bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a crucialINO2allele for enhancing ethanol resistance in an industrial fermentation strain ofSaccharomyces cerevisiae
Authors: Albillos-Arenal Sonia , Alonso del Real Javier , Lairón-Peris María , Barrio Eladio , Querol Amparo 
Published: September 2024

ABSTRACTEthanol toxicity is a major challenge forS. cerevisiaeduring fermentation, affecting its growth and influencing the process. This study investigated the molecular mechanisms of ethanol tolerance using transcriptomic analysis of threeS. cerevisiaestrains with varying ethanol resistance. We identified distinct responses in membrane lipid synthesis genes, particularly in ergosterol biosynthesis, regulated by the Ino2p transcription factor. A variant of Ino2p with V263I and H86R amino acid replacements was exclusive to ethanol-tolerant strains. CRISPR-Cas9-mediated point mutations in theINO2gene of the highly tolerant strain AJ4 resulted in decreased ethanol tolerance. Our findings demonstrate the crucial role of Ino2p in ethanol tolerance through regulation of lipid synthesis and membrane composition, highlighting the complex interplay of trans elements in strain-specific ethanol resistanceIMPORTANCEThis study provides critical insights into the molecular basis of ethanol tolerance inS. cerevisiae, a key trait for improving industrial fermentation processes. By identifying specific genetic variants in the Ino2p transcription factor and their impact on ethanol resistance, we reveal potential targets for enhancing yeast strain performance in high-ethanol environments. Our findings not only contribute to the fundamental understanding of stress response mechanisms in yeast but also offer practical implications for strain engineering in the biotechnology and beverage industries. The unexpected magnitude of the Ino2p variants’ effect on ethanol tolerance underscores the importance of considering strain-specific genetic backgrounds in metabolic engineering strategies
Absent, but not glucocorticoid-modulated, corticotropin-releasing hormone (Crh) regulates anxiety-like behaviors in mice
Authors: Friedman Hannah R. , Gaston Lindsey S. , Chan Li F. , Majzoub Joseph A. 
Published: September 2024

AbstractThe hypothalamic-pituitary-adrenal (HPA) axis is a well characterized endocrine response system. Hypothalamic Crh in the paraventricular nucleus of the hypothalamus (PVH) initiates HPA axis signaling to cause the release of cortisol (or corticosterone in rodents) from the adrenal gland. PVH-specific deletion ofCrhreduces anxiety-like behaviors in mice. Here we report that manipulation of PVHCrhexpression in primary adrenal insufficiency or by dexamethasone (DEX) treatment do not alter mouse anxiety behaviors. In Experiment 1, we compared wildtype (WT) mice to those with primary adrenal insufficiency (MrapKO) or global deletion of Crh (CrhKO). We analyzed behaviors using open field (OF) and elevated plus maze (EPM), PVH Crh mRNA expression by spatial transcriptomics, and plasma ACTH and corticosterone after a 15-minute restraint test with ELISAs. EPM analysis showedCrhKO mice were less anxious than WT andMrapKO mice, andMrapKO mice had no distinguishing behavioral phenotype. In Experiment 2, we evaluated HPA axis habituation to chronically elevatedCrhexpression by comparing mice treated with 5-8 weeks of DEX with those similarly treated followed by DEX withdrawal for 1 week. All mice regardless of genotype and treatment showed no significant behavioral differences. Our findings suggest that reduced anxiety associated with lowCrhexpression requires extreme deficiency, perhaps outside of those PVH Crh neurons negatively regulated by glucocorticoids. If these findings extend to humans, they suggest that increases in Crh expression with primary adrenal insufficiency, or decreases with exogenous glucocorticoid therapy, may not alter anxiety behaviors via modulation of Crh expression.
The role of vibration amplitude in the escape hatching response of red-eyed treefrog embryos
Authors: Jung Julie , Caldwell Michael S. , McDaniel J. Gregory , Warkentin Karen M. 
Published: September 2024

AbstractThe function and adaptive significance of defensive behaviors depend on the contexts in which they naturally occur. Amplitude properties of predator cues are widely used by prey to assess predation risk, yet rarely studied in the context of the stimuli relevant to defensive decisions in nature. Red-eyed treefrog embryos,Agalychnis callidryas, hatch precociously in response to attacks on their arboreal egg clutches by snakes and wasps. They use vibrations excited during attacks to detect predators, but wind and rainstorms also excite intense vibrations. Past work has demonstrated that to avoid costly decision errors,A. callidryasnon-redundantly combine information from the temporal and frequency properties of clutch vibrations. Here we demonstrate that embryos also use absolute amplitude and fine-scale amplitude modulation information to refine their hatching decision. We used vibration recordings to characterize the amplitude properties of the most common predator and benign-source disturbances toA. callidryasegg clutches in nature and tested whether embryos at three ages across the onset of mechanosensory-cued hatching (4–6 days) respond to amplitude variation during playback of synthetic vibrations to eggs. Older embryos responded to much lower-amplitude vibrations, reflecting a >88-fold decrease in response threshold from 4 to 5 days. To assess how embryos combine amplitude with other vibration properties, we played embryos recorded exemplars of snake attack and rain vibrations of varying amplitudes and patterns of amplitude modulation. The amplitude response curve was steeper for snake recordings than for rain. While amplitude information alone is insufficient to discriminate predator attack from benign-source vibrations,A. callidryasemploy an impressively complex strategy combining absolute amplitude, amplitude modulation, temporal, and frequency information for their hatching decision.
Quorum sensing orchestrates parallel cell death pathways inVibrio choleraevia Type 6 secretion dependent and independent mechanisms
Authors: Mashruwala Ameya A. , Bassler Bonnie L. 
Published: September 2024

AbstractQuorum sensing (QS) is a cell-to-cell communication process that enables bacteria to coordinate group behaviors. InVibrio choleraecolonies, a program of spatial-temporal cell death is among the QS-controlled traits. Cell death occurs in two phases, first along the colony rim, and subsequently, at the colony center. Both cell death phases are driven by the type VI secretion system (T6SS). Here, we show that HapR, the master QS regulator, does not controlt6ssgene expression nor T6SS-mediated killing activity. Nonetheless, a ΔhapRstrain displays no cell death at the colony rim. RNA-Seq analyses reveal that HapR activates expression of an operon containing four genes of unknown function,vca0646-0649. Epistasis and overexpression studies show that two of the genes,vca0646andvca0647, are required to drive cell death in both a ΔhapRand a ΔhapRΔt6ssstrain. Thus,vca0646-0649are regulated by HapR but act independently of the T6SS machinery to cause cell death, suggesting that a second, parallel pathway to cell death exists inV. cholerae.SignificanceCell death is a fundamental biological process. In mammals, cell death sculpts tissues during development, enables injury recovery, and regulates immunity. In bacteria, cell death mechanisms remain little explored. Recently, colonies formed by the pathogenVibrio choleraewere demonstrated to undergo a spatio-temporal program of cell death. The program is controlled by quorum sensing (QS) and driven by the Type VI secretion system. Here, we discover QS-controlled genes, calledvca0646-0649, that cause cell death inV. choleraecolonies independently of the Type VI secretion system. These findings indicate that a second cell death pathway exists inV. cholerae. The results expand our understanding of bacterial cell death mechanisms and provide insight into how cell death shapes bacterial community structure.
Distinct Disruptions in CA1 and CA3 Place Cell Function in Alzheimer’s Disease Mice
Authors: Park Sanggeon , Park Mijeong , Kim Eun Joo , Kim Jeansok J. , Huh Yeowool , Cho Jeiwon 
Published: September 2024

AbstractThe hippocampus, a critical brain structure for spatial learning and memory, is susceptible to neurodegenerative disorders such as Alzheimer’s disease (AD). The APPswe/PSEN1dE9 (APP/PS1) transgenic mouse model is widely used to study the pathology of AD. Although previous research has established AD-associated impairments in hippocampal-dependent learning and memory, the neurophysiological mechanisms underlying these cognitive dysfunctions remain less understood. To address this gap, we investigated the activities of place cells in both CA1 and CA3 hippocampal subregions, which have distinct yet complementary computational roles. Behaviorally, APP/PS1 mice demonstrated impaired spatial recognition memory compared to wild-type (WT) mice in the object location test. Physiologically, place cells in APP/PS1 mice showed deterioration in spatial representation compared to WT. Specifically, CA1 place cells exhibited significant reductions in coherence and spatial information, while CA3 place cells displayed a significant reduction in place field size. Both CA1 and CA3 place cells in APP/PS1 mice also showed significant disruptions in their ability to stably encode the same environment. Furthermore, the burst firing properties of these cells were altered to forms correlated with reduced cognition. Additionally, the theta rhythm was significantly attenuated in CA1 place cells of APP/PS1 mice compared to WT. Our results suggest that distinct alteration in the physiological properties of CA1 and CA3 place cells, coupled with disrupted hippocampal theta rhythm in CA1, may collectively contribute to impaired hippocampal-dependent spatial learning and memory in AD.
Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences
Authors: Wijesekara Yasas , Wu Ling-Yi , Beeloo Rick , Rozwalak Piotr , Hauptfeld Ernestina , Doijad Swapnil P. , Dutilh Bas E. , Kaderali Lars 
Published: September 2024

ABSTRACTViruses are integral to every biome on Earth, yet we still need a more comprehensive picture of their identity and global distribution. Global metagenomics sequencing efforts revealed the genomic content of tens of thousands of environmental samples, however identifying the viral sequences in these datasets remains challenging due to their vast genomic diversity. Here, we address identifying bacteriophage sequences in unlabeled sequencing data. In a recent benchmarking paper, we observed that existing deep-learning tools show a high true positive rate, but may also produce many false positives when confronted with divergent sequences. To tackle this challenge, we introduce Jaeger, a novel deep-learning method designed specifically for identifying bacteriophage genome fragments. Extensive benchmarking on the IMG/VR database and real-world metagenomes reveals Jaeger’s consistent high sensitivity (0.87) and precision (0.92). Applying Jaeger to over 16,000 metagenomic assemblies from the MGnify database yielded over five million putative phage contigs. On average, Jaeger is around 20 times faster than the other state-of-the-art methods. Jaeger is available athttps://github.com/MGXlab/Jaeger.
The electrogenicity of the Na+/K+-ATPase poses challenges for computation in highly active spiking cells
Authors: Weerdmeester Liz , Schleimer Jan-Hendrik , Schreiber Susanne 
Published: September 2024

1SummaryThe evolution of the Na+/K+-ATPase laid the foundation for ion homeostasis and electrical signalling. While not required for restoration of ionic gradients, the electrogenicity of the pump (resulting from its 3:2 stoichiometry) is useful to prevent runaway activity. As we show here, electrogenicity also comes with disadvantageous side effects: (1) an activity-dependent shift in a cell’s baseline firing and (2) interference with computation, disturbing network entrainment when inputs change strongly. We exemplify these generic effects in a mathematical model of the weakly electric fish electrocyte, which spikes at hundreds of Hz and is exposed to abrupt rate changes when producing behaviourally-relevant communication signals. We discuss biophysical strategies allowing cells to mitigate the consequences of electrogenicity at additional metabolic cost and postulate an interesting role for a voltage-dependence of the Na+/K+-ATPase. Our work shows that the pump’s electrogenicity opens an additional axis of vulnerability that is likely to play a role in brain disease.
A genome-wide CRISPR screen inAnophelesmosquito cells identifies essential genes and required components of clodronate liposome function
Authors: Mameli Enzo , Samantsidis George-Rafael , Viswanatha Raghuvir , Kwon Hyeogsun , Hall David R. , Butnaru Matthew , Hu Yanhui , Mohr Stephanie E. , Perrimon Norbert , Smith Ryan C. 
Published: September 2024

AbstractAnophelesmosquitoes are the sole vector of human malaria, the most burdensome vector-borne disease worldwide. Strategies aimed at reducing mosquito populations and limiting their ability to transmit disease show the most promise for disease control. Therefore, gaining an improved understanding of mosquito biology, and specifically that of the immune response, can aid efforts to develop new approaches that limit malaria transmission. Here, we use a genome-wide CRISPR screening approach for the first time in mosquito cells to identify essential genes inAnophelesand identify genes for which knockout confers resistance to clodronate liposomes, which have been widely used in mammals and arthropods to ablate immune cells. In the essential gene screen, we identified a set of 1280Anophelesgenes that are highly enriched for genes involved in fundamental cell processes. For the clodronate liposome screen, we identified several candidate resistance factors and confirm their roles in the uptake and processing of clodronate liposomes throughin vivovalidation inAnopheles gambiae, providing new mechanistic detail of phagolysosome formation and clodronate liposome function. In summary, we demonstrate the application of a genome-wide CRISPR knockout platform in a major malaria vector and the identification of genes that are important for fitness and immune-related processes.
Dual roles of EGO-1 and RRF-1 in regulating germline exo-RNAi efficiency inCaenorhabditis elegans
Authors: Dejima Katsufumi , Yoshida Keita , Mitani Shohei 
Published: September 2024

AbstractRNA interference (RNAi) is widely used in life science research and is critical for diverse biological processes, such as germline development and antiviral defense. InCaenorhabditis elegans, RNA-dependent RNA polymerases, with redundant involvement of EGO-1 and RRF-1, facilitate small RNA amplification in germline exogenous RNAi (exo-RNAi). However, their coordination during the regulation of exo-RNAi processes in the germline remains unclear. Here, we examined non-null mutants of theego-1gene and found thatego-1(S1198L)animals exhibited germline exo-RNAi defects with normal fertility, abnormalities in germ granules, and synthetic temperature-dependent sterility withrrf-1. The exo-RNAi defects inego-1(S1198L)were partially restored by inhibitinghrde-1,cde-1, andznfx-1. Similar defects were observed in wild-type andego-1(S1198L)heterozygous descendants derived fromego-1(S1198L), but these were suppressed by ancestral inhibition ofrrf-1. These data reveal a dual role for EGO-1 in the positive regulation of germline exo-RNAi: it not only mediates target silencing through its RNA-dependent RNA polymerase activity, but also fine-tunes germ granule function or downstream processes, which are antagonized by RRF-1.
Motor preparation tracks decision boundary crossing in temporal decision-making
Authors: Ofir Nir , Landau Ayelet N. 
Published: September 2024

AbstractInterval timing, the ability of animals to estimate the passage of time, is thought to involve diverse neural processes rather than a single central “clock” (Paton & Buonomano, 2018). Each of the different processes engaged in interval timing follows a different dynamic path, according to its specific function. For example, attention tracks anticipated events, such as offsets of intervals (Rohenkohl & Nobre, 2011), while motor processes control the timing of the behavioral output (De Lafuente et al., 2024). Hence, different processes provide complimentary perspectives on mechanisms of time perception. The temporal bisection task, where participants categorize intervals as “long” or “short”, is thought to rely on the same mechanisms as other perceptual decisions (Balcı & Simen, 2014). In line with this hypothesis, we previously described an EEG potential that tracks the formation of decision following the end of the timed interval (Ofir & Landau, 2022). Here, we track the dynamics of motor preparation to investigate the formation of decision within the timed interval. In contrast to typical perceptual decisions, where motor plans for all response alternatives are prepared simultaneously (Shadlen & Kiani, 2013), we find that different temporal decisions develop sequentially. While preparation for “long” responses was already underway before interval offset, no preparation was found for “short” responses. Furthermore, within intervals categorized as “long”, motor preparation was stronger at interval offset for faster responses. Our findings shed light on the unique dynamics of temporal decisions and demonstrate the importance of considering neural activity in timing tasks from multiple perspectives.
Corrosion resistance of MWCNTs-nanoZnO composite reinforced chromium-free Zn-Al coating
Authors: Fu Yu , Zhao Junwen , Li Xujia , Peng Yiwen 
Published: September 2024

Purpose
This paper aims to prepare high corrosion-resistant chromium-free zinc-aluminum (Zn–Al) coatings reinforced with multi-walled carbon nanotubes (MWCNTs) and nano-ZnO particle composites.

Design/methodology/approach
The morphology, composition and corrosion resistance of the coatings were analyzed by electrochemical tests, water contact angle tests, immersion tests, scanning electron microscopy/energy dispersive spectrometer and X-ray diffraction.

Findings
The composite coating with 0.3% MWCNTs and 0.5% nano-ZnO particles demonstrated both high shielding performance and cathodic protection performance, which was attributed to the porosity filling of MWCNTs and nano-ZnO particles together with the electrical connection of MWCNTs between the zinc and aluminum powders.

Originality/value
This work laid an experimental foundation for the preparation and corrosion mechanism of high corrosion-resistant chromium-free Zn–Al coating reinforced with MWCNTs and nano-ZnO particles.
Actor opportunism, social capital and coping strategies in the sharing economy: drivers, outcomes and marketing implications
Authors: Saravade Swapnil , Felix Reto 
Published: September 2024

Purpose
This paper aims to provide a conceptual understanding of the drivers and outcomes of actor opportunism in the context of the three key actors of the sharing economy – the service provider, the platform and the consumer.

Design/methodology/approach
The research uses a conceptual approach by drawing on literature from within and outside of marketing.

Findings
The current research introduces a conceptual framework of opportunism in the sharing economy with seven underlying propositions. The framework posits a U-shaped moderating effect of social capital for the relationship between opportunism and its drivers, actor vulnerability and asset specificity. Furthermore, a 2 × 2 matrix consisting of two types of opportunistic behaviors (active and passive) and two coping strategies by other actors (defensive and nondefensive) suggests that passive opportunism tends to lead to value codestruction independently of the coping strategies employed by other actors. Counterintuitively, the combination of active opportunism and defensive coping strategy presents an opportunity for value cocreation due to its potential to break up older structures and generate new ones.

Research limitations/implications
While our research provides a higher-level understanding of opportunism pertaining to platform, consumers and service providers in the sharing economy, future research could situate our framework within specific regulatory environments, incorporate the role of competitors and examine individual interaction effects between type of opportunism and coping strategies.

Practical implications
The framework enables service providers, platforms and consumers to identify drivers of opportunistic behaviors of their partners and discern instances in which opportunistic behaviors lead to value codestruction for all actors.

Originality/value
This research transcends prior work on the bright and dark sides of the sharing economy by identifying its dynamic nature and examining the contributing role of opportunism.
Developmentalism, technocracy and legitimacy crises of humanities: A Third World perspective
Authors: Bhattacharyya Sanchari , Sanasam Reena 
Published: September 2024

PurposeThe visible ill-effects of the developmental enterprises in the ex-colonies and the tendency towards technocratic totalitarianism, in many ways, have altered the way modern humans perceived the idea of “progress” and “development” historically since the Cold War. This paper presents a deconstructive-transdisciplinary critique of the pervasive ideology by focusing on three nodal points in the stages of “development”: (1) the rise of technocratic modern science; (2) the making of the Third World; and (3) de-legitimisation of its indigenous knowledge paradigms.Design/methodology/approachDrawing on the first-hand accounts of the researchers, social scientists, activists and environmentalists, this paper presents an extensive critique of the violence involved in the development enterprises and recommends possible ways to move beyond the developmental hegemony. This paper is a theoretical investigation that adopts an interpretative, pluralistic, transdisciplinary approach, in order to deconstruct the development ideology and analyse the ramifications of the developmental propaganda and practice as they unfolded in the Global South.FindingsThis paper highlights the need to decondition the social imaginary from the hegemony of developmentalism and its by-product scientism and “technological rationality” for an inclusive, pluralistic, democratic social order.Research limitations/implicationsThe focal area of this work is India in particular and Global South in general. It studies the era between the 1950s and 1980s when the major development enterprises took place and studies the consequences they entailed.Social implicationsThe scope of this paper encompasses every socio-economic, ecological and epistemological domain affected by the detrimental effects of the developmental enterprises in the Global South.Originality/valueThe originality of this work lies in its transdisciplinary approach. The scope of this paper is extensive and covers nearly every domain of human existence that has been affected by the development debacle and technocratic totalitarianism in the post-War era.