bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole-genome re-sequencing of the Baikal seal and other phocid seals for a glimpse into their genetic diversity, demographic history, and phylogeny
Authors: Nebenführ Marcel , Arnason Ulfur , Janke Axel
Published: October 2024

Background

The iconic Baikal seal (Pusa sibirica), the smallest true seal, is a freshwater seal that is endemic to Lake Baikal where it became landlocked some million years ago. It is a rather abundant species of least concern, despite the limited habitat. Until recently, research on its genetic diversity has only been done on mitochondrial genes, restriction fragment analyses, and microsatellites, before its reference genome has been published.

Findings

Here we report the genome sequences of six Baikal seals, and one individual of the Caspian seal, ringed seal, and the harbor seal, re-sequenced from Illumina paired-end short read data. Heterozygosity calculations of the six newly sequenced individuals are like the previously reported genomes. In addition, the novel genome data of the other species contributed to a more complete phocid seal phylogeny based on whole-genome data.

Conclusions

Despite the long isolation of the land-locked Baikal seal population, the genetic diversity of this species is in the same range as other seal species. The Baikal seal appears to form a single, diverse population. However, targeted genome studies are needed to explore the genomic diversity throughout their distribution.
Global, Regional, and National Burdens of Ischemic Stroke Attributed to High Body-mass Index from 1990 to 2021
Authors: Zhang Yuan , Ren Xuesong , Zhao Xiaofeng , Meng Lina , Lu Hai , Zhang Chunhong
Published: October 2024

Background

Ischemic stroke (IS) is a significant contributor to the global disease burden, with overweight/obesity recognized as one of the primary risk factors. This study aims to evaluate the distribution and changes in the global burden of IS attributable to high body-mass index (BMI) from 1990 to 2021, providing a foundation for the development of targeted prevention and treatment strategies.

Methods

Based on the modeling strategies of the 2021 global burden of disease (GBD) dataset, the burden of IS attributable to high BMI was estimated. The assessment covered the global disease burden and its distribution by region, country, development level, age group, and gender, as well as temporal trends. Age-standardized rates, along with the estimated annual percentage change (EAPC) in these rates, were utilized to describe this burden and its evolving trends. Locally estimated scatterplot smoothing (LOESS) regression was employed to analyze the trends of disease burden in relation to changes in socio-demographic index (SDI).

Results

From 1990 to 2021, although the age-standardized death rate and disability-adjusted life years (DALY) rate for IS attributable to high BMI have declined globally, the absolute number of deaths and DALYs nearly doubled, reaching 172,390.65 (95% UI, 347,912.75 to 25,064.57) and 4,439,186.31 (95% UI, 8,647,485.11 to 649,030.21) respectively. Meanwhile, significant disparities in disease burden existed across different regions, genders, and age groups. In high-middle SDI regions, the burden of IS caused by high BMI significantly exceeded that in other regions, while in low-income areas, this burden was rapidly increasing. Additionally, the increase in burden among men was significantly greater than that among women, and the previously concentrated burden in the elderly is now rapidly shifting toward younger groups.

Conclusions

The overweight and obese populations continue to present significant challenges in managing the burden of IS. In light of future population growth and aging trends, more effective stroke prevention strategies and practical solutions are urgently needed, particularly in low- and middle-income countries. Additionally, given the increasing disease burden among men and younger populations, it is essential to establish targeted preventive measures to address the specific needs of different groups and improve overall health outcomes.
Connectomic Organization of the Suprachiasmatic Nucleus
Authors: Liu Jing , Yu Jing , Shen Lijun , Chen Xi , Ma Lei , Zhai Hao , Li Linlin , Zhang Lina , Wang Lu , Yuan Jingbin , Chen Bohao , Hong Bei , Liu Jiazheng , Lv Yanan , Cai Yu , Zhang Yanchao , Chang Sheng , Guo Jinyue , Chen Haoran , Liu Mianzhi , Wang Zichen , Xin Tong , Zhou Fangxu , Zhao Xinghui , Zhang Dandan , Xie Qiwei , Ma Hongtu , Xu Ying , Cheng Heping , Han Hua
Published: October 2024

The suprachiasmatic nucleus (SCN), the mammalian master clock, is a special structure dedicated to the time computation. However, a connectomic understanding of the nucleus as a whole is lacking. Using serial section electron microscopy, we reconstructed multiscale and multimodal SCN communication networks. Intra-SCN synaptic network consists of 9,566 morphologically similar neurons and 4.3 million synapses, organized into multiscale circuitries that interact with SCN-traversing axon fascicles. Strikingly, SCN neurons engage in unique soma-soma ephaptic interaction, forming 2,038 electrotonic integrative units with the largest overlapping the light-responsive area (LRA). SCN’s paracrine modality contains 47,396 μm3dense core vesicles, with notable scarcity in the LRA, suggesting cross-modal coordination and functional integration. These distinct network features provide comprehensive insights into the system architecture of the mammalian circadian clock.
The Zoonotic Potential of Poultry-Associated Nitrofurantoin-ResistantEscherichia coli
Authors: Sealey Jordan E , Astley Beth , Avison Matthew B
Published: October 2024

Escherichia coliis the most common cause of urinary tract infection (UTI) in humans. Nitrofurantoin is the most frequent UTI therapy in the United Kingdom. Here we identify poultry as a potential zoonotic reservoir of nitrofurantoin resistant (NFT-R) and pre-resistant (one mutation away from NFT-R)E. coli. We found NFT-RE. coliexcreted by dogs fed a raw meat diet, as well as NFT-R and pre-resistantE. colicontaminating chicken meat sold for human consumption and chicken-based raw dog food. By whole genome sequence analysis, with reference to additional data from public repositories, we identified NFT-R or pre-resistantE. coliclones. These were ST919/8874, ST665, ST6805, ST69, ST752 and ST7529, which were dominated by isolates from poultry sources in Europe, though the ST752 clone is globally disseminated. Five of these clones included isolates from human clinical samples, of which several were confirmed urinary isolates. Our findings have important implications for public health and domestic hygiene, particularly for people being treated for UTI. They also increase concerns about the roles of raw-fed dogs as vectors for the entry of resistantE. coliinto the home. It is likely that nitrofuran use in poultry production was the initial driver for the emergence of NFT-R on poultry farms. Therefore, whilst NFT-RE. colisample-level positivity in poultry meat was far lower than resistance to more recently used fluoroquinolones, NFT-R and pre-resistantE. coliappear to have persisted among poultry flocks despite 30 years of zero legal use in Europe.
Hijacking and Integration of Algal Plastids and Mitochondria in a Polar Planktonic Host
Authors: Rao Ananya Kedige , Yee Daniel , Chevalier Fabien , LeKieffre Charlotte , Pavie Marie , Olivetta Marine , Dudin Omaya , Gallet Benoit , Hehenberger Elisabeth , Seifi Mehdi , Jug Florian , Deschamps Joran , Wu Ting-Di , Gast Rebecca , Jouneau Pierre-Henri , Decelle Johan
Published: October 2024

In oceanic plankton, various host organisms are capable of engulfing and temporarily integrating microalgae (photosymbiosis) or just their photosynthetic plastids (kleptoplastidy) as a solar-powered energy source. These cellular interactions can be considered to be representative of evolutionary steps in plastid acquisition in eukaryotes, but the underlying cellular mechanisms and dynamics are not fully understood. Here, we studied a kleptoplastidic dinoflagellate (RSD: Ross Sea Dinoflagellate), which is known to steal plastids of the microalgaPhaeocystis antarctica. We tracked the morphology and activity of stolen plastids over several months by combining multimodal subcellular imaging and photophysiology. Upon integration inside a host vacuole, the volume of plastids and pyrenoids significantly increased and photosynthetic activity was boosted along with carbon fixation and transfer to the host. This may be supported by the retention of a 50-fold larger algal nucleus for ∼1 week. Once the algal nucleus was lost, there was a decrease in plastid volume and photosynthesis, but plastids were still beneficial for the host after > 2 months. Unlike other kleptoplastidic interactions, we showed that the algal mitochondrion was also stolen and retained for several months, transforming into an extensive network in close proximity with plastids. This highlights a new strategy in plankton along the continuum of plastid symbioses where both the energy-producing plastid and mitochondrion of a microalga are hijacked for several months by a host. This symbiosis that we found to be widely-distributed in polar regions suggests that plastid-mitochondrion interaction may have played a role in the evolution of plastid acquisition.
Genetic differentiation is constrained to chromosomal inversions and putative centromeres in locally adapted populations with higher gene flow
Authors: Akopyan Maria , Tigano Anna , Jacobs Arne , Wilder Aryn P. , Therkildsen Nina O.
Published: October 2024

The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes in shaping genetic diversity across genomes and among populations. This is particularly relevant when local adaptation occurs despite gene flow, where clustering of differentiated loci can maintain locally adapted variants by reducing recombination between them. However, the limited genomic resources for non-model species, including reference genomes and recombination maps, has constrained our understanding of these patterns. In this study, we leverage the Atlantic silverside—a non-model fish with extensive local adaptation across a steep latitudinal gradient—as an ideal system to explore how genome structure influences adaptation under varying levels of gene flow, using a newly available reference genome and multiple recombination maps. Analyzing 168 genomes from four populations, we found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. With increasing gene flow, the number and clustering of FSToutlier loci also increased, with differentiated loci tightly clustered in large haploblocks harboring inversions and smaller peaks overlapping putative centromeres. Notably, sequence divergence was only evident in inversions, supporting their role in adaptive divergence with gene flow, whereas centromeres appeared differentiated because of low recombination and reduced diversity, with no indication of elevated sequence divergence. Our results support the hypothesis that clustered genomic architectures evolve with high gene flow and enhance our understanding of how inversions and centromeres are linked to different evolutionary processes.

Significance Statement

How populations preserve favorable combinations of genes adapted to their local environment despite reproducing with populations adapted to different conditions is a longstanding question in evolutionary biology. By analyzing the genomes of 168 Atlantic silverside fish from four populations, we found that when populations adapted to different environments frequently interbreed, genetic differences concentrate in specific parts of the genome, particularly in chromosomal inversions—where segments of DNA are flipped. These inversions help preserve locally adapted gene combinations, enabling populations to maintain differences essential for survival in their habitats. This research enhances our understanding of genomic adaptation, a fundamental evolutionary question with increasing relevance as environmental changes pose new challenges globally.
Outpatient Portal Use and Blood Pressure Management during Pregnancy
Authors: Stamos Athena , Fareed Naleef
Published: October 2024

We investigated the association between systole and diastole, and outpatient portal use during pregnancy. We used electronic and administrative data from our academic medical center. We categorized patients into two groups: (<140 mm Hg; <90 mm Hg), and out-of-range (≥140 mm Hg, ≥ 90 mm Hg). Random effects linear regression models examined the association between mean trimester blood pressure (BP) levels and portal use, adjusting for covariates. As portal use increased, both systole and diastole levels decreased for the out-of-range group. These differences were statistically significant for patients who were initially out-of-range. For the in-range group, systole and diastole levels were stable as portal use increased. Results provide evidence to support a relationship between outpatient portal use and BP outcomes during pregnancy. More research is needed to expand on our findings, especially those focused on the implementation and design of outpatient portals for pregnancy.
Bifidobacterium animalis subsp. lactisBL-11 Promotes Height Growth in Children Aged 3-7 Years: A Self-controlled Cohort Study
Authors: Wang Qian , Yang Yanan , Xiao Yin , Liu Ziyi , Li Mingxi , Yu Yue , Wang Nannan , Li Junyan , Li Xiaohui , Xu Chuanhui , Liu Deyun , Wu Chongming
Published: October 2024

Background

Short status of children has captured extensive attention since it reflects the health status of children and affects physical and psychological health throughout children’s life. Compelling evidences have revealed that gut microbiota participates in the skeletal development directly or indirectly. Currently, the calcium agent and growth hormone-like drugs have provided potential opportunities to promote growth and development among children, yet limited trials existed with probiotic intake as a primary strategy.

Objectives

Present cohort study was designed to evaluate the height-promoting effect of gut probioticBifidobacterium animalis subsp. lactisBL-11 among 3-7 years old children. Registered underClinicalTrials.govIdentifier no. ChiCTR2400089723.

Methods

This study was conducted with Chinese children aged 3 to 7 years (n = 124) who fall between the 3rd and 25th percentiles (P3-P25) for height, and whose annual growth rate in height is less than 5 cm. TheBifidobacterium animalis subsp. lactisBL-11 oiling agent were taken every day with total live bacteria ≥ 30 billion. The height of each participant was measured and recorded before and after three-monthsBifidobacterium animalis subsp. lactisBL-11 intervention.

Results

Bifidobacterium animalis subsp. lactisBL-11 could strikingly promote the height growth of children, and shift the height percentile rage from P3-P10 to P10-P25. Importantly, this promoting effect has no specificity between age and sex. Comparatively, children with shorter height (P3-P10) were more sensitive toBifidobacterium animalis subsp. lactisBL-11.

Conclusions

Administration ofBifidobacterium animalis subsp. lactisBL-11 as early as possible is in favor of the child’s growth and development, which provided a strategy for pediatricians to address some plights that how to promote children’s growth effectively and safely.
Insights into the Structural Regulation of Polo-Like Kinase Activity using AlphaFold
Authors: Wyatt Michael D. , McInnes Campbell
Published: October 2024

The Polo Like Kinases including the major family member, PLK1 are key regulatory enzymes controlling the cell cycle and mitosis. PLK1 is associated with poor survival rates in cancer and has been extensively investigated as an oncology drug target. Each member of the Polo like kinase family (PLKs 1-5) have two subdomains with independent functions and include the well conserved N-terminal kinase domain (KD) and the C-terminal polobox domain (PBD). The PBD is involved in the recognition of substrates primed by other kinases and in the PLK1 context is responsible for subcellular localization to specific sites in the nucleus including centrosomes and kinetochores. While the phosphosubstrate recognition site in PLKs 1-3 is highly conserved, its role in PLKs 2 and 3 is not well characterized and phosphopeptides that inhibit PLK1 have dramatically lower affinity for PLKs 2 and 3. An additional role of the PBD is its ability through domain-domain interactions with the KD to regulate PLK1 activity by an autoinhibited state of PLK1, conceptually similar to that which occurs through other kinases. Other mechanisms regulating PLK activity include the interchange between monomeric and dimeric forms, which inhibit or activate PLK1 during the cell cycle. Furthermore, PLK1 may exist as heterodimers with PLK2 and/or PLK3 and thus play context dependent roles. Here, through the use of the AlphaFold (AF) algorithm, structural insights into regulation of activity of the PLK1 and other family members have been obtained. These include dramatically different tertiary arrangement of the individual domains in each individual PLK. Analysis of the domain-domain interactions, interdomain and intradomain loops in each PLK sheds light onto plausible mechanisms by which the activity of each PLK is regulated and provides insights into the selectivity of phosphopeptides. The results also suggest a mechanism for the heterodimerization of PLK1 and PLK2 which has been observed in the literature.
Fatty acid desaturases link cell metabolism pathways to promote proliferation of Epstein-Barr virus-infected B cells
Authors: Bonglack Emmanuela N. , Hill Kaeden K. , Barry Ashley P. , Bartlett Alexandria , Castellano-Escuder Pol , Hirschey Matthew D. , Luftig Micah A.
Published: October 2024

Epstein-Barr virus (EBV) is a gamma herpesvirus that infects up to 95% of the human population by adulthood, typically remaining latent in the host memory B cell pool. In immunocompromised individuals, EBV can drive the transformation and rapid proliferation of infected B cells, ultimately resulting in neoplasia. The same transformation process can be inducedin vitro, with EBV-infected peripheral blood mononuclear cells (PBMCs) forming immortalized lymphoblastoid cell lines (LCLs) within weeks. In this study, we found that the fatty acid desaturases stearoyl-CoA desaturase 1 (SCD1) and fatty acid desaturase 2 (FADS2) are upregulated by EBV, and crucial for EBV-induced B cell proliferation. Additionally, we found that pharmacological and genetic inhibition of both SCD1 and FADS2 results in a significantly greater reduction in proliferation and cell cycle arrest, compared to perturbing either enzyme individually. Additionally, we found that inhibiting either SCD1 or FADS2 alone hypersensitizes LCLs to palmitate-induced apoptosis, recapitulating studies in other tissue types. Further lipidomic and metabolic analysis of dual SCD1/FADS2-inhibited LCLs revealed an increase in free unsaturated fatty acids, a reduction of oxidative phosphorylation, and a reduction of glycolysis, thereby linking the activity of SCD1 and FADS2 to overall growth-promoting metabolism. Lastly, we show that SCD1 and FADS2 are important in the growth of clinically derived EBV+ immunoblastic lymphoma cells. Collectively, these data demonstrate a previously uncharacterized role of lipid desaturation in EBV+ transformed B cell proliferation, revealing a metabolic pathway that can be targeted in future anti-lymphoma therapies.
Investigating the barley methylome, its variation and association with genomic, transcriptomic, and phenotypic variation
Authors: Kühl Marius , Wu Po-Ya , Shrestha Asis , Engelhorn Julia , Hartwig Thomas , Stich Benjamin
Published: October 2024

Epigenetic variation contributes to explaining the missing heritability of complex traits. In order to understand the genome-wide methylation variation in spring barley, our objectives were to gain fundamental insight into the barley methylome through whole genome bisulfite sequencing, characterizing methylation variation among 23 parental inbreds of a community resource for genetic mapping of phenotypic traits, and assessing the association of differentially methylated regions (DMRs) with single nucleotide polymorphisms (SNPs) and gene expression variation. Compared to other angiosperms, barley was found to have a highly methylated genome with an average genome wide methylation level of 88.6%, 58.1%, and 1.4% in the CpG, CHG, and CHH sequence context, respectively. We identified just below 500 000 differentially methylated regions (DMRs) among the inbreds. About 64%, 64%, and 83% of the DMRs were not associated with genomic variation in the CpG, CHG, and CHH context, respectively. The methylation level of around 6% of all DMRs was significantly associated with gene expression, where the directionality of the correlation was depended on the relative location of the DMR to the respective gene with a recognizable pattern. Notably, this pattern was much more specific and spatially confined than the association of methylation with gene expression across genes in a singular inbred line. We exemplified this association between DNA methylation and gene expression on the known flowering promoting geneVRN-H1and identified a highly methylated epiallele associated with earlier flowering time. Finally, methylation was shown to improve the prediction abilities of genomic prediction models for a variety of traits over models using solely SNPs and gene expression as predictors. These observations highlight the independence of DNA methylation to sequence variation and their difference in information content. Our discoveries suggest that epigenetic variation provides a layer of information likely not predictable by other means and is therefore a valuable addition to genomic prediction models.
Scrutinized lipid utilization disrupts Amphotericin-B responsiveness in clinical isolates ofLeishmania donovani
Authors: Pradhan Supratim , Dhar Dhruba , Manna Debolina , Chakraborty Shubhangi , Bhattacharyya Arkapriya , Chauhan Khushi , Mukherjee Rimi , Sen Abhik , Pandey Krishna , Das Soumen , Mukherjee Budhaditya
Published: October 2024

The management ofLeishmania donovani (LD), responsible for fatal visceral leishmaniasis (VL), faces increasing challenges due to rising drug-unresponsiveness, leading to increasing treatment failures. While hypolipidemia characterizes VL, LD, a cholesterol auxotroph, relies on host lipid scavenging for its intracellular survival. The aggressive pathology, in terms of increased organ parasite load, observed in hosts infected with antimony-unresponsive-LD (LD-R) as compared to their sensitive counterparts (LD-S), highlights LD-R’s heightened reliance on host lipids. Here we report that LD-R-infection promotes fluid-phase endocytosis in the host, selectively accumulating neutral lipids while excluding oxidized-LDL. LD-R enhances the fusion of endocytosed LDL- vesicles with its phagolysosomal membrane and inhibits cholesterol mobilization from these vesicles by suppressing NPC-1. This provides LD-R amastigotes with excess lipids, supporting their rapid proliferation and membrane synthesis. This excess LDL-influx leads to an eventual accumulation of neutral lipid droplets around LD-R amastigotes, thereby increasing their unresponsiveness towards Amphotericin-B, a second-line amphiphilic antileishmanial. Notably, VL patients showing relapse with Amphotericin-B treatment exhibited significantly lower serum LDL and cholesterol than cured cases. Treatment with Aspirin, a lipid droplet blocker, reduced lipid droplets around LD-R amastigotes, restoring Amphotericin-B responsiveness.
This is SPRTA: assessing phylogenetic confidence at pandemic scales
Authors: De Maio Nicola , Ly-Trong Nhan , Minh Bui Quang , Goldman Nick
Published: October 2024

Phylogenetics plays a central role in evolutionary biology and genomic epidemiology. Assessing phylogenetic confidence and reliability is therefore crucial and methods to do this, such as Felsenstein’s bootstrap, are among the most used in modern science. However, methods based on Felsenstein’s bootstrap suffer from excessive computational demand, and are unsuitable for large datasets. Furthermore, most of these methods emerge from a cladistic framework which makes their results hard to interpret in the context of genomic epidemiology.

We propose SPRTA (“ SPR-based Tree Assessment”), an efficient and interpretable approach to assess confidence in phylogenetic trees. SPRTA shifts the paradigm of phylogenetic support measurement from evaluating the confidence in clades (groupings of taxa) to genome evolution histories, for example assessing if a lineage evolved from another considered lineage or not. This focus on evolutionary histories is particularly valuable in genomic epidemiology, where typically the evolutionary and transmission history of a pathogen are of interest, not clade content.

We illustrate the use of SPRTA by investigating a global SARS-CoV-2 phylogenetic tree relating>2M genomes, highlighting plausible alternative evolutionary origins of many SARS-CoV-2 variants. We have implemented SPRTA within the free and open source maximum likelihood phylogenetic software MAPLE, available fromhttps://github.com/NicolaDM/MAPLE.
Crystallographic and NMR studies of Streptococcus pneumonia LCP protein PsrSpindicate the importance of dynamics in four long loops for ligand specificity
Authors: Sandalova Tatyana , Sala Benedetta Maria , Moche Martin , Ljunggren Hans-Gustaf , Alici Evren , Henriques-Normark Birgitta , Agback Tatiana , Lesovoy Dmitry , Agback Peter , Achour Adnane
Published: October 2024

The crystal structure of the extracellular region of the second pneumococcal LCP, a polyisoprenyl-teichoic acid-peptidoglycan teichoic acid transferase PsrSp, was determined and refined to 2.15Å resolution. Despite the low sequence homology with other LCP proteins, the PsrSpmaintains the fold of the LCP domain and the positions of the 15 residues suggested to participate in the transferase function are conserved. The empty tunnel found in the PsrSpbetween the central β-sheet and three α-helices is wide enough to accommodate polyisoprenyl-teichoic acid. Comparison of the crystallographic temperature factors of LCP from distinct bacteria demonstrated that the four long loops located close to the teichoic acid and peptidoglycan binding sites have different relative mobility. To compare the dynamics of the PsrSpin crystalline state and in solution, NMR spectra were recorded, and 88% of the residues were assigned in the1H-15N TROSY HSQC spectra. Comparison of the secondary structure of the crystal structure of PsrSpwith NMR data demonstrated a perfect concordance between the results using these two methods. Moreover, the relative mobility of the essential loops estimated from the crystallographic B-factor is in good agreement with order parameter S2, predicted from chemical shift. We hypothesize that the dynamics of these loops are important for the substrate promiscuity of LCP proteins.
Engineered Bxb1 variants improve integrase activity and fidelity
Authors: Rose Joshua , Kim Hyaeyeong , Von Stetina Jessica , Thangavelu Mahant , Conway Hasahn , O'Hara Mollie S , Hanna Patrick , Biondi Thomas , Dunyak Maike Thamsen , Finn Jonathan D , Kumar Sandeep , Cochrane Jesse C
Published: October 2024

Many current genome editing technologies rely on the action of large serine integrases (LSIs) to insert gene-sized DNA sequences into the genome. Bxb1 is the most commonly used LSI for therapeutic efforts, including PASTE, PASSIGE and I-PGI. While Bxb1 demonstrated good activity in vitro in cycling cells, the activity in non-dividing hepatocytes was significantly less efficient. Further, wild-type Bxb1 is known to have detectable off-target activity at cryptic genomic sites, which presents a potential safety risk for therapeutic development. To address these issues, we developed Bxb1 variants that demonstrate increased specificity and potency in vitro and have engineered stabilized Bxb1 variants that increase in vivo activity over 25-fold enabling targeted integration at therapeutically relevant levels.
Computational redesign of TALE proteins for DNA-templated assembly of protein fibers
Authors: de Haas Robbert J. , Langowski Mark D. , Borst Andrew J. , Pillai Visakh V. S. , Hoffmann Gwendolyn E. , Bongers Martin , Cheng Suna , Treichel Catherine , Leaf Elizabeth M. , Wu Mengyu , Lynch Eric M. , Kollman Justin M. , Ruggeri Francesco S. , Walkey Carl , de Vries Renko , King Neil P.
Published: October 2024

Many viral proteins self-assemble into capsid structures, often using their genetic material as a template for assembly. To date,de novodesigned capsid-like proteins do not require genetic material as a template for assembly, which can be both an advantage and a disadvantage depending on the use case. Templates are indispensable, for example, in the assembly of linear structures with well-defined lengths. As a first step towards fullyde novodesigned templated assembly, here we redesign proteins from the Transcription activator-like effector (TALE) family of transcriptional regulators to polymerize on double-stranded DNA (dsDNA) templates. Starting from natural TALE protein sequences, we created idealized repeat proteins with sequence-independent DNA binding properties that cooperatively self-assemble to form linear protein-DNA complexes with template-controlled lengths. We used high-resolution atomic force microscopy (AFM) and cryo electron microscopy (cryo-EM) to characterize the three-dimensional structures of the DNA-protein hybrid complexes. In these structures, a protein filament helically wraps around the dsDNA using a binding mode similar to that of natural TALE proteins. As an example application of these materials, we show the system can be used for repetitive peptide antigen display at precisely controlled repeat distances, and that such immunogens elicit robust antigen-specific antibodies in mice.
An all-in-one pipeline for thein vitrodiscovery andin vivotesting ofPlasmodium falciparummalaria transmission blocking drugs
Authors: Brancucci Nicolas M. B. , Gumpp Christin , van Gemert Geert-Jan , Yu Xiao , Passecker Armin , Nardella Flore , Thommen Basil T. , Chambon Marc , Turcatti Gerardo , Halby Ludovic , Blasco Benjamin , Duffey Maëlle , Arimondo Paola B. , Bousema Teun , Scherf Artur , Leroy Didier , Kooij Taco W. A. , Rottmann Matthias , Voss Till S.
Published: October 2024

Elimination and eradication of malaria will depend on new drugs with potent activity againstPlasmodium falciparummature stage V gametocytes, the only stages able to infect the mosquito vector for onward parasite transmission. The identification of molecules active against these quiescent stages is difficult due to the specific biology of gametocyte maturation and challenges linked to their cultivationin vitro. Furthermore, the antimalarial drug development pipeline lacks a suitable animal model for evaluating the transmission-blocking potential of promising lead compounds and preclinical and clinical drug candidatesin vivo. Here, we established a transmission-blocking drug discovery and development platform based on transgenicP. falciparumparasites engineered to produce large numbers of pure stage V gametocytes expressing a red-shifted firefly luciferase as reporter for cellular viability. This NF54/iGP1_RE9Hulg8line facilitated the development of a highly efficient and robustin vitroscreening assay for the identification of stage V gametocytocidal compounds. Importantly, by infecting humanized NODscidIL2Rγnullmice with pure NF54/iGP1_RE9Hulg8stage V gametocytes, we also established a preclinicalP. falciparum in vivotransmission model. Using whole animal bioluminescence imaging and quantification of gametocyte densities over a period of 14 days, we assessed the gametocyte killing and clearance kineticsin vivoof antimalarial reference drugs as well as five clinical drug candidates and identified markedly different pharmacodynamic response profiles. Furthermore, we successfully integrated this mouse model with mosquito feeding assays and thus firmly established a valuable tool for the systematicin vivoevaluation of gametocytocidal and transmission-blocking drug efficacy.

One sentence summary

We applied robust new assays for gametocytocidal drug discovery andin vivoefficacy testing using a humanized mouse model for malaria transmission
DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria
Authors: Dalia Triana N. , Machouri Mérick , Lacrouts Céline , Fauconnet Yoann , Guerois Raphaël , Andreani Jessica , Radicella J. Pablo , Dalia Ankur B.
Published: October 2024

Natural transformation (NT) represents one of the major modes of horizontal gene transfer in bacterial species. During NT, cells can take up free DNA from the environment and integrate it into their genome by homologous recombination. While NT has been studied for >90 years, the molecular details underlying this recombination remain poorly understood. Recent work has demonstrated that ComM is an NT-specific hexameric helicase that promotes recombinational branch migration in Gram-negative bacteria. How ComM is loaded onto the post-synaptic recombination intermediate during NT, however, remains unclear. Another NT-specific recombination mediator protein that is ubiquitously conserved in both Gram-positive and Gram-negative bacteria is DprA. Here, we uncover that DprA homologs in Gram-negative species contain a C-terminal winged helix domain that is predicted to interact with ComM by AlphaFold. UsingHelicobacter pyloriandVibrio choleraeas model systems, we demonstrate that ComM directly interacts with the DprA winged-helix domain, and that this interaction is critical for DprA to recruit ComM to the recombination site to promote branch migration during NT. These results advance our molecular understanding of recombination during this conserved mode of horizontal gene transfer. Furthermore, they demonstrate how structural modeling can help uncover unexpected interactions between well-studied proteins to provide deep mechanistic insight into the molecular coordination required for their activity.

SIGNIFICANCE STATEMENT

Bacteria can acquire novel traits like antibiotic resistance and virulence through horizontal gene transfer by natural transformation. During this process, cells take up free DNA from the environment and integrate it into their genome by homologous recombination. Many of the molecular details underlying this process, however, remain incompletely understood. In this study, we identify a new protein-protein interaction between ComM and DprA, two factors that promote homologous recombination during natural transformation in Gram-negative species. Through a combination of bioinformatics, structural modeling, cell biological assays, and complementary genetic approaches, we demonstrate that this interaction is required for DprA to recruit ComM to the site of homologous recombination.
High Throughput Viral Enumeration of Aquatic Ecosystems via Flow Cytometry
Authors: Bellanger Madeline , Visscher Pieter T , White Richard Allen
Published: October 2024

For the past 25 years, flow cytometry has been a gold standard for the direct measurement of viral-like particles (VLP) in aquatic ecosystems. Flow cytometry allows for higher throughput and costs less than alternative enumeration methods, leading to its broad usage in aquatic viral ecology. A major challenge associated with flow cytometry is the degradation of VLPs over time, making the use of high throughput plates not possible, thus lowering overall throughput. It has also been difficult to maintain a method with low contamination, high signal-to-noise ratios, and observations of real VLPs vs. fake particles. For these reasons, the use of flow cytometry has rapidly declined over the years due to the advent of massively parallel sequencing. Here, we describe a high throughput method in a 96 well plate format that provides a hands-free approach to viral enumeration. Our approach limits fake particles, noise levels, and cross-sample contamination. In a standard run, 60 samples can be measured for VLPs within 2.25 hours, which is ∼1 hour faster than the standard single tube approach and ∼1.5 hours faster than epifluorescence microscopy (EFM). Direct measurement of VLPs still provides a window into the viral-host interactions within aquatic ecosystems, which can be rapidly measured and resolved in a high throughput manner.
Opto2P-FCM: A MEMS based miniature two-photon microscope with two-photon patterned optogenetic stimulation
Authors: Futia Gregory L. , Zohrabi Mo , McCullough Connor , Teel Alec , Simoes de Souza Fabio , Oroke Ryan , Miscles Eduardo J. , Ozbay Baris N. , Kilborn Karl , Bright Victor M. , Restrepo Diego , Gopinath Juliet T. , Gibson Emily A.
Published: October 2024

Multiphoton microscopy combined with optogenetic photostimulation is a powerful technique in neuroscience enabling precise control of cellular activity to determine the neural basis of behavior in a live animal. Two-photon patterned photostimulation has taken this further by allowing interrogation at the individual neuron level. However, it remains a challenge to implement imaging of neural activity with spatially patterned two-photon photostimulation in a freely moving animal. We developed a miniature microscope for high resolution two-photon fluorescence imaging with patterned two-photon optogenetic stimulation. The design incorporates a MEMS scanner for two-photon imaging and a second beam path for patterned two-photon excitation in a compact and lightweight design that can be head-attached to a freely moving animal. We demonstrate cell-specific optogenetics and high resolution MEMS based two-photon imaging in a freely moving mouse. The new capabilities of this miniature microscope design can enable cell-specific studies of behavior that can only be done in freely moving animals.
Transmission of SARS-CoV-2 on aircraft: A scoping review
Authors: Vardavas Constantine I. , Nikitara Katerina , Aslanoglou Katerina , Kamekis Apostolos , Ramesh Nithya , Symvoulakis Emmanouil , Phalkey Revati , Leonardi-Bee Jo , Mouchtouri Varvara , Hadjichristodoulou Christos , Baka Agoritsa , Lamb Favelle , Suk Jonathan E. , Robesyn Emmanuel
Published: October 2024

Introduction

The assessment of empirical epidemiological data is needed to assess the transmissibility of SARS-CoV-2 in aircraft settings. This review summarises reported contact- tracing data and evaluates the secondary attack rates (SAR) and factors associated with SARS- CoV-2 transmission in aircraft, to provide insight for future decision making in the context of future respiratory pandemics.

Methods

This scoping literature review assessed studies published between December 2020 to November 2023 in Ovid Medline, Embase and Cochrane Library databases. The inclusion criteria were based on the PCC framework (P-Population, C-Concept, C-Context). The study population was restricted to passengers and crew (population) to assess transmission (concept) in an aircraft setting (context).

Results

Thirty-one studies which assess SARS-CoV-2 transmission in 521 domestic and international flights were included in this systematic review. The SAR reported in the studies with an identified index case ranged from 0% to 16%. Significant variation in the reporting across studies was noted. Overall, the studies reported that using face masks or respirators by passengers and crew members during flight seemed to be a possible strategy for mitigating SARS-CoV-2 transmission while sitting within close proximity to index cases (≤2 seats in every direction) was associated with a higher SAR.

Conclusions

Our results are consistent with sporadic clusters happening onboard aircraft. Close proximity to COVID-19 cases within the aircraft was associated with a higher SAR. Our findings further underscore the need for a systematic approach to examining and reporting SARS-CoV-2 transmission onboard aircraft. This evidence may assist policymakers and transportation authorities in the development of emergency preparedness measures and travel guidance during the post-pandemic COVID-19 era.
Ecological and social factors lead to variation in parental care between sexes in a burying beetle
Authors: Ma Donghui , Ma Long , Komdeur Jan
Published: October 2024

Sexual conflict over parental care represents a divergence in the evolutionary interests between males and females, consequently leading to distinct sex roles in parental care and reproductive strategies. However, whether and how various ecological and social environments influence such sex differences remains largely unclear. In the present study, using the burying beetlesNicrophorus vespilloides, we experimentally investigated the impacts of resource availability and inter- and intra-specific competition pressure on individual parental care and reproduction in males and females. We manipulated the resource availability for the breeding pairs by providing them with either large or small mouse carcasses, and constructed the presence of intra- and inter-specific competition, by introducing an additional, small pair of beetles and blowfly maggotsCalliphora, respectively. We expected that males would decrease their parental care, while females would increase theirs, in response to smaller carcass. We also expected that the presence of intra- and inter-specific competition differentially affected the cares of males and females. We found that, compared to males and females breeding on large carcasses, males did not change their care, whereas females increased their care, when breeding on small carcasses. In the presence of another pair of adults, both males and females increased their parental care, whereas in the presence of blowfly maggots they both decreased their parental care. Our results showed that males and females adjust their parental care based on resource availability and competition pressure, with sex-specific differences driven by ecological and social factors. Our study sheds light on the importance of sex-specific parental care in response to various external drivers which contributes to a better understanding of the evolution of sex conflict over parental care.
Control of spatiotemporal activation of organ-specific fibers in the vagus nerve by intermittent interferential current stimulation
Authors: Rossetti Nicolò , Song Weiguo , Schnepel Philipp , Jayaprakash Naveen , Koutsouras Dimitrios A. , Fichman Mark , Wong Jason , Levy Todd , Elgohary Mohamed , Qanud Khaled , Giannotti Alice , Barbe Mary F , Chen Frank Liu , Langereis Geert , Datta-Chaudhuri Timir , Mihajlović Vojkan , Zanos Stavros
Published: October 2024

Vagus nerve stimulation (VNS) is emerging as potential treatment for several chronic diseases, however, limited control of fiber activation to promote desired effects over side effects restricts clinical translation. Here we describe a new VNS method that relies on intermittent, interferential sinusoidal current stimulation (i2CS) through implanted, multi-contact epineural cuffs. In swine, i2CS elicits specific nerve potentials and end organ responses, distinct from equivalent non-interferential sinusoidal stimulation. Comparing experimental results with anatomical trajectories of nerve fascicles from end organs to the stimulation electrode indicates that i2CS activates organ-specific fascicles rather than the entire nerve. Experimental results and anatomically realistic, physiologically validated biophysical models of the vagus nerve demonstrate that i2CS reduces fiber activation at the focus of interference. Current steering and repetition frequency determine spatiotemporal pattern of vagal fiber activation, allowing tunable and precise control of neural and organ responses. In experiments in a cohort of anesthetized swine, i2CS has improved selectivity for a desired effect, mediated by smaller bronchopulmonary fibers, over a side effect, mediated by larger laryngeal fibers, compared to non-interferential sinusoidal or square pulse VNS.
A construction contract administration (CCA) framework for graduate architects’ professional development
Authors: Tiew Si Yee
Published: October 2024

Purpose

Construction contract administration should be carried out by a person (normally engineer or architect depending on the type of contract) with expert technical knowledge of the construction process, strong leadership quality, highly developed interpersonal skills and an understanding of contractual, legislative and statutory underpinnings. However, due to a shortage of architects, graduate architects have been assigned to perform a partial role. Architectural firms are disappointed with the quality of the graduates and still note that they have to mentor them to be competent for their jobs. This paper aims to develop a construction contract administration (CCA) framework for graduate architects that aids the smooth running of a construction contract.

Design/methodology/approach

Seven housing projects in Malaysia have been selected as case studies. Documentation review and semi-structured interviews relevant to selected case studies were conducted to collect data to develop the CCA framework. The draft framework will then be validated through a focus group study.

Findings

A total of 5 themes and 11 sub-themes with core tasks were developed in the CCA framework. The themes involved are claims and legal matters management, communication and relationship management, project management, design management and quality assessment and management. Sub-themes are authority matters, building certification, meetings, coordination checklist, letter writing, contract documentation, building material, design brief, building sustainability and workmanship quality standards, contractors’ submission and building details.

Originality/value

The contribution of this study can be utilized for developing further models in the future that would improve the work performance of graduate architects. The framework assists the university by moving forward to the professional practice stage. In addition, it indirectly enhances the potential of graduate architects to perform efficiently and intensifies the bonding between project stakeholders.
Silence in the workplace: what do we know from research?
Authors: Kim Hee Sun , Wang Jia
Published: October 2024

Purpose

The purpose of this article is to examine the antecedents and consequences of organizational silence and employee silence to determine whether these two concepts should be distinguished rather than used interchangeably in research.

Design/methodology/approach

This study conducted a systematic literature review of 79 studies on organizational silence and 113 on employee silence, leading to three major findings.

Findings

First, this study shows that organizational silence is a collective phenomenon and employee silence occurs at the individual level; therefore, indicating they should be treated as two distinct concepts. Second, both types of silence are influenced by contextual factors (internal and external) and leadership. Third, organizational silence impacts both individual and organizational outcomes, whereas employee silence mainly affects an individual’s psychological health and performance.

Originality/value

This research clarifies the distinction between organizational silence and employee silence, offering guidance for researchers on how to approach these concepts. It also highlights the critical need to address workplace silence and the potential harm it may cause to both organizational and individual well-being if left unaddressed. Furthermore, this research supports organizational leaders and human resource developers in fostering a healthier work culture, improving performance and driving continuous improvement.