bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying functional and regional differences in chimpanzee stone tool technology
Authors: Proffitt Tomos , Reeves Jonathan. S. , Pacome Soiret Serge , Luncz Lydia. V.
Published: September 2022

The earliest hominin archaeological sites preserve a record of stone tools used for cutting and pounding. Traditionally, sharp-edged flakes were seen as the primary means by which our earliest ancestors interacted with the world. The importance of pounding tools is increasingly apparent. In some cases, they have been compared with stone hammers and anvils used by chimpanzees for nut-cracking. However, there has been little focus on providing a robust descriptive and quantitative characterization of chimpanzee stone tools, allowing for meaningful comparisons between chimpanzee groups and with archaeological artefacts. Here we apply a primate archaeological approach to characterize the range of chimpanzee nut-cracking stone tools from Djouroutou in the Taï National Park. By combining a techno-typological analysis, and two- and three-dimensional measures of damage, we identify clear differences in the location and extent of damage between nut-cracking hammerstones and anvils used at Djouroutou and when compared with other wild chimpanzee populations. Furthermore, we discuss these results in relation to interpretations of Plio-Pleistocene percussive technology. We highlight potential difficulties in identifying the underlying function of percussive artefacts based on morphological or techno-typological attributes alone. The material record from Djouroutou represents an important new datum of chimpanzee regional and material culture.
Lower respiratory tract microbiome composition and community interactions in smokers
Authors: Campos Michael , Cickovski Trevor , Fernandez Mitch , Jaric Melita , Wanner Adam , Holt Gregory , Donna Elio , Mendes Eliana , Silva-Herzog Eugenia , Schneper Lisa , Segal Jonathan , Amador David Moraga , Riveros Juan Daniel , Aguiar-Pulido Vanessa , Banerjee Santanu , Salathe Matthias , Mathee Kalai , Narasimhan Giri
Published: September 2022

The lung microbiome impacts lung function, making any smoking-induced changes in the lung microbiome potentially significant. The complex co-occurrence and co-avoidance patterns between the bacterial taxa in the LRT microbiome were explored for a cohort of active (AS), former (FS), and never (NS) smokers. Bronchoalveolar lavages (BAL) were collected from 55 volunteer subjects (nine NS, 24 FS, and 22 AS). The LRT microbiome composition was assessed using 16S rRNA amplicon sequencing. Identification of differentially abundant taxa, co-occurrence patterns, discriminant analysis, and biomarker inferences were performed. The data show that smoking results in a loss in the diversity of the lower respiratory tract (LRT) microbiome, change in the co-occurrence patterns, and a weakening of the tight community structure present in healthy microbiomes. The increased abundance of Ralstonia taxa in the lung microbiomes of both former and active smokers is significant.
 
Partial least square discriminant and DESeq2 analyses suggested a compositional difference between the cohorts in the LRT microbiome. The groups were sufficiently distinct from each other, suggesting that cessation of smoking may not be sufficient for      the lung microbiota to return to a composition similar to that of never smokers. The LEfSe analyses identified several bacterial taxa as potential biomarkers of smoking status. Network-based clustering analysis highlighted different co-occurring and co-avoiding microbial taxa in the three groups. The analysis found a cluster of bacterial taxa that co-occur in smokers and non-smokers alike. The clusters exhibited tighter and more significant associations in NS compared to FS and AS. Higher degree of rivalry between clusters was observed in the AS.
Acrocarpospora catenulata sp. nov., a novel actinobacterium isolated from lake sediment
Authors: Liu Chaolan , Guo Yidong , Li Li , Li Jianghua , Wang Limei , Lin Jiafu , Wang Xinrong , Chu Yiwen
Published: September 2022

A novel actinobacterium, designated strain H8750T, was isolated from sediment sampled at Lugu Lake, southwest PR China and its polyphasic taxonomy was studied. Strain H8750Tproduced well-developed substrate mycelium, and formed club-shaped and hooked structures borne on the tip of the aerial mycelia. It containedmeso-diaminopimelic, glucose, ribose and madurose in whole-cell hydrolysates. The predominant menaquinones were MK-9(H4), MK-9(H2) and MK-9(H6). The phospholipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, unidentified phospholipids and unidentified aminophospholipids. The major fatty acid (>10 %) werecis9 C17 : 1, iso-C16 : 0and C15 : 0. The DNA G+C content was 69.7 mol% based on the whole genome sequence. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences indicated that strain H8750Twas closely related toAcrocarpospora macrocephalaJCM 10982T(98.0 %),Acrocarpospora pleiomorphaJCM 10983T(97.9 %) andAcrocarpospora phusangensisDSM 45867T(97.8 %) and formed a monophyletic clade within the genusAcrocarposporain the phylogenetic trees. The average nucleotide identity and digital DNA–DNA hybridization values between strain H8750Tand its closely relatedAcrocarposporaspecies were 79.8~87.2 % and 25.9~28.0 %, respectively, which showed that it belonged to a distinct species. Furthermore, the morphological and phenotypic characteristics allowed the isolate to be differentiated from its closely related species. Therefore, it is concluded that strain H8750Tcan be classified as representing a novel species of the genusAcrocarpospora, for which the nameAcrocarpospora catenulatasp. nov. is proposed. The type strain is H8750T(=JCM 34849T=CICC 25116T). Moreover, based on the gene prediction results, strain H8750Tmay have the genetic potential to synthesize many new secondary metabolites, which further increases its bioactive value.
Local Control Comparison of Early-Stage Epidermal Skin Cancers Treated With and Without Dermal Image Guidance: A Meta-Analysis
Authors: Yu Lio , Moloney Mairead , Tran Alison , Zheng Songzhu , Rogers James
Published: September 2022

Background

Various treatments exist for non-melanoma skin cancer (NMSC), but the mainstay is surgical removal. Superficial radiotherapy (SRT) is one non-surgical technique that has been used for over a century but fell out of favor due to the advent of Mohs micrographic surgery (MMS). A new technology that combines a 22 megahertz (MHz) dermal ultrasound with SRT (US-SRT) enables tumor visualization before, during, and after treatment, and demonstrates increased cure rates and reduced recurrences.

Methods

We conducted a meta-analysis comparing the local control (LC) of four studies using traditional non-image-guided forms of radiotherapy for NMSC treatment to two seminal studies utilizing high-resolution dermal ultrasound-guided SRT (HRUS-SRT). The four traditional radiotherapy studies were obtained from a comprehensive literature search used in an article published by the American Society of Radiation Oncology (ASTRO) on curative radiation treatment of basal cell carcinoma (BCC), squamous cell carcinoma (SCC) and squamous cell carcinoma in-situ (SCCIS) lesions. The meta-analysis employed a logit as the effect size indicator with Q-statistic to test the null hypothesis.

Results

LC rates for the 2 US-SRT studies were statistically superior to the 4 traditional therapies individually and collectively. When stratified by histology, statistically superior outcomes for US-SRT were observed in all subtypes with p-values ranging from p < 0.0001 to p = 0.0438. These results validated an earlier analysis using a logistic regression statistical method showing the same results.

Conclusion

US-SRT is statistically superior to non-image-guided radiotherapies for NMSC treatment. This modality may represent the future standard of non-surgical treatment for early-stage NMSC.
Regionally enriched rare deleterious exonic variants in the UK and Ireland
Authors: Halachev Mihail , Gountouna Elvina , Meynert Alison ,   Regeneron Genetics Center, Tzoneva Gannie , Shuldiner Alan R. , Semple Colin A. , Wilson James F.
Published: September 2022

Geographic clustering of haplotypes appears to have emerged in the UK as a result of differing patterns of immigration and drift in regions that have been relatively isolated from each other. However, until recently it has been unclear how such patterns of regional genetic differentiation might impact the protein-coding fraction of the genome. Here, we exploit UK Biobank (UKB) and Viking Genes whole exome sequencing data to study regional genetic differentiation across the UK and Ireland in protein coding genes, encompassing 20 regions of origin and 44,696 unrelated individuals. We rediscover the strong influence of genetic drift in shaping variation in the Northern Isles of Scotland and among those with full or partial Ashkenazi Jewish (AJ) ancestry. For full AJ, almost half the known rare exonic variants (45%) are at least two-fold more or less frequent than in a Europe-wide reference sample, while the degree of variant frequency differences in Shetland and Orkney are comparable to part AJ (19%, 17%, 16%, respectively). We also demonstrate substantial genetic differentiation among several mainland regions of origin, particularly north and south Wales, SE Scotland and Ireland. With stringent filtering criteria we found 67 variants likely to have adverse biomedical consequences, enriched by at least five-fold in frequency in one or more British or Irish regions relative to a European reference group, and we calculate that this may lead to tens or hundreds of affected individuals. We conclude that regional genetic variation across the UK and Ireland should be considered in the design of genetic studies, and may inform effective genetic screening and counselling.
origamiFISH allows universal, label-free, single molecule visualization of DNA origami nanodevices across biological samples
Authors: Wang Wendy Xueyi , Douglas Travis R. , Zhang Haiwang , Bhattacharya Afrin , Rothenbroker Meghan , Jia Zhengping , Muffat Julien , Li Yun , Chou Leo Y. T.
Published: September 2022

Structural DNA nanotechnology enables user-prescribed design of DNA nanostructures (DNs) for biological applications, but how DN design determines their bio-distribution and cellular interactions remain poorly understood. One challenge is that current methods for tracking DN fatesin situ, including fluorescent-dye labeling, suffer from low sensitivity and dye-induced artifacts. Here we present origamiFISH, a label-free and universal method for single-molecule fluorescence detection of DNA origami nanostructures in cells and tissues. origamiFISH targets pan-DN scaffold sequences with hybridization chain reaction (HCR) probes to achieve thousand-fold signal amplification. We identify cell-type and shape-specific spatiotemporal uptake patterns within 1 minute of uptake and at picomolar DN concentrations, 10,000x lower than field standards. We additionally optimized compatibility with immunofluorescence and tissue clearing to visualize DN distribution within tissue cryo/vibratome-sections, slice cultures, and whole-mount organoids. Together, origamiFISH enables faithful mapping of DN interactions across subcellular and tissue barriers for guiding the development of DN-based therapeutics.
The genetic architecture ofArabidopsis thalianain response to native non-pathogenic leaf bacterial species revealed by GWA mapping in field conditions
Authors: Ramírez-Sánchez Daniela , Duflos Rémi , Gibelin-Viala Chrystel , Zamar Rémy , Vailleau Fabienne , Roux Fabrice
Published: September 2022

Non-pathogenic bacteria can largely contribute to plant health by mobilizing and supplying nutrients and by providing protection against pathogens and resistance to abiotic stresses. Yet, the number of GWAS reporting the genetic architecture of the response to individual members of the beneficial microbiota remains limited. In this study, we established a GWAS under field conditions to estimate the level of genetic variation and the underlying genetic architecture, among 162 accessions ofArabidopsis thalianaoriginating from 54 natural populations located south-west of France, in response to 13 strains of seven of the most abundant and prevalent non-pathogenic bacterial species isolated from the leaf compartment ofA. thalianain the same geographical region. Using a high-throughput phenotyping methodology to score vegetative growth-related traits, extensive genetic variation was detected within our local set ofA. thalianaaccessions in response to these leaf bacteria, both at the species and strain levels. The presence of crossing reaction norms among strains indicates that declaring a strain as a plant-growth promoting bacterium is highly dependent on the host genotype tested. In line with the strong genotype-by-genotype interactions, we detected a complex and highly flexible genetic architecture between the 13 strains. Finally, the candidate genes underlying the QTLs revealed a significant enrichment in several biological pathways, including cell, secondary metabolism, signalling and transport. Altogether, plant innate immunity appears as a significant source of natural genetic variation in plant-microbiota interactions and opens new avenues for better understanding the ecologically relevant molecular dialog during plant-microbiota interactions.
A quantitative universal NGS-based ctDNA assay for hepatoblastoma
Authors: Kahana-Edwin Smadar , Torpy James , Cain Lucy E. , Mullins Anna , McCowage Geoffrey , Woodfield Sarah E. , Vasudevan Sanjeev A. , Shea Dan P.T. , Minoche Andre E , Kummerfeld Sarah , Goldstein Leonard D. , Karpelowsky Jonathan
Published: September 2022

Driver mutations inCTNNB1are a hallmark of hepatoblastoma and offer a common biomarker for a liquid biopsy approach based on the presence ofCTNNB1circulating tumor DNA (ctDNA). We developed and investigated the utility of a quantitative universal next-generation sequencing (NGS) ctDNA assay for hepatoblastoma (QUENCH) to detectCTNNB1ctDNA and assessed the links between ctDNA and current clinical indicators/biomarkers in hepatoblastoma. Applied to patients with hepatoblastoma, we demonstrate quantitation of various variants including single base substitutions and deletions down to 0.3% variant allele frequency, with 65% sensitivity and 100% specificity at the patient level, to allow biopsy-free tumor genotyping and sensitive ctDNA quantitation. CtDNA positivity correlates with tumor burden and ctDNA levels correlate with macroscopic residual disease and treatment response, thus providing promising evidence for the utility of quantitative ctDNA detection in hepatoblastoma.
Clinical Performance and Trends During the First Two Months of Monkeypox Virus PCR Testing at Two United States Reference Labs
Authors: Lieberman Nicole A. P. , Mathias Patrick C. , Bradley Benjamin T. , Greninger Alexander L.
Published: September 2022

Recently, a sustained human-to-human outbreak of monkeypox virus (MPXV), a member of the Orthopoxvirus genus, which includes the etiologic agent of smallpox, has been documented in multiple non-endemic countries including the United States. Prior to June 2022, US testing was limited to public health labs and the Centers for Disease Control and Prevention. Following recognition of the scope of the outbreak, testing for MPXV has expanded into clinical laboratories. Here, we examine epidemiological characteristics, specimen collection practices, and cycle threshold (Ct) values for MPXV PCR tests performed at two reference laboratories.Results from both laboratories support public health data showing a high positivity rate in men (>30%) and those ages 30-49 (25-35%). The overall positivity rate decreased during the study period but remains elevated (∼20%). There was a significant difference in Ct values between laboratories (ARUP 23.86 vs. UW 25.40) and collection method (22.79 for dry swab vs. 24.44 for VTM). These viral load differences likely reflect slight differences in specimen processing. When multiple specimens were collected for a single individual, the overall result concordance rate was greater than 95%, with less than 1.5% of individuals having three or more tests receive a single positive result. As compared to the overall positive cohort, individuals three or more swabs and a single positive result had significantly higher Ct values (22.9 vs 35.0). These results provide an early snapshot of testing in the US during the monkeypox virus outbreak and support restricting the number of swabs collected per individual.
Asymmetrical gene flow between coastal and inland dunes in a threatened digger wasp
Authors: Batsleer Femke , Gallin Matthieu , Delafonteyne Moyra , Dekeukeleire Daan , T’Jollyn Filiep , Vantieghem Pieter , Broeck An Vanden , Mergeay Joachim , Maes Dirk , Bonte Dries
Published: September 2022

1.

Connectivity is a species- and landscape-specific measure that is key to species conservation in fragmented landscapes. However, information on connectivity is often lacking, especially for insects which are known to be severely declining. Patterns of gene flow constitute an indirect measure of functional landscape connectivity. We studied the population genetic structure of the rare digger wasp Bembix rostrata in coastal and inland regions in and near Belgium. The species is restricted to sandy pioneer vegetations for nesting and is well known for its philopatry as it does not easily colonize vacant habitat. It has markedly declined in the last century, especially in the inland region where open sand habitat has decreased in area and became highly fragmented. To assess within and between region connectivity, we used mating system independent population genetic methods suitable for haplodiploid species. We found more pronounced genetic structure in the small and isolated inland populations as compared to the well-connected coastal region. We also found a pattern of asymmetrical gene flow from coast to inland, including a few rare dispersal distances up to 200 to 300 km based on assignment tests. We point to demography, wind and difference in dispersal capacities as possible underlying factors that can explain the discrepancy in connectivity and asymmetrical gene flow between the different regions. Despite B. rostrata being a poor colonizer, gene flow between existing populations appeared not highly restricted, especially at the coast. Therefore, to improve the conservation status of B. rostrata, the primary focus should be to preserve and create sufficient habitat for this species to increase the number and quality of (meta)populations, rather than focusing on landscape connectivity itself.
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
Authors: Knudsen Teresa E. , Hamilton William , Proks Martin , Lykkegaard Maria , Nielsen Alexander V. , Trusina Ala , Brickman Joshua M.
Published: September 2022

Cooperative DNA binding of transcription factors (TFs) integrates external stimuli and context across tissues and time. Naïve mouse embryonic stem cells are derived from early development and can sustain the pluripotent identity indefinitely. Here we ask whether TFs associated with pluripotency evolved to directly support this state, or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is not present, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB quantitatively influences differentiation, and in silico modeling of bipartite TF activity suggests ESRRB safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of highly stable stem cell models.
Neuraminidase activity modulates cellular co-infection during influenza A virus multicycle growth
Authors: Guo Zijian , He Yuanyuan , Benegal Ananya N. , Vahey Michael D.
Published: September 2022

Infection of individual cells by multiple virions plays critical roles in the replication and spread of many viruses, but mechanisms that control cellular co-infection during multi-cycle viral growth remain unclear. Here, we investigate virus-intrinsic factors that control cellular co-infection by influenza A virus (IAV). Using quantitative fluorescence to track the spread of virions from single infected cells, we identify the IAV surface protein neuraminidase (NA) as a key determinant of cellular co-infection. We map this effect to NA’s ability to deplete viral receptors from both infected and neighboring uninfected cells. In cases where viral infectious potential is low, genetic or pharmacological inhibition of NA increases the local spread of infection by increasing the viral load received by neighboring cells. These results identify virus-intrinsic factors that contribute to cellular multiplicity of infection, and suggest that optimal levels of NA activity depend on the infectious potential of the virus in question.
Using Packing Defects in Heterogeneous Biological Membrane as a Lens to Explore Protein Localization Propensity and Small Molecule Permeability
Authors: Tripathy Madhusmita , Srivastava Anand
Published: September 2022

Plasma membrane (PM) heterogeneity has long been implicated in various cellular functions. However, mechanistic principles governing functional regulations of lipid environment is not well understood due to the inherent complexities associated with the relevant length and time scales that limit both direct experimental measurements and their interpretation. In this context, computer simulation holds immense potential to investigate molecular-level interactions that lead to PM heterogeneity and the related functions. Herein, we investigate spatial and dynamic heterogeneity in model membranes with coexisting liquid ordered and liquid disordered phases and characterize the membrane order in terms of the topological changes in lipid local environment using the non-affine parameter (NAP) frame-work. Furthermore, we probe the packing defects in membrane with coexisting fluid phases, which can be considered as the conjugate of membrane order assessed in terms of the NAP. In doing so, we formalize the connection between membrane packing and local membrane order and use that to explore the mechanistic principles behind preferential localization of proteins in mixed phase membranes and membrane permeability of small molecules. Our observations suggest that heterogeneity in mixed phase membranes follow some generic features, where functions may arise based on packing-related basic design principles.

Significance

Functionally important complex lateral and transverse structures in biological membrane result from the differential molecular interactions among a rich variety of lipids and other building blocks. The nature of molecular packing in membrane is a manifestation of these interactions. In this work, using some of the ideas from the Physics of amorphous materials and glasses, we quantify the correlation between heterogeneous membrane organization and the three dimensional packing defects. Subsequently, we investigate the packing-based molecular design-level features that drive preferential localization of peptides in heterogeneous membrane and membrane permeation of small molecules.
The Arabidopsis MCTP member QUIRKY regulates the formation of the STRUBBELIG receptor kinase complex
Authors: Chen Xia , Leśniewska Barbara , Vaddepalli Prasad , Schneitz Kay
Published: September 2022

Intercellular communication plays a central role in organogenesis. Tissue morphogenesis inArabidopsis thalianarequires signaling mediated by a cell surface complex containing the atypical receptor kinase STRUBBELIG (SUB) and the multiple C2 domains and transmembrane region protein QUIRKY (QKY). QKY is required to stabilize SUB at the plasma membrane. However, it is unclear what the in vivo architecture of the QKY/SUB signaling complex is, how it is controlled, and how it relates to the maintenance of SUB at the cell surface. Using a combination of yeast two-hybrid assays and Förster resonance energy transfer (FRET)/fluorescence lifetime imaging microscopy (FLIM) in epidermal cells of seedling roots we find that QKY promotes the formation of SUB homo-oligomers in vivo, a process that appears to involve an interaction between the extracellular domains of SUB. We also show that QKY and SUB physically interact and form a complex at the cell surface in vivo. In addition, the data show that the N-terminal C2A-B region of QKY interacts with the intracellular domain of SUB. They further reveal that this interaction is essential to maintain SUB levels at the cell surface. Finally, we provide evidence that QKY forms homo-multimers in vivo in a SUB-independent manner. We suggest a model in which the physical interaction of QKY with SUB mediates the oligomerization of SUB and attenuates its internalization, thereby maintaining sufficiently high levels of SUB at the cell surface required for the control of tissue morphogenesis.
An endosymbiont harvest: Phylogenomic analysis of Wolbachia genomes from the Darwin Tree of Life biodiversity genomics project
Authors: Vancaester Emmelien , Blaxter Mark
Published: September 2022

The Darwin Tree of Life project aims to sequence all described terrestrial and aquatic eukaryotic species found in Britain and Ireland. Reference genome sequences are generated from single individuals for each target species. In addition to the target genome, sequenced samples often contain genetic material from microbiomes, endosymbionts, parasites and other cobionts. Wolbachia endosymbiotic bacteria are found in a diversity of terrestrial arthropods and nematodes, with supergroups A and B the most common in insects. We identified and assembled 110 complete Wolbachia genomes from 93 host species spanning 92 families by filtering data from 368 insect species generated by the Darwin Tree of Life project. From 15 infected species we assembled more than one Wolbachia genome, including cases where individuals carried simultaneous supergroup A and B infections. Different insect orders had distinct patterns of infection, with Lepidopteran hosts mostly infected with supergroup B, while infections in Diptera and Hymenoptera were dominated by A-type Wolbachia. Other than these large-scale order-level associations, host and Wolbachia phylogenies revealed no (or very limited) cophylogeny. This points to the occurrence of frequent host switching events, including between insect orders, in the evolutionary history of the Wolbachia pandemic. While supergroup A and B genomes had distinct GC% and GC skew, and B genomes had a larger core gene set and tended to be longer, it was the abundance of active and pseudogenised copies of bacteriophage WO who was a strong determinant of Wolbachia genome size. Mining raw genome data generated for reference genome assemblies is a robust way of identifying and analysing cobiont genomes and giving greater ecological context for their hosts.
Down-regulated GAS6 impairs synovial macrophage efferocytosis and promotes obesity-associated osteoarthritis
Authors: Zihao Yao , Weizhong Qi , Liangliang Liu , Yan Shao , Hongbo Zhang , Jianbin Yin , Haoyan Pan , Xiongtian Guo , Anling Liu , Daozhang Cai , Xiaochun Bai , Haiyan Zhang
Published: September 2022

Obesity has always been considered a significant risk factor in OA progression, but the underlying mechanism of obesity-related inflammation in OA synovitis remains unclear. The present study found that synovial macrophages infiltrated and polarized in the obesity microenvironment and identified the essential role of M1 macrophages in impaired macrophage efferocytosis using pathology analysis of obesity-associated OA. The present study revealed that obese OA patients and ApoE−/− mice showed a more pronounced synovitis and enhanced macrophage infiltration in synovial tissue, accompanied by dominant M1 macrophage polarization. Obese OA mice had a more severe cartilage destruction and increased levels of synovial apoptotic cells than OA mice in the control group. Enhanced M1-polarized macrophages in obese synovium decreased growth arrest-specific 6 (GAS6) secretion, resulting in impaired macrophage efferocytosis in synovial apoptotic cells. Intracellular contents released by accumulated apoptotic cells further triggered an immune response and lead to a release of inflammatory factors, such as TNF-α, IL-1β, and IL-6, which induce chondrocyte homeostasis dysfunction in obese OA patients. Intra-articular injection of GAS6 restored the phagocytic capacity of macrophages, reduced the accumulation of local apoptotic cells, and decreased the levels of TUNEL- and caspase-3-positive cells, preserving cartilage thickness and preventing the progression of obesity-associated OA. Therefore, blocking M1 macrophage polarization or intra-articular injection of GAS6 is a potential therapeutic strategy for obesity-associated OA.
DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network
Authors: Carraro Massimo , Hendriks Ivo A. , Hammond Colin M. , Solis Victor , Völker-Albert Moritz , Elsborg Jonas D. , Weisser Melanie B. , Spanos Christos , Montoya Guillermo , Rappsilber Juri , Imhof Axel , Nielsen Michael L. , Groth Anja
Published: September 2022

A multitude of histone chaperones are required to protect histones after their biosynthesis until DNA deposition. They cooperate through the formation of co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using explorative interactomics approaches, we characterize the organization of the histone H3–H4 chaperones network and define the interplay between histone chaperone systems. We identify and validate several novel histone dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX acts separately from the rest of the network, recruiting heterochromatin factors and promoting lysine 9 tri-methylation of new histone H3.3 prior to deposition onto DNA. With its functionality, DAXX provides a molecular mechanism for de novo heterochromatin assembly. Collectively, our findings provide a new framework for understanding how cells orchestrate histone supply and comply with chromatin dynamics throughout the cell cycle.
VLA-4 suppression by senescence signals regulates meningeal immunity and leptomeningeal metastasis
Authors: Li Jiaqian , Huang Di , Lei Bingxi , Huang Jingying , Zhao Qiyi , Su Shicheng , Wang Ying
Published: September 2022

Leptomeningeal metastasis is associated with dismal prognosis and has few treatment options. However, very little is known about the immune response to leptomeningeal metastasis. Here, by establishing an immunocompetent mouse model of breast cancer leptomeningeal metastasis, we found that tumor-specific CD8+T cells were generated in deep cervical lymph nodes (dCLNs) and played an important role in controlling leptomeningeal metastasis. Mechanistically, T cells in dCLNs displayed a senescence phenotype and their recruitment was impaired in mice bearing cancer cells that preferentially colonized in leptomeningeal space. Upregulation of p53 suppressed the transcription of VLA-4 in senescent dCLN T cells and consequently inhibited their migration to the leptomeningeal compartment. Clinically, CD8+T cells from cerebrospinal fluid of patients with leptomeningeal metastasis exhibited senescence and VLA-4 downregulation. Collectively, our findings demonstrated that CD8+T cell immunosenescence drives leptomeningeal metastasis.
Amphibian larvae benefit from a warm environment under simultaneous threat from chytridiomycosis and ranavirosis
Authors: Herczeg Dávid , Holly Dóra , Kásler Andrea , Bókony Veronika , Papp Tibor , Takács-Vágó Hunor , Ujszegi János , Hettyey Attila
Published: September 2022

Rising temperatures can facilitate epizootic outbreaks, but disease outbreaks may be suppressed if temperatures increase beyond the optimum of the pathogens while still within the temperature range that allows for effective immune function in hosts. The two most devastating pathogens of wild amphibians, Batrachochytrium dendrobatidis (Bd) and ranaviruses (Rv), co-occur in large areas, yet little is known about the consequences of their co-infection and how these consequences depend on temperature. Here we tested how co-infection and elevated temperatures (28 and 30°C vs. 22°C) affected Bd and Rv prevalence, infection intensities, and resulting mortalities in larval agile frogs and common toads. We found multiple pieces of evidence that the presence of one pathogen influenced the prevalence and/or infection intensity of the other pathogen in both species, depending on temperature and initial Rv concentration. Generally, the 30°C treatment lowered the prevalence and infection intensity of both pathogens, and, in agile frogs, this was mirrored by higher survival. These results suggest that if temperatures naturally increase or are artificially elevated beyond what is ideal for both Bd and Rv, amphibians may be able to control infections and survive even the simultaneous presence of their most dangerous pathogenic enemies.
Comprehensive identification, isolation, and culture of human breast cell types
Authors: Thi Kate , Del Toro Katelyn , Licon-Munoz Yamhilette , Sayaman Rosalyn W. , Hines William C.
Published: September 2022

Tissues are formed and shaped by cells of many different types and are orchestrated through countless interactions among the cells—and the myriad of molecules they synthesize. Deciphering a tissue’s biological complexity thus requires studying it at cell-level resolution, where molecular and biochemical features of different cell types can be explored and thoroughly dissected. Unfortunately, the lack of comprehensive methods to identify, isolate, and culture each cell type from many tissues has impeded progress. Here, we present a method for the breadth of cell types composing the human breast. Our goal has long been to understand the essence of each of these different breast cell types, that is, to reveal the underlying biology explaining their intrinsic features, the consequences of interactions, and their contributions to the tissue as a whole. This biological exploration has required cell purification, deep-RNA sequencing—and a thorough dissection of the genes and pathways defining each cell type, which we present in an adjoining article. Here, we present an exhaustive cellular dissection of the human breast, where we explore its cellular composition and histological organization. Moreover, we introduce a novel fluorescence-activated cell sorting (FACS) antibody panel and rigorous gating strategy capable of isolating each of the twelve major breast cell types to purity. Finally, we describe the creation of primary cell models from nearly every one of these breast cell types—some being the first of their kind— and submit these as critical tools for studying the dynamic cellular interactions within breast tissues and tumors. Together, this body of work and derived resources deliver a unique perspective of the breast, revealing insights into its cellular, molecular, and biochemical composition.
Proteome-Wide Photo-Crosslinking Enables Residue-Level Visualization of Protein Interaction Networks in vivo
Authors: Faustino Anneliese M. , Sharma Piyoosh , Yadav Divya , Fried Stephen D.
Published: September 2022

Crosslinking mass spectrometry (XL-MS) is emerging as a unique method at the crossroads of structural and cellular biology, uniquely capable of identifying protein-protein interactions with residue-level resolution and on the proteome-wide scale. With the development of crosslinkers that can form linkages inside cells and easily cleave during fragmentation on the mass spectrometer (MS-cleavable crosslinks), it has become increasingly facile to identify contacts between any two proteins in complex samples, including in live cells or tissues. Photo-crosslinkers possess the advantages of high temporal resolution and high reactivity, thereby engaging all residue-types (rather than just lysine); nevertheless, photo-crosslinkers have not enjoyed widespread use, and have yet to be employed for proteome-wide studies, because their products are challenging to identify, and an MS-cleavable photo-crosslinker has not yet been reported. Here, we demonstrate the synthesis and application of two heterobifunctional photo-crosslinkers that feature diazirines and N-hydroxy-succinimidyl carbamate groups, the latter of which unveil MS-cleavable linkage upon acyl transfer to protein targets. Moreover, these crosslinkers demonstrate high water-solubility and cell-permeability. Using these compounds, we demonstrate the feasibility of proteome-wide photo-crosslinking mass spectrometry (photo-XL-MS), both in extracts and in cellulo. These studies provide a partial interaction map of the E. coli cytosol with residue-level resolution. We find that photo-XL-MS has a propensity to capture protein-protein interactions, particularly involving low-abundance uncharacterized proteins, suggesting it could be a powerful tool to shed light on the “darker” corners of the proteome. Overall, we describe methods that enable the detection of protein quinary interaction networks in their native environment at residue-level resolution proteome-wide, and we expect they will prove useful toward the effort to explore the molecular sociology of the cell.

TOC graphic
Structural characterization of human tryptophan hydroxylase 2 reveals L-Phe as the superior regulatory domain ligand relevant for serotonin biosynthesis
Authors: Vedel Ida M. , Prestel Andreas , Zhang Zhenwei , Skawinska Natalia T. , Stark Holger , Harris Pernille , Kragelund Birthe B. , Peters Günther H. J.
Published: September 2022

Tryptophan hydroxylase 2 (TPH2) catalyzes the rate-limiting step in the biosynthesis of serotonin in the brain. Consequently, regulation of TPH2 is relevant for serotonin related diseases, yet, the regulatory mechanism of TPH2 is poorly understood and structural as well as dynamical insights are missing. Here, we use NMR spectroscopy to determine the structure of a 47 N-terminally truncated variant of the regulatory domain (RD) dimer of human TPH2 in complex with L-Phe, and show that L-Phe is the superior RD ligand compared to the natural substrate, L-Trp. Using cryo-EM we obtain a low-resolution structure of a similarly truncated variant of the complete tetrameric enzyme with dimerized RDs. The cryo-EM 2D class averages additionally indicate that the RDs are dynamic in the tetramer and likely exist in a monomer-dimer equilibrium. Our results provide structural information on the RD both as an isolated domain and in the TPH2 tetramer, which will facilitate future elucidation of TPH2’s regulatory mechanism affecting serotonin regulation.
A small molecule RIG-I agonist serves to adjuvant broad multifaceted influenza virus vaccine immunity
Authors: Hemann Emily A. , Knoll Megan L. , Wilkins Courtney R. , Subra Caroline , Green Richard , García-Sastre Adolfo , Thomas Paul G. , Trautmann Lydie , Ireton Renee , Loo Yueh-Ming , Gale Michael
Published: September 2022

Retinoic acid-inducible gene I (RIG-I) is essential for activating host cell innate immunity to regulates the immune response against many RNA viruses. We identified a small molecule compound, KIN1148, that directly binds RIG-I to drive IRF3activation to impart the expression of IRF3-target genes, including specific immunomodulatory cytokines and chemokines. KIN1148 does not lead to ATPase activity or compete with ATP for binding but activates RIG-I to induce antiviral gene expression programs distinct from type I interferon (IFN) treatment. When administered in combination with a vaccine against influenza A virus (IAV), KIN1148 induces both neutralizing antibody and broadly cross-protective IAV-specific T cell responses compared to vaccination alone, which induces comparatively poor responses. This robust KIN1148-adjuvanted immune response protects mice from lethal H1N1 and H5N1 IAV challenge. Importantly, KIN1148 also augments human CD8+ T cell activation. Thus, we have identified a small molecule RIG-I agonist that serves as an effective adjuvant in inducing non-canonical RIG-I activation for induction of innate immune programs that enhance adaptive immune protection of antiviral vaccination.

Hemann, et. al. identify a small-molecule RIG-I agonist (KIN1148) that directly binds RIG-I for non-canonical activation and adjuvants pandemic and avian influenza virus vaccination. KIN1148 augments broadly neutralizing antibody and T cell responses in mice and enhances human DC maturation and CD8+ T cell activation.
Mitochondrial protein import stress augments α-synuclein aggregation and neurodegeneration independent of bioenergetics
Authors: Coyne Liam P. , Rana Arnav , Wang Xiaowen , Bhagwagar Sanaea , Umino Yumiko , Solessio Eduardo C. , Middleton Frank , Chen Xin Jie
Published: September 2022

Several genetic and environmental risk factors for Parkinson’s disease have been identified that converge on mitochondria as central elements in the disease process. However, the mechanisms by which mitochondrial dysfunction contributes to neurodegeneration remain incompletely understood. Non-bioenergetic pathways of the mitochondria are increasingly appreciated, but confounding bioenergetic defects are a major barrier to experimental validation. Here, we describe a novel bioenergetics-independent mechanism by which mild mitochondrial protein import stress augments neurodegeneration. We induced this mitochondrial protein import stress in an established mouse model of Parkinson’s disease expressing the A53T mutated form of α-synuclein (SNCA). Mice with import stress in addition to the A53T mutation demonstrated increased size of α-synuclein aggregates, co-aggregation of mitochondrial preproteins with α-synuclein, and worsened neurodegeneration. Importantly, we found no evidence of bioenergetic defects in any of the mutant mice, even with the added import stress. These data suggest that mitochondrial protein import stress contributes to neurodegeneration through cytosolic proteostatic stress and co-aggregation of mitochondrial and neuropathogenic proteins independent of bioenergetics. Given that protein import efficiency is affected by many types of mitochondrial stress, our findings add a new layer to understanding why the pathogenic mitochondrial dysfunction and cytosolic protein misfolding pathways converge in neurodegenerative diseases such as Parkinson’s disease.
Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in Amazonas, a Brazilian setting with high levels of hybrid immunity
Authors: Arantes Ighor , Bello Gonzalo , Nascimento Valdinete , Souza Victor , da Silva Arlesson , Silva Dejanane , Nascimento Fernanda , Mejía Matilde , Brandão Maria Júlia , Gonçalves Luciana , Silva George , da Costa Cristiano Fernandes , Abdalla Ligia , Santos João Hugo , Ramos Tatyana Costa Amorim , Piantham Chayada , Ito Kimihito , Siqueira Marilda Mendonça , Resende Paola Cristina , Wallau Gabriel Luz , Delatorre Edson , Gräf Tiago , Naveca Felipe
Published: September 2022

The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively, with variable impact according to the immune population landscape. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil’s most heavily affected regions. We sequenced the virus genome from 4,128 patients collected in Amazonas between July 1st, 2021 and January 31st, 2022 and investigated the lineage replacement dynamics using a phylodynamic approach. The VOCs Delta and Omicron displayed similar patterns of phylogeographic spread but significantly different epidemic dynamics. The Delta and Omicron epidemics were fueled by multiple introduction events, followed by the successful establishment of a few local transmission lineages of considerable size that mainly arose in the Capital, Manaus. The VOC Omicron spread and became dominant much faster than the VOC Delta. We estimate that under the same epidemiological conditions, the average Re of Omicron was ∼3.3 times higher than that of Delta and the average Re of the Delta was ∼1.3 times higher than that of Gamma. Furthermore, the gradual replacement of Gamma by Delta occurred without an upsurge of COVID-19 cases, while the rise of Omicron fueled a sharp increase in SARS-CoV-2 infection. The Omicron wave displayed a shorter duration and a clear decoupling between the number of SARS-CoV-2 cases and deaths compared with previous (B.1.* and Gamma) waves in the Amazonas state. These findings suggest that the high level of hybrid immunity (infection plus vaccination) acquired by the Amazonian population by mid-2021 was able to limit the spread of the VOC Delta and was also probably crucial to curb the number of severe cases, although not the number of VOC Omicron new infections.
Under the shadow: Old-biased genes are subject to weak purifying selection at both the tissue and cell type-specific levels
Authors: Yıldız Melih , İzgi Hamit , Rahimova Firuza , Altıntaş Umut Berkay , Turan Zeliha Gözde , Somel Mehmet
Published: September 2022

The mutation accumulation theory predicts that aging is caused by accumulation of late-acting deleterious variants in the germ-line, due to weak purifying selection at old age. In accordance with this model, we and others have shown that sequence conservation among old-biased genes (with higher expression in old versus young adults) is weaker than among young-biased genes across a number of mammalian and insect species. However, questions remained regarding the source and generality of this observation. It was especially unclear whether the observed patterns were driven by tissue and cell type composition shifts or by cell-autonomous expression changes during aging. How wide this trend would extend to non-mammalian metazoan aging was also uncertain. Here we analyzed bulk tissue as well as cell type-specific RNA sequencing data from diverse animal taxa across six different datasets from five species. We show that the previously reported age-related decrease in transcriptome conservation (ADICT) is commonly found in aging tissues of non-mammalian species, including non-mammalian vertebrates (chicken brain, killifish liver and skin) and invertebrates (fruit fly brain). Analyzing cell type-specific transcriptomes of adult mice, we further detect the same ADICT trend at the single cell type level. Old-biased genes are less conserved across the majority of cell types analyzed in the lung, brain, liver, muscle, kidney, and skin, and these include both tissue-specific cell types, and also ubiquitous immune cell types. Overall, our results support the notion that aging in metazoan tissues may be at least partly shaped by the mutation accumulation process.
Pharmacologic hyperstabilisation of the HIV-1 capsid lattice induces capsid failure
Authors: Faysal K.M. Rifat , Walsh James C , Renner Nadine , Marquez Chantal L , Shah Vaibhav , Tuckwell Andrew J , Christie Michelle P , Parker Michael W , Turville Stuart Grant , James Leo , Towers Greg J , Jacques David A , Boecking Till
Published: September 2022

The HIV-1 capsid has emerged as a tractable target for antiretroviral therapy. Lenacapavir, developed by Gilead Sciences, is the first capsid-targeting drug approved for medical use. Here we investigate the effect of Lenacapavir on HIV capsid stability and uncoating. We employ a single particle approach that simultaneously measures capsid content release and lattice persistence. We demonstrate that Lenacapavir's potent antiviral activity is predominantly due to lethal hyperstabilisation of the capsid lattice and resultant loss of compartmentalisation. This study highlights that disrupting capsid metastability is a powerful strategy for the development of novel antivirals.