bluuebunny/crossref_metadata_2025_split huggingface dataset:
The bacterial microbiome in Spider and Deathwatch beetles
Authors: Hendricks Austin , Philips T. Keith , Engl Tobias , Plarre Rüdiger (Rudy) , Martinson Vincent G. 
Published: July 2024

AbstractThe beetle family Ptinidae contains a number of economically important pests, such as the Cigarette beetleLasioderma serricorne, the Drugstore beetleStegobium paniceum, and the diverse Spider beetles. Many of these species are stored product pests which target a diverse range of food sources from dried tobacco to books made with organic materials. Despite the threat that the 2,200 species of Ptinidae beetles pose, fewer than 50 have been surveyed for microbial symbionts, and only a handful have been screened using contemporary genomic methods. In this study, we screen 116 individual specimens that cover most subfamilies of Ptinidae, with outgroup beetles from closely related families Dermestidae, Endecatomidae, and Bostrichidae. We used 16S ribosomal RNA gene amplicon data to characterize the bacterial microbiomes of these specimens. The majority of these species had never been screened for microbes. We found that, unlike in their sister family Bostrichidae that has two mutualistic bacteria seen in most species, there are no consistent bacterial members of ptinid microbiomes. For specimens which hadWolbachiainfections, we did additional screening using multilocus sequence typing, and showed that our populations have different strains ofWolbachiathan has been noted in previous publications.ImportancePtinid beetles are both household pests of pantry goods and economic pests of dried good warehouses and cultural archives such as libraries and museums. Currently, the most common pest control measures for ptinid beetles are phosphine and/or heat treatments. Many ptinid beetles have been observed to have increasing resistance to phosphine, and heat treatments are not appropriate for many of the goods commonly infested by ptinids. Pest control techniques focused on symbiotic bacteria have been shown to significantly decrease populations, and often have the beneficial side effect of being more specific than other pest control techniques. This survey provides foundational information about the bacteria associated with diverse ptinid species, which may be used for future control efforts.
Beyond Static Models: The Dynamic Interplay of Facial Emotions and Attentional Scope
Authors: Hu Kesong , He Shuchang , Li Qi , Li Chiang-Shan R. 
Published: July 2024

AbstractThe interplay between emotion and attention has long been intensely scrutinized, with competing theories proposing divergent mechanisms. Building on our previous work, here we present evidence that refines these perspectives, revealing a nuanced, temporally dynamic relationship between emotional stimuli and attentional focus. Using a modified Flanker task with facial emotion cues, we demonstrate that the effects of emotional stimuli on attention evolve over time, contrary to traditional fixed-effect assumptions. Our results show distinct temporal patterns: Neutral faces elicited typical flanker effects initially, but only interference persisted later. Early-stage happy faces amplified flanker facilitation but not interference, while threat faces augmented flanker interference but not facilitation. In the late stage, flanker facilitation disappeared across all emotion conditions, and interference patterns converged, mirroring the neutral face condition. These findings indicate emotion’s influence on attention is more complex and dynamic than previously recognized, potentially reflecting learning or habituation processes. We propose a new framework for understanding emotion-attention interactions that transcends traditional dichotomies of attention focus and approach-avoidance, offering a more nuanced perspective on this critical cognitive interface.
Comparative genomic analysis ofLatilactobacillus sakeistrains provides new insights into their association with different niche adaptations
Authors: Ito Kohei , Ito Yutaro 
Published: July 2024

AbstractLatilactobacillus sakei, a lactic acid bacterium in diverse environments such as fermented foods, meat, and the human gastrointestinal tract, exhibits significant genetic diversity and niche-specific adaptations. This study conducts a comprehensive comparative genomic analysis of 30 completeL. sakeigenomes to uncover the genetic mechanisms underlying these adaptations. Phylogenetic analysis divided the species into three distinct clades that did not correlate with the source of isolation and did not suggest any niche-specific evolutionary direction. The pan-genome analysis revealed a substantial core genome alongside a diverse genetic repertoire, indicating both high genetic conservation and adaptability. Predicted growth rates based on codon use bias analysis suggest thatL. sakeistrains have an overall faster growth rate and may be able to efficiently dominant in competitive environments. Plasmid analysis revealed a variety of plasmids carrying genes essential for carbohydrate metabolism, enhancingL. sakei’s ability to thrive in various fermentation substrates. It was also found that the number of genes belonging to the GH1 family among sugar metabolism-related genes present on chromosomes and plasmids varies between strains, and that AA1, which is involved in alcohol oxidation, has been acquired from plasmids. BLAST analysis revealed that some strains have environmental adaptation gene clusters of cell surface polysaccharides that may mediate attachment to food and mucosa. These findings not only underscore the genetic and functional diversity ofL. sakeibut also highlight its potential as a potent starter culture in fermentation and as a probiotic. The knowledge gleaned from this study lays a solid foundation for future research aimed at harnessing the genetic traits ofL. sakeistrains for industrial and health-related applications.
Ancient tree-topologies and gene-flow processes among human lineages in Africa
Authors: Breton Gwenna , Sjödin Per , Zervakis Panagiotis I. , Laurent Romain , Froment Alain , Sjöstrand Agnès E. , Hewlett Barry S. , Barreiro Luis B. , Perry George H. , Soodyall Himla , Heyer Evelyne , Schlebusch Carina M. , Jakobsson Mattias , Verdu Paul 
Published: July 2024

AbstractThe deep history of humans in Africa and the complex divergences and migrations among ancient human genetic lineages remain poorly understood and are the subject of ongoing debate. We produced 73 high-quality whole genome sequences from 14 Central and Southern African populations with diverse, well-documented, languages, subsistence strategies, and socio-cultural practices, and jointly analyze this novel data with 104 African and non-African previously-released whole genomes. We find vast genome-wide diversity and individual pairwise differentiation within and among African populations at continental, regional, and even local geographical scales, often uncorrelated with linguistic affiliations and cultural practices. We combine populations in 54 different ways and, for each population combination separately, we conduct extensive machine-learning Approximate Bayesian Computation inferences relying on genome-wide simulations of 48 competing evolutionary scenarios. We thus reconstruct jointly the tree-topologies and migration processes among ancient and recent lineages best explaining the diversity of extant genomic patterns. Our results show the necessity to explicitly consider the genomic diversity of African populations at a local scale, without merging population samples indiscriminately into largera prioricategories based on geography, subsistence-strategy, and/or linguistics criteria, in order to reconstruct the diverse evolutionary histories of our species. We find that, for all different combinations of Central and Southern African populations, a tree-like evolution with long periods of drift between short periods of unidirectional gene-flow among pairs of ancient or recent lineages best explain observed genomic patterns compared to recurring gene-flow processes among lineages. Moreover, we find that, for 25 combinations of populations, the lineage ancestral to extant Southern African Khoe-San populations diverged around 300,000 years ago from a lineage ancestral to Rainforest Hunter-Gatherers and neighboring agriculturalist populations. We also find that short periods of ancient or recent asymmetrical gene-flow among lineages often coincided with epochs of major cultural and ecological changes previously identified by paleo-climatologists and archaeologists in Sub-Saharan Africa.
A distant TANGO1 family member promotes vitellogenin export from the ER inC. elegans
Authors: Mo Jimmy H. , Zhai Chao , Jung Kwangsek , Li Yan , Yan Yonghong , Dong Meng-Qiu , Mak Ho Yi 
Published: July 2024

SummaryVitellogenin belongs to the Large Lipid Transfer Protein superfamily and is thought to share a common ancestor with human Apolipoprotein B (ApoB) for systemic lipid transport1–5. Vitellogenin forms part of yolk granules (also known as yolk organelles), as maternal contribution of nutrients that support the embryonic development of oviparous animals6,7. InCaenorhabditis elegans, vitellogenin proteins (VIT-1 to VIT-6) are synthesized in the hermaphrodite intestine, secreted into the pseudocoelom and internalized by oocytes8–13. Although a general route for inter-tissue vitellogenin transport has been described, the full mechanism that underlies its intracellular trafficking within the intestine remains obscure9,12,13. In humans, transport and Golgi organization protein 1 (TANGO1) and TANGO1-like (TALI) proteins generate super-sized membrane carriers to accommodate bulky ApoB-containing lipoprotein particles for their export from ER exit sites14–17. Transport facilitated by TANGO1 family of proteins is considered as an alternative, COPII-independent ER exit pathway18–24. Thus far, TANGO1 orthologs have been discovered in most metazoans, except nematodes24,25. Here, we report theC. elegansprotein R148.3 (nowTransport andGolgi organization 1-like or TNGL-1) as a mediator of vitellogenin export from the ER. TNGL-1 depletion triggers VIT-2 accumulation in the intestinal ER lumen. TNGL-1 requires its C-terminal unstructured domain for its localization to ER exit sites. Like TANGO1, it utilizes a luminal globular domain for cargo engagement. Our findings support TNGL-1 as a distant TANGO1 family member.
A second wave of Notch signaling diversifies the intestinal secretory lineage
Authors: Zagoren Eleanor , Dias Nicolas , Smith Zachary D. , Ameen Nadia A. , Sumigray Kaelyn 
Published: July 2024

SummaryThe small intestine is well known for the function of its nutrient-absorbing enterocytes; yet equally critical for the maintenance of homeostasis is a diverse set of secretory cells, all of which are presumed to differentiate from the same intestinal stem cell. Despite major roles in intestinal function and health, understanding how the full spectrum of secretory cell types arises remains a longstanding challenge, largely due to their comparative rarity. Here, we investigate the fate specification of a rare and distinct population of small intestinal epithelial cells found in rats and humans but not mice:CFTRHighExpressers (CHEs). We use pseudotime trajectory analysis of single-cell RNA-seq data from rat intestinal jejunum to provide evidence that CHEs are specified along the secretory lineage and appear to employ a second wave of Notch-based signal transduction to distinguish these cells from other secretory cell types. We further validate the general order of transcription factors that direct these cells from unspecified progenitors within the crypt and experimentally demonstrate that Notch signaling is necessary to induce CHE fate bothin vivoandin vitro. Our results suggest a model in which Notch is reactivated along the secretory lineage to specify the CHE population: a rare secretory cell type with putative functions in localized coordination of luminal pH and direct relevance to cystic fibrosis pathophysiology.
Not All Is Lost: Resilience of Microbiome Samples to Freezer Failures and Long-term Storage
Authors: Pulido-Chavez M. Fabiola , Randolph James W. J. , Glassman Sydney I. 
Published: July 2024

AbstractAdvances in technology have facilitated extensive sample collection to explore microbiomes across diverse systems, leading to a growing reliance on ultracold freezers for storing both samples and extracted DNA. However, freezer malfunctions can jeopardize data integrity. In this study, we investigated the effects of an unforeseen short-term thaw event (∼1 week) resulting from a freezer malfunction on soil samples stored at -80°C and extracted uncompromised DNA stored long-term at -20°C. We compared these samples against previously sequenced Illumina MiSeq data to assess whether the process of thawing soil or multi-year extracted DNA storage affected the resilience of bacterial or fungal richness or community composition, thereby impacting our ability to accurately determine treatment effects. Our results reveal substantial resilience in fungal richness and both bacterial and fungal beta-diversity to soil sample thawing and extended frozen DNA storage. This resilience facilitated biological inferences that closely mirrored those observed in the original study. Notably, fungi exhibited greater resilience to short-term thawing compared to bacteria, which showed sensitivity to both thawing and long-term freezing. Moreover, taxonomic composition analysis revealed the persistence of dominant microbial taxa under thawing and prolonged freezing, suggesting that dominant microbes remain viable for tracking across temporal studies. In conclusion, our study highlights that beta-diversity is more robust than alpha-diversity and fungi are more resilient than bacteria. Furthermore, our findings underscore the effectiveness of soil storage at -80°C compared to storage of extracted DNA at -20°C, despite potential freezer failures, as the most robust method for long-term storage in microbiome studies.
Biofilm dispersal patterns revealed using far-red fluorogenic probes
Authors: Prentice Jojo A. , Kasivisweswaran Sandhya , van de Weerd Robert , Bridges Andrew A. 
Published: July 2024

AbstractBacteria frequently colonize niches by forming multicellular communities called biofilms. To explore new territories, cells exit biofilms through an active process called dispersal. Biofilm dispersal is essential for bacteria to spread between infection sites, yet how the process is executed at the single-cell level remains mysterious. Here, we characterize dispersal at unprecedented resolution for the global pathogenVibrio cholerae. To do so, we first developed a far-red cell-labeling strategy that overcomes pitfalls of fluorescent protein-based approaches. We reveal that dispersal initiates at the biofilm periphery and ∼25% of cells never disperse. We define novel micro-scale patterns that occur during dispersal, including biofilm compression and the formation of dynamic channels. These patterns are attenuated in mutants that reduce overall dispersal or that increase dispersal at the cost of homogenizing local mechanical properties. Collectively, our findings provide fundamental insights into the mechanisms of biofilm dispersal, advancing our understanding of how pathogens disseminate.
Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program
Authors: Palikyras Spiros , Varamogiani-Mamatsi Vassiliki , Zhu Yajie , Ramasamy Shyam , Mizi Athanasia , Liebermann Isabel , Stavropoulou Athanasia , Papadionysiou Ioanna , Bartsch Deniz , Kargapolova Yulia , Sofiadis Konstantinos , Nikolaou Christoforos , Kurian Leo , Oudelaar A. Marieke , Barbieri Mariano , Papantonis Argyris 
Published: July 2024

ABSTRACTSenescence —the endpoint of replicative lifespan for normal cells— is established via a complex sequence of molecular events. One such event is the dramatic reorganization of CTCF into senescence-induced clusters (SICCs). However, the molecular determinants, genomic consequences, and functional purpose of SICCs remained unknown. Here, we combine functional assays, super-resolution imaging, and 3D genomics with computational modelling to dissect SICC emergence. We establish that the competition between CTCF-bound and non-bound loci dictates clustering propensity. Upon senescence entry, cells repurpose SRRM2 —a key component of nuclear speckles— and BANF1 —a ‘molecular glue’ for chromosomes— to cluster CTCF and rewire genome architecture. This CTCF-centric reorganization in reference to nuclear speckles functionally sustains the senescence splicing program, as SICC disruption fully reverts alternative splicing patterns. We therefore uncover a new paradigm, whereby cells translate changes in nuclear biochemistry into architectural changes directing splicing choices so as to commit to the fate of senescence.GRAPHICAL ABSTRACTHIGHLIGHTSHMGB2-bound loci compete with CTCF-bound ones for nuclear speckle associationSenescent cells repurpose SRRM2 and BANF1 to cluster CTCF on specklesBANF1 is essential, but not sufficient for CTCF clusteringThe SRRM2 RNA-binding domain directs CTCF clusteringSICCs rewire chromatin positioning to sustain the senescence splicing program
Novel Imaging Tools to Study Mitochondrial Dynamics inCaenorhabditis elegans
Authors: Valera-Alberni Miriam , Yao Pallas , Romero-Sanz Silvia , Lanjuin Anne , Mair William B. 
Published: July 2024

AbstractMitochondria exhibit a close interplay between their structure and function. Understanding this intricate relationship requires advanced imaging techniques that can capture the dynamic nature of mitochondria and their impact on cellular processes. However, much of the work on mitochondrial dynamics has been done in single celled organisms or in vitro cell culture. Here, we introduce novel genetic tools for live imaging of mitochondrial networks in the nematodeCaenorhabditis elegans, addressing a pressing need for advanced techniques in studying organelle dynamics within live intact multicellular organisms. Through a comprehensive analysis, we directly compare our tools with existing methods, demonstrating their advantages for visualizing mitochondrial morphology and contrasting their impact on organismal physiology. We reveal limitations of conventional techniques, while showcasing the utility and versatility of our approaches, including endogenous CRISPR tags and ectopic labeling. By providing a guide for selecting the most suitable tools based on experimental goals, our work advances mitochondrial research inC. elegansand enhances the strategic integration of diverse imaging modalities for a holistic understanding of organelle dynamics in living organisms.
Dark photon constraints from a 7.139 GHz cavity haloscope experiment
Authors: He Dong , Fan Jie , Gao Xin , Gao Yu , Houston Nick , Ji Zhongqing , Jin Yirong , Li Chuang , Li Jinmian , Li Tianjun , Liu Shi-hang , Niu Jia-Shu , Peng Zhihui , Sun Liang , Sun Zheng , Wang Jia , Wei Puxian , Wu Lina , Xiang Zhongchen , Yang Qiaoli , Zhang Chi , Zhang Wenxing , Zhang Xin , Zheng Dongning , Zheng Ruifeng , Zhou Jian-yong ,   APEX Collaboration
Published: July 2024

The dark photon is a promising candidate for the dark matter which comprises most of the matter in our visible Universe. Via kinetic mixing with the Standard Model it can also be resonantly converted to photons in an electromagnetic cavity, offering novel experimental possibilities for the discovery and study of dark matter. We report the results of a pathfinder dark photon dark matter cavity search experiment performed at Hunan Normal University and the Institute of Physics, Chinese Academy of Sciences, representing the first stage of the Axion and dark Photon EXperiment program. Finding no statistically significant excess, we place an upper limit on the kinetic mixing parameter |χ|<3.7×10−13 around mA≃29.5  μeV at 90% confidence level. This result exceeds other constraints on dark photon dark matter in this frequency range by roughly an order of magnitude.

Published by the American Physical Society
2024
Determinants and impact of production planning and control accounting techniques on competitiveness of manufacturing companies: a structural equation modelling approach
Authors: Oyewo Babajide , Alta'any Mohammad , ALo Kolawole Adeyemi , Dube Negroes Tembo 
Published: July 2024

Purpose
This study aims to investigate four internal (organisational structure, quality of information technology, business strategy and market orientation) and two external (competition intensity and perceived environmental uncertainty) contextual factors affecting the use of production planning and control accounting techniques (PPC), as well as the impact of PPC usage on organisational competitiveness.

Design/methodology/approach
Seven major PPC techniques were investigated, namely: attribute costing, lifecycle costing, quality costing, target costing, value-chain costing, activity-based costing and activity-based management. By deploying a multi-informant strategy, a structured questionnaire was used to gather survey data from 129 senior accounting, finance and production personnel of publicly quoted manufacturing companies in Nigeria.

Findings
The results, using structural equation modelling, show that market orientation is the strongest determinant of PPC usage. The inability of competition intensity and perceived environmental uncertainty to notably affect PPC usage suggests that external environmental pressure to use PPC is weak. Although PPC can engender organisational competitiveness, their interactive usage yields optimal results.

Originality/value
The study contributes to knowledge by: (i) presenting evidence that although PPC techniques can engender organisational competitiveness, it is their interactive usage that yields optimal results; (ii) empirically demonstrating that contextual factors influence PPC usage in line with the contingency theory; and (iii) validating the diffusion of innovation theory that organisations will typically deploy PPC techniques because of their relative advantage of improving organisational competitiveness.