bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and cellular rhythms in excitatory and inhibitory neurons in the mouse prefrontal cortex
Authors: Burns Jennifer N. , Jenkins Aaron K. , Yin RuoFei , Zong Wei , Vadnie Chelsea A. , DePoy Lauren M. , Petersen Kaitlyn A , Tsyglakova Mariya , Scott Madeline R. , Tseng George C. , Huang Yanhua H. , McClung Colleen A. 
Published: July 2024

AbstractPrevious studies have shown that there are rhythms in gene expression in the mouse prefrontal cortex (PFC); however, the contribution of different cell types and potential variation by sex has not yet been determined. Of particular interest are excitatory pyramidal cells and inhibitory parvalbumin (PV) interneurons, as interactions between these cell types are essential for regulating the excitation/inhibition balance and controlling many of the cognitive functions regulated by the PFC. In this study, we identify cell-type specific rhythms in the translatome of PV and pyramidal cells in the mouse PFC and assess diurnal rhythms in PV cell electrophysiological properties. We find that while core molecular clock genes are conserved and synchronized between cell types, pyramidal cells have nearly twice as many rhythmic transcripts as PV cells (35% vs. 18%). Rhythmic transcripts in pyramidal cells also show a high degree of overlap between sexes, both in terms of which transcripts are rhythmic and in the biological processes associated with them. Conversely, in PV cells, rhythmic transcripts from males and females are largely distinct. Moreover, we find sex-specific effects of phase on action potential properties in PV cells that are eliminated by environmental circadian disruption. Together, this study demonstrates that rhythms in gene expression and electrophysiological properties in the mouse PFC vary by both cell type and sex. Moreover, the biological processes associated with these rhythmic transcripts may provide insight into the unique functions of rhythms in these cells, as well as their selective vulnerabilities to circadian disruption.Significance statementThis is the first study to examine translatomic rhythms in the mouse PFC with cell-type specificity. We find that the core molecular clock cycles in phase across cell types, indicating that previously described daily oscillations in the cortical excitation/inhibition balance are not the consequence of a phase offset between PV and pyramidal cells. Nevertheless, rhythmic transcripts and their associated biological processes differ by both sex and cell type, suggesting that molecular rhythms may play a unique role in different cell types and between sexes. Therefore, our results, such as the enrichment of transcripts associated with mitochondrial function in PV cells from males, point towards possible cell and sex-specific mechanisms that could contribute to psychiatric and cognitive diseases upon rhythm disruption.
Insights into gene conversion and crossing-over processes from long-read sequencing of human, chimpanzee and gorilla testes and sperm
Authors: Porsborg Peter Soerud , Charmouh Anders Poulsen , Singh Vinod Kumar , Winge Sofia Boeg , Hvilsom Christina , Pelizzola Marta , Laurentino Sandra , Neuhaus Nina , Hobolth Asger , Bataillon Thomas , Almstrup Kristian , Besenbacher Søren , Schierup Mikkel Heide 
Published: July 2024

AbstractHomologous recombination rearranges genetic information during meiosis to generate new combinations of variants. Recombination also causes new mutations, affects the GC content of the genome and reduces selective interference. Here, we use HiFi long-read sequencing to directly detect crossover and gene conversion events from switches between the two haplotypes along single HiFi-reads from testis tissue of humans, chimpanzees and gorillas as well as human sperm samples. Furthermore, based on DNA methylation calls, we classify the cellular origin of reads to either somatic or germline cells in the testis tissue. We identify 1692 crossovers and 1032 gene conversions in nine samples and investigate their chromosomal distribution. Crossovers are more telomeric and correlate better with recombination maps than gene conversions. We show a strong concordance between a human double-strand break map and the human samples, but not for the other species, supporting different PRDM9-programmed double-strand break loci. We estimate the average gene conversion tract lengths to be similar and very short in all three species (means 40-100 bp, fitted well by a geometric distribution) and that 95-98% of non-crossover events do not involve tracts intersecting with polymorphism and are therefore not detectable. Finally, we detect a GC bias in the gene conversion of both single and multiple SNVs and show that the GC-biased gene conversion affects SNVs flanking crossover events. This implies that gene conversion events associated with crossover events are much longer (estimated above 500 bp) than those associated with non-crossover events. Highly accurate long-read sequencing combined with the classification of reads to specific cell types provides a new, powerful way to make individual, detailed maps of gene conversion and crossovers for any species.
Transovarial transmission in field caught mosquitoes identifies a mechanism for the establishment of Usutu virus in a temperate country
Authors: Schilling Mirjam , Lawson Becki , Spiro Simon , Jagdev Madhujot , Vaux Alexander G.C. , Bruce Robert C. , Johnston Colin J. , Abbott Anthony J. , Wrigglesworth Ethan , Pearce-Kelly Paul , Cunningham Andrew A. , Medlock Jolyon M. , Johnson Nicholas , Folly Arran J. 
Published: July 2024

AbstractUsutu virus (USUV) is an emerging zoonotic flavivirus in Europe, and the first zoonotic mosquito-borne virus to be confirmed in animal hosts in the United Kingdom (UK). Phylogenetic analysis of USUV in the three years following its initial detection in 2020 indicated that the virus is overwintering in the UK. In 2023, USUV was identified outside Greater London for the first time. Therefore, USUV should now be considered endemic within southeast England. Surveillance of avian hosts and mosquito vectors has been insufficient to elucidate the mechanism by which USUV has persisted through temperate winters. It is likely that mosquitoes play a significant role in facilitating the establishment of USUV in temperate areas, as is the case for related mosquito-borne viruses. Here we undertake enhanced targeted vector surveillance at the index site to investigate the role of mosquitoes in facilitating USUV establishment in the UK.Between 2021 and 2024 inclusive, we detected USUV in host-seeking adult femaleCulex pipienss.l. (n = 8/554 pools), a key vector of the virus in Europe. During 2023, enhanced surveillance detected transovarial transmission of USUV in wildCx. pipienss.l. (n = 1/202 pools), by screening adults following captive rearing of mosquito larvae collected from the field. This is, to our knowledge, the first description of vertical transmission of USUV in an arthropod vector. Consequently, transovarial transmission should be considered a viable mechanism for the persistence of USUV in temperate areas. Our results highlight the importance of undertaking detailed vector surveillance, across life stages, to inform the epidemiology of vector-borne viruses.
A general Bioluminescence Resonance Energy Transfer (BRET) protocol to measure and analyze protein interactions in mammalian cells
Authors: Duval Carla Jane , Steffen Candy Laura , Pavic Karolina , Abankwa Daniel Kwaku 
Published: July 2024

SummaryBioluminescence resonance energy transfer (BRET) allows to quantitate protein interactions in intact cells. Here we provide a step-by-step protocol for measuring BRET due to transient interactions of oncogenic K-RasG12V in plasma membrane nanoclusters of HEK293-EBNA cells. We describe how to seed, transfect and replate cells, followed by their preparation for BRET-measurements on a microplate reader and detailed data analysis steps. For details on how to apply this protocol, please refer to Steffen et al., 20241.Graphical abstract
Glycoengineering with neuraminic acid analogs to label lipooligosaccharides and detect native sialyltransferase activity in Gram-negative bacteria
Authors: Alvarado Melendez Erianna I. , de Jong Hanna , Hartman Jet E. M. , Ong Jun Yang , Wösten Marc M. S. M. , Wennekes Tom 
Published: July 2024

AbstractLipooligosaccharides (LOS) are the most abundant cell surface glycoconjugates on the outer membrane of Gram-negative bacteria. They play important roles in host-microbe interactions. Certain Gram-negative pathogenic bacteria cap their LOS with the sialic acid,N-acetylneuraminic acid (Neu5Ac), to mimic host glycans that among others protects these bacteria from recognition by the hosts immune system. This process of molecular mimicry is not fully understood and remains under investigated. To explore the functional role of sialic acid-capped lipooligosaccharides (LOS) at the molecular level, it is important to have tools readily available for the detection and manipulation of both Neu5Ac on glycoconjugates and the involved sialyltransferases, preferably in live bacteria. We and others have shown that the native sialyltransferases of some Gram-negative bacteria can incorporate extracellular unnatural sialic acid nucleotides onto their LOS. We here report on the expanded use of native bacterial sialyltransferases to incorporate neuraminic acids analogs with a reporter group into the LOS of a variety of Gram-negative bacteria. We show that this approach offers a quick strategy to screen bacteria for the expression of functional sialyltransferases and the ability to use exogenous CMP-Neu5Ac to decorate their glycoconjugates. For selected bacteria we also show this strategy complements two other glycoengineering techniques, Metabolic Oligosaccharide Engineering (MOE) and Selective Exo-Enzymatic Labelling (SEEL), and that together they provide tools to modify, label, detect and visualize sialylation of bacterial LOS.
Glia control experience-dependent plasticity in an olfactory critical period
Authors: Leier Hans C. , Foden Alexander J. , Jindal Darren A. , Wilkov Abigail J. , Costello Paola Van der Linden , Vanderzalm Pamela J. , Coutinho-Budd Jaeda C. , Tabuchi Masashi , Broihier Heather T. 
Published: July 2024

AbstractSensory experience during developmental critical periods has lifelong consequences for circuit function and behavior, but the molecular and cellular mechanisms through which experience causes these changes are not well understood. The Drosophila antennal lobe houses synapses between olfactory sensory neurons (OSNs) and downstream projection neurons (PNs) in stereotyped glomeruli. Many glomeruli exhibit structural plasticity in response to early-life odor exposure, indicating a general sensitivity of the fly olfactory circuitry to early sensory experience. We recently found that glia shape antennal lobe development in young adults, leading us to ask if glia also drive experience-dependent plasticity during this period. Here we define a critical period for structural and functional plasticity of OSN-PN synapses in the ethyl butyrate (EB)-sensitive glomerulus VM7. EB exposure for the first two days post-eclosion drives large-scale reductions in glomerular volume, presynapse number, and post-synaptic activity. Crucially, pruning during the critical period has long-term consequences for circuit function since both OSN-PN synapse number and spontaneous activity of PNs remain persistently decreased following early-life odor exposure. The highly conserved engulfment receptor Draper is required for this critical period plasticity as ensheathing glia upregulate Draper, invade the VM7 glomerulus, and phagocytose OSN presynaptic terminals in response to critical-period EB exposure. Loss of Draper fully suppresses the morphological and physiological consequences of critical period odor exposure, arguing that phagocytic glia engulf intact synaptic terminals. These data demonstrate experience-dependent pruning of synapses and argue that Drosophila olfactory circuitry is a powerful model for defining the function of glia in critical period plasticity.
An adaptor for feedback regulation of heme biosynthesis by the mitochondrial protease CLPXP
Authors: Cottle Thomas , Joh Lydia , Posner Cori , DeCosta Adam , Kardon Julia R. 
Published: July 2024

ABSTRACTHeme biosynthesis is tightly coordinated such that essential heme functions including oxygen transport, respiration, and catalysis are fully supplied without overproducing toxic heme precursors and depleting cellular iron. The initial heme biosynthetic enzyme, ALA synthase (ALAS), exhibits heme-induced degradation that is dependent on the mitochondrial AAA+ protease complex CLPXP, but the mechanism for this negative feedback regulation had not been elucidated. By biochemical reconstitution, we have discovered that POLDIP2 serves as a heme-sensing adaptor protein to deliver ALAS for degradation. Similarly, loss of POLDIP2 strongly impairs ALAS turnover in cells. POLDIP2 directly recognizes heme-bound ALAS to drive assembly of the degradation complex. The C-terminal element of ALAS, truncation of which leads to a form of porphyria (XLDPP), is dispensable for interaction with POLDIP2 but necessary for degradation. Our findings establish the molecular basis for heme-induced degradation of ALAS by CLPXP, establish POLDIP2 as a substrate adaptor for CLPXP, and provide mechanistic insight into two forms of erythropoietic protoporphyria linked to CLPX and ALAS.
Healthcare professionals’ attitudes towards digital health interventions and perspectives on digital health inequalities: a qualitative study
Authors: Ramasawmy Mel , Sunkersing David , Poole Lydia , Blandford Ann , Gill Paramjit , Khunti Kamlesh , Modha Shivali H , Patel Kiran , Potts Henry WW , Sajid Madiha , Khan Nushrat , Banerjee Amitava 
Published: July 2024

AbstractBackgroundUse of Digital Health Interventions (DHIs) for the management of cardiometabolic diseases has increased, but may exacerbate existing health inequalities. Healthcare professionals (HCPs) play a vital role in recommending and supporting patients to use these tools. There is a need to understand the role of HCPs in managing the implementation of digital health in communities at risk of health inequalities.ObjectiveTo explore the views of health care professionals about digital health and its impact on health inequalities, focusing on cardiometabolic diseases and the South Asian population in the UK.MethodsOnline interviews and focus-groups with HCPs (n=18), exploring participants’ experiences and attitudes towards digital health, perceptions of patients’ barriers and facilitators to use, whether they perceived any populations to be particularly at risk of digital inequalities, and the impact of the COVID-19 pandemic on their practice in relation to digital health. After informed consent, transcription and coding, a reflexive thematic approach was taken to analysis.ResultsHCPs recognised the potential benefits of DHIs to improve access and delivery of care and patient outcomes, but described several barriers to successful implementation. HCPs demonstrated a good understanding of the challenges their patients face in relation to wider inequalities, barriers to health behaviours and healthcare access, and digital health. Of particular concern was the impact of increasing reliance of digital interventions in health care on the exclusion of some patient groups. Participants recommended improvement of the design and implementation of DHIs offered to patients through working with at-risk populations throughout the process. Finally, participants emphasised the importance of ensuring non-digital services remained available to ensure equitable access to health and social care.ConclusionsHCPs described the complexities of delivering care to underserved communities. DHIs were identified as a potential way to improve health outcomes for some, while over-reliance risked exacerbating inequalities. Participant recommendations related to design, implementation, and engaging target populations providing practical examples to address digital health inequalities, such as working with other sectors to take a community approach.
How a year of pandemic and related public health measures impacted youth and young adults and the foundations they build upon: Qualitative interviews in Ontario Canada
Authors: Austin Laurel C. , Gomes Makayla Nunes , Chavez Sebastian , Degano Celina 
Published: July 2024

AbstractIntroductionDuring youth and young adult (YYA) years education, employment, relationships with family and friends, and important rituals representing transition to new phases of life are foundations on which personal identity and future well-being are established. These were shaken by the COVID-19 pandemic. We explore how Ontario YYAs and the foundations they build upon (education, employment, relationships, transitional events) were impacted by over a year of pandemic and public health responses to prevent spread.MethodsIn-depth semi-structured interviews with 19 Ontario YYAs age 16-21 were conducted during April - June 2021. Reflexive thematic analysis aided by MAXQDA software was used to iteratively engage with data to search for patterns and shared meaning.ResultsThirteen themes were identified, organized into four meta-themes: impacts on self, impacts on foundations (educational, employment, transitional events/rituals), impacts on relationships, and coping responses. Many, especially those living with loved ones believed to risk a fatal outcome from COVID-19, felt the weight of needing to avoid the virus to protect loved ones. YYAs who were in their last year of secondary school in spring 2020 or 2021 missed important transitional endings, e.g., graduation. Those graduating in 2020 and going on to post-secondary school also missed transitional beginnings, e.g., experiencing in-person on-campus higher education classrooms, living in residence, and meeting new friends. Perceived negative impacts on education quality and professional development were common. Virtual learning models and changes to in-person schooling, hastily introduced and evolving over the next year, did not measure up to traditional learning models.ConclusionsAll of these impacts took a toll. Respondents routinely volunteered concerns about stress, loneliness, and their mental health. There is need for further research to assess long-term impacts of these experiences, especially among YYAs who had family members at severe risk, and those finishing secondary school in spring of 2020.
Co-option of mitochondrial nucleic acid sensing pathways by HSV-1 UL12.5 for reactivation from latent Infection
Authors: Cuddy Sean R. , Flores Matthew E. , Krakowiak Patryk A. , Whitford Abigail L. , Dochnal Sara A. , Babnis Aleksandra , Miyake Tsuyoshi , Tigano Marco , Engel Daniel A. , Cliffe Anna. R 
Published: July 2024

SummaryAlthough viruses subvert innate immune pathways for their replication, there is evidence they can also co-opt anti-viral responses for their benefit. The ubiquitous human pathogen, Herpes Simplex Virus-1 (HSV-1), encodes a protein (UL12.5) that induces the release of mitochondrial nucleic acid into the cytosol, which activates immune sensing pathways and reduces productive replication in non-neuronal cells. HSV-1 establishes latency in neurons and can reactivate to cause disease. We found that UL12.5 is required for HSV-1 reactivation in neurons and acts to directly promote viral lytic gene expression during initial exit from latency. Further, the direct activation of innate immune sensing pathways triggered HSV reactivation and compensated for a lack of UL12.5. Finally, we found that the induction of HSV-1 lytic genes during reactivation required intact RNA and DNA sensing pathways, demonstrating that HSV-1 can both respond to and active antiviral nucleic acid sensing pathways to reactivate from a latent infection.
Interspecies interaction reshapes the fitness landscape of evolved genotypes
Authors: Sun Xinli , Xu Zhihui , Hu Guohai , Xie Jiyu , Li Yun , Tao Lili , Zhang Nan , Xun Weibing , Miao Youzhi , Zhang Ruifu , Shen Qirong , Kovács Ákos T. 
Published: July 2024

AbstractMicrobial interaction and their evolution is vital for shaping the structure and function of microbial communities. However, the mechanisms governing the directionality and stability of the evolution of interactions within microbial communities remain poorly understood. Here, we used a syntrophic two-species biofilm consortium composed ofBacillus velezensisSQR9 andPseudomonas stutzeriXL272 that promotes plant growth through their metabolic interactions and investigated how the interactions within the consortium change over evolutionary timescale to characterize the phenotypic and genetic diversification. The focal speciesB. velezensisSQR9 rapidly diversified into diverse colony morphotypes, both in the presence and absence of its interactor,P. stutzeriXL272, with variable frequencies. These morphotypes displayed phenotypic differentiation among biofilm formation, planktonic growth, and spore formation. The evolvedP. stutzerialtered the fitness landscape ofB. velezensismorphotypes, allowing the weaker rough morphotype to outcompete the biofilm-enhanced slimy morphotype. Whole genome re-sequencing correlated these phenotypic changes with mutations in specific genes encoding regulators ofB. velezensis, includingywcC,comA,comP,degS,degQandspo0F. The coevolutionary partner,P. stutzeriincreased its exopolysaccharide production that could be explained by a frame shift mutation incpsAgene encoding capsular polysaccharide (CPS) biosynthesis protein. Compared with the mono-evolution, co-evolvedB. velezensispopulations showed greater mutation accumulation in intergenic regions, which led to greater genetic parallelism. Furthermore, the dissimilarity between mono-evolved and co-evolved populations increased over time. Our study reveals intricate genetic diversification and fitness differentiation within a biofilm consortium, shaped by both abiotic conditions and biotic interactions.