilic Neuroglian interactions provides strong binding between cells of a same lineage, while a weaker interaction through Neurexin-IV exists between CG to NSC lineages. Their loss leads to random, aberrant grouping of several NSC lineages together, and to altered axonal projection of newborn neurons. Further, we link the loss of these two adhesion complexes during development to locomotor hyperactivity in the resulting adults. Altogether, our findings identify a corset of adhesions building a neurogenic niche at the scale of individual stem cell and provide the proof-of-principle that mechanisms supporting niche formation during development define adult behaviour.
Geometric constraints on human brain function
Authors: Pang James C. , Aquino Kevin M. , Oldehinkel Marianne , Robinson Peter A. , Fulcher Ben D. , Breakspear Michael , Fornito Alex
Published: October 2022

The brain’s anatomy constrains its function, but precisely how remains unclear. Here, we show that human cortical and subcortical activity, measured with magnetic resonance imaging under spontaneous and diverse task-evoked conditions, can be parsimoniously understood as resulting from excitations of fundamental, resonant modes of the brain’s geometry (i.e., its shape) rather than modes from complex inter-regional connectivity, as classically assumed. We then use these modes to show that task-evoked activations across >10,000 brain maps are not confined to focal areas, as widely believed, but instead excite brain-wide modes with wavelengths spanning >60 mm. Finally, we confirm theoretical predictions that the close link between geometry and function is explained by a dominant role for wave-like dynamics, showing that such dynamics can reproduce numerous canonical spatiotemporal properties of spontaneous and evoked recordings. Our findings challenge prevailing views of brain function and identify a previously under-appreciated role of brain geometry that is predicted by a unifying and physically principled approach.
Analysis of the structure and time-series evolution of knowledge label network from a complex perspective
Authors: Wang Xu , Feng Xin , Guo Yuan
Published: October 2022

Purpose

The research on social media-based academic communication has made great progress with the development of the mobile Internet era, and while a large number of research results have emerged, clarifying the topology of the knowledge label network (KLN) in this field and showing the development of its knowledge labels and related concepts is one of the issues that must be faced. This study aims to discuss the aforementioned issue.

Design/methodology/approach

From a bibliometric perspective, 5,217 research papers in this field from CNKI from 2011 to 2021 are selected, and the title and abstract of each paper are subjected to subword processing and topic model analysis, and the extended labels are obtained by taking the merged set with the original keywords, so as to construct a conceptually expanded KLN. At the same time, appropriate time window slicing is performed to observe the temporal evolution of the network topology. Specifically, the basic network topological parameters and the complex modal structure are analyzed empirically to explore the evolution pattern and inner mechanism of the KLN in this domain. In addition, the ARIMA time series prediction model is used to further predict and compare the changing trend of network structure among different disciplines, so as to compare the differences among different disciplines.

Findings

The results show that the degree sequence distribution of the KLN is power-law distributed during the growth process, and it performs better in the mature stage of network development, and the network shows more stable scale-free characteristics. At the same time, the network has the characteristics of “short path and high clustering” throughout the time series, which is a typical small-world network. The KLN consists of a small number of hub nodes occupying the core position of the network, while a large number of label nodes are distributed at the periphery of the network and formed around these hub nodes, and its knowledge expansion pattern has a certain retrospective nature. More knowledge label nodes expand from the center to the periphery and have a gradual and stable trend. In addition, there are certain differences between different disciplines, and the research direction or topic of library and information science (LIS) is more refined and deeper than that of journalism and media and computer science. The LIS discipline has shown better development momentum in this field.

Originality/value

KLN is constructed by using extended labels and empirically analyzed by using network frontier conceptual motifs, which reflects the innovation of the study to a certain extent. In future research, the influence of larger-scale network motifs on the structural features and evolutionary mechanisms of KLNs will be further explored.
Testing spillover-crossover effects of work-family conflict and family-work conflict on Indonesian spouses
Authors: Ratnaningsih Ika Zenita , Idris Mohd Awang , Yulita Yulita
Published: October 2022

Purpose

This study aims to investigate the spillover–crossover effects on the work–family interface, with an emphasis on work–family conflict (WFC) and family–work conflict (FWC) on marital satisfaction and personal burnout.

Design/methodology/approach

Data were collected from matched dyads by 300 teachers and their spouses (N = 600) in Indonesia. Multiple regression analysis served to test the hypotheses.

Findings

The results showed significant spillover–crossover effects of WFC on personal burnout amongst working wives to their spouses, but not working husbands to their spouses. Moreover, there was a spillover effect of FWC on personal burnout amongst working wives, and a crossover effect of FWC on spouses' personal burnout amongst working husbands to their spouses. However, there was no spillover–crossover effect of WFC and FWC on marital satisfaction for both working wives and husbands.

Practical implications

The findings have implications for occupational stress management. Decision-makers have to create a positive atmosphere that reduces WFC in the workplace by providing support to the workers.

Originality/value

This study contributes to the literature by exploring the crossover effects of WFC and FWC amongst marital spouses in a country with inherent conservatism and traditional gender role perspectives.
Corporate social responsibility performance and its effects on climate for innovation and opportunism: evidence from Vietnamese architectural design firms
Authors: Nguyen Minh Van
Published: October 2022

Purpose

The purpose of this research is to expand a better understanding of how corporate social responsibility (CSR) initiatives affect climate for innovation and opportunism within architectural design firms (ADFs).

Design/methodology/approach

The literature review and discussions with industry practitioners identified an initial list of variables. A questionnaire survey was developed, validated and delivered to employees working in ADFs. 226 valid responses were collected. Then, the structural equation modeling (SEM) method was employed to empirically investigate the relationships between CSR performance, climate for innovation and opportunism in a single integrative model.

Findings

The results empirically support that CSR performance has a positive effect on climate for innovation and a negative effect on opportunism. In addition, climate for innovation shows a negative effect on opportunism.

Research limitations/implications

This research highlights that CSR performance is essential for ADFs to better achieve sustainable development. By doing CSR activities, climate for innovation in ADFs is expected to be improved, and a sense of opportunism is mitigated. The findings of this paper are explicitly delivered in the context of Vietnamese ADFs and could not be straightforwardly generalized or translated to the construction industry or other sectors in different research contexts.

Practical implications

The findings show that a climate for innovation is crucial in ADFs. Business managers are encouraged to employ CSR initiatives to foster an innovation climate and reduce a sense of opportunism within ADFs.

Originality/value

This study is one of the first attempts to investigate the relationships between CSR performance, climate for innovation, and opportunism within ADFs. While the findings highlight the critical role of CSR performance, the study argues that CSR should be carefully implemented because there are no “one-size-fits-all” CSR strategies for different business contexts.