bluuebunny/crossref_metadata_2025 huggingface dataset:
The Scalable Variant Call Representation: Enabling Genetic Analysis Beyond One Million Genomes
Authors: Poterba Timothy , Vittal Christopher , King Daniel , Goldstein Daniel , Goldstein Jacqueline I. , Schultz Patrick , Karczewski Konrad J. , Seed Cotton , Neale Benjamin M.
Published: January 2024

The Variant Call Format (VCF) is widely used in genome sequencing but scales poorly. For instance, we estimate a 150,000 genome VCF would occupy 900 TiB, making it both costly and complicated to produce and analyze. The issue stems from VCF’s requirement to densely represent both reference-genotypes and allele-indexed arrays. These requirements lead to unnecessary data duplication and, ultimately, very large files.

To address these challenges, we introduce the Scalable Variant Call Representation (SVCR). This representation reduces file sizes by ensuring they scale linearly with samples. SVCR achieves this by adopting reference blocks from the Genomic Variant Call Format (GVCF) and employing local allele indices. SVCR is also lossless and mergeable, allowing for N+1 and N+K incremental joint-calling.

We present two implementations of SVCR: SVCR-VCF, which encodes SVCR in VCF format, and VDS, which uses Hail’s native format. Our experiments confirm the linear scalability of SVCR-VCF and VDS, in contrast to the super-linear growth seen with standard VCF files. We also discuss the VDS Combiner, a scalable, open-source tool for producing a VDS from GVCFs and unique features of VDS which enable rapid data analysis. SVCR, and VDS in particular, ensure the scientific community can generate, analyze, and disseminate genetics datasets with millions of samples.
Reannotation of the zebra finch genome reveals undiscovered transcriptional complexity
Authors: Richard Hugues , Wiedenhoeft John , Scharff Constance , Adam Iris
Published: January 2024

The zebra finch has become a paradigmatic model system to mechanistically investigate vocal communication from genes to behavior. Here, we report 1) a comprehensive map of the polyadenylated fraction of the transcriptome of the male zebra finch telencephalon at two ages, during the song learning phase at 50 days and when fully adult at 2 years as well as 2) as an expanded and refined annotation of the zebra finch genome based on our transcriptome data. Using high‐throughput next generation sequencing of paired‐end strand‐ specific cDNA fragments, we detected over 50% of the annotated protein coding transcripts (ENSEMBL v.55) in the telencephalon at both stages. We exploited the information gained from the paired‐end sequence reads and from reads falling onto splice junctions to update the existing annotation (ENS55) with new transcript structures and alternative splicing events. The dataset allowed to refine 2822 of the available gene models by extending them in the 3’‐UTR and to detect 11391 undiscovered transcriptional units in non‐coding regions. Our results illustrate the value of continuously incorporating new transcriptional evidence into existing annotations.
Reduced intra-tendinous sliding in Achilles tendinopathy during active plantarflexion regardless of horizontal foot position
Authors: Lecompte Laura , Crouzier Marion , Bogaerts Stijn , Scheys Lennart , Vanwanseele Benedicte
Published: January 2024

The Achilles tendon consists of three subtendons with the ability to slide relative to each other. As optimal intra-tendinous sliding is thought to reduce the overall stress in the tendon, alterations in sliding behavior could potentially play a role in the development of Achilles tendinopathy. The aims of this study were to investigate the difference in intra-tendinous sliding within the Achilles tendon during isometric contractions between asymptomatic controls and patients with Achilles tendinopathy and the effect of changing the horizontal foot position on intra-tendinous sliding in both groups. 29 participants (13 Achilles tendinopathy, 16 controls) performed isometric plantarflexion contractions at 60% of their maximal voluntary contraction (MVC), in toes-neutral, and at 30% MVC in toes-neutral, toes-in and toes-out positions during which ultrasound images were recorded. Intra-tendinous sliding was estimated as the superficial-to-middle and middle-to-deep relative displacement. Our results indicate that patients with Achilles tendinopathy present lower intra-tendinous sliding compared to asymptomatic controls. Regarding the horizontal foot position in both groups, the toes-out foot position resulted in increased sliding compared to both toes-neutral and toes-out foot position. We provided evidence that patients with Achilles tendinopathy show lower intra-tendinous sliding compared to asymptomatic controls. Since intra-tendinous sliding is a physiological feature of the Achilles tendon, the external foot position holds promise to increase sliding in patients with Achilles tendinopathy and promote healthy tendon behavior. Future research should investigate if implementing this external foot position in rehabilitation programs stimulates sliding within the Achilles tendon and improves clinical outcome.
A multi-host mechanistic model of African swine fever emergence and control in Romania
Authors: Hayes Brandon H. , Vergne Timothée , Rose Nicolas , Mortasivu Cristian , Andraud Mathieu
Published: January 2024

African swine fever (ASF) has devastating effects on swine production, farmer livelihood, animal welfare, and biodiversity. Extremely difficult to control, epidemic management is further complicated when spillover between domestic pig and wild boar populations is suspected. To quantify ASF viral transmission between domestic pigs and wild boar, a spatially-explicit stochastic mechanistic model was constructed using village centroids to represent aggregated backyard pig herds and a hexagonal raster of forest coverage to represent wild boar abundance. The model was parameterized to the initial six months of the ongoing Romanian epidemic through approximate Bayesian computation. It was estimated that a median of 69.4% (interquartile range: 53.0–80.0%) of domestic pig herd cases came from other infected domestic pig herds while 20.4% (11.2–33.8%) originated from infected wild boar sources, and 8.4% (4.7–14.2%) stemmed from external sources not explicitly represented. Also, 31.9% of infected wild boar habitat (16.7–56.2%) originated from domestic pig herds and 68.1% (43.8–83.3%) came from neighboring infected wild boar populations. Furthermore, it was found that habitats with a forest coverage greater than 15% were 2.6 times more infectious and 5.3 times more susceptible than other habitats. All alternative control scenarios, including culling domestic pig herds upon local domestic pig or wild boar case detection, improved epidemic outcomes, with the greatest decrease in final epidemic size being observed from the reactive culling of entire villages following case detection. These results can be used to further inform policy recommendations in ASF-epidemic regions.

Significance Statement

The current African swine fever (ASF) pandemic is devastating to affected nations, and quantifying transmission parameters is critical to informing control strategies. Disease spillover between wild and domestic hosts further complicates control efforts, yet the influence of spillover events on epidemic propagation remains unknown. Using the context of Romania—one of the European nations with the most severe epidemic and where spillover transmission is strongly suspected—we show that targeting spillover mechanisms is critical for achieving holistic disease control, and then demonstrate the impact of alternative control scenarios had they been enacted. These results can inform control strategy policy decisions in the many nations at-risk for or actively experiencing ASF epidemics.
A conserved Pol II elongator SPT6L mediates Pol V transcription elongation to regulate RNA-directed DNA methylation inArabidopsis
Authors: Liu Yujuan , Shu Jie , Zhang Zhi , Ding Ning , Liu Jinyuan , Liu Jun , Cui Yuhai , Wang Changhu , Chen Chen
Published: January 2024

In plants, the plant-specific RNA polymerase V (Pol V) transcripts non-coding RNAs and provides a docking platform for the association of accessory proteins in the RNA-directed DNA methylation (RdDM) pathway. Various components have been uncovered that are involved in the process of DNA methylation, but it is still not clear how the transcription of Pol V is regulated. Here, we found that the conserved Pol II elongator, SPT6L, bound to thousands of intergenic regions in an RNA polymerase II (Pol II) independent manner. The intergenic enrichment of SPT6L, interestingly, co-occupied with the largest subunit of Pol V (NRPE1) and mutation of SPT6L led to the reduction of DNA methylation but not Pol V enrichment. Furthermore, the association of SPT6L at Pol V loci was dependent on the Pol V associated factor, SPT5L, rather than the presence of Pol V, and the interaction between SPT6L and NRPE1 was compromised inspt5l. Finally, Pol V RIP-seq revealed that SPT6L is required to maintain the amount and length of Pol V transcripts. Our findings thus uncovered the critical role of a Pol II conserved elongator in Pol V mediated DNA methylation and transcription, and shed light on the mutual regulation between Pol V and II in plants.
MprF-mediated immune evasion is necessary forLactiplantibacillus plantarumresilience inDrosophilagut during inflammation
Authors: Arias-Rojas Aranzazu , Arifah Adini , Angelidou Georgia , Alshaar Belal , Schombel Ursula , Forest Emma , Frahm Dagmar , Brinkmann Volker , Paczia Nicole , Beisel Chase , Gisch Nicolas , Iatsenko Igor
Published: January 2024

Background

Multiple peptide resistance factor (MprF) confers resistance to cationic antimicrobial peptides (AMPs) in several pathogens, thereby enabling evasion of the host immune response. While MprF has been proven to be crucial for the virulence of various pathogens, its role in commensal gut bacteria remains uncharacterized. To close this knowledge gap, we used a common gut commensal of animals,Lactiplantibacillus plantarum, and its natural host, the fruit flyDrosophila melanogaster, as an experimental model to investigate the role of MprF in commensal-host interactions.

Results

TheL. plantarumΔmprFmutant that we generated exhibited deficiency in the synthesis of lysyl-phosphatidylglycerol (Lys-PG), resulting in increased negative cell surface charge and increased susceptibility to AMPs. Susceptibility to AMPs had no effect on ΔmprFmutant’s ability to colonize guts of uninfected flies. However, we observed significantly reduced abundance of the ΔmprFmutant after infection-induced inflammation in the guts of wild-type flies but not flies lacking AMPs. These results demonstrate that host AMPs reduce the abundance of the ΔmprFmutant during infection. We found in addition that the ΔmprFmutant compared to wild-typeL. plantaruminduces a stronger intestinal immune response in flies due to the increased release of immunostimulatory peptidoglycan fragments, indicating an important role of MprF in promoting host tolerance to commensals.

Conclusion

Overall, our results demonstrate that MprF, besides its well-characterized role in pathogen immune evasion and virulence, is also an important resilience factor in maintaining stable microbiota-host interactions during intestinal inflammation.
Mitochondrial respiration is essential for photosynthesis-dependent ATP supply of the plant cytosol
Authors: Vera-Vives Antoni M. , Novel Piero , Zheng Ke , Tan Shun-ling , Schwarzländer Markus , Alboresi Alessandro , Morosinotto Tomas
Published: January 2024

Plants rely on solar energy to synthesize ATP and NADPH for photosynthetic carbon fixation. Since a substantial proportion of cellular ATP is consumed in the cytosol, photosynthesis-derived ATP needs to be supplied there. While the triose phosphate shuttle and mitochondrial respiration can both deliver ATP to the cytosol, the significance of the different mechanismsin vivohas been difficult to assess. Although mitochondrial respiration is essential in plants, whether this is due to heterotrophic bottlenecks during plant development or rather a need for respiration in photosynthetically active cells, has not been resolved. In this study, we examinedin vivochanges of cytosolic ATP concentration in response to light, employing a biosensing strategy in the mossPhyscomitrium patens. Our measurements revealed increased cytosolic ATP concentration caused by photosynthetic activity. Moss tissue depleted of respiratory complex I showed decreased cytosolic ATP accumulation, highlighting a critical role of mitochondrial respiration in light-dependent ATP supply of the cytosol. Consistently, targeting mitochondrial ATP production directly, through the construction of mutants deficient in mitochondrial ATPase (complex V), led to drastic growth reduction, despite only minor alterations in photosynthetic electron transport activity. SinceP. patensis photoautotrophic throughout its development, we conclude that heterotrophic bottlenecks cannot account for the indispensable role of mitochondrial respiration in plants. Instead, our results offer compelling evidence that mitochondrial respiration is essential for ATP provision to the cytosol in actively photosynthesizing cells. Mitochondrial respiration provides metabolic integration, ensuring a reliable supply of cytosolic ATP essential for supporting plant growth and development.
Identification of phospholipase Ds and phospholipid species involved in circadian clock alterations using CRISPR/Cas9-based multiplex editing of Arabidopsis
Authors: Kim Sang-Chul , Nusinow Dmitri A. , Wang Xuemin
Published: January 2024

Reciprocal regulation between the circadian clock and lipid metabolism is emerging, but its mechanisms remain elusive. We reported that a lipid metabolite phosphatidic acid (PA) bound to the core clock transcription factors LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and chemical suppression of phospholipase D (PLD)-catalyzed PA formation perturbed the clock in Arabidopsis. Here, we identified, among 12 members, specific PLDs critical to regulating clock function. We approached this using a multiplex CRISPR/Cas9 system to generate a library of plants bearing randomly mutatedPLDs,then screening the mutants for altered rhythmic expression ofCCA1. AllPLDs, except forβ2, were effectively edited, and the mutations were heritable. Screening of T2 plants identified some with an altered rhythm ofCCA1expression, and this trait was observed in many of their progenies. Genotyping revealed that at least two of sixPLDs (α1, α3,γ1,δ,εandζ2) were mutated in the clock-altered plants. Those plants also had reduced levels of PA molecular species that bound LHY and CCA1. This study identifies combinations of two or more PLDs and changes in particular phospholipid species involved in clock outputs and also suggests a functional redundancy of the six PLDs for regulating the plant circadian clock.

One sentence summary

This study identifies combinations of two or more phospholipase Ds involved in altering clock outputs and the specific phosphatidic acid species impacting the clock rhythms.
Discovery and binding mode of small molecule inhibitors of the apo form of human TDO2
Authors: Lotz-Jenne Carina , Lange Roland , Cren Sylvaine , Bourquin Geoffroy , Goglia Laksmei , Kimmerlin Thierry , Wicki Micha , Müller Manon , Artico Nadia , Ackerknecht Sabine , Pfaff Philippe , Joesch Christoph , Mac Sweeney Aengus
Published: January 2024

Tryptophan-2,3-dioxygenase (TDO2) and indoleamine-2,3-dioxygenase (IDO1) catalyze the conversion of L-tryptophan to N-formyl-kynurenine and play important roles in metabolism, inflammation, and tumor immune surveillance. Their enzymatic activities depend on their heme contents, which vary dynamically according to biological conditions. Inhibitors binding to heme-containing holo-TDO2 are known, but to date no inhibitor that binds to the heme-free state (apo-TDO2) has been reported. We describe the discovery of the first apo-TDO2 targeting inhibitors, to our knowledge, together with their co-crystal structures and inhibition of cellular TDO2 activity at low nanomolar concentrations.
Continuous structural neuroplasticity during motor learning - a diffusion MRI study
Authors: Friedman Naama , Malovani Cfir , Perets Inbar , Kenin Etai , Bernstein-Eliav Michal , Tavor Ido
Published: January 2024

How does our brain transform when we encounter a new task? To fully answer this question, comparing brain states before and after learning may not be enough, but rather an on-going, continuous monitoring of brain changes during learning is required. While such continuous examinations of functional learning-induced changes are widely available using functional magnetic resonance imaging (fMRI), a continuous investigation of microstructural brain modifications during learning is yet to be reported.

Here, we continuously acquire diffusion MRI images during task performance. We then compute the mean diffusivity (MD) using a sliding-window approach, resulting in a continuous measure of microstructural changes throughout learning. We demonstrate the utility of this method on a motor sequence learning (finger tapping) task (n=58). MD decrease was detected in task-related brain regions, including the parahippocampal gyrus, hippocampus, inferior temporal gyrus, and cerebellum. Analysis of the temporal patterns of decrease revealed a rapid MD reduction in the right temporal gyrus after 11 minutes of learning, with additional decrease in the right parahippocampal gyrus and left cerebellum after 22 minutes. We further computed “neuroplasticity networks” of brain areas showing similar change patterns and detected similarities between these networks and canonical functional connectivity networks.

Our findings offer novel insights on the spatio-temporal dynamics of microstructural neuroplasticity by demonstrating continuous modifications during the encoding phase of learning itself, rather than comparing pre- and post-learning states.
Prevotella timonensisdegrades the vaginal epithelial glycocalyx through high fucosidase and sialidase activities
Authors: Segui-Perez Celia , de Jongh Rivka , Jonkergouw Robin , Pelayo Paula , Balskus Emily P. , Zomer Aldert , Strijbis Karin
Published: January 2024

Bacterial vaginosis (BV) is a polymicrobial infection of the female reproductive tract (FRT). BV is characterized by replacement of health-associatedLactobacillusspecies by diverse anaerobic bacteria, including the well-knownGardnerella vaginalis.Prevotella timonensisandPrevotella biviaare anaerobes that are found in a significant percentage of BV patients, but their pathogenic properties are yet to be determined. Defining characteristics of anaerobic overgrowth in BV are adherence to the mucosal surface and the increased activity of mucin-degrading enzymes such as sialidases in vaginal secretions. Here, we demonstrate thatP. timonensisbut notP. biviastrongly adhered to vaginal and endocervical cells to a similar level asG. vaginalisbut did not elicit a comparable pro-inflammatory response. TheP. timonensisgenome uniquely encodes a large set of mucus-degrading enzymes including 4 putative fucosidases and 2 putative sialidases, PtNanH1 and PtNanH2. Enzyme assays demonstrated that fucosidase and sialidase activity inP. timonensiscell-bound and secreted fractions was significantly higher than for other vaginal anaerobes. Infection assays revealed thatP. timonensisfucosidases and sialidases efficiently removed fucose and α2,3- and α2,6-linked sialic acid moieties from the epithelial glycocalyx. Recombinantly expressedP. timonensisNanH1 and NanH2 efficiently removed α2,3 and α2,6-linked sialic acids from the epithelial surface and sialic acid removal byP. timonensiscould be blocked using inhibitors. This study demonstrates thatP.timonensishas distinct virulence properties that include initial adhesion and a high capacity for mucin degradation at the vaginal epithelial mucosal surface. Our results underline the importance of understanding the role of different anaerobic bacteria in BV.

Significance statement (Layman)

Bacterial vaginosis (BV) is a common vaginal infection that affects a high percentage of women and is associated with reduced fertility and increased risk of secondary infections.Gardnerella vaginalisis the most well-known BV-associated bacterium, butPrevotellaspecies includingP. timonensisandP. biviamay also play an important role. We showed that, similar toG. vaginalis,P. timonensisadhered well to the vaginal epithelium, suggesting that both bacteria could be important in the first stage of infection. Compared to the other bacteria,P. timonensiswas unique in efficiently removing the protective mucin sugars that cover the vaginal epithelium. These results underscore that vaginal bacteria play different roles in the initiation and development of BV.
Exploratory and risk-taking behaviours in coexisting rodents
Authors: Hughes Bryan , Bowman Jeff , Schulte-Hostedde Albrecht
Published: January 2024

There has been an increasing interest in modelling the influence of animal personality on species interactions within ecosystems. Animal personality traits associated with dispersal, movement within a home range and risk-taking, including docility and exploration, have been shown to influence an array of environmental variables including seed dispersal and habitat availability. Despite growing interest however, little information is available to model the effects of differences in personality phenotypes among coexisting species. Since coexisting or sympatric species often compete for resources, differences in movement patterns can help mitigate the impact of intra- and interspecific competition. We used two standardized behavioural tests with three species of coexisting rodents in Algonquin Provincial Park, Ontario, Canada to measure exploration and docility personality phenotypes. To evaluate personalities, we modelled plastic changes in behaviours within species and phenotypic variation in behavioural strategies among species. We show empirical evidence to support differences in personality phenotypes in coexisting species and consider the importance of alternative personality strategies in shaping community dynamics.
Long-read sequencing reveals novel structural variation markers for key agronomic and quality traits of soybean
Authors: Wang Zhibo , Belay Kassaye , Paterson Joe , Bewick Patrick , Singer William , Song Qijian , Zhang Bo , Li Song
Published: January 2024

In plant genomic research, long read sequencing has been widely used to detect structure variations that are not captured by short read sequencing. In this letter, we described an analysis of whole genome re-sequencing of 29 soybean varieties using nanopore long-read sequencing. The compiled germplasm reflects diverse applications, including livestock feeding, soy milk and tofu production, as well as consumption of natto, sprouts, and vegetable soybeans (edamame). We have identified 365,497 structural variations in these newly re-sequenced genomes and found that the newly identified structural variations are associated with important agronomic traits. These traits include seed weight, flowering time, plant height, oleic acid content, methionine content, and trypsin inhibitor content, all of which significantly impact soybean production and quality. Experimental validation supports the roles of predicted candidate genes and structural variant in these biological processes. Our research provides a new source for rapid marker discovery in crop genomes using structural variation and whole genome sequencing.
Associations between common genetic variants and income provide insights about the socioeconomic health gradient
Authors: Kweon Hyeokmoon , Burik Casper A.P. , Ning Yuchen , Ahlskog Rafael , Xia Charley , Abner Erik , Bao Yanchun , Bhatta Laxmi , Faquih Tariq O. , de Feijter Maud , Fisher Paul , Gelemanović Andrea , Giannelis Alexandros , Hottenga Jouke-Jan , Khalili Bita , Lee Yunsung , Li-Gao Ruifang , Masso Jaan , Myhre Ronny , Palviainen Teemu , Rietveld Cornelius A. , Teumer Alexander , Verweij Renske M. , Willoughby Emily A. , Agerbo Esben , Bergmann Sven , Boomsma Dorret I. , Børglum Anders D. , Brumpton Ben M. , Davies Neil Martin , Esko Tõnu , Gordon Scott D. , Homuth Georg , Ikram M. Arfan , Johannesson Magnus , Kaprio Jaakko , Kidd Michael P. , Kutalik Zoltán , Kwong Alex S.F. , Lee James J. , Luik Annemarie I. , Magnus Per , Marques-Vidal Pedro , Martin Nicholas G. , Mook-Kanamori Dennis O. , Mortensen Preben Bo , Oskarsson Sven , Pedersen Emil M. , Polašek Ozren , Rosendaal Frits R. , Smart Melissa C. , Snieder Harold , van der Most Peter J. , Vollenweider Peter , Völzke Henry , Willemsen Gonneke , Beauchamp Jonathan P. , DiPrete Thomas A. , Linnér Richard Karlsson , Lu Qiongshi , Morris Tim T. , Okbay Aysu , Harden K. Paige , Abdellaoui Abdel , Hill W. David , de Vlaming Ronald , Benjamin Daniel J. , Koellinger Philipp D.
Published: January 2024

We conducted a genome-wide association study (GWAS) on income among individuals of European descent and leveraged the results to investigate the socio-economic health gradient (N=668,288). We found 162 genomic loci associated with a common genetic factor underlying various income measures, all with small effect sizes. Our GWAS-derived polygenic index captures 1 - 4% of income variance, with only one-fourth attributed to direct genetic effects. A phenome-wide association study using this polygenic index showed reduced risks for a broad spectrum of diseases, including hypertension, obesity, type 2 diabetes, coronary atherosclerosis, depression, asthma, and back pain. The income factor showed a substantial genetic correlation (0.92,s.e. = .006) with educational attainment (EA). Accounting for EA’s genetic overlap with income revealed that the remaining genetic signal for higher income related to better mental health but reduced physical health benefits and increased participation in risky behaviours such as drinking and smoking.
Transient frequency preference responses in cell signaling systems
Authors: Szischik Candela Lucia , Szemere Juliana Reves , Balderrama Rocío , de la Vega Constanza Sánchez , Ventura Alejandra C.
Published: January 2024

Ligand-receptor systems, covalent modification cycles, and transcriptional networks are the fundamental components of cell signaling and gene expression systems. While their behavior in reaching a steady state regime under step-like stimulation is well understood, their response under repetitive stimulation, particularly at early time stages is poorly characterized. This is despite the fact that early-stage responses to external inputs are arguably as informative as late-stage ones.

In simple systems, a periodic stimulation elicits an initial transient response, followed by periodic behavior. Transient responses are relevant when the stimulation has a limited time span, or when the stimulated component’s timescale is slow as compared to the timescales of the downstream processes, in which case these fast processes may be capturing only those transients. In this study, we analyze the frequency response of simple motifs at different time stages. We use dose-conserved pulsatile input signals, meaning that the amplitude or the duration of the pulses varies along with frequency to conserve input dose, and consider different metrics versus frequency curves.

We show that in ligand-receptor systems, there is a frequency preference response (band-pass filter) in some specific metrics during the transient stages, which is not present in the periodic regime. We suggest this is a general system-level mechanism that cells may use to filter input signals that have consequences for higher order circuits.

Additionally, we evaluate how the described behavior in isolated motifs is reflected in similar types of responses in cascades and pathways of which they are a part. Our studies suggest that transient frequency preferences are important dynamic features of cell signaling and gene expression systems, which have been overlooked.
Tracing back the expansion of the endomembrane rescue systems in parasitic Parabasalids to the ancestral origin in its free-living sister lineage
Authors: Shinde Abhishek P , Kucerova Jitka , Dacks Joel B , Tachezy Jan
Published: January 2024

Early Endosomes sort transmembrane cargo whether for lysosomal degradation or retrieval to the plasma membrane or the Golgi complex. Endosomal retrieval in eukaryotes is governed by the anciently homologous Retromer or Retriever complexes. Each comprises a core tri-protein subcomplex, membrane-deformation proteins, and interacting partner complexes, together retrieving a variety of known cargo proteins. Trichomonas vaginalis; a sexually transmitted human parasite uses the endomembrane system for pathogenesis. It has massively and selectively expanded its endomembrane protein complement, the evolutionary path of which has been largely unexplored. Our molecular evolutionary study of Retromer, Retriever and associated machinery in parabasalids and its free-living sister lineage of Anaeramoeba, demonstrates specific expansion of the Retromer machinery, contrasting with the Retriever components. We also observe partial loss of Commander complex and Sorting Nexins in Parabasalia but complete retention in Anaeramoeba. Notably, we identify putative parabasalid Sorting Nexin analogues. Finally, we report the first Retriever protein localization in a non- metazoan group along with Retromer protein localization in T. vaginalis. Therefore, we provide a unique genome expansion study of endomembrane trafficking system in parasitic and free- living protists alike.
Energy allocation theory for bacterial growth control in and out of steady state
Authors: Cylke Arianna , Serbanescu Diana , Banerjee Shiladitya
Published: January 2024

Efficient allocation of energy resources to key physiological functions allows living organisms to grow and thrive in diverse environments and adapt to a wide range of perturbations. To quantitatively understand how unicellular organisms utilize their energy resources in response to changes in growth environment, we introduce a theory of dynamic energy allocation which describes cellular growth dynamics based on partitioning of metabolizable energy into key physiological functions: growth, division, cell shape regulation, energy storage and loss through dissipation. By optimizing the energy flux for growth, we develop the equations governing the time evolution of cell morphology and growth rate in diverse environments. The resulting model accurately captures experimentally observed dependencies of bacterial cell size on growth rate, superlinear scaling of metabolic rate with cell size, and predicts nutrient-dependent trade-offs between energy expended for growth, division, and shape maintenance. By calibrating model parameters with available experimental data for the model organismE. coli, our model is capable of describing bacterial growth control in dynamic conditions, particularly during nutrient shifts and osmotic shocks. The model captures these perturbations with minimal added complexity and our unified approach predicts the driving factors behind a wide range of observed morphological and growth phenomena.
The loss of the PDIM/PGL virulence lipids causes differential secretion of ESX-1 substrates inMycobacterium marinum
Authors: Jones Bradley S , Hu Daniel D , Nicholson Kathleen R , Cronin Rachel M , Champion Matthew , Champion Patricia A.
Published: January 2024

The mycobacterial cell envelope is a major virulence determinant in pathogenic mycobacteria. Specific outer lipids play roles in pathogenesis, modulating the immune system and promoting the secretion of virulence factors. ESX-1 (ESAT-6 system-1) is a conserved protein secretion system required for mycobacterial pathogenesis (1, 2). Previous studies revealed that mycobacterial strains lacking the outer lipid PDIM have impaired ESX-1 function during laboratory growth and infection (3-5). The mechanisms underlying changes in ESX-1 function are unknown. We used a proteo-genetic approach to measure PDIM and PGL-dependent protein secretion inM. marinum, a non-tubercular mycobacterial pathogen that causes tuberculosis-like disease in ectothermic animals (6, 7). Importantly,M. marinumis a well-established model for mycobacterial pathogenesis (8, 9). Our findings showed thatM. marinumstrains without PDIM and PGL showed specific, significant reductions in protein secretion compared to the WT and complemented strains. We recently established a hierarchy for the secretion of ESX-1 substrates in four (I-IV) groups (10). Loss of PDIM differentially impacted secretion of Groups III and IV ESX-1 substrates, which are likely the effectors of pathogenesis. Our data suggests that the altered secretion of specific ESX-1 substrates is responsible for the observed ESX-1-related effects in PDIM-deficient strains.
ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism
Authors: Rashan Edrees H. , Bartlett Abigail K. , Khana Daven B. , Zhang Jingying , Jain Raghav , Smith Andrew J. , Baker Zakery N. , Cook Taylor , Caldwell Alana , Chevalier Autumn R. , Pfleger Brian F. , Yuan Peng , Amador-Noguez Daniel , Simcox Judith A. , Pagliarini David J.
Published: January 2024

Fatty acid β-oxidation (FAO) is a central catabolic pathway with broad implications for organismal health. However, various fatty acids are largely incompatible with standard FAO machinery until they are modified by other enzymes. Included among these are the 4-hydroxy acids (4-HAs)—fatty acids hydroxylated at the 4 (γ) position—which can be provided from dietary intake, lipid peroxidation, and certain drugs of abuse. Here, we reveal that two atypical and poorly characterized acyl-CoA dehydrogenases (ACADs), ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains N-terminal to their ACAD domains that phosphorylate the 4-OH position as a requisite step in the conversion of 4-hydroxyacyl-CoAs into 2-enoyl-CoAs—conventional FAO intermediates. Our ACAD11 cryo-EM structure and molecular modeling reveal a unique binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain 4-HAs, whereas ACAD11 is peroxisomal and enables longer-chain 4-HA catabolism. Mice lacking ACAD11 accumulate 4-HAs in their plasma while comparable 3- and 5-hydroxy acids remain unchanged. Collectively, this work defines ACAD10 and ACAD11 as the primary gatekeepers of mammalian 4-HA catabolism and sets the stage for broader investigations into the ramifications of aberrant 4-HA metabolism in human health and disease.
Chlamydia trachomatismodulates the expression of JAK-STAT signaling components to attenuate the Type II interferon response of epithelial cells
Authors: Fontanilla Francis L. , Carabeo Rey A. , Brinkworth Amanda J.
Published: January 2024

Chlamydia trachomatishas adapted to subvert signaling in epithelial cells to ensure successful intracellular development. Interferon-γ (IFNγ) produced by recruited lymphocytes signals through the JAK/STAT pathway to restrict chlamydial growth in the genital tract. However, duringChlamydiainfectionin vitro, addition of IFNγ does not fully induce nuclear localization of its transcription factor STAT1 and target gene, IDO1. We hypothesize that this altered interferon response is a result ofChlamydiatargeting components of the IFNγ-JAK/STAT pathway. To assess the ability of replicatingChlamydiato dampen interferon signaling, HEp2 human epithelial cells were infected withC. trachomatisserovar L2 for 24 hours prior to exposure to physiologically relevant levels of IFNγ (500 pg/mL). This novel approach enabled us to observe reduced phospho-activation of both STAT1 and its kinase Janus Kinase 2 (JAK2) in infected cells compared to mock-infected cells. Importantly, basal JAK2 and STAT1 transcript and protein levels were dampened by infection even in the absence of interferon, which could have implications for cytokine signaling beyond IFNγ. Additionally, target genes IRF1, GBP1, APOL3, IDO1, and SOCS1 were not fully induced in response to IFNγ exposure. Infection-dependent decreases in transcript, protein, and phosphoprotein were rescued whende novobacterial protein synthesis was inhibited with chloramphenicol, restoring expression of IFNγ-target genes. SimilarChlamydia-dependent dampening of STAT1 and JAK2 transcript levels were observed in infected END1 endocervical cells and in HEp2s infected withC. trachomatisserovar D, suggesting a conserved mechanism of dampening the interferon response by reducing the availability of key signaling components.

Importance

As an obligate intracellular pathogen that has evolved to infect the genital epithelium,Chlamydiahas developed strategies to prevent detection and antimicrobial signaling in its host to ensure its survival and spread. A major player in clearingChlamydiainfections is the inflammatory cytokine interferon-γ (IFNγ), which is produced by immune cells that are recruited to the site of infection. Reports of IFNγ levels in vaginal and cervical swabs fromChlamydia-infected patients range from 1-350 pg/mL, while mostin vitrostudies of the effects of IFNγ on chlamydial growth have used 15-85 fold higher concentrations. By using physiologically-relevant concentrations of IFNγ we were able assessChlamydia’sability to modulate its signaling. We found thatChlamydiadecreases the expression of multiple components that are required for inducing gene expression by IFNγ, providing a possible mechanism by whichC. trachomatiscan attenuate the immune response in the female genital tract to cause long-term infections.
Characterization of Recombinant Human Lactoferrin Expressed inKomagataella Phaffii
Authors: Lu Xiaoning , Cummings Chad , Osuala Udodili A. , Yennawar Neela H. , Namitz Kevin E. W. , Hellner Brittney , Besada-Lombana Pamela B. , Peterson Ross D. , Clark Anthony J.
Published: January 2024

We performed a thorough analysis and characterization of multiple batches of Helaina recombinant human lactoferrin (rhLF, Effera™) expressed at an industrial scale in a yeast system. Bottom-up LC-MS/MS-based proteomics analysis detected the full sequence of Helaina rhLF protein and confirmed that its amino acid sequence is identical to that of native human LF (Uniprot i.d. P02788). Helaina rhLF had a protein purity of 98% or higher as determined by three orthogonal methods; reversed-phase HPLC, SDS-PAGE, and LC-MS proteomics analysis. N-linked glycans were detected at three known glycosylation sites, namely, Asparagines-156, -497, and -642. The identified N-glycans of Helaina rhLF were predominantly oligomannose structures with five to nine mannoses (M5-M9), which we also report to be present in both the native human and bovine LF. human milk LF (hmLF) possessed lower levels of oligomannose structures and were mainly M5 and M6. Helaina rhLF protein secondary structure was nearly identical to that of hmLF, as revealed by microfluidic modulation spectroscopy. Results of small-angle X-ray scattering (SAXS) and analytical ultracentrifugation analyses confirmed that, like hmLF, Helaina rhLF displayed well-folded globular structures in solution. Reconstructed solvent envelopes of Helaina rhLF, obtained through the SAXS analysis, demonstrated a remarkable fit with the reported crystalline structure of iron-bound native hmLF. Differential scanning calorimetry investigations into the thermal stability of Helaina rhLF revealed two distinct denaturation temperatures at 68.7±0.9 °C and 91.9±0.5 °C, consistently mirroring denaturation temperatures observed for apo-and holo-hmLF. Overall, the characterization analysis results affirmed that Helaina rhLF was of high purity and exhibited globular structures closely akin to that of hmLF.
Stacking effects on mutation detection by T4 DNA ligation within dimeric DNA origami triangle barcodes for single-molecule nanopore analysis
Authors: Aboagye-Mensah Dorothy , Confederat Samuel , Alammar Fahad , Kailas Lekshmi , Adedeji-Olulana Abimbola F. , Stopar Alex , Nicholson Allen W. , Thomson Neil H. , Actis Paolo , Castronovo Matteo
Published: January 2024

Solid-state nanopores represent an emerging technology for the highly sensitive detection of biomolecular markers, but the detection of DNA point mutations is challenged by the high noise levels associated with solid-state nanopore reading. In contrast, barcoded DNA origami nanostructures can provide unique single-molecule nanopore fingerprints. In this work, we have integrated nanopore-barcoded DNA nanostructures with enzymatic DNA ligation, the latter of which is routinely involved in clinical protocols for DNA mutation detection. We designed two triangular DNA origami variants containing three elongated staples that provide strands extensions on one side that are complementary to a target sequence. Addition of the latter in solution promotes the formation of a DNA triangle dimer. Since T4 DNA ligase repairs a nick in a dsDNA segment only if there is Watson-Crick base-pairing at the nick, the two DNA triangles can be covalently linked only if the DNA sequence bridging the two triangles carries the targeted mutation. We have found striking differences between ligation detection by gel electrophoresis, AFM, and quartz capillary-based nanopores. The stacking interaction between DNA triangles is enhanced by the formation of dimers, and promote the formation of higher order nanostructure, which serve as molecular weight amplification for DNA ligation in gels. The triangle-triangle stacking dynamics presumably involves a clam-like folding mechanism, which is detectable by quartz nanopore analysis, and which hinders ligation by T4 DNA ligase. The results provide the basis for development of rapid, highly sensitive, and affordable high-throughput approaches for profiling genetic variations in point-of-care settings.
WITHDRAWN: The relationship between antibiotic use in humans and poultry and antibiotic resistance prevalence in humans: an ecological regression study of Campylobacter in the UK
Authors: Emes Eve , Guitian Javier , Knight Gwenan , Naylor Nichola
Published: January 2024

Withdrawal Statement

The authors have withdrawn this manuscript because, upon running further robustness tests, some of the results presented in the preprint were determined not to be robust. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Proteomic Changes in the Human Cerebrovasculature in Alzheimer’s Disease and Related Tauopathies Linked to Peripheral Biomarkers in Plasma and Cerebrospinal Fluid
Authors: Wojtas Aleksandra M. , Dammer Eric B. , Guo Qi , Ping Lingyan , Shantaraman Ananth , Duong Duc M. , Yin Luming , Fox Edward J. , Seifar Fatemeh , Lee Edward B. , Johnson Erik C. B. , Lah James J. , Levey Allan I. , Levites Yona , Rangaraju Srikant , Golde Todd E. , Seyfried Nicholas T.
Published: January 2024

Dysfunction of the neurovascular unit stands as a significant pathological hallmark of Alzheimer’s disease (AD) and age-related neurodegenerative diseases. Nevertheless, detecting vascular changes in the brain within bulk tissues has proven challenging, limiting our ability to characterize proteomic alterations from less abundant cell types. To address this challenge, we conducted quantitative proteomic analyses on both bulk brain tissues and cerebrovascular-enriched fractions from the same individuals, encompassing cognitively unimpaired control, progressive supranuclear palsy (PSP), and AD cases. Protein co-expression network analysis identified modules unique to the cerebrovascular fractions, specifically enriched with pericytes, endothelial cells, and smooth muscle cells. Many of these modules also exhibited significant correlations with amyloid plaques, cerebral amyloid angiopathy (CAA), and/or tau pathology in the brain. Notably, the protein products within AD genetic risk loci were found concentrated within modules unique to the vascular fractions, consistent with a role of cerebrovascular deficits in the etiology of AD. To prioritize peripheral AD biomarkers associated with vascular dysfunction, we assessed the overlap between differentially abundant proteins in AD cerebrospinal fluid (CSF) and plasma with a vascular-enriched network modules in the brain. This analysis highlighted matrisome proteins, SMOC1 and SMOC2, as being increased in CSF, plasma, and brain. Immunohistochemical analysis revealed SMOC1 deposition in both parenchymal plaques and CAA in the AD brain, whereas SMOC2 was predominantly localized to CAA. Collectively, these findings significantly enhance our understanding of the involvement of cerebrovascular abnormalities in AD, shedding light on potential biomarkers and molecular pathways associated with CAA and vascular dysfunction in neurodegenerative diseases.
A Systematic Review and Meta-Analysis on the Effectiveness of Bivalent mRNA Booster Vaccines against Omicron Variants
Authors: Song Shangchen , Madewell Zachary J. , Liu Mingjin , Miao Yu , Xiang Shaolin , Huo Yanan , Sarkar Shoumi , Chowdhury Amily , Longini Ira M. , Yang Yang
Published: January 2024

Background

A global shift to bivalent mRNA vaccines is ongoing to counterbalance diminishing monovalent vaccine effectiveness (VE) due to the evolution of SARS-CoV-2 variants, yet substantial variation in the bivalent VE exists across studies and a complete picture is lacking.

Methods

We searched papers evaluating SARS-CoV-2 bivalent mRNA vaccines on PubMed, Web of Science, Cochrane Library, Google Scholar, Embase, Scopus, bioRxiv, and medRxiv published from September 1st, 2022, to November 8th, 2023. Pooled VE against Omicron-associated infection and severe events was estimated in reference to unvaccinated, ≥2 monovalent doses, and ≥3 monovalent doses.

Results

From 630 citations identified, 28 studies were included, involving 55,393,303 individuals. Bivalent boosters demonstrated superior protection against symptomatic or any infection compared to unvaccinated, ≥2 monovalent doses, and ≥3 monovalent doses, with corresponding relative VE estimated as 53.5% (95% CI: - 22.2-82.3%), 30.8% (95% CI: 22.5-38.2%), and 28.4% (95% CI: 10.2-42.9%) for all ages, and 22.5% (95% CI: 16.8-39.8%), 31.4% (95% CI: 27.7-35.0%), and 30.6% (95% CI: -13.2-57.5%) for adults ≥60 years old. Pooled bivalent VE estimates against severe events were higher, 72.9% (95% CI: 60.5-82.4%), 57.6% (95% CI: 42.4-68.8%), and 62.1% (95% CI: 54.6-68.3%) for all ages, and 72.0% (95% CI: 51.4-83.9%), 63.4% (95% CI: 41.0-77.3%), and 60.7% (95% CI: 52.4-67.6%) for adults ≥60 years old, compared to unvaccinated, ≥2 monovalent doses, and ≥3 monovalent doses, respectively.

Conclusions

Bivalent boosters demonstrated higher VE against severe outcomes than monovalent boosters across age groups, highlighting the critical need for improving vaccine coverage, especially among the vulnerable older subpopulation.
A randomized controlled trial of alpha phase-locked auditory stimulation to treat symptoms of sleep onset insomnia
Authors: Bressler Scott , Neely Ryan , Yost Ryan , Wang David
Published: January 2024

Sleep onset insomnia is a pervasive problem that contributes significantly to the poor health outcomes associated with insufficient sleep. Auditory stimuli phase-locked to slow-wave sleep oscillations have been shown to augment deep sleep, but it is unknown whether a similar approach can be used to accelerate sleep onset. The present randomized controlled crossover trial enrolled adults with objectively verified sleep onset latencies (SOLs) greater than 30 minutes to test the effect of auditory stimuli delivered at specific phases of participants’ alpha oscillations prior to sleep onset. During the intervention week, participants wore an electroencephalogram (EEG)-enabled headband that delivered acoustic pulses timed to arrive anti-phase with alpha for 30 minutes (Stimulation). During the Sham week, the headband silently recorded EEG. The primary outcome was SOL determined by blinded scoring of EEG records. For the 21 subjects included in the analyses, stimulation had a significant effect on SOL according to a linear mixed effects model (p = 0.0019), and weekly average SOL decreased by 10.5 ± 15.9 minutes (29.3 ± 44.4%). These data suggest that phase-locked acoustic stimulation can be a viable alternative to pharmaceuticals to accelerate sleep onset in individuals with prolonged sleep onset latencies.