bluuebunny/crossref_metadata_2025_split huggingface dataset:
Possible acquisition and molecular evolution ofvpugenes inferred from comprehensive sequence analysis of human and simian immunodeficiency viruses
Authors: Naruki Miu , Saito Motofumi , Nomaguchi Masako , Kanai Akio 
Published: April 2024

AbstractVpu, an accessory protein ofHuman immunodeficiency virus 1(HIV-1), plays a crucial role in viral particle production and release, contributing to HIV virulence and its associated pandemic. Despite its significance, the acquisition and evolution of thevpugene remain poorly understood. In this study, we conducted a comprehensive computational analysis of approximately 38,000 sequences fromSimian immunodeficiency viruses(SIV) and HIV. From these, we obtained 141 representative Vpu protein sequences, while preserving their diversity by removing redundant sequences. We then created a phylogenetic tree, which revealed that SIV and HIV strains can be classified into four major types based on the Vpu proteins they express: Vpu-type 1, the putative ancestral type, which includes SIVs from Dent’s mona monkey, mona monkey, and moustached guenon; Vpu-type 2, which includes SIVgor from gorillas and HIV-1 group O; Vpu-type 3, which includes SIVcpz from chimpanzees; and Vpu-type 4, which includes HIV-1 group M, HIV-1 pandemic strain (subtype 4a), and HIV-1 group N (subtype 4b). Vpu-types 1 and 2 show variations invpulength, whereas Vpu-types 3 and 4 show less variability. Notably, the gene encoding Vpu-type 1 varies in the length of its overlap with theenvgene. To clarify the evolutionary relationship between Vpu-type 1 SIVs and SIVs lacking Vpu, we constructed a phylogenetic tree based on the nucleotide sequence between thepolandenvgenes, using 401 sequences derived from HIV-1, HIV-2, and SIVs. Vpu-type 1 (SIVden and SIVmon), SIVasc (red-tailed monkey), and SIVsyk (Sykes’ monkeys) clustered closely on the phylogenetic tree. Considering the observed similarities between thevpu, vprandenvgenes in SIVdeb and SIVsyk, we speculated that thevpugene originated within the SIV genome. A phylogenetic tree constructed with 242 Vpu-type 4a sequences from the HIV pandemic strain and 135 sequences of circulating recombinant forms of HIV-1 revealed that the viral subtypes can be further classified into 18 distinct protein subtypes, surpassing the number of previously known subtypes. Collectively, our results suggest an evolutionary model for thevpugene that sheds light on its origin and divergence, and their implications in the context of HIV-1 and SIV evolution.
Variable orthogonality of RDF – large serine integrase interactions within the ϕC31 family
Authors: MacDonald Alasdair I. , Baksh Aron , Holland Alex , Shin Heewhan , Rice Phoebe A. , Stark W. Marshall , Olorunniji Femi J. 
Published: April 2024

AbstractLarge serine integrases are phage- (or mobile element-) encoded enzymes that catalyse site-specific recombination reactions between a short DNA sequence on the phage genome (attP) and a corresponding host genome sequence (attB), thereby integrating the phage DNA into the host genome. Each integrase has its unique pair ofattPandattBsites, a feature that allows them to be used as orthogonal tools for genome modification applications. In the presence of a second protein, the Recombination Directionality Factor (RDF), integrase catalyses the reverse, excisive reaction, generating new recombination sites,attRandattL. In addition to promotingattRxattLreaction, the RDF inhibitsattPxattBrecombination. This feature makes the directionality of integrase reactions programmable, allowing them to be useful for building synthetic biology devices. In this report, we describe the degree of orthogonality of both integrative and excisive reactions for three related integrases (ϕC31, ϕBT1, and TG1) and their RDFs. Among these, TG1 integrase is the most active, showing near complete recombination in bothattPxattBandattRxattLreactions, and the most directional in the presence of its RDF. Our findings show that there is varying orthogonality among these three integrases – RDF pairs: ϕC31 integrase was the least selective, with all three RDFs activating it forattRxattLrecombination. Similarly, ϕC31 RDF was the least effective among the three RDFs in promoting the excisive activities of the integrases, including its cognate ϕC31 integrase. ϕBT1 and TG1 RDFs were noticeably more effective than ϕC31 RDF at inhibitingattPxattBrecombination by their respective integrases, making them more suitable for building reversible genetic switches. AlphaFold-Multimer predicts very similar structural interactions between each cognate integrase – RDF pair. The binding surface on RDF is much more conserved than the binding surface on integrase, an indication that specificity is determined more by the integrase than the RDF. Overall, the observed weak integrase/RDF orthogonality across the three enzymes emphasizes the need for identifying and characterizing more integrase – RDF pairs. Additionally, the ability of a particular integrase’s preferred reaction direction to be controlled to varying degrees by non-cognate RDFs provides a path to tunable, non-binary genetic switches.
A Tunable and Druggable Mechanism to Delay Forgetting of Olfactory Memories inC. elegans
Authors: Berliner Dana Landschaft , Goldstein Kesem , Teichman Guy , Anava Sarit , Gingold Hila , Rieger Itai , Levi Noam , Pechuk Vladyslava , Salzberg Yehuda , Agarwal Priti , Sagi Dror , Cohen Dror , Nikelshparg Evelina , Ben-Zvi Anat , Zaidel-Bar Ronen , Vizuete Antonio Miranda , Oren-Suissa Meital , Rechavi Oded 
Published: April 2024

AbstractThe poet W.B Yeats wrote that“All that is personal soon rots, it must be packed in ice or salt”. Here we show that inCaenorhabditis elegansnematodes, simple animals with just 302 neurons, memories are preserved on ice and in lithium salt.C. elegansnematodes can form associative memories, which are typically forgotten quickly. We discovered that when placed on ice, worms delay forgetting of specific olfactory memories by at least 8-fold. Delayed forgetting was canceled completely when the worms were gradually adapted to low temperatures, owing to a genetically-encoded program that turns acclimated worms cold-tolerant. RNA-seq, mutant analyses, and pharmacological assays revealed that regulation of membrane properties switches cold-induced delayed forgetting ON and OFF, and, remarkably, that lithium delays forgetting only in cold-sensitive but not cold-tolerant worms. We found that downregulation of the diacylglycerol pathway in the AWC sensory neurons is essential for lithium-mediated delayed forgetting, and using neuronal activity recordings located the memory trace to the downstream AIY interneurons. We suggest that the awesome genetic tractability ofC. elegansmight be harnessed to study the effects of lithium and cold temperatures on the brain, why it influences psychiatric disorders, and even more fundamentally how memory is stored and lost.
Extracellular vesicles isolated from frozen and fresh human melanoma tissue are similar in purity and protein composition
Authors: D’Arrigo Daniele , Lässer Cecilia , Urzì Ornella , Park Kyong-Su , Bagge Roger Olofsson , Lötvall Jan , Crescitelli Rossella 
Published: April 2024

ABSTRACTExtracellular vesicles (EVs) isolated from tumor tissues represent a precious source of EVs because they are enriched in disease-associated biomarkers and are highly concentrated. However, a fundamental question is whether freezing of tissues influences the EVs’ integrity and function and whether non-EVs are co-isolated with the EVs. In this work, we isolated EVs from metastatic melanoma tissue both immediately after tissue resection and after being frozen for at least two weeks. Specifically, the samples were divided into two parts: one was immediately processed for EV isolation (hereafter called fresh), and the other was frozen on dry ice and stored for two weeks before being processed for EV isolation (hereafter called frozen). Large and small EVs were isolated through ultracentrifugation, pooled, and further purified on an iodixanol density cushion. The EVs were analyzed by transmission electron microscopy, nanoparticle tracking analysis, and protein quantification as well as by quantitative mass spectrometry. The results did not show any significant difference between EVs isolated from fresh and frozen tissue. Importantly, there was no enrichment of either intracellular proteins or mitochondrial proteins in EVs isolated from frozen tissues vs. fresh tissues. Moreover, there were no significant differences in the quantity of proteins like MT-CO2, Cox6, SLC24A22, HLA-DR, and Erlin2, which were previously identified as potential markers of melanoma, ovarian cancer, and breast cancer. Overall, this study supports the use of frozen tissues as a source of EVs for research purposes because frozen tissue-derived EVs do not differ in purity or protein composition compared to their fresh counterparts.
Pseudovibriamides fromPseudovibriomarine sponge bacteria promote swarming motility via transcriptional modulation
Authors: Dai Yitao , Lourenzon Vitor , Ióca Laura P. , Al-Smadi Dua , Arnold Lydia , McIntire Ian , Berlinck Roberto G. S. , Eustáquio Alessandra S. 
Published: April 2024

AbstractPseudovibrioα-Proteobacteria have been repeatedly isolated from marine sponges and proposed to be beneficial to the host. Bacterial motility is known to contribute to host colonization. We have previously identified pseudovibriamides A and B, produced in culture byPseudovibrio brasiliensisAb134, and shown that pseudovibriamide A promotes flagellar motility. Pseudovibriamides are encoded in a hybrid nonribosomal peptide synthetase-polyketide synthase gene cluster that also includes several accessory genes. Pseudovibriamide A is a linear heptapeptide and pseudovibriamide B is a nonadepsipeptide derived from pseudovibriamide A. Here we define the borders of the pseudovibriamides gene cluster, assign function to biosynthetic genes using reverse genetics and test the hypothesis that pseudovibriamides impact motility by modulating gene transcription. RNA-seq transcriptomic analyses of strains having different compositions of pseudovibriamides suggested that both pseudovibriamides A and B affect genes potentially involved in motility, and that a compensatory mechanism is at play in mutants that produce only pseudovibriamide A, resulting in comparable swarming motility as the wild type. The data gathered suggest that pseudovibriamides A and B have opposite roles in modulating a subset of genes, with pseudovibriamide B having a primary effect in gene activation, and pseudovibriamide A on inhibition. Finally, we observed many differentially expressed genes (up to 29% of the total gene number) indicating that pseudovibriamides have a global effect on transcription that goes beyond motility.ImportanceMarine sponges are found throughout the oceans from tropical coral reefs to polar sea floors, playing crucial roles in marine ecosystems.Pseudovibriobacteria have been proposed to contribute to sponge health. We have previously shown that pseudovibriamides produced byPseudovibrio brasiliensispromote bacterial motility, a behavior that is beneficial to bacterial survival and to host colonization. The gene cluster that encodes pseudovibriamide biosynthesis is found in two thirds ofPseudovibriogenomes. This gene cluster is also present inPseudomonasbacteria that interact with terrestrial plants and animals. Here we first assign function to pseudovibriamide biosynthetic genes using reverse genetics. We then show that pseudovibriamides play a major role in transcriptional regulation, affecting up to 29% ofP. brasiliensisgenes, including motility genes. Thus, this work gives insights into pseudovibriamide biosynthesis and provides evidence that they are signaling molecules relevant to bacterial motility and to other yet to be identified phenotypes.
PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking
Authors: Forman Thomas E. , Sajek Marcin P. , Larson Eric D. , Mukherjee Neelanjan , Fantauzzo Katherine A. 
Published: April 2024

AbstractSignaling through the platelet-derived growth factor receptor alpha (PDGFRα) plays a critical role in craniofacial development, as mutations inPDGFRAare associated with cleft lip/palate in humans andPdgframutant mouse models display varying degrees of facial clefting. Phosphatidylinositol 3-kinase (PI3K)/Akt is the primary effector of PDGFRα signaling during skeletal development in the mouse. We previously demonstrated that Akt phosphorylates the RNA-binding protein serine/arginine-rich splicing factor 3 (Srsf3) downstream of PI3K-mediated PDGFRα signaling in mouse embryonic palatal mesenchyme (MEPM) cells, leading to its nuclear translocation. We further showed that ablation ofSrsf3in the murine neural crest lineage results in severe midline facial clefting, due to defects in proliferation and survival of cranial neural crest cells, and widespread alternative RNA splicing (AS) changes. Here, we sought to determine the molecular mechanisms by which Srsf3 activity is regulated downstream of PDGFRα signaling to control AS of transcripts necessary for craniofacial development. We demonstrated via enhanced UV-crosslinking and immunoprecipitation (eCLIP) of MEPM cells that PDGF-AA stimulation leads to preferential binding of Srsf3 to exons and loss of binding to canonical Srsf3 CA-rich motifs. Through the analysis of complementary RNA-seq data, we showed that Srsf3 activity results in the preferential inclusion of exons with increased GC content and lower intron to exon length ratio. Moreover, we found that the subset of transcripts that are bound by Srsf3 and undergo AS upon PDGFRα signaling commonly encode regulators of PI3K signaling and early endosomal trafficking. Functional validation studies further confirmed that Srsf3 activity downstream of PDGFRα signaling leads to retention of the receptor in early endosomes and increases in downstream PI3K-mediated Akt signaling. Taken together, our findings reveal that growth factor-mediated phosphorylation of an RNA-binding protein underlies gene expression regulation necessary for mammalian craniofacial development.
RNA-binding proteins identified by R-DeeP/TripepSVM are involved in heterocyst differentiation
Authors: Brenes-Álvarez Manuel , Ropp Halie R. , Papagiannidis Dimitrios , Potel Clement , Stein Frank , Savitski Mikhail M , Vioque Agustín , Muro-Pastor Alicia M. , Hess Wolfgang R. 
Published: April 2024

AbstractRNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria is an example of cell differentiation in prokaryotes. Although multiple non-coding transcripts are involved in this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation of RNA-protein complexes after RNase treatment in density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates inNostocsp. PCC 7120. We validatedin vivothe RNA-binding capacity of 6 RBP candidates. Some participate in essential physiological aspects, such as photosynthesis (Alr2890), thylakoid biogenesis (Vipp1) or heterocyst differentiation (PrpA, PatU3), but their association with RNA was unknown. Validated RBPs Asl3888 and Alr1700 were not previously characterized. Alr1700 is an RBP with two OB-fold domains that is differentially expressed in heterocysts. Deletion ofalr1700led to complete deregulation of the cell differentiation process, a striking increase in the number of heterocyst-like cells, and was ultimately lethal in the absence of combined nitrogen. These observations characterize this RBP as a master regulator of the heterocyst patterning and differentiation process, leading us to rename Alr1700 to PatR. The data can be accessed athttps://sunshine.biologie.uni-freiburg.de/R-DeeP-Nostoc/.
Intracellular pocket conformations determine signaling efficacy through the μ opioid receptor
Authors: Cooper David A. , DePaolo-Boisvert Joseph , Nicholson Stanley A. , Gad Barien , Minh David D. L. 
Published: April 2024

ABSTRACTIt has been challenging to determine how a ligand that binds to a receptor activates downstream signaling pathways and to predict the strength of signaling. The challenge is compounded by functional selectivity, in which a single ligand binding to a single receptor can activate multiple signaling pathways at different levels. Spectroscopic studies show that in the largest class of cell surface receptors, 7 transmembrane receptors (7TMRs), activation is associated with ligand-induced shifts in the equilibria of intracellular pocket conformations in the absence of transducer proteins. We hypothesized that signaling through the μ opioid receptor, a prototypical 7TMR, is linearly proportional to the equilibrium probability of observing intracellular pocket conformations in the receptor-ligand complex. Here we show that a machine learning model based on this hypothesis accurately calculates the efficacy of both G protein and β-arrestin-2 signaling. Structural features that the model associates with activation are intracellular pocket expansion, toggle switch rotation, and sodium binding pocket collapse. Distinct pathways are activated by different arrangements of the ligand and sodium binding pockets and the intracellular pocket. While recent work has categorized ligands as active or inactive (or partially active) based on binding affinities to two conformations, our approach accurately computes signaling efficacy along multiple pathways.
The link between socially responsible human resource management and eco-helping behavior in aviation industry – a moderated mediation model
Authors: Nguyen Thi Lan Phuong , Nguyen Thi Thu Huong 
Published: April 2024

Purpose
This study aims to propose a research model that emphasizes the moderating influence of ethical leadership (ELS) and the link between socially responsible human resource management (SRHRM) and leaders’ eco-helping behavior (LEH) in the aviation industry.

Design/methodology/approach
The authors used a time-lag research design. Data were gathered from 397 respondents working for aviation companies in Vietnam and analyzed using SmartPLS 4.0.

Findings
The findings show that SRHRM has a beneficial effect on LEH through employees’ voluntary workplace green behavior (EVB). Based on social cognitive theory, this study developed a theoretical model of how SRHRM influences LEH through EVB. The authors discovered that SRHRM increased LEH and that EVB mediated this favorable relationship. Furthermore, the results demonstrate that ELS mitigates the indirect impact of SRHRM on LEH via EVB.

Research limitations/implications
Future studies should assess constructs with numerous observations across time, with a larger sample size and in different industrial settings.

Practical implications
Volunteerism is one of the most important values in the aviation industry given that it is vulnerable to practices such as overbooking, delaying, postponing flights and pressure weather.

Originality/value
This study emphasized the impact of SRHRM and ELS on LEH while fulfilling their professional obligations. EVB may be best positioned to mediate the relationship between SRHRM and LEH.
Unveil the benefit of independent leadership structure on employee welfare
Authors: Nguyen Thanh Dung , Harvison Thuong , Ashraf Ali 
Published: April 2024

PurposeEmployees play a vital role in the success of a corporation. While boards of directors are created to protect shareholders’ interests, it is unclear if these directors also ensure employee welfare. In this vein, our paper examines the relationship between board leadership structure and employee well-being.Design/methodology/approachThe authors employ several analysis techniques, including univariate analysis, ordinary least squares (OLS) regressions, two-stage least squares (2SLS) regressions, propensity score matching methodology, the Heckman Selection model and difference-in-differences analysis. The sample comprises USA public firms for the period 1998–2018.FindingsOur findings indicate that having an independent chairperson can significantly benefit the welfare of employees, especially for firms with overly powerful chief executive officers (CEOs) and during times of financial distress.Originality/valueIndependent leadership structure is one of the crucial board characteristics that have not been examined to explain employee welfare at firms. We find that an independent chairperson can mitigate the negative effect of overly powerful CEOs on employee benefits. Importantly, independent chairpersons are beneficial for employees in difficult times and when CEOs are busy with daily activities.
Does my school teach me entrepreneurship? School entrepreneurship curriculum and students’ entrepreneurial intention: a serial mediation-moderation analysis
Authors: Patel Jayesh , Vannai Sanjay , Dasani Vikrant , Sharma Mahendra 
Published: April 2024

PurposeIn order to achieve a sustained level of entrepreneurship in India, it is very important that the spirit and culture of entrepreneurship are ingrained in students, right at the “school” level. Specifically, in this study we examine how student entrepreneurial behavior is influenced by entrepreneurial activities at school.Design/methodology/approachWe chose schools in India to recruit the students’ samples; 520 higher secondary school students were approached in-person to understand their entrepreneurial intentions (EI). We applied PLS-SEM to test the relationships of serial mediation.FindingsOur findings imply that the students' entrepreneurial intentions are largely influenced by the school’s entrepreneurship program (e.g. labs, lectures and exercises). Further, we noted that school career guidance and students’ entrepreneurship attitude effectively mediate the relationship between school entrepreneurship curriculum and EI.Practical implicationsEntrepreneurship education beginning in schools does foster stronger entrepreneurial intent over the short-term. It also helps in fostering entrepreneurs, who create jobs and support in achieving the country’s desired SDGs.Originality/valueThe study contributes new dimensions to entrepreneurship research focusing on school children hence anchoring at early stages.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-05-2023-0350