bluuebunny/crossref_metadata_2025 huggingface dataset:
Stoichiometric expression of messenger polycistrons by eukaryotic ribosomes (SEMPER) for compact, ratio-tunable multi-gene expression from single mRNAs
Authors: Duan Mengtong , Dev Ishaan , Lu Andrew , You Mei Yi , Shapiro Mikhail G.
Published: May 2023

Applications of mammalian synthetic biology increasingly require the ability to express multiple proteins at user-determined stoichiometries from single, compactly encoded transcripts. Here we present an approach for expressing multiple open reading frames (ORFs) from a single transcript, taking advantage of the leaky scanning model of translation initiation. In this method, adjacent ORFs are translated from a single messenger RNA at tunable ratios determined by their order in the sequence and the strength of their translation initiation sites. We call this approach Stoichiometric Expression of Messenger Polycistrons by Eukaryotic Ribosomes (SEMPER). We demonstrate the principles of this approach by expressing up to three fluorescent proteins from one plasmid in two different cell lines. We then use it to encode a stoichiometrically tuned polycistronic construct encoding gas vesicle acoustic reporter genes, showing that enforcing the optimal ratio in every cell enables efficient formation of the multi-protein complex while minimizing cellular toxicity. Finally, we demonstrate the polycistronic expression of two fluorescent proteins from single mRNAs made throughin vitrotranscription and delivered to cells. SEMPER will enable a broad range of applications requiring tunable expression from compact eukaryotic constructs.
SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors
Authors: Palmer Theron , Kessler Michael D , Shao Xiaoshan M. , Balan Archana , Yarchoan Mark , Zaidi Neeha , Lopez-Vidal Tamara Y , Saeed Ali , Gore Jessica , Azad Nilofer S , Jaffee Elizabeth M , Favorov Alexander V , Anagnostou Valsamo , Karchin Rachel , Gaykalova Daria A , Danilova Ludmila , Fertig Elana J
Published: May 2023

Aberrant alternative splicing can generate neoantigens, which can themselves stimulate immune responses and surveillance. Previous methods for quantifying splicing-derived neoantigens are limited by independent references and potential batch effects. Here, we introduce SpliceMutr, a bioinformatics approach and pipeline for identifying splicing derived neoantigens from tumor and normal data. SpliceMutr facilitates the identification of tumor-specific antigenic splice variants, predicts MHC-binding affinity, and estimates splicing antigenicity scores per gene. By applying this tool to genomic data from The Cancer Genome Atlas (TCGA), we generate splicing-derived neoantigens and neoantigenicity scores per sample and across all cancer types and find numerous correlations between splicing antigenicity and well-established biomarkers of anti-tumor immunity. Notably, carriers of mutations within splicing machinery genes have higher splicing antigenicity, which provides support for our approach. Further analysis of splicing antigenicity in cohorts of melanoma patients treated with mono-or combined immune checkpoint inhibition suggest that the abundance of splicing antigens is reduced post-treatment from baseline in patients who progress, likely because of an immunoediting process. We also observe increased splicing antigenicity in responders to immunotherapy, which may relate to an increased capacity to mount an immune response to splicing-derived antigens. We find the splicing antigenicity to be higher in tumor samples when compared to normal, that mutations in the splicing machinery result in increased splicing antigenicity in some cancers, and higher splicing antigenicity is associated with positive response to immune checkpoint inhibitor therapies. Further, this new computational pipeline provides novel analytical capabilities for splicing antigenicity and is openly available for further immuno-oncologic analysis.
Protein-mediated genome folding allosterically enhances site-specific integration of foreign DNA into CRISPRs
Authors: Santiago-Frangos Andrew , Henriques William S. , Wiegand Tanner , Gauvin Colin C. , Buyukyoruk Murat , Graham Ava B. , Wilkinson Royce A. , Triem Lenny , Neselu Kasahun , Eng Edward T. , Lander Gabriel C. , Wiedenheft Blake
Published: May 2023

Bacteria and archaea acquire resistance to viruses and plasmids by integrating fragments of foreign DNA into the first repeat of a CRISPR array. However, the mechanism of site-specific integration remains poorly understood. Here, we determine a 560 kDa integration complex structure that explains how Cas (Cas1-2/3) and non-Cas proteins (IHF) fold 150 base-pairs of host DNA into a U-shaped bend and a loop that protrude from Cas1-2/3 at right angles. The U-shaped bend traps foreign DNA on one face of the Cas1-2/3 integrase, while the loop places the first CRISPR repeat in the Cas1 active site. Both Cas3s rotate 100-degrees to expose DNA binding sites on either side of the Cas2 homodimer, that each bind an inverted repeat motif in the leader. Leader sequence motifs direct Cas1-2/3-mediated integration to diverse repeat sequences that have a 5’-GT.
The folding-limited nucleation of curli hints at an evolved safety mechanism for functional amyloid production
Authors: Claridge Jolyon K. , Martens Chloe , Pradhan Brajabandhu , Sobott Frank , Sleutel Mike , Remaut Han
Published: May 2023

It is nearly two decades ago that the ‘thin aggregative fimbriae’ which had been shown to enhance the biofilm formation ofSalmonella enteriditisandEscherichia coliwere identified as amyloid fibers. The realization that natural proteins can develop amyloidogenic traits as part of their functional repertoire instigated a search for similar proteins across all kingdoms of life. That pursuit has since unearthed dozens of candidates which now constitute the family of proteins referred to as functional amyloids (FA). FAs are promising candidates for future synthetic biology applications in that they marry the structural benefits of the amyloid fold (self-assembly and stability) while steering clear of the cytotoxicity issues that are typically linked to amyloid associated human pathologies. Unfortunately, the extreme aggregation propensity of FAs and the associated operational difficulties are restricting their adoption in real-world applications, underscoring the need for additional processes to control the amyloid reaction. Here we untangle the molecular mechanism of amyloid formation of the canonical functional amyloid curli using NMR, native mass spectrometry and cryo-electron microscopy. Our results are consistent with folding-limited one-step amyloid nucleation that has emerged as an evolutionary balance between efficient extracellular polymerization, while steering clear of pre-emptive nucleation in the periplasm. Sequence analysis of the amyloid curlin kernel suggests a finetuning of the rate of monomer folding via modulation of the secondary structure propensity of the pre-amyloid species, opening new potential avenues towards control of the amyloid reaction.
Network Pharmacology and molecular docking approach to unveil the mechanism ofHypericum perforatumin the management of Alzheimer’s disorder
Authors: Dogra Vishali , Choudhary Manjusha , Parashar Arun , Choudhary Nitesh
Published: May 2023

The pathogenesis of Alzheimer’s disease (AD) is not fully understood which limits the availability of safer and more efficient therapeutic strategies for the management of AD. There has been growing interest in recent years in exploring the potential of herbal medicines as a source of safer and alternative therapeutic strategies for the management of AD. This study aims to discover the mechanism ofHypericum perforatumin the management of AD using network pharmacology and molecular docking approach. The results of network pharmacology suggest that 39 bioactive molecules ofH. perforatumtarget 127 genes associated with AD, amongst which ATP-dependent translocase, acetylcholinesterase, amyloid-β precursor protein, β-secretase 1, carbonic anhydrase 2, dipeptidyl peptidase 4, epidermal growth factor receptor, tyrosine-protein phosphatase non-receptor type 1, α-synuclein, and vascular endothelial growth factor A seems to be the prominent target of these molecules. Further, the results of molecular docking predicted amentoflavone, I3,II8-biapigenin, rutin, miquelianin, quercetin, luteolin, and nicotiflorin as a promising modulator of target proteins which were determined from network pharmacology to be associated with AD. Our findings suggest thatH. perforatumcould be a safer and more promising alternative therapeutic strategy for the management of AD by targeting multiple pathways of AD pathogenesis.
Nunchaku: Optimally partitioning data into piece-wise linear segments
Authors: Huo Yu , Li Hongpei , Wang Xiao , Du Xiaochen , Swain Peter S.
Published: May 2023

When analysing two-dimensional data sets, scientists are often interested in regions where one variable depends linearly on the other. Typically they use anad hocmethod to do so. Here we develop a statistically rigorous, Bayesian approach to infer the optimal partitioning of a data set into contiguous piece-wise linear segments. Ournunchakualgorithm is freely available. Focusing on microbial growth, we usenunchakuto identify the range of optical density where the density is linearly proportional to the number of cells and to automatically find the regions of exponential growth for bothEscherichia coliandSaccharomyces cerevisiae. For budding yeast, we consequently are able to infer the Monod constant for growth on fructose. Our algorithm lends itself to automation and high throughput studies, increases reproducibility, and will facilitate data analysis for a broad range of scientists.
Assessing the role of trypsin in quantitative plasma- and single-cell proteomics towards clinical application
Authors: Woessmann Jakob , Petrosius Valdemaras , Üresin Nil , Kotol David , Aragon-Fernandez Pedro , Hober Andreas , Keller Ulrich auf dem , Edfors Fredrik , Schoof Erwin M.
Published: May 2023

Mass spectrometry-based bottom-up proteomics is rapidly evolving and routinely applied in large biomedical studies. Proteases are a central component of every bottom-up proteomics experiment, digesting proteins into peptides. Trypsin has been the most widely applied protease in proteomics, due to its characteristics. With ever-larger cohort sizes and possible future clinical application of mass spectrometry-based proteomics, the technical impact of trypsin becomes increasingly relevant. To assess possible biases introduced by trypsin digestion, we evaluated the impact of eight commercially available trypsins in a variety of bottom-up proteomics experiments, and across a range of protease concentrations and storage times. To investigate the universal impact of these technical attributes, we included bulk HeLa-cell lysate, human plasma and single HEK293 cells, which were analyzed over a range of Selected Reaction Monitoring (SRM), Data-Independent Acquisition (DIA), and Data-Dependent Acquisition (DDA) instrument methods on three LC-MS instruments. Quantification methods employed encompassed both label-free approaches and absolute quantification utilizing spike-in heavy-labeled recombinant protein fragment standards. Based on this extensive dataset, we report variations between commercial trypsins, their source, as well as their concentration. Furthermore, we provide suggestions on the handling of trypsin in large scale studies.
Trypanosoma bruceibloodstream form mitochondrion is capable of ATP production by substrate phoshorylation
Authors: Gergana Taleva , Michaela Husova , Brian Panicucci , Carolina Hierro-Yap , Erika Pineda , Biran Marc , Moos Martin , Šimek Petr , Frederic Bringaud , Alena Zíková
Published: May 2023

The bloodstream formTrypanosoma bruceimaintains essential mitochondrial membrane potential (ΔΨm) through the reverse activity of FoF1-ATP synthase. The ATP that drives this activity is thought to be generated by glycolysis and imported from the cytosol via an ATP/ADP carrier (AAC). We have shown that this carrier is the only carrier that can import ATP into the mitochondrial matrix to power the FoF1-ATPase. Contrary to expectations, its deletion has no effect on parasite growth, virulence and levels of ΔΨm, suggesting that ATP is produced intramitochondrially by substrate phosphorylation pathways. Therefore, we knocked out the succinyl-CoA synthetase (SCoAS) gene, a key enzyme that produces ATP through substrate phosphorylation. Its absence resulted in changes in the metabolic landscape of the parasite, lower virulence, and reduced mitochondrial ATP content. This minimal mitochondrial ATP pool was maintained by AAC activity as evidenced by the 25- fold increase in sensitivity of the mutant parasites to AAC inhibitor carboxyatractyloside. Under nutrient-limited conditions, suppression of SCoAS expression by RNA interference negatively affected cell growth and levels of ΔΨm. We concluded that the bloodstream mitochondrion is capable of generating ATP via substrate phosphorylation pathways, the importance of which depends on environmental conditions.
A cytological and functional framework of the meiotic spindle assembly checkpoint inArabidopsis thaliana
Authors: Lampou Konstantinos , Böwer Franziska , Komaki Shinichiro , Köhler Maren , Schnittger Arp
Published: May 2023

The spindle assembly checkpoint (SAC) is a surveillance mechanism active during metaphase to prevent aneuploidy. The SAC is especially important during meiosis to maintain genome stability over generations and sustain fertility. However, despite its crucial role for reproduction and breeding, little is known about the plant meiotic SAC. Here, we present a cytological and functional framework of the SAC in male meiocytes ofArabidopsis thaliana. Using live-cell imaging, we have dissected the temporal association of SAC components with the kinetochore and have identified the three conserved kinases BMF1, MPS1 and AURORA as crucial regulators of the loading of BMF3 to kinetochores. Functionally characterizing core SAC components, we found that BUB3.3 has a predominant and previously not recognized role in chromosome congression. We suggest that BUB3.3 is involved in efficient kinetochore-microtubule interactions. Furthermore, the meiotic SAC is only active for a limited time under severe microtubule destabilizing conditions leading to the hypothesis that the relaxed nature of the meiotic SAC is a gateway to polyploidization and hence might contribute to genome evolution in plants.
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex
Authors: Jaksch Dhaarsini , Irnstorfer Johanna , Kalman Petra-Franziska , Martinez Javier
Published: May 2023

The mammalian tRNA ligase complex (tRNA-LC) catalyzes the splicing of intron-containing pre-tRNAs in the nucleus and the splicing ofXBP1mRNA during the unfolded protein response (UPR) in the cytoplasm. We recently reported that the tRNA-LC co-evolved with PYROXD1, an essential oxidoreductase that protects the catalytic cysteine of RTCB, the catalytic subunit of the tRNA-LC, against aerobic oxidation. In this study we show that the oxidoreductase Thioredoxin (TRX) preserves the enzymatic activity of RTCB under otherwise inhibiting concentrations of oxidants. TRX physically interacts with oxidized RTCB, and reduces and re-activates RTCB through the action of its redox-active cysteine pair. We further show that TRX interacts with RTCB at late stages of UPR. Since the interaction requires oxidative conditions, our findings suggest that prolonged UPR generates reactive oxygen species. Thus, our results support a functional role for TRX in securing and repairing the active site of the tRNA-LC, thereby allowing pre-tRNA splicing and UPR to occur when cells encounter mild, but still inhibitory levels of reactive oxygen species.
SOX7: Novel Autistic Gene Identified by Analysis of Multi-Omics Data
Authors: Gonzales Samantha , Zhao Jane Zizhen , Choi Na Young , Acharya Prabha , Jeong Sehoon , Lee Moo-Yeal
Published: May 2023

Background

Genome-wide association studies and next generation sequencing data analyses based on DNA information have identified thousands of mutations associated with autism spectrum disorder (ASD). However, more than 99% of identified mutations are non-coding. Thus, it is unclear which of these mutations might be functional and thus potentially causal variants. Transcriptomic profiling using total RNA-sequencing has been one of the most utilized approaches to link protein levels to genetic information at the molecular level. The transcriptome captures molecular genomic complexity that the DNA sequence solely does not. Some mutations alter a gene’s DNA sequence but do not necessarily change expression and/or protein function. To date, few common variants reliably associated with the diagnosis status of ASD despite consistently high estimates of heritability. In addition, reliable biomarkers used to diagnose ASD or molecular mechanisms to define the severity of ASD do not exist.

Objectives

It is necessary to integrate DNA and RNA testing together to identify true causal genes and propose useful biomarkers for ASD.

Methods

We performed gene-based association studies with adaptive test using genome-wide association studies (GWAS) summary statistics with two large GWAS datasets (ASD 2019 data: 18,382 ASD cases and 27,969 controls [discovery data]; ASD 2017 data: 6,197 ASD cases and 7,377 controls [replication data]) which were obtained from the Psychiatric Genomics Consortium (PGC). In addition, we investigated differential expression for genes identified in gene-based GWAS with a RNA-seq dataset (GSE30573: 3 cases and 3 controls) using the DESeq2 package.

Results

We identified 5 genes significantly associated with ASD in ASD 2019 data (KIZ-AS1, p=8.67×10−10; KIZ, p=1.16×10−9; XRN2, p=7.73×10−9; SOX7, p=2.22×10−7; PINX1-DT, p=2.14×10−6). Among these 5 genes, gene SOX7 (p=0.00087), LOC101929229 (p=0.009), and KIZ-AS1 (p=0.059) were replicated in ASD 2017 data. KIZ (p=0.06) was close to the boundary of replication in ASD 2017 data. Genes SOX7 (p=0.0017, adjusted p=0.0085), LOC101929229 (also known as PINX1-DT, p=5.83×10−7, adjusted p=1.18×10−5), and KIZ (p=0.00099, adjusted p=0.0055) indicated significant expression differences between cases and controls in the RNA-seq data. SOX7 encodes a member of the SOX (SRY-related HMG-box) family of transcription factors pivotally contributing to determining of the cell fate and identity in many lineages. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins leading to autism.

Conclusion

Gene SOX7 in the transcription factor family could be associated with ASD. This finding may provide new diagnostic and therapeutic strategies for ASD.
SIX4 Controls STING Expression Enhancing anti-PD-1 Efficacy
Authors: Liang Beiyuan , Zhang Evan H. , Ye Zhen , Storts Hayden , Zheng Xinru , Zaleski Olivia , Jin Wei , Xing Xuanxuan , Wang Jing J.
Published: May 2023

The cGAS/STING cytosolic DNA sensing pathway plays a central role in anti-tumor immunity. Expression of STING is tightly regulated and commonly reduced or defective in many types of cancer. We have identified SIX4 as a significant regulator of STING expression in colon cancer cells. We showed that knockout of SIX4 decreased STING expression at the mRNA and protein levels while ectopic expression of SIX4 increased STING expression. Depletion of SIX4 led to attenuated STING activation and downstream signaling. Re-expression of SIX4 or ectopic expression of STING in SIX4 knockout cells reversed the effect. Ectopic expression of SIX4 enhanced DMXAA and cGAMP-induced STING activation and downstream signaling. Importantly, decrease of SIX4 expression substantially decreased tumor infiltration of CD8+T-cells and reduced the efficacy of PD-1 antibodies to diminish tumor growth in immune competent micein vivo. Finally, analysis of TCGA colon cancer dataset indicated that tumors with high SIX4 expression were significantly enriched in the Inflammatory Response pathway. SIX4 expression also correlated with expression of multiple IFN-stimulated genes, inflammatory cytokines and CD8A. Taken together, our results implicate that SIX4 is a principal regulator of STING expression in colon cancer cells, providing an additional mechanism and genetic marker to predict effective immune checkpoint blockade therapy responses.
Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS
Authors: Keller Andrew , Tang Xiaoting , Bruce James E.
Published: May 2023

XL-MS provides low-resolution structural information of proteins in cells and tissues. Combined with quantitation, it can identify changes in the interactome between samples, for example, control and drug-treated cells, or young and old mice. A difference can originate from protein conformational changes altering the solvent-accessible distance separating the cross-linked residues. Alternatively, a difference can result from conformational changes localized to the cross-linked residues, for example, altering the solvent exposure or reactivity of those residues or post-translational modifications on the cross-linked peptides. In this manner, cross-linking is sensitive to a variety of protein conformational features. Dead-end peptides are cross-links attached only at one end to a protein, the other terminus being hydrolyzed. As a result, changes in their abundance reflect only conformational changes localized to the attached residue. For this reason, analyzing both quantified cross-links and their corresponding dead-end peptides can help elucidate the likely conformational changes giving rise to observed differences of cross-link abundance. We describe analysis of dead-end peptides in the XLinkDB public cross-link database and, with quantified mitochondrial data isolated from failing heart versus healthy mice, show how a comparison of abundance ratios between cross-links and their corresponding dead-end peptides can be leveraged to reveal possible conformational explanations.
Kinetic trapping organizes actin filaments within liquid-like protein droplets
Authors: Chandrasekaran Aravind , Graham Kristin , Stachowiak Jeanne C. , Rangamani Padmini
Published: May 2023

Abstract

Actin is essential for various cellular functions such as growth, migration, and endocytosis. Recent evidence suggests that several actin-binding proteins phase separate to form condensates and that actin networks have different architectures in these droplets. In this study, we use computational modeling to investigate the conditions under which actin forms different network organizations in VASP droplets. Our simulations reveal that the binding and unbinding rates of actin and VASP determine the probability of formation of shells and rings, with shells being more probable than rings. The different actin networks are highly dependent on the kinetics of VASP-actin interactions, suggesting that they arise from kinetic trapping. Specifically, we showed that reducing the residence time of VASP on actin filaments promotes assembly of shells rather than rings, where rings require a greater degree of actin bundling. These predictions were tested experimentally using a mutant of VASP, which has decreased bundling capability. Experiments reveal an increase in the abundance of shells in VASP droplets, consistent with our predictions. Finally, we investigated the arrangements of filaments within deformed droplets and found that the filament length largely determines whether a droplet will straighten into a bundle or remain kinetically trapped in a ring-like architecture. The sphere-to-ellipsoid transition is favored under a wide range of conditions while the ellipse-to-rod transition is only permitted when filaments have a specific range of lengths. Our findings have implications for understanding how the interactions between phase-separated actin binding proteins and actin filaments can give rise to different actin network architectures.
StressME: unified computing framework ofEscherichia colimetabolism, gene expression, and stress responses
Authors: Zhao Jiao , Chen Ke , Palsson Bernhard O. , Yang Laurence
Published: May 2023

Generalist microbes have adapted to a multitude of environmental stresses through their integrated stress response system. Individual stress responses have been quantified byE. colimetabolism and expression (ME) models under thermal, oxidative and acid stress, respectively. However, the systematic quantification of crosstalk among these stress responses remains lacking. Here, we present StressME: the unified stress response model ofE. colicombining thermal (FoldME), oxidative (OxidizeME) and acid (AcidifyME) stress responses. StressME is the most up to date ME model forE. coliand it reproduces all published single-stress ME models. Additionally, it includes refined rate constants to improve prediction accuracy for wild-type and stress-evolved strains. StressME revealed certain optimal proteome allocation strategies associated with cross-stress responses. These stress-optimal proteomes were shaped by trade-offs between protective vs. metabolic enzymes; cytoplasmic vs. periplasmic chaperones; and expression of stress-specific proteins. As StressME is tuned to compute metabolic and gene expression responses under mild acid, oxidative, and thermal stresses, it is useful for engineering and health applications. The modular design of our open-source package also facilitates model expansion (e.g., to new stress mechanisms) by the computational biology community.

Author summary

A fundamental understanding of multi-stress adaptation inE.colihas potential industrial relevance. While individual stress responses have been quantified through the protein regulatory network inE.coli, the systematic quantification of the crosstalk among stress responses remains lacking. Here, we develop a new modeling pipeline by which thermal, oxidative and acid stress response can be coupled to each other, and the metabolic activities, protein and metabolic flux redistribution due to cross stress can be quantified. We optimize the effective rate constants in the integrated model. We then confirm the model robustness by validating against the published data under single stress. Finally, we use the model to characterize the cross-adaptation between protective and catalytic proteins as well as between chaperones present in different cellular compartments. We find effective cross-protection against cross stress by adapting theE.colicells to the thermal stress first. We also indicate the presence of trade-offs by which the cell may refuse to give up more protein allocation away from one stress response to the other, because doing so would decrease stress tolerance further. The single stress plug-in design makes the model build-up pipeline flexible and expandable, allowing incorporation of more stressors into the model architecture for industrial applications.
TPR domain assigns versatility of BcTir/Tpr system against viral infection
Authors: Liu Yingying , Zhang Chen , Khudaverdyan Nelli , Wang Junyi , Zhang Lei , Golovko Mikhail Y , Golovko Svetlana A , Guo Ang , Song Jikui , Wu Min , Combs Colin
Published: May 2023

NAD+-derived signal produced by TIR domain triggered the host immune responses. The ubiquitous TPR domain involved in signal recognition and effector activation were found widely assembled with the TIR domain. However, the immune roles of these assemblies remain elusive. Here, a two-gene operon, one containing a TIR domain, designated as BcTir, and the other, BcTpr, fromBacillus cereus, exhibited anti-phage immunity. BcTpr, but not BcTir, exhibited NADase activity to produce the cyclic ADPR (cADPR) isomer and mediate NAD+depletion. Noticeably, the truncated N terminus of BcTpr only depleted NAD+unless at the presence of TPR domain to generate cADPR isomer unveiling its role played for glycosite selection. In addition, the BcTir/Tpr system significantly repressed viral proliferation and increased oxidation resistance by scavenging excessive reactive oxygen species (ROS) upon phage infection. These findings unraveled a multifunctional role of the BcTir/Tpr system during immune responses.

In Brief

The bacterial BcTir/Tpr system was identified with the ability to protect against phage infection via NAD+depletion, viral replication repression, and ROS homeostasis, in which BcTpr played a dual role in NAD+-derived signal production and NAD+depletion.

Highlights

The BcTir/Tpr system works as a BcTir-BcTpr complex against phage infection.

BcTpr, instead of BcTir, generates the NAD+-derived cADPR isomer through its glycosidase domain at N terminus.

The amount of cADPR isomer production is regulated by the helix numbers of the TPR domain at C terminus of BcTpr.

The BcTir/Tpr system can depress phage proliferation and decrease ROS production upon phage infection.
Student perceptions of cardiovascular physiology module format in a preclinical medical science course
Authors: Scherrer Kristen , Sullivan Spencer , Dallaghan Gary Beck , Moorefield Emily
Published: May 2023

Positive active learning outcomes require student engagement with foundational, preparatory material prior to class. The current study involved thorough updating of cardiovascular physiology module format. It then examined preclinical medical student perceptions, and midterm exam performance, after using different preparatory module formats that were reviewed prior to participating in interactive classroom sessions. Modules that were initially created in Articulate Storyline were updated in Articulate Rise360 and introduced over a 3-year period. Both module styles contained the same cardiovascular physiology content, but updated Rise360 modules presented content in multiple formats to capture a variety of student learning preferences and divided each concept into several smaller topics to maintain student attention. Although midterm exam performance remained unchanged, student evaluations revealed that the updated Rise360 modules were more helpful with fewer technical issues indicating that students preferred the interactive online modules to prepare for collaborative classroom exercises. Students find updated preparatory modules to be more helpful and may therefore be more likely to engage with them before class and ultimately lead to a more productive interactive classroom learning experience.
Auditory cortex conveys non-topographic sound localization signals to visual cortex
Authors: Mazo Camille , Baeta Margarida , Petreanu Leopoldo
Published: May 2023

Perception requires binding spatiotemporally congruent multimodal sensory stimuli. The auditory cortex (AC) sends projections to the primary visual cortex (V1), which could provide signals for binding spatially corresponding audio-visual stimuli. However, it is unknown whether AC inputs in V1 encode sound location. We used dual-color two-photon axonal calcium imaging and an array of speakers to measure the auditory spatial information that AC transmits to V1. We found that AC relays information about the location of ipsilateral and contralateral sound sources to V1. Sound location could be accurately decoded by sampling AC axons in V1, providing a substrate for making location-specific audiovisual associations. However, AC inputs were not retinotopically arranged in V1, and audio-visual modulations of V1 neurons did not depend on the spatial congruency of the sound and light stimuli. The distributed, non-topographic sound localization signals provided by AC might allow the association of specific audiovisual spatial patterns in V1 neurons.
Targeting retrovirus-derivedRtl8aand8bcauses late onset obesity and neurodevelopmental defects
Authors: Fujioka Yoshifumi , Shiura Hirosuke , Ishii Masayuki , Ono Ryuichi , Endo Tsutomu , Kiyonari Hiroshi , Hirate Yoshikazu , Ito Hikaru , Kanai-Azuma Masami , Kohda Takashi , Kaneko-Ishino Tomoko , Ishino Fumitoshi
Published: May 2023

Retrotransposon Gag-like (RTL) 8A, 8B and 8C are triplet genes of uncertain function that form a cluster on the X chromosome. They are eutherian-specific genes presumably derived from a certain retrovirus. Here, we demonstrate thatRtl8aandRtl8bplay an important role in growth and behavior via brain functions in the hypothalamus and prefrontal cortex.Rtl8aandRtl8bdouble knockout (DKO) mice exhibited overgrowth due to hyperphagia from young adulthood and reduced social responses, increased apathy-like behavior. RTL8A and RTL8B proteins are localized to both the nucleus and cytoplasm of neurons presumably due to an N-terminal nuclear localization signal-like sequence. An increment in nucleus size was also detected in the neurons in the prefrontal cortex, suggesting neuronal dysfunction. These data give another strong evidence that retrovirus-derived acquired genes contributed to the establishment of the current eutherian developmental system in a wide variety of ways.

Summary statement

Rtl8aandRtl8bdouble knockout mice exhibited late onset obesity and neurodevelopmental defects, demonstrating that these eutherian specific retrovirus-derived acquired genes encoding proteins with only 113 amino acids play important roles in the brain presumably via their functions in the hypothalamus and prefrontal cortex.
Ghrelin signalling in AgRP neurons links metabolic state to the sensory regulation of AgRP neural activity
Authors: So Wang Lok , Hu Jiachen , Jeffs Lotus , Dempsey Harry , Lockie Sarah H. , Zigman Jeffrey M , Stark Romana , Reichenbach Alex , Andrews Zane B.
Published: May 2023

Objective

The sensory detection of food and food cues suppresses Agouti related peptide (AgRP) neuronal activity prior to consumption with greatest suppression in response to high caloric food or energy need. Although external sensory cues regulate AgRP neuronal activity, the interoceptive mechanisms priming an appropriate AgRP neural response to sensory information of caloric availability remain unexplored. Since hunger increases plasma ghrelin, we hypothesized that ghrelin receptor (GHSR) signalling on AgRP neurons is a key interoceptive mechanism integrating energy need with external sensory cues predicting caloric availability.

Methods

We used in vivo photometry to measure the effects of ghrelin administration or fasting on AgRP neural activity with GCaMP6s and dopamine release in the nucleus accumbens with GRAB-DA in mice lacking ghrelin receptors in AgRP neurons.

Results

The deletion of GHSR on AgRP neurons prevented ghrelin-induced food intake, motivation and AgRP activity. The presentation of food (peanut butter pellet) or a wooden dowel suppressed AgRP activity in fasted WT but not mice lacking GHSRs in AgRP neurons. Similarly, peanut butter and a wooden dowel increased dopamine release in the nucleus accumbens after ip ghrelin injection in WT but not mice lacking GHSRs in AgRP neurons. No difference in dopamine release was observed in fasted mice. Finally, ip ghrelin administration did not directly increase dopamine neural activity in the ventral tegmental area.

Conclusions

Our results suggest that AgRP GHSRs integrate an interoceptive state of energy need with external sensory information to produce an optimal change in AgRP neural activity. Thus, ghrelin signalling on AgRP neurons is more than just a feedback signal to increase AgRP activity during hunger.
A Study on multiple isotherms of Cr6+ions usingBrevibacillus brevisUS575 isolated from tannery effluents
Authors: Bhattacharjee Arghyadeep , Sahoo Om Saswat , Karmakar Srabani , Mitra Arup Kumar
Published: May 2023

Various leather factories in West Bengal have resulted in an enormous amount of leather that is processed annually. Regular discharges of tannery effluents into land and open water have led to significant soil and water pollution, with one of the most dangerous inorganic pollutants being chromium (Cr). This study aims to recover the most harmful components from industrial water using efficient biosorbents.Brevibacillus brevisUS575 has been initially found in tannery effluents, where it has a high tolerance level to Cr6+ions. The Cr(VI) adsorbed from the solution in aqueous phase during the course of the 60-minute contact period in this experiment was nearly 74%. Studies on the concentration of biomass, pH of the medium, and the starting concentration of metal ions have also been seen to affect the rate of biosorption. According to the desorption investigation, 1 M HCl outperformed all other concentrations of HCl, NaOH and pure water. Highest capacity of adsorption of the bio-adsorbent was calculated using the Langmuir model. The monolayer adsorption process was determined, and since the Freundlich model’s 1/n value fell inside 1, favourable adsorption has been postulated. According to the results of this study, the bacterium isolated from tannery wastewater was found to be the best alternative and could be used to create plans for using biosorption to combat current environmental pollution.
Exomap1 mouse: a transgenic model forin vivostudies of exosome biology
Authors: Fordjour Francis K. , Abuelreich Sarah , Hong Xiaoman , Chatterjee Emeli , Lallai Valeria , Ng Martin , Saftics Andras , Deng Fengyan , Carnel-Amar Natacha , Wakimoto Hiroaki , Shimizu Kazuhide , Bautista Malia , Phu Tuan Anh , Vu Ngan K. , Geiger Paige C. , Raffai Robert L. , Fowler Christie D. , Das Saumya , Christenson Lane K. , Jovanovic-Talisman Tijana , Gould Stephen J.
Published: May 2023

Exosomes are small extracellular vesicles (sEVs) of ∼30-150 nm in diameter that have the same topology as the cell, are enriched in selected exosome cargo proteins, and play important roles in health and disease. To address large unanswered questions regarding exosome biologyin vivo, we created theexomap1transgenic mouse model. In response to Cre recombinase,exomap1mice express HsCD81mNG, a fusion protein between human CD81, the most highly enriched exosome protein yet described, and the bright green fluorescent protein mNeonGreen. As expected, cell type-specific expression of Cre induced the cell type-specific expression of HsCD81mNG in diverse cell types, correctly localized HsCD81mNG to the plasma membrane, and selectively loaded HsCD81mNG into secreted vesicles that have the size (∼80 nm), topology (outside out), and content (presence of mouse exosome markers) of exosomes. Furthermore, mouse cells expressing HsCD81mNG released HsCD81mNG-marked exosomes into blood and other biofluids. Using high-resolution, single-exosome analysis by quantitative single molecule localization microscopy, we show here that that hepatocytes contribute ∼15% of the blood exosome population whereas neurons contribute <1% of blood exosomes. These estimates of cell type-specific contributions to blood EV population are consistent with the porosity of liver sinusoidal endothelial cells to particles of ∼50-300 nm in diameter, as well as with the impermeability of blood-brain and blood-neuron barriers to particles >5 nm in size. Taken together, these results establish theexomap1mouse as a useful tool forin vivostudies of exosome biology, and for mapping cell type-specific contributions to biofluid exosome populations. In addition, our data confirm that CD81 is a highly-specific marker for exosomes and is not enriched in the larger microvesicle class of EVs.
Ripply1 and Gsc collectively suppress anterior endoderm differentiation from prechordal plate progenitors
Authors: Cheng Tao , Liu Xiang , Dong Yang , Tian Yi-Meng , Xing Yan-Yi , Chen Chen-Yi , Liu Cong , Li Yun-Fei , Huang Ying , Zhuo Ding-Hao , Xu Xiao , Luan Jing-Yun , Fu Xin-Xin , Jin Zi-Xin , Mo Jing , Xu Xiang , Liang Hong-Qing , Xu Peng-Fei
Published: May 2023

During gastrulation, the mesendoderm is firstly specified by morphogens such as Nodal, and then segregates into endoderm and mesoderm in a Nodal concentration-dependent manner. However, the mechanism underlying the segregation and crosstalk of different sub-groups within the meso- and endoderm lineages remains unclear. Here, taking zebrafish prechordal plate (PP) and anterior endoderm (Endo) as research model, using single-cell multi-omics and live imaging analyses, we show that anterior Endo progenitors originate directly from PP progenitors. A single-cell transcriptomic trajectory analysis of wild-type,ndr1knockdown andlft1knockout Nodal explants confirms the diversification of anterior Endo fate from PP progenitors. Gene Ontology (GO) enrichment analysis indentifies that the change of chromatin organization potentiates the segregation of endodermal cell fate from PP progenitors. Single-cell ATAC & RNA sequencing further reveals that two transcriptional regulators,gscandripply1, exhibit varied activation patterns in PP and Endo lineages at both the chromatin and RNA expression levels. We further demonstrate that Ripply1 functions coordinately with Gsc to repress endodermal cell fate by directly binding to thecis-elements ofsox32andsox17. Modulating the expression levels of these regulators tilts the cell fate decision between the PP and Endo lineages.
The variable domain from the mitochondrial fission mechanoenzyme Drp1 promotes liquid-liquid phase separation
Authors: Posey Ammon E. , Bagheri Mehran , Ross Kyle A. , Lanum Elizabeth N. , Khan Misha A. , Jennings Christine M. , Harwig Megan C. , Kennedy Nolan W. , Hilser Vincent J. , Harden James L. , Hill R. Blake
Published: May 2023

Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a “variable domain” (VD) important for regulation. For the mitochondrial fission dynamin, Drp1, a regulatory role for the VD is demonstrated by mutations that can elongate, or fragment, mitochondria. How the VD encodes inhibitory and stimulatory activity is unclear. Here, isolated VD is shown to be intrinsically disordered (ID) yet undergoes a cooperative transition in the stabilizing osmolyte TMAO. However, the TMAO stabilized state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, raising the possibility that phase separation may enable rapid tuning of Drp1 assembly necessary for fission.
Unleashing the power of support: how co-worker and supervisor support mediate firm performance through performance management
Authors: Tenakwah Emmanuel Senior , Erdiaw-Kwasie Michael Odei , Asiedu Esther , Al Aina Riham
Published: May 2023

Purpose

This paper investigates the impact of performance management (PM) practices on firms' financial performance and the mediating role of co-worker and supervisor support.

Design/methodology/approach

Data were collected through a two-wave survey. The authors tested the hypotheses using data from 439 employees.

Findings

The authors find that PM practices positively influence a firm financial performance. The results also show a positive indirect relationship between PM practices and firm financial performance through co-worker support. The mediated effect is about 0.2 times as large as the direct effect of PM practices on firm financial performance. The results also show that supervisor support partially mediates the relationship between PM practices and firm financial performance.

Research limitations/implications

The authors extend our knowledge of PM practices–firm financial performance relationships. The study advances the existing knowledge on this relationship beyond the traditional input-output models by exploring the mediating role of employee involvement in the relationship between PM practices and firm financial performance. Specifically, the authors' findings reveal that co-worker and supervisory support can act as a mediator in this relationship, shedding new light on the importance of employee/supervisor involvement in PM practices.

Practical implications

The findings highlight the need for managers to take a crucial look at the importance of co-worker and supervisor support. This suggests that organisations can focus on providing adequate training to managers and supervisors to enhance their ability to provide social support to their employees. Organisations can also encourage a positive and supportive workplace culture to foster an environment that promotes employee engagement, motivation and performance.

Originality/value

The results of this study enrich the literature on PM practices–firm financial performance by conceptualising supervisor and co-worker support as mechanisms through which this relationship occurs. By so doing, the authors clarify how PM practices affect firm financial performance.
Generic analytical models of memelement and inverse memelement with time-dependent memory effects
Authors: Banchuin Rawid
Published: May 2023

Purpose

The purpose of this paper is to originally present the generic analytical models of memelement and inverse memelement with time-dependent memory effect.

Design/methodology/approach

The variable order forward Grünwald–Letnikov fractional derivative and the memristor and inverse memristor models proposed by Fouda et al. have been adopted as the basis. Both analytical and numerical studies have been conducted. The applications to the candidate practical memristor and inverse memelements have also been presented.

Findings

The generic analytical models of memelement and inverse memelement with time-dependent memory effect, the simplified ones for DC and AC signal-based analyses and the equations of crucial parameters have been derived. Besides the well-known opposite relationships with frequency, the Lissajous patterns of memelement and inverse memelement also use the opposite relationships with the time. The proposed models can be well applied to the practical elements.

Originality/value

To the best of the authors’ knowledge, for the first time, the models’ memelement and inverse memelement with time-dependent memory effect have been presented. A new contrast between these elements has been discovered. The resulting models are applicable to the practical elements.
Women entrepreneurship in the internationalization of SMEs: a bibliometric analysis for future research directions
Authors: Anggadwita Grisna , Indarti Nurul
Published: May 2023

Purpose

This study aims to systematically review papers on women’s entrepreneurship in the internationalization of small and medium enterprises (SMEs) by examining the research profile (i.e. publication trends, publishers, domain and quality of journals, methodologies and units of analysis and regional classifications), internationalization entry modes and the theories underpinning, key variables using AMO framework (i.e. antecedents, mediators, moderators and outcomes) and suggestions for potential future studies.

Design/methodology/approach

This study used bibliometric analysis by selecting 62 relevant papers from 3,016 papers collected from the Web of Science, Scopus, Google Scholar and EBSCO databases. Content analysis was conducted to identify key research issues and gaps, which were then mapped on an AMO framework to address potential future research.

Findings

This study found that the number of papers published during the period 1994–September 2022 fluctuated, indicating an increasing trend of women’s entrepreneurship research in the internationalization of SMEs being published in various reputable journals by well-known publishers. This study also found several alternatives of internationalization entry modes, although export is still the most widely used alternative. Various theories that underlie this research include internationalization theory, resource-based theory, feminist theory and international entrepreneurship. This study proposes a future research framework on women’s entrepreneurship in the internationalization of SMEs: AMO.

Originality/value

This study contributes to the intersection of gender-focused international business and entrepreneurship domains. This study proposes a conceptual model of women’s entrepreneurship in internationalization of SMEs by mapping the antecedents, mediators/moderators and outcomes and offers promising opportunities for future research directions.