bluuebunny/crossref_metadata_2025 huggingface dataset:
Low-cost 3D printed lenses for brightfield and fluorescence microscopy
Authors: Christopher Jay , Rooney Liam M. , Donnachie Mark , Uttamchandani Deepak , McConnell Gail , Bauer Ralf
Published: November 2023

We present the fabrication and implementation of low-cost optical quality 3D printed lenses, and their application as microscope objectives with different prescriptions. The imaging performance of the 3D printed lenses was benchmarked against commercially available optics including a 20 mm focal length 12.7 mm diameter NBK-7 plano-convex lens used as a low magnification objective, and a separate high magnification objective featuring three 6 mm diameter NBK-7 lenses with different positive and negative focal lengths. We describe the design and manufacturing processes to produce high-quality 3D printed lenses. We tested their surface quality using a stylus profilometer, showing that they conform to that of commercial glass counterpart lenses. The 3D printed lenses were used as microscope objectives in both brightfield and epi-fluorescence imaging of specimens including onion, cyanobacteria, and variegatedHostaleaves, demonstrating a sub-cellular resolution performance obtained with low-cost 3D printed optical elements within brightfield and fluorescence microscopy.
Mice Models to Bioinformatics Methods Led to the Discovery of Antidiabetic Compounds in the F. racemosa Plant Extracts
Authors: Hossain Mohammad Uzzal , Rahman A.B.Z Naimur , Hossain Md. Shahadat , Dey Shajib , Chowdhury Zeshan Mahmud , Bhattacharjee Arittra , Ahammad Ishtiaque , Hasan Mohammad Kamrul , Ahmed Istiak , Hosen Md. Billal , Das Keshob Chandra , Keya Chaman Ara , Salimullah Md.
Published: November 2023

One of the primary health issues caused by inadequate blood sugar regulation is Diabetes Mellitus (DM). Diabetes and its consequences remain clinically significant even with the development of oral hypoglycemic medications. Therefore, Ficus racemosa (F. racemosa) plant has been studied for assessing of its antidiabetic potential coupling with animal model and in silico experiments. Drug Alloxan (150 mg/kg) was injected to induce the experimental diabetes in Swiss Albino mice, and two doses methanol extract of the F. racemosa fruit (300 and 500 mg/kg) along with glibenclamide (5 mg/kg) were given orally. Oral Glucose Tolerance Test (OGTT) and acute toxicity were performed as well in both diabetic and non-diabetic mice. Later, in silico experiments including ADMET profiling, molecular docking and simulations were performed. The administration of a dosage less than 3000 mg/kg has been observed to be well-tolerated by mice, with no reported instances of mortality or adverse effects. Following oral administration for 7 days, the blood glucose level (BGL) was significantly decreased in mice model in both doses of extracts, indicating the effect of F. racemosa. Subsequent to this, molecular docking and simulations have indicated that the SIRT1 receptor exhibits a higher binding affinity towards four specific compounds, namely Friedelin, Lupeol Acetate, Gluanol, and Ferulic Acid, as indicated by the dynamics parameters and interacting residues. The current investigation provided evidence that the fruit extract of F. racemosa significantly mitigated the hyperglycemic impact. Moreover, a total of four substances have been found that play a crucial role in the mechanisms behind the reduction of diabetic effects. Hence, the current investigation could potentially serve as a viable therapeutic approach in the treatment of diabetes.
DNA methylation carries signatures of sublethal effects under thermal stress in loggerhead sea turtles
Authors: Yen Eugenie C. , Gilbert James D. , Balard Alice , Afonso Inês O. , Fairweather Kirsten , Newlands Débora , Lopes Artur , Correia Sandra M. , Taxonera Albert , Rossiter Stephen J. , Martín-Durán José M. , Eizaguirre Christophe
Published: November 2023

Rising global temperatures are a major threat to biodiversity. Whilst research generally focuses on thermal tolerance and mortality, sublethal effects may alter population dynamics and subsequently the adaptive potential of species. However, detecting such effects in the wild can be challenging, particularly for endangered and long-lived species with cryptic life histories. This necessitates the development of molecular tools to identify their signatures. In a split-clutch design experiment, we relocated clutches of wild, nesting loggerhead sea turtles (Caretta caretta) to a protected,in-situhatchery. Eggs were then split into two sub-clutches incubated under shallow (35cm) or deep (55cm) conditions, with those in the shallow treatment experiencing significantly higher temperatures. Whilst no difference in hatching success was observed between treatments, hatchlings that emerged from the shallow, warmer treatment had altered length-mass relationships, and were weaker at fitness tests of locomotion capacity than their siblings incubated in the deep, cooler treatment. To characterise the molecular signatures of these thermal effects, we performed whole genome bisulfite sequencing on blood samples collected upon emergence. This identified 714 differentially methylated sites between treatments, including on genes with neuronal development, cytoskeleton, and sex determination functions. Taken together, our results show that higher incubation temperatures can induce sublethal effects in hatchlings, which are reflected in their DNA methylation status at identified sites. Such sites could be used as biomarkers of thermal stress, especially if they are retained across life stages. Overall, this study suggests that global warming may have population-level consequences for loggerhead sea turtles, by reducing hatchling quality, dispersal capacity and the adaptive potential of this species. Conservation efforts for climate-threatened taxa like endangered sea turtles will therefore benefit from strategies that monitor and mitigate exposure to incubation temperatures that lead to sublethal effects.
Multi-protein chimeric antigens, a novel combined approach for efficiently targeting and blocking the blood stage ofPlasmodium falciparum
Authors: Deshmukh Bhagyashree , Khatri Dhruv , Kochar Sanjay Kumar , Athale Chaitanya , Karmodiya Krishanpal
Published: November 2023

Plasmodium falciparum-induced malaria remains a fatal disease affecting millions of people worldwide. Mainly, the blood stage of malaria is highly pathogenic and symptomatic, rapidly damaging the host organs and occasionally leading to death. Currently, no vaccines are approved for use against the blood stage of malaria. Canonical vaccines in the past have selected the most immunodominant or essential protein to block the growth of the parasite. This strategy works efficiently for low-complexity organisms such as viruses and a few bacteria but has not shown promising results for a malaria vaccine.Plasmodiumhas a complex life cycle and vaccine candidates especially during blood stage are ineffective due to multiple gene families showing redundancy, immune evasion, and insufficient antibody titer. Herein, we demonstrate a novel strategy of combining multiple antigens from the blood stage ofPlasmodium falciparumusing only the most immunodominant peptide sequences as a way of tackling polymorphism and redundancy. We created three chimeric antigens targeting eight PfEMP1 proteins (chimeric varB) and eight merozoite surface proteins (chimeric MSP and InvP) by selecting and stitching B-cell epitopes. Our chimeric constructs show naturally circulating antibodies against individual peptides using epitope-mapping microarray as well as entire proteins in malaria-infected patients. We demonstrate that anti-varB antibodies are neutralizing in nature and significantly reduce the cytoadhesion on an organ-on-chip system with a microfluidic device mimicking physiological conditions. We have applied a Deep Learning based method to quantify the number of adhered RBCs under fluidic conditions that is used to study cytoadhesion. Furthermore, the anti-MSP and InvP antibodies show complete growth inhibition in a single cycle at a combined concentration of 0.13 mg/ml. Overall, our results show that a combination of antigenic peptides from multiple antigens can function as a next-generation vaccine and effectively block the blood stage by reducing cytoadhesion and inhibiting the parasite growth.
Group-common and individual-specific effects of structure-function coupling in human brain networks with graph neural networks
Authors: Chen Peiyu , Yang Hang , Zheng Xin , Jia Hai , Hao Jiachang , Xu Xiaoyu , Li Chao , He Xiaosong , Chen Runsen , Okubo Tatsuo S. , Cui Zaixu
Published: November 2023

The human cerebral cortex is organized into functionally segregated but synchronized regions bridged by the structural connectivity of white matter pathways. While structure-function coupling has been implicated in cognitive development and neuropsychiatric disorders, it remains unclear to what extent the structure-function coupling reflects a group-common characteristic or varies across individuals, at both the global and regional brain levels. By leveraging two independent, high-quality datasets, we found that the graph neural network accurately predicted unseen individuals’ functional connectivity from structural connectivity, reflecting a strong structure-function coupling. This coupling was primarily driven by network topology and was substantially stronger than that of the correlation approaches. Moreover, we observed that structure-function coupling was dominated by group-common effects, with subtle yet significant individual-specific effects. The regional group and individual effects of coupling were hierarchically organized across the cortex along a sensorimotor-association axis, with lower group and higher individual effects in association cortices. These findings emphasize the importance of considering both group and individual effects in understanding cortical structure-function coupling, suggesting insights into interpreting individual differences of the coupling and informing connectivity-guided therapeutics.
Sec7 regulatory domains scaffold autoinhibited and active conformations
Authors: Brownfield Bryce A. , Richardson Brian C. , Halaby Steve L. , Fromme J. Christopher
Published: November 2023

The late stages of Golgi maturation involve a series of sequential trafficking events in which cargo-laden vesicles are produced and targeted to multiple distinct subcellular destinations. Each of these vesicle biogenesis events requires activation of an Arf GTPase by the Sec7/BIG guanine nucleotide exchange factor (GEF). Sec7 localization and activity is regulated by autoinhibition, positive feedback, and interaction with other GTPases. Although these mechanisms have been characterized biochemically, we lack a clear picture of how GEF localization and activity is modulated by these signals. Here we report the cryoEM structure of full-length Sec7 in its autoinhibited form, revealing the architecture of its multiple regulatory domains. We use functional experiments to determine the basis for autoinhibition and use structural predictions to produce a model for an active conformation of the GEF that is supported empirically. This study therefore elucidates the conformational transition that Sec7 undergoes to become active on the organelle membrane surface.
Modulation of dysbiotic vaginal complications by cervical mucus revealed in linked human vagina and cervix chips
Authors: Gutzeit Ola , Gulati Aakanksha , Izadifar Zohreh , Stejskalova Anna , Rhbiny Hassan , Cotton Justin , Budnik Bogdan , Shahriar Sanjid , Goyal Girija , Junaid Abidemi , Ingber Donald E.
Published: November 2023

Background

The cervicovaginal mucus that coats the upper surface of the vaginal epithelium is thought to serve as a selective barrier that helps to clear pathogens, however, its role in modulating the physiology and pathophysiology of the human vagina is poorly understood. Bacterial vaginosis (BV), a common disease of the female reproductive tract that increases susceptibility to sexually transmitted infections, pelvic inflammatory disease, infertility, preterm birth, and both maternal and neonatal infections is characterized by the presence of a wide array of strict and facultative anaerobes, often includingGardnerella vaginalis.

Objective

To assess the role of cervical mucus in preventing dysbiosis-associated complications and preserving vaginal health.

Study Design

To better understand the role of cervicovaginal mucus in vaginal health, we used human organ-on-a-chip (Organ Chip) microfluidic culture technology to analyze the effects of cervical mucus produced in a human Cervix Chip when transferred to a human Vagina Chip BV model. Both chips are lined by primary human organ-specific (cervical or vaginal) epithelium interfaced with organ-specific stromal fibroblasts.

Results

Our data show that mucus-containing effluents from Cervix Chips protect Vagina Chips from inflammation and epithelial cell injury caused by co-culture with dysbiotic microbiome containingG. vaginalis. Proteomic analysis of proteins produced by the Vagina Chip following treatment with the Cervix Chip mucus also revealed a collection of differentially abundant proteins that may contribute to the vaginal response to dysbiotic microbiome, which could represent potential diagnostic biomarkers or therapeutic targets for management of BV.

Conclusions

This study highlights the importance of cervical mucus in control of human vaginal physiology and pathophysiology, and demonstrates the potential value of Organ Chip technology for studies focused on health and diseases of the female reproductive tract.
A Simple Strategy for Identifying Conserved Features across Non-independent Omics Studies
Authors: Reed Eric , Sebastiani Paola
Published: November 2023

False discovery is an ever-present concern in omics research, especially for burgeoning technologies with unvetted specificity of their biomolecular measurements, as such unknowns obscure the ability to characterize biologically informative features from studies performed with any single platform. Accordingly, performing replication studies of the same samples using different omics platforms is a viable strategy for identifying high-confidence molecular associations that are conserved across studies. However, an important caveat of replication studies that include the same samples is that they are inherently non-independent, leading to overestimating conservation if studies are treated otherwise. Strategies for accounting for such inter-study dependencies have been proposed for meta-analysis methods devised to increase statistical power to detect molecular associations in one or more studies. Still, they are not immediately suited for identifying conserved molecular associations across multiple studies. Here, we present a unifying strategy for performing inter-study conservation analysis as an alternative to meta-analysis strategies for aggregating summary statistical results of shared features across complementary studies while accounting for inter-study dependency. This method, which we call “adjusted maximum p-value” (AdjMaxP), is easy to implement with inter-study dependency and conservation estimated directly from the p-values from each study’s molecular feature-level association testing results. Through simulation-based assessment, we demonstrate AdjMaxP’s improved performance for accurately identifying conserved features over a related meta-analysis strategy for non-independent studies. AdjMaxP offers an easily implementable strategy for improving the precision of analyses for biomarker discovery from cross-platform omics study designs, thereby facilitating the adoption of such protocols for robust inference from emerging omics technologies.
Structure guided mutagenesis of Henipavirus Receptor Binding Proteins reveals molecular determinants of receptor usage and antibody binding epitopes
Authors: Oguntuyo KY , Haas GD , Azarm KD , Stevens CS , Brambilla L , Kowdle S , Avanzato VA , Pryce R , Freiberg AN , Bowden TA , Lee B
Published: November 2023

Nipah virus (NiV) is a highly lethal, zoonotic henipavirus (HNV) that causes respiratory and neurological signs and symptoms in humans. Similar to other paramyxoviruses, HNVs mediate entry into host cells through the concerted actions of two surface glycoproteins: a receptor binding protein (RBP) that mediates attachment and a fusion glycoprotein (F) that triggers fusion in an RBP-dependent manner. NiV uses ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3) as entry receptors. Ghana virus (GhV), a novel HNV identified in a Ghanaian bat, use EFNB2 but not EFNB3. In this study, we employ a structure-informed approach to identify receptor interfacing residues and systematically introduce GhV-RBP residues into a NiV-RBP backbone to uncover the molecular determinants of EFNB3 usage. We reveal two regions that severely impair EFNB3 binding by NiV-RBP and EFNB3-mediated entry by NiV pseudotyped viral particles. Further analyses uncovered two point mutations (NiVN557SGhVandNiVY581TGhV) pivotal for this phenotype. Moreover, we identify NiV interaction with Y120 of EFNB3 as important for usage of this receptor. Beyond these EFNB3-related findings, we reveal two domains that restrict GhV binding of EFNB2, identify the HNV-head as an immunodominant target for polyclonal and monoclonal antibodies, and describe putative epitopes for GhV and NiV-specific monoclonal antibodies. Cumulatively, the work presented here generates useful reagents and tools that shed insight to residues important for NiV usage of EFNB3, reveals regions critical for GhV binding of EFNB2, and describes putative HNV antibody binding epitopes.
Exposure to sounds during sleep impairs hippocampal sharp wave ripples and memory consolidation
Authors: Salgado-Puga Karla , Rothschild Gideon
Published: November 2023

Sleep is critical for the consolidation of recent experiences into long-term memories. As a key underlying neuronal mechanism, hippocampal sharp-wave ripples (SWRs) occurring during sleep define periods of hippocampal reactivation of recent experiences and have been causally linked with memory consolidation. Hippocampal SWR-dependent memory consolidation during sleep is often referred to as occurring during an “offline” state, dedicated to processing internally generated neural activity patterns rather than external stimuli. However, the brain is not fully disconnected from the environment during sleep. In particular, sounds heard during sleep are processed by a highly active auditory system which projects to brain regions in the medial temporal lobe, reflecting an anatomical pathway for sound modulation of hippocampal activity. While neural processing of salient sounds during sleep, such as those of a predator or an offspring, is evolutionarily adaptive, whether ongoing processing of environmental sounds during sleep interferes with SWR-dependent memory consolidation remains unknown. To address this question, we used a closed-loop system to deliver non-waking sound stimuli during or following SWRs in sleeping rats. We found that exposure to sounds during sleep suppressed the ripple power and reduced the rate of SWRs. Furthermore, sounds delivered during SWRs (On-SWR) suppressed ripple power significantly more than sounds delivered 2 seconds after SWRs (Off-SWR). Next, we tested the influence of sound presentation during sleep on memory consolidation. To this end, SWR-triggered sounds were applied during sleep sessions following learning of a conditioned place preference paradigm, in which rats learned a place-reward association. We found that On-SWR sound pairing during post-learning sleep induced a complete abolishment of memory retention 24 h following learning, while leaving memory retention immediately following sleep intact. In contrast, Off-SWR pairing weakened memory 24 h following learning as well as immediately following learning. Notably, On-SWR pairing induced a significantly larger impairment in memory 24 h after learning as compared to Off-SWR pairing. Together, these findings suggest that sounds heard during sleep suppress SWRs and memory consolidation, and that the magnitude of these effects are dependent on sound-SWR timing. These results suggest that exposure to environmental sounds during sleep may pose a risk for memory consolidation processes.
Individual cell fate and population dynamics revealed by a mathematical model linking telomere length and replicative senescence
Authors: Rat Anaïs , Doumic Marie , Teixeira Maria Teresa , Xu Zhou
Published: November 2023

Progressive shortening of telomeres ultimately causes replicative senescence and is linked with aging and tumor suppression. Studying the intricate link between telomere shortening and senescence at the molecular level and its population-scale effects over time is challenging with current approaches but crucial for understanding behavior at the organ or tissue level. In this study, we developed a mathematical model for telomere shortening and the onset of replicative senescence using data fromSaccharomyces cerevisiaewithout telomerase. Our model tracks individual cell states, their telomere length dynamics, and lifespan over time, revealing selection forces within a population. We discovered that both cell genealogy and global telomere length distribution are key to determine the population proliferation capacity. We also discovered that cell growth defects unrelated to telomeres also affect subsequent proliferation and may act as confounding variables in replicative senescence assays. Overall, while there is a deterministic limit for the shortest telomere length, the stochastic occurrence of non-terminal arrests drive cells into a totally different regime, which may promote genome instability and senescence escape. Our results offer a comprehensive framework for investigating the implications of telomere length on human diseases.

One-sentence Summary

Key determinants of population proliferation capacity in the context of telomere shortening.
Focal adhesion-derived liquid-liquid phase separations regulate mRNA translation
Authors: Kumar Abhishek , Tanaka Keiichiro , Schwartz Martin A
Published: November 2023

Liquid-liquid phase separation (LLPS) has emerged as a major organizing principle in cells. Recent work showed that multiple components of integrin-mediated focal adhesions including p130Cas can form LLPS, which govern adhesion dynamics and related cell behaviors. In this study, we found that the focal adhesion protein p130Cas drives formation of structures with the characteristics of LLPS that bud from focal adhesions into the cytoplasm. Condensing concentrated cytoplasm around p130Cas-coated beads allowed their isolation, which were enriched in a subset of focal adhesion proteins, mRNAs and RNA binding proteins, including those implicated in inhibiting mRNA translation. Plating cells on very high concentrations of fibronectin to induce large focal adhesions inhibited message translation which required p130Cas and correlated with droplet formation. Photo-induction of p130Cas condensates using the Cry2 system also reduced translation. These results identify a novel regulatory mechanism in which high adhesion limits message translation via induction of p130Cas-dependent cytoplasmic LLPS. This mechanism may contribute to the quiescent state of very strongly adhesive myofibroblasts and senescent cells.
Homologies and evolution of male tail characters in rhabditid and diplogastrid nematodes
Authors: Kiontke Karin , Kolysh Simone , Ng Rocio , Fitch David H. A.
Published: November 2023

A major question in evolutionary biology is how often the same developmental events, mechanisms and genes are reused in the recurrent evolution of similar phenotypes. If this happens frequently, it would suggest that evolution is often constrained by developmental genetic mechanisms. To help address this question, we used adherens junction staining and laser ablation to analyze the development underlying several features of nematode male tails have evolved recurrently. We find that recurrent evolution has sometimes employed similar developmental events (parallel evolution) and sometimes different events (convergent evolution). Specifically, phasmid position changed four times via cell migration and never by switches in cell lineage polarity; different genital papillae are missing in species with less than nine; and tail tip morphogenesis was gained at least twice (once with tail tip cell fusions and once without) and lost at least twice. As in previous analyses, we also find that genital papilla positions have shifted differently in different lineages relative to their conserved positions of origin in the lateral hypodermis. In particular, the v1 papilla homolog in diplogastrids has moved dorsally relative to the other v-papillae and lies posterior to the v2 papilla. The prevalence of recurrently evolved characters (homoplasy) suggests that caution should be exercised when using these characters for phylogenetic inference. On the other hand, because of their recurrent evolution, these characters provide good models for investigating how developmental and genetic systems may bias, constrain or allow phenotypic evolution.
Anodal M1 tDCS enhances online learning of rhythmic timing videogame skill
Authors: Meek Anthony W. , Greenwell Davin , Poston Brach , Riley Zachary A.
Published: November 2023

Transcranial direct current stimulation (tDCS) has been shown to modify excitability of the primary motor cortex (M1) and influence online motor learning. However, research on the effects of tDCS on motor learning has focused predominantly on simplified motor tasks. The purpose of the present study was to investigate whether anodal stimulation of M1 over a single session of practice influences online learning of a relatively complex rhythmic timing video game. Fifty-eight healthy young adults were randomized to either a-tDCS or SHAM conditions and performed 2 familiarization blocks, a 20-minute 5 block practice period while receiving their assigned stimulation, and a post-test block with their non-dominant hand. To assess performance, a performance index was calculated that incorporated timing accuracy elements and incorrect key inputs. The results showed that M1 a-tDCS enhanced the learning of the video game based skill more than SHAM stimulation during practice, as well as overall learning at the post-test. These results provide evidence that M1 a-tDCS can enhance acquisition of skills where quality or success of performance depends on optimized timing between component motions of the skill, which could have implications for the application of tDCS in many real-world contexts.
Stable isotopes disentangle niche partitioning and species co-occurrence in a multi-level marine mutualism
Authors: Titus Benjamin M. , Froehlich Catheline Y. M. , Vondriska Clayton , Baker Ronald , Caves Eleanor M.
Published: November 2023

Ecologists have long sought general explanations for the co-occurrence of ecologically similar taxa. Niche theory explains co-occurrence via functional differences among taxa that reduce competition and promote resource partitioning. Alternatively, the unified neutral theory of biodiversity and biogeography suggests that co-occurrence can be attributed to stochastic processes, and thus, presupposes that ecologically similar species that occur in sympatry are functionally analogous. We test these alternative hypotheses in multiple dimensions using the most diverse crustacean-sea anemone symbiosis from coral reefs in the Tropical Western Atlantic. δ13C and δ15N stable isotope analyses of six crustacean symbionts that co-occur around the host anemoneBartholomea annulataexhibit highly differentiated isotopic niche space spanning three trophic levels. As multiple crustacean species within the symbiosis have been documented as cleaners that remove parasites from reef fishes, we extended our investigation into the broader cleaner community. Our stable isotope analyses of cleaners shows that only Pederson’s cleaner shrimpAncylomenes pedersoniexhibits δ15N isotopic signatures that are consistent with a dedicated cleaning lifestyle. Co-occurring species that have been previously described to clean reef fishes such asPericlimenes yucatanicus, Stenopus hispidus,andStenorhynchus seticornisall occupy trophic levels well belowAn. pedersoni. Taken together, our data are consistent with the expectations of niche theory: co-occurring symbiotic crustaceans have highly partitioned niche space with low levels of functional redundancy. Finally, our findings reinforce and extend the ecological importance ofAn. pedersonias likely the only dedicated cleaner shrimp on coral reefs in the Tropical Western Atlantic.
Unraveling cryptic diversity: Genomic approaches to study the taxonomy and evolution of Woolly-necked storks using museum specimens
Authors: Ghimire Prashant , Palacios Catalina , Tremble Jeremiah , Lamichhaney Sangeet
Published: November 2023

The availability of large-scale genomics data for current research in evolutionary biology has enabled a comprehensive examination of the intricate interplay between diverse evolutionary processes associated with speciation. Despite these advancements, the genomic basis of taxonomic classification remains challenging in many species, one such example being the Woolly-necked storks(Ciconia sps.). The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification(C. episcopus and C. microcelis)that has been a matter of contention and ambiguity. Asian and African Woollynecks were just recently recognized as different species based on their morphological differences, however genetic/genomic studies on Woolly-necked storks are lacking. In this study, we have used ∼70-year-old museum samples to explore the taxonomy and evolution of the Woolly-necked storks. We used a whole-genome sequencing strategy and generated 13.5 million single nucleotide polymorphisms (SNPs) that were polymorphic among populations of Asian and African Woollynecks. Our study has revealed that Asian and African Woollyneck are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspeciesC. e. neglectaandC. e. episcopussuggesting this classification harbors cryptic diversity that requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results suggest populations-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds. Moreover, our study also provides historical genomic resources to examine genomic signatures of local adaptation associated with the distribution, ecology, and evolution of African and Asian Woollynecks.
Co-exposure to Polyethylene Fiber andSalmonella entericaTyphimurium Alters Microbiome and Metabolome ofin vitroChicken Cecal Mesocosms
Authors: Chatman Chamia C. , Olson Elena G. , Freedman Allison J. , Dittoe Dana K. , Ricke Steven C. , Majumder Erica L-W.
Published: November 2023

Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations where there could be an interaction withSalmonella entericaTyphimurium, one of the commonly isolated serovars from processed chicken. In this study, the microbiota response to a 24-hour co-exposure toSalmonella entericaTyphimurium and/or low-density polyethylene (PE) microplastics in anin vitrobroiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and withoutS.Typhimurium yielded a lowerFirmicutes/Bacteroidesratio compared to other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence ofS.Typhimurium. Additionally, the co-exposure to PE Fiber andS. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in anin vitrochicken cecal model.

IMPORTANCE

Researching the exposome, a summation of exposure of one’s lifespan, will aid in determining the environmental factors that contribute to disease states. There is an emerging concern that microplastic-pathogen interactions in the gastrointestinal tract of broiler chickens may lead to an increase inSalmonellainfection across flocks and eventually increased incidence of human salmonellosis cases. In this research article, we elucidated the effects of co-exposure to polyethylene microplastics andSalmonella entericaserovar Typhimurium on the ceca microbial community.Salmonellapresence caused strong shifts in the cecal metabolome but not the microbiome. The inverse was true for polyethylene fiber. Polyethylene powder had almost no effect. The co-exposure had worse effects than either alone. This demonstrates that exposure effects to the gut microbial community are contaminant specific. When combined, the interactions between exposures exacerbate changes to the gut environment. The results herein support currentSalmonellamitigation efforts and understanding microplastics-pathogen interactions.
Spatial and temporal profiling of the complement system uncovered novel functions of the alternative complement pathway in brain development
Authors: Zhang Yingying , Watson Brianna , Rattan Ajitanuj , Lee Tyrone , Chawla Smriti , Geistlinger Ludwig , Guan Yilin , Ma Minghe , Caldarone Barbara J. , Song Wenchao , Moffitt Jeffrey R. , Carroll Michael C.
Published: November 2023

Mounting evidence implicated the classical complement pathway (CP) in normal brain development, and the pathogenesis of neuropsychiatric and neurodegenerative diseases. However the source and regulation of complement in the brain remain unclear. Using MERFISH, a spatial transcriptomic method with single-cell resolution, we established a developmental brain atlas of the complement system. We showed that the brain synthesizes essential building blocks of the complement system locally with remarkable cellular and spatial heterogeneity. We provided transcriptional evidence supporting the presence of the alternative pathway (AP), but lack of lectin pathway (LP) activity in postnatal brain development. Cell type, temporal and spatial expression patterns of genes involved indicate non-redundant functions of the CP and AP. In addition, deficiency in Masp3-driven AP resulted in developmental and cognitive defects, indicating essential functions of the AP, an observation that highlights the necessity to disentangle differential involvement of the three complement activation pathways in development and diseases.
Preventing evolutionary rescue in cancer
Authors: Patil Srishti , Ahmed Armaan , Viossat Yannick , Noble Robert
Published: November 2023

Abstract

First-line cancer treatment frequently fails due to initially rare therapeutic resistance. An important clinical question is then how to schedule subsequent treatments to maximize the probability of tumour eradication. Here, we provide a theoretical solution to this problem by using mathematical analysis and extensive stochastic simulations within the framework of evolutionary rescue theory to determine how best to exploit the vulnerability of small tumours to stochastic extinction. Whereas standard clinical practice is to wait for evidence of relapse, we confirm a recent hypothesis that the optimal time to switch to a second treatment is when the tumour is close to its minimum size before relapse, when it is likely undetectable. This optimum can lie slightly before or slightly after the nadir, depending on tumour parameters. Given that this exact time point may be difficult to determine in practice, we study windows of high extinction probability that lie around the optimal switching point, showing that switching after the relapse has begun is typically better than switching too early. We further reveal how treatment dose and tumour demographic and evolutionary parameters influence the predicted clinical outcome, and we determine how best to schedule drugs of unequal efficacy. Our work establishes a foundation for further experimental and clinical investigation of this evolutionarily-informed “extinction therapy” strategy.
The uniqueLegionella longbeachaecapsule favors intracellular replication and immune evasion
Authors: Schmidt Silke , Mondino Sonia , Gomez-Valero Laura , Escoll Pedro , Mascarenhas Danielle P. A. , Gonçalves Augusto , Rusniok Christophe , Sachse Martin , Nilges Maryse Moya- , Fontaine Thierry , Zamboni Dario S. , Buchrieser Carmen
Published: November 2023

Legionella longbeachaeandLegionella pneumophilacause Legionnaires’ disease despite species-specific differences in environmental niches, disease epidemiology, and genomic content. Here, we characterized a newL. longbeachaevirulence factor, a capsule that is expressed in post-exponential growth phase as shown by electron microscopy. Analysis of the capsule compositionviaHLPC revealed the presence of a highly anionic polysaccharide absent in a capsule mutant. The capsule is crucial for replication and virulencein vivoin a mouse model of infection and in the natural hostAcanthamoeba castellanii. It has anti-phagocytic function when encountering innate immune cells, it is involved in a low cytokine responses in mice and in human monocyte derived macrophages and helps to dampen the innate immune response. TheL. longbeachaecapsule is a novel virulence factor, unique among knownLegionellaspecies, that aidsL. longbeachaeto survive in specific niches and partly confersL. longbeachaeits unique infection characteristics.
Phylogenetic analysis reveals unexplored fungal diversity on skin
Authors: Brito Pedro Nicolas , Paulino Luciana Campos
Published: November 2023

Despite recent advances, to date there is not full knowledge of microbial diversity inhabiting various organs of human body. Skin harbors a complex microbiome that might affect our health positively and negatively. Fungal communities from skin are dominated byMalasseziayeasts. Traditionally, they were thought to be causative agents of skin diseases; however, their role is controversial, and the possible implication of specific species and subtypes remains unclear. Previously, we have conducted two fungal community surveys in healthy skin and dandruff/sebohrreic dermatitis, and have detected prevalentMalasseziaorganisms that could not be assigned to any known species. The usage of distinct ITS rDNA regions did not allow sequence comparison between studies. Here we report molecular characterization and phylogenetic analysis of unidentifiedMalasseziaorganisms, aiming to increase knowledge in fungal microbiome from skin. Findings suggested that a highly prevalent organism might belong to a novelMalasseziaspecies. Results also revealed uncertain taxonomic assignments, even in the case of accepted species. Correct assignment of species and intraspecific variants is relevant considering that specific taxa might be directly involved in disease development. Despite high prevalence, organisms might have remained undiscovered due to difficulties in culturingMalassezia. Challenges and future perspectives for skin fungal microbiome studies are discussed. We address issues to be overcome for unraveling the complete skin microbial diversity and its relation to health and disease.
eSVD-DE: Cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings
Authors: Lin Kevin Z. , Qiu Yixuan , Roeder Kathryn
Published: November 2023

Background

Single-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes.

Results

We develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals’ posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression.

Conclusions

eSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.
Mutational destabilisation accelerates the evolution of novel sensory and network functions
Authors: Kimura Yuki , Kawai-Noma Shigeko , Umeno Daisuke
Published: November 2023

Binding-induced folding1–4(BIF) is a promising mechanism that can be used to rapidly convert binders into sensors/regulators without allosteric design. Here we showed that allosteric regulatory proteins AraC can acquire BIF mechanism without compromising their inherent allosteric mechanisms, with high frequency upon mutations. This opened an opportunity to compare the evolutionary capacity of the allosteric and non-allosteric modes of a specific sensory protein. We found that AraC evolved novel sensory function far more rapidly in BIF mode than in allosteric mode. This newly acquired (non-allosteric) sensory function is distinguishable both in its response logic and in sensitivity from original (allosteric) one, and they can be operated simultaneously, independently, and cooperatively, allowing the construction of complex regulatory networks behaviours such as a selective NIMPLY/OR converter and width-tuneable band-pass filter. Together with its high frequency of emergence, BIF can be an overlooked evolutionary driver of the invention of novel biosensors and complex regulatory networks in nature and laboratory.
An unmanned aerial vehicle pipeline to estimate body volume at scale for ecological monitoring
Authors: Stone Thomas C , Davis Katrina J
Published: November 2023

Demographic data are essential to construct mechanistic models to understand how populations change over time and in response to global threats like climate change. Existing demographic data are either lacking or insufficient for many species, particularly those that are challenging to study, such as marine mammals. A pipeline for collecting accurate demographic data to construct robust demographic models at scale would fill this knowledge gap for many species, including marine mammals like pinnipeds (seals, sea lions, and walruses).

We introduce a non-invasive pipeline to estimate the 3D body size (volume) of species that will allow monitoring at high spatial and temporal scales. Our pipeline integrates 3D structure-from-motion photogrammetry data collected via planned flight missions using off-the-shelf, multirotor unmanned aerial vehicles (UAVs). We apply and validate this pipeline on the grey sealHalichoerus grypus, a marine species that spends much of its time at sea but is predictably observable during its annual breeding season. We investigate the optimal ground sampling distance (GSD) for surveys by calculating the success rates and accuracy of volume estimates of individuals at different elevations.

We establish an optimal GSD of 0.8 cm px-1for animals similar in size to UK grey seals (∼1.4 - 2.5 m length), making our pipeline reproducible and applicable to a broad range of organisms. Volume estimates were accurate and could be made for up to 68% of hauled-out seals in the study areas. Finally, we highlight six key traits that make a species well-suited to estimating body volume following this pipeline. Good candidates include large reptiles like crocodiles, large mammals such as hippopotamus, and shrubs or bushes in deserts and Mediterranean habitats.

Our pipeline accurately estimates individual body volume of marine macrovertebrates in a time-and cost-effective manner whilst minimising disturbance. Whilst the approach is applied to pinnipeds here, the pipeline is adaptable to many different taxa that are otherwise challenging to study. Our proposed approach therefore opens up previously inaccessible areas of the Tree of Life to demographic studies, which will improve our ability to protect and conserve these species into the future.
Causal Role of the Medial Prefrontal Cortex in Learning Social Hierarchy
Authors: Qu Chen , Huang Yulong , Philippe Rémi , Cai Shenggang , Derrington Edmund , Moisan Frédéric , Shi Mengke , Dreher Jean-Claude
Published: November 2023

Social hierarchy is a fundamental principle of social organization and an important attribute of community stability and development. Yet, little is known about the causal role of specific brain regions in learning hierarchies. Here, using transcranial direct current stimulation (tDCS), we investigated the causal role of the medial prefrontal cortex (mPFC) in learning social and non-social hierarchies. In the Training phase, participants(N=128) acquired knowledge of social and non-social hierarchy in parallel, by trial and error. During the Test phase, they were presented with two items from hierarchies that were never encountered together and required to make transitive inferences. Anodal stimulation over mPFC impaired social hierarchy learning compared with non-social learning and this modulation was influenced by the relative social rank of the members (i.e. higher or lower status). Anodal stimulation also impaired transitive inference making, but only during early blocks before learning was established. Together, our results provide causal evidence of mPFC engagement in learning social ranks by observation.
Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics
Authors: Bortel Patricia , Piga Ilaria , Koenig Claire , Gerner Christopher , Martinez del Val Ana , Olsen Jesper V.
Published: November 2023

Improving coverage, robustness and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography tandem mass spectrometry (LC-MS/MS) runs from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-beads phosphoproteomics sample preparation with focus on low input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample and loading buffer volumes, allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 µg of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA).

Graphical abstract