bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiological safety and antimicrobial resistance profiles of ready-to-eat seafood in Bayelsa, Nigeria
Authors: Omeje Faith I , Beshiru Abeni , Igbinosa Isoken H , Igbinosa Etinosa O 
Published: July 2024

Abstract
The global significance of processed seafood necessitates vigilant monitoring for health risks, particularly in the ready-to-eat (RTE) sector. This study assessed the microbiological safety and antimicrobial resistance (AMR) profiles of 520 RTE seafood samples collected from Bayelsa, Nigeria. Escherichia coli identification was conducted using culture-based and polymerase chain reaction (PCR) methods. The isolates were further characterized using standard bacteriological techniques. PCR screening was employed to detect virulence and resistance genes. Of the processed RTE seafood samples assessed, 12.1% tested positive for E. coli. Extended-spectrum beta-lactamase (ESBL)-producing E. coli accounted for 2.3% of the samples. Various diarrheagenic determinants were identified, with aggregative adherence regulator-activated island (aaiC) and attaching and effacing (eae) being the most prevalent. Higher AMR levels were observed in ESBL-producing strains. Additionally, extracellular virulence factors, biofilm formation, and hydrophobicity assays revealed diverse pathogenic potentials among the isolates. The detection of beta-lactamase AMR genes, such as blaTEM (15.9%), blaCTX−M−15 (3.2%), and blaCTX−M−1 (1.6%), underscores the genetic mechanisms responsible for resistance in E. coli strains recovered from RTE seafood. These findings underscore the need for thorough monitoring and strict control procedures to ensure the safety of RTE seafood and mitigate the risks associated with AMR in food consumption.
Pandemic preparedness—political perspectives
Authors: Brüssow Harald 
Published: July 2024

Abstract
Pandemic preparedness is explored for the antibiotic resistance crisis and the threat of a next viral pandemic. Bacterial pathogens escaping from control by antibiotics are well defined, and resistance develops over decades while a next viral pandemic occurs suddenly with a novel virus. The death toll for resistant bacterial infections is reviewed, and the scientific and economic hurdles to the development of new antibiotics are discussed. Regulatory adaptations and financial push and pull programs to restimulate new antibiotic development are explored. The COVID-19 pandemic caused not only millions of deaths, but also economic losses in excess of 10 trillion US dollars. Coronaviruses and influenza viruses remain usual suspects for new viral pandemics, followed by paramyxoviruses. Viral infections at the animal–human interface in wet markets and in disturbed environments need active virus surveillance programs. Learning lessons from the COVID-19 for non-pharmaceutical interventions is difficult to draw since measures were frequently applied in combination against different variant viruses and against changing population immunity levels. The Randomised Evaluation of COVID-19 Therapy (RECOVERY) clinical trials demonstrated that even under emergency situations clinical trials can rapidly provide solid treatment data. Various novel vaccine approaches were the most efficient control measures for the COVID-19 pandemic. Pandemic preparedness also requires a fact-based discussion both in the public and in parliaments to settle the conflict between individual freedom and necessary restrictions during a pandemic. Mature and educated citizens are needed not only for coping with pandemics but also for creating stress-resistant democratic societies. Learned scientific societies should contribute to this discussion.
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis
Authors: Wang Huaying , Zhang Wei , Yu Yanan , Fang Xiaoxue , Zhang Tengjiao , Xu Luyuan , Gong Lei , Xiao Hongxing 
Published: July 2024

Abstract
—Chloroplast capture, a phenomenon that can occur through interspecific hybridization and introgression, is frequently invoked to explain cytonuclear discordance in plants. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential for driving species differentiation and possible functional differences in the context of chloroplast capture. To address this crucial question, we chose the Aquilegia genus, which is known for having minimal sterility among species, and inferred that A. amurensis captured the plastome of A. parviflora based on cytonuclear discordance and gene flow between the 2 species. We focused on the introgression region and its differentiation from corresponding regions in closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes (CECs; i.e., organelle-targeted genes) of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast-receiving species due to cytonuclear interactions during introgression. Notably, the intrinsic correlation of CEC introgression was a greater degree of evolutionary distance for these CECs between A. amurensis and A. parviflora. Terpene synthase activity genes (GO: 0010333) were overrepresented among the introgressed genes, and more than 30% of these genes were CEC genes. These findings support our observations that floral terpene release pattern is similar between A. amurensis and A. parviflora compared with A. japonica. Our study clarifies the mechanisms of cytonuclear coevolution, species differentiation, and functional differences in the context of chloroplast capture and highlights the potential role of chloroplast capture in adaptation.
The neurovascular coupling response of the aged brain is brain-state dependent
Authors: Zhang Xiao , Tao Lechan , Nygaard Amalie H. , Dong Yiqiu , Hong Xiaoqi , Goddard Carolyn M. , He Chen , Postnov Dmitry , Allodi Ilary , Lauritzen Martin J. , Cai Changsi 
Published: July 2024

AbstractBrain aging lead to reduced cerebral blood flow and cognitive decline, but how normal aging affects neurovascular coupling (NVC) in the awake brain is unclear. Here, we investigated NVC in relation to calcium changes in vascular mural cells (VMCs) in awake adult and aged mice. We show that NVC responses are reduced and prolonged in the aged brain and that this is more pronounced at the capillary level than in arterioles. However, the overall NVC response, measured as the time integral of vasodilation, is the same in two age groups. In adult, but not in aged mice, the NVC response correlated with Ca2+ signaling in VMCs, while the overall Ca2+ kinetics were slower in aged than in adult mice. In particular, the rate of Ca2+ transport, and the Ca2+ sensitivity of VMCs were reduced in aged mice, explaining the reduced and prolonged vasodilation. Spontaneous locomotion was less frequent and reduced in aged mice as compared to young adult mice, and this was reflected in the ‘slow but prolonged’ NVC and vascular Ca2+ responses. Taken together, our data characterize the NVC in the aged awake brain as slow but prolonged, and underscoring the importance of brain state in understanding age-related mechanisms.
A draft Arab pangenome reference
Authors: Nassir Nasna , Almarri Mohamed A. , Kumail Muhammad , Mohamed Nesrin , Balan Bipin , Hanif Shehzad , AlObathani Maryam , Jamalalail Bassam , Elsokary Hanan , Kondaramage Dasuki , Shiyas Suhana , Kosaji Noor , Satsangi Dharana , Abdelmotagali Madiha Hamdi Saif , Abou Tayoun Ahmad , Ahmed Olfat Zuhair Salem , Youssef Douaa Fathi , Al Suwaidi Hanan , Albanna Ammar , Du Plessis Stefan , Khansaheb Hamda Hassan , Alsheikh-Ali Alawi , Uddin Mohammed 
Published: July 2024

SummaryPangenomes represent a significant shift from relying on a single reference sequence to a robust set of assemblies, Arab populations remain significantly underrepresented; hence, we present the first Arab Pangenome Reference (APR) utilizing 53 individuals of diverse Arab ethnicities. We assembled nuclear and mitochondrial pangenomes using 35.27X high-fidelity long reads, 54.22X ultralong reads and 65.46X Hi-C reads yielded contiguous haplotype-phasedde novoassemblies of exceptional quality, with an average N50 of 124.28 Mb. We discovered 111.96 million base pairs of novel euchromatic sequences absent from existing human pangenomes, the T2T-CHM13, GRCh38 reference human genomes, and other public datasets. We identified 8.94 million population-specific small variants and 235,195 structural variants within the Arab pangenome. We detected 883 gene duplications including 15.06% associated with recessive diseases and 1,436 bp of novel mitochondrial pangenome sequence. Our study provides a valuable resource for future genomic medicine initiatives in Arab population and other global populations.
Transient TELC and transmembrane potential in a laser flashed bacteriorhodopsin purple membrane open flat sheet
Authors: Lee James Weifu 
Published: July 2024

AbstractThe transmembrane-electrostatically localized protons/cations charges (TELC, also known as TELP) model may serve as a unified framework to explain a wide range of bioenergetic phenomenon. Transient TELC and transmembrane potential in a laser flash-energized bacteriorhodopsin (bR) purple membrane (PM) open flat sheet are now better analyzed. Under the Heberle et al. 1994 experimental conditions, the number of bR molecules is now calculated to be 8200 per PM open flat sheet with a diameter of 600 nm. With a single-turnover laser flash intensity of 3 mJ/cm2to photoexcite 10% of the bR molecules, the number of laser flash-induced peak TELC density is calculated to be 2900 per µm2of PM, which translates to a peak transient transmembrane potential of 50 mV. The bR protonic outlet protrudes into the liquid phase outside the putative “potential well/barrier”. The observation is in line with the TELP model; but does not support the “potential well/barrier” model. The author encourages research on more relevant protonic cell systems that have transmembrane potential with TELC comprising excess positive charges at one side and excess anions at the other side of the membrane.
Microglia-specific transduction via AAV11 armed with IBA1 promoter and miRNA-9 targeting sequences
Authors: Luo Nengsong , Lin Kunzhang , Cai Yuxiang , Sui Xiaokai , Zhang Zilian , Xing Jiayong , Liu Gangning , Yuan Wenjia , Wang Jie , Xu Fuqiang 
Published: July 2024

AbstractMicroglia, as resident immune cells in the central nervous system (CNS), are closely related to human health and the pathogenesis of various CNS diseases, making them compelling targets for therapeutic interventions. However, functional and therapeutic studies of microglia remain significant challenges largely due to the lack of tools capable of efficiently and specifically transducing microglia. Herein, we evaluated the specificity and efficiency of various adeno-associated virus (AAV) vectors armed with the mIBA1 promoter and miRNA-9 targeting sequences in transducing microglia within the caudate putamen (CPu) brain region, and found that AAV11 mediates more specific and efficient transduction of microglia. Subsequently, we further demonstrated that AAV11 also exhibits high transduction specificity for microglia across various brain areas and within the spinal cord. Finally, by reducing the injection dosage, we employed AAV11 for sparse labeling of microglia. This work provides a promising tool for advancing both the functional investigation and therapeutic targeting of microglia.
Realisation threshold revisited: does the minimum tooth size scale with body size?
Authors: Christensen Mona M. , Laakkonen Juha , Jernvall Jukka 
Published: July 2024

AbstractBased on his analyses of lynx and brown bear teeth, Björn Kurtén coined the concept of ‘realisation threshold’, the smallest size at which a tooth can form and erupt properly. Kurtén found the smallest sizes of the studied lynx and bear teeth to be 2.5 mm and 3.5 mm, respectively, much larger than for example the smallest rodent teeth known to readily erupt. A recent study comparing developing teeth from shrews to elephants suggested a relatively unchanged theoretical minimum tooth size for mammalian teeth. Together, these studies have left open the question of whether realisation thresholds of teeth are larger in larger mammals than in small ones. In this study, we follow Kurtén’s line of thought and compare the sizes of teeth that are variably present in dentitions, and therefore likely cross the realisation threshold only occasionally. First, we show using published reports that variably present teeth are relatively small in large mammals, but larger than the previously suggested theoretical minimum tooth size. Next, we examine the canines of mares that are known to be variably present. We report one canine that, compared with information found in the literature, is by far the smallest compared to the body size. In conclusion, whereas the variably present teeth tend to be larger in large mammals, there may be overlooked potential for large mammals to develop very small teeth. This information can be helpful in extrapolating findings from common small model organisms, such as mice, to larger mammals, including humans.
HDAC4 Inhibits NMDA Receptor-Mediated Stimulation of Neurogranin Expression
Authors: de Andrés Raquel , Martínez-Blanco Elena , Díez-Guerra F. Javier 
Published: July 2024

AbstractThe coordination of neuronal wiring and activity within the central nervous system (CNS) is crucial for cognitive function, particularly in the context of aging and neurological disorders. Neurogranin (Ng), an abundant forebrain protein, modulates calmodulin (CaM) activity and deeply influences synaptic plasticity and neuronal processing. This study investigates the regulatory mechanisms of Ng expression, a critical but underexplored area for combating cognitive impairment. Utilizing both in vitro and in vivo hippocampal models, we show that Ng expression arises during late developmental stages, coinciding with synaptic maturation and neuronal circuit consolidation of. We observed that Ng expression increases in neuronal networks with heightened synaptic activity and identified GluN2B-containing N-methyl-D-aspartate (NMDA) receptors as key drivers of this expression. Additionally, we discovered that nuclear-localized HDAC4 inhibits Ng expression, establishing a regulatory axis that is counteracted by NMDA receptor stimulation. Analysis of the Ng gene promoter activity revealed regulatory elements between the −2.4 and −0.85 Kbp region, including a binding site for RE1-Silencing Transcription factor (REST), which may mediate HDAC4’s repressive effect on Ng expression. Further analysis of the promoter sequence revealed conserved binding sites for the myocyte enhancer factor-2 (MEF2) transcription factor, a target of HDAC4-mediated transcription regulation. Our findings elucidate the interplay between synaptic activity, NMDAR function, and transcriptional regulation in controlling Ng expression, offering insights into synaptic plasticity mechanisms and potential therapeutic strategies to prevent cognitive dysfunction.
Moderate Cold Stress Enhance Drought Resistance throughCCA1via -an ABA-independent Pathway
Authors: Yang Xue , Liu Yan , Jia Zi-Chang , Li Ming , Hou Xuan-Xuan , Hou Sheng-Qiang , Shi Xi-Long , Gao Bei , Zhang Dao-Yuan , Zhu Fu-Yuan , Chen Mo-Xian , Liu Ying-Gao 
Published: July 2024

AbstractIn nature, plants frequently encounter concurrent stresses, particularly the simultaneous occurrence of cold and drought stress poses a challenge to plants in middle and high latitudes. However, the molecular mechanisms underlying the plants response to this double-stress scenario remain unclear. Although some responses suggest that drought stress can improve cold resistance in plants, through ABA signaling pathways. In our study, we discovered that moderate low temperature treatment significantly enhanced Arabidopsis drought tolerance. Low temperature rapidly triggers the transcription factor CCA1, a prototypical response to cold stress, which inturn directly regulates the expression ofOST1andP5CS1by binding to their promoters. This leads to the premature closure of stomata and accumulation of proline through a non-ABA-dependent pathway even before plants experience drought stress, ultimately improving plant resistance against drought and cold. Moreover, this mechanism is conserved across plant species, and the synergistic resistance mechanism enables perennial plants to survive winter conditions and annual plants to withstand multi-stresses.
Genome report: Genome sequence of the tuliptree scale insect,Toumeyella liriodendri(Gmelin)
Authors: Mongue Andrew J. , Markee Amanda , Grebler Ethan , Liesenfelt Tracy , Powell Erin C. 
Published: July 2024

AbstractScale insects are of interest both to basic researchers for their unique reproductive biology and to applied researchers for their pest status. In spite of this interest, there remain few genomic resources for this group of insects. To begin addressing this lack of data, we present the genome sequence of the tuliptree scale insect,Toumeyella liriodendri(Gmelin) (Hemiptera: Coccomorpha: Coccidae). The genome assembly spans 536Mb, with over 96% of sequence assembled into one of 17 chromosomal scaffolds. We characterize roughly 66% of this sequence as repetitive and annotate 16,508 protein coding genes. Then we use the reference genome to explore the phylogeny of soft scales (Coccidae) and evolution of karyotype within the family. We find thatT. liriodendriis an early-diverging soft scale, less closely related to most sequenced soft scales than a species of the family Aclerdidae is. This molecular result bolsters a previous, character-based phylogenetic placement of Aclerdidae within Coccidae. In terms of genome structure,T. liriodendrihas nearly twice as many chromosomes as the only other soft scale assembled to the chromosome level,Ericerus pela(Chavannes). In comparing the two, we find that chromosome number evolution can largely be explained by simple fissions rather than more complex rearrangements. These genomic natural history observations lay a foundation for further exploration of this unique group of insects.
Chronic β3 adrenergic agonist treatment improves brain microvascular endothelial function and cognition in aged mice
Authors: Natarajan Duraipandy , Ekambaram Shoba , Tarantini Stefano , Yelahanka Nagaraja Raghavendra , Yabluchanskiy Andriy , Hedrick Andria F , Awasthi Vibhudutta , Subramanian Madhan , Csiszar Anna , Balasubramanian Priya 
Published: July 2024

AbstractMicrovascular endothelial dysfunction, characterized by impaired neurovascular coupling, reduced glucose uptake, blood-brain barrier disruption, and microvascular rarefaction, plays a critical role in the pathogenesis of age-related vascular cognitive impairment (VCI). Emerging evidence points to non-cell autonomous mechanisms mediated by adverse circulating milieu (an increased ratio of pro-geronic to anti-geronic circulating factors) in the pathogenesis of endothelial dysfunction leading to impaired cerebral blood flow and cognitive decline in the aging population. In particular, age-related adipose dysfunction contributes, at least in part, to an unfavorable systemic milieu characterized by chronic hyperglycemia, hyperinsulinemia, dyslipidemia, and altered adipokine profile, which together contribute to microvascular endothelial dysfunction. Hence, in the present study, we aimed to test whether thermogenic stimulation, an intervention known to improve adipose and systemic metabolism by increasing cellular energy expenditure, could mitigate brain endothelial dysfunction and improve cognition in the aging population. Eighteen-month-old old C57BL/6J mice were treated with saline or CL (β3-adrenergic agonist) for 6 weeks followed by functional analysis to assess endothelial function and cognition. CL treatment improved neurovascular coupling responses and rescued brain glucose uptake in aged animals. In addition, CL treatment also attenuated blood-brain barrier leakage and associated neuroinflammation in the cortex of aged animals. More importantly, these beneficial changes in microvascular function translated to improved cognitive performance in radial arm water maze and Y-maze tests. Our results suggest that β3-adrenergic agonist treatment improves multiple aspects of brain microvascular endothelial function and can be potentially repurposed for treating age-associated cognitive decline.
Msh3 and Pms1 Set Neuronal CAG-repeat Migration Rate to Drive Selective Striatal and Cortical Pathogenesis in HD Mice
Authors: Wang Nan , Zhang Shasha , Langfelder Peter , Ramanathan Lalini , Plascencia Mary , Gao Fuying , Vaca Raymond , Gu Xiaofeng , Deng Linna , Dionisio Leonardo E. , Prasad Brinda C. , Vogt Thomas , Horvath Steve , Aaronson Jeffrey S. , Rosinski Jim , Yang X. William 
Published: July 2024

SUMMARYModifiers of Huntington’s disease (HD) include mismatch repair (MMR) genes; however, their underlying disease-altering mechanisms remain unresolved. Knockout (KO) alleles for 9 HD GWAS modifiers/MMR genes were crossed to the Q140 Huntingtin (mHtt) knock-in mice to probe such mechanisms. Four KO mice strongly (Msh3andPms1) or moderately (Msh2andMlh1) rescue a triad of adult-onset, striatal medium-spiny-neuron (MSN)-selective phenotypes: somaticHttDNA CAG-repeat expansion, transcriptionopathy, and mHtt protein aggregation. Comparatively, Q140 cortex also exhibits an analogous, but later-onset, pathogenic triad that isMsh3-dependent. Remarkably, Q140/homozygous Msh3-KO lacks visible mHtt aggregates in the brain, even at advanced ages (20-months). Moreover,Msh3-deficiency prevents striatal synaptic marker loss, astrogliosis, and locomotor impairment in HD mice. Purified Q140 MSN nuclei exhibit highly linear age-dependent mHtt DNA repeat expansion (i.e. repeat migration), with modal-CAG increasing at +8.8 repeats/month (R2=0.98). This linear rate is reduced to 2.3 and 0.3 repeats/month in Q140 with Msh3 heterozygous and homozygous alleles, respectively. Our study defines somaticHttCAG-repeat thresholds below which there are no detectable mHtt nuclear or neuropil aggregates. Mild transcriptionopathy can still occur in Q140 mice with stabilizedHtt140-CAG repeats, but the majority of transcriptomic changes are due to somatic repeat expansion. Our analysis reveals 479 genes with expression levels highly correlated with modal-CAG length in MSNs. Thus, our study mechanistically connects HD GWAS genes to selective neuronal vulnerability in HD, in whichMsh3andPms1set the linear rate of neuronal mHtt CAG-repeat migration to drive repeat-length dependent pathogenesis; and provides a preclinical platform for targeting these genes for HD suppression across brain regions.One Sentence SummaryMsh3 and Pms1 are genetic drivers of sequential striatal and cortical pathogenesis in Q140 mice by mediating selective CAG-repeat migration in HD vulnerable neurons.