bluuebunny/crossref_metadata_2025_split huggingface dataset:
StressME: unified computing framework ofEscherichia colimetabolism, gene expression, and stress responses
Authors: Zhao Jiao , Chen Ke , Palsson Bernhard O. , Yang Laurence 
Published: May 2023

AbstractGeneralist 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 summaryA 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

SummaryNAD+-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 BriefThe 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.HighlightsThe 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

AbstractPositive 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

ABSTRACTPerception 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

AbstractRetrotransposon 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 statementRtl8aandRtl8bdouble 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

AbstractObjectiveThe 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.MethodsWe 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.ResultsThe 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.ConclusionsOur 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

AbstractVarious 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

ABSTRACTExosomes 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

AbstractDuring 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

AbstractDynamins 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

PurposeThis 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/approachData were collected through a two-wave survey. The authors tested the hypotheses using data from 439 employees.FindingsThe 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/implicationsThe 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 implicationsThe 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/valueThe 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.