bluuebunny/crossref_metadata_2025 huggingface dataset:
T cells in testicular germ cell tumors: new evidence of fundamental contributions by rare subsets
Authors: Islam Rashidul , Heyer Jannis , Figura Miriam , Wang Xiaoyan , Nie Xichen , Nathaniel Benedict , Indumathy Sivanjah , Hartmann Katja , Pleuger Christiane , Fijak Monika , Kliesch Sabine , Dittmar Florian , Pilatz Adrian , Wagenlehner Florian , Hedger Mark , Loveland Bruce , Hotaling James H. , Guo Jingtao , Loveland Kate , Schuppe Hans-Christian , Fietz Daniela
Published: October 2023

BACKGROUND

Immune cell infiltration is heterogeneous but common in testicular germ cell tumors (TGCT) and pre-invasive germ cell neoplasia in situ (GCNIS). Tumor-infiltrating T cells including regulatory T (Treg) and follicular helper T (Tfh) cells are found in other cancer entities, but their contributions to TGCT are unknown.

METHODS

Human testis specimens from independent patient cohorts were analyzed using immunohistochemistry, flow cytometry and single-cell RNA sequencing (scRNA-seq) with special emphasis on delineating T cell subtypes.

RESULTS

Profound changes in immune cell composition within TGCT, shifting from macrophages in normal testes to T cells plus B and dendritic cells in TGCT, were documented. In most samples (96%), the CD4+ T cell frequency exceeded that of CD8+ cells, with decreasing numbers from central to peripheral tumor areas, and to tumor-free, contralateral testes. T cells including Treg and Tfh were most abundant in seminoma compared to mixed tumors and embryonal carcinoma.

CONCLUSION

Despite considerable heterogeneity between patients, T cell subtypes form a key part of the TGCT microenvironment. The novel finding of rare Treg and Tfh cells in human testis suggests their involvement in TGCT pathobiology, with implications for understanding tumor progression, to assess patients’ prognosis, and as putative targets for personalized immunotherapy.
A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)
Authors: Baca S.M. , Gustafson G.T. , DeRaad D.A. , Alexander A. , Hime P.M. , Short A.E.Z.
Published: October 2023

TheNotomicrus trailispecies group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this group, with multiple distinct clades sharing overlapping distributions and lineages attributed toN. trailiand the closely relatedN. gracilipesrecovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within theN. trailigroup. First, we use short-read whole genome sequencing of four noterid genera to design a noterid-specific UCE probe set (Noteridae 3.4Kv1) targeting over 3,400 unique loci. Using this probe set, we capture UCE data from population-level sampling of 44trailigroup specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putativeN. trailigroup populations overlap. We subject the resulting data matrix to various trimming and data completeness treatments and reconstruct the phylogeny with both concatenated maximum likelihood and coalescent congruent methods. We recover robust phylogenetic estimates that identify several phylogenetically distinct clades within thetrailigroup that share overlapping distributions. To test for the genetic distinctiveness of populations, we extract single nucleotide polymorphism (SNP) data from UCE alignments and examine patterns of genetic clustering using principal component analyses (PCAs) and STRUCTURE. Population genetic results are highly concordant with recovered phylogenetic structure, revealing a high degree of co-ancestry shared within identified clades, contrasting with limited ancestry sharing between clades. We recover a pattern consistent with repeated diversification and dispersal of thetrailigroup in the Neotropics, highlighting the efficacy of a tailored UCE approach for facilitating shallow-scale phylogenetic reconstructions and population genetic analyses, which can reveal novel aspects of coleopteran phylogeography.
Adaptation to space conditions of novel bacterial species isolated from the International Space Station revealed by functional gene annotations and comparative genome analysis
Authors: Szydlowski Lukasz M. , Bulbul Alper A. , Simpson Anna C. , Kaya Deniz E. , Singh Nitin K. , Sezerman Ugur O. , Łabaj Paweł P. , Kosciolek Tomasz , Venkateswaran Kasthuri J.
Published: October 2023

Background

The extreme environment of the International Space Station (ISS) puts selective pressure on microorganisms unintentionally introduced during its 20+ years of service as a low-orbit science platform and human habitat. Such pressure leads to the development of new features not found in the Earth-bound relatives, which enable them to adapt to unfavorable conditions.

Results

In this study, we generated the functional annotation of the genomes of five newly identified species of Gram-positive bacteria, four of which are non-spore-forming and one spore-forming, all isolated from the ISS. Using a deep-learning based tool - deepFRI - we were able to functionally annotate close to 100% of protein-coding genes in all studied species, overcoming other annotation tools. Our comparative genomic analysis highlights common characteristics across all five species and specific genetic traits that appear unique to these ISS microorganisms. Proteome analysis mirrored these genomic patterns, revealing similar traits. The collective annotations suggest adaptations to life in space, including the management of hypoosmotic stress related to microgravity via mechanosensitive channel proteins, increased DNA repair activity to counteract heightened radiation exposure, and the presence of mobile genetic elements enhancing metabolism. In addition, our findings suggest the evolution of certain genetic traits indicative of potential pathogenic capabilities, such as small molecule and peptide synthesis and ATP-dependent transporters. These traits, exclusive to the ISS microorganisms, further substantiate previous reports explaining why microbes exposed to space conditions demonstrate enhanced antibiotic resistance and pathogenicity.

Conclusion

Our findings indicate that the microorganisms isolated from ISS we studied have adapted to life in space. Evidence such as mechanosensitive channel proteins, increased DNA repair activity, as well as metallopeptidases and novel S-layer oxidoreductases suggest a convergent adaptation among these diverse microorganisms, potentially complementing one another within the context of the microbiome. The common genes that facilitate adaptation to the ISS environment may enable bioproduction of essential biomolecules need during future space missions, or serve as potential drug targets, if these microorganisms pose health risks.
Removing bias in sequence models of protein fitness
Authors: Shaw Ada , Spinner Hansen , Shin June , Gurev Sarah , Rollins Nathan , Marks Debora
Published: October 2023

Unsupervised sequence models for protein fitness have emerged as powerful tools for protein design in order to engineer therapeutics and industrial enzymes, yet they are strongly biased towards potential designs that are close to their training data. This hinders their ability to generate functional sequences that are far away from natural sequences, as is often desired to design new functions. To address this problem, we introduce a de-biasing approach that enables the comparison of protein sequences across mutational depths to overcome the extant sequence similarity bias in natural sequence models. We demonstrate our method’s effectiveness at improving the relative natural sequence model predictions of experimentally measured variant functions across mutational depths. Using case studies proteins with very low functional percentages further away from the wild type, we demonstrate that our method improves the recovery of top-performing variants in these sparsely functional regimes. Our method is generally applicable to any unsupervised fitness prediction model, and for any function for any protein, and can thus easily be incorporated into any computational protein design pipeline. These studies have the potential to develop more efficient and cost-effective computational methods for designing diverse functional proteins and to inform underlying experimental library design to best take advantage of machine learning capabilities.
QUANTIFYING INTRASPECIFIC VARIATION IN HOST RESISTANCE AND TOLERANCE TO A LETHAL PATHOGEN
Authors: Hardy Bennett M. , Muths Erin , Funk W. Chris , Bailey Larissa L.
Published: October 2023

Due to the ubiquity of disease in natural systems, hosts have evolved strategies of disease resistance and tolerance to defend themselves from further harm once infected. Resistance strategies directly limit pathogen growth, typically leading to lower infection burdens in the host. A tolerance approach limits the fitness consequences caused by the pathogen but does not directly inhibit pathogen growth. Testing for intraspecific variation in wild host populations is important for informing conservation decisions about captive breeding, translocation, and disease treatment. Here, we test for the relative importance of tolerance and resistance in multiple populations of boreal toads (Anaxyrus boreas boreas) againstBatrachochytrium dendrobatidis(Bd), the amphibian fungal pathogen responsible for the greatest host biodiversity loss due to disease. Boreal toads have severely declined in Colorado (CO) due to Bd, but toad populations challenged with Bd in western Wyoming (WY) appear to be less affected. We used a common garden infection experiment to expose post-metamorphic toads sourced from four populations (2 in CO and 2 in WY) to Bd and monitored changes in mass, pathogen burden, and survival for eight weeks. We used a multi-state modeling approach to estimate weekly survival and transition probabilities between infected and cleared states, reflecting a dynamic infection process that traditional approaches fail to capture. We found that WY boreal toads are highly tolerant to Bd infection with higher survival probabilities than those in CO when infected with identical pathogen burdens. WY toads also had higher probabilities of clearing infections and took an average of five days longer to reach peak infection burdens. Our results demonstrate strong intraspecific differences in tolerance and resistance that explain why population declines vary regionally across the species. We used a robust, multi-state framework to gain inference on typically hidden disease processes when testing for host tolerance or resistance and demonstrated that describing an entire species as ‘tolerant’ or ‘resistant’ is unwise without testing for intraspecific variation in host defenses.
Isolation and Identification of possible pathogenic bacteria on carrots sold at community market, Ahmadu Bello University, Zaria
Authors: Ojodomo Blessing , Ashar Saaondo James
Published: October 2023

Carrots (Daucus carota) are root vegetables that can be purple, red, yellow or white colour based on their pigmentation and variety. Due to the awareness of its high nutritional content such as vitamins, minerals and carotene, they are mainly consumed raw, possibly exposing one to the risk of being infected. Studies on the pathogenic Bacteria associated with fresh carrots sold in the community market at Ahmadu Bello University, main campus Samaru Zaria, were carried out using cultural techniques. Salmonella Shigella agar, MacConkey agar and Eosin methylene blue agar were the growth media for the isolation of the pathogenic Bacteria. Twelve fresh carrots were randomly bought from different food vendors in the community market, and then 10g of the outer layer (epidermal) scrapings were collected from each sample and homogenized in 90 ml of buffered peptone water. It was then serially diluted and 0.1ml of each 104and 105dilutions were plated on EMB, SSA, and MacConkey agar. Isolates were identified by gram staining and biochemical tests. The bacteria were identified to beProteusspecies,Citrobacterspecies,Klebsiellaspecies, andSalmonellaspecies.Proteusspp was predominantly isolated among the bacterial isolates (41%) followed byCitrobacterspp (25%),Klebsiellaspp (17%) andSalmonellaspp (17%). These organisms may have been introduced to the carrots during growth, harvesting, handling, storage and distribution. The presence of the organisms is a public health risk because of the diseases known to be caused by them. It is therefore imperative that adequate hygienic practices be put in place during the cultivating and handling of carrots. A high level of susceptibility was observed in Ciprofloxacin at (100%) and Augmentin at (50%), while the high level of resistance was observed to be high in Gentamicin at (100%).
Phylogenetic analysis ofABCEgenes across the plant kingdom
Authors: Jakobson Liina , Mõttus Jelena , Suurväli Jaanus , Sõmera Merike , Tarassova Jemilia , Nigul Lenne , Smolander Olli-Pekka , Sarmiento Cecilia
Published: October 2023

ATP-BINDING CASSETTE SUBFAMILY E MEMBER (ABCE) proteins are one of the most conserved proteins across eukaryotes and archaea. Yeast and the vast majority of animals possess a singleABCEgene encoding the vital ABCE1 protein. We retrievedABCEgene sequences of 76 plant species from public genome databases and analyzed them with the reference toArabidopsis thaliana ABCE2gene (AtABCE2). Over half of the studied plant species possess two or moreABCEgenes. There can be as many as eightABCEgenes in a plant species. This suggest thatABCEgenes in plants can be classified as a low-copy gene family, rather than a single-copy gene family. Plant ABCE proteins showed overall high sequence conservation, sharing at least 78% of amino acid sequence identity with AtABCE2. The phylogenetic trees of full-length ABCE amino acid and CDS sequences demonstrated thatBrassicaceaeandPoaceaefamilies have independently undergone lineage-specific split of the ancestralABCEgene. Other plant species have gainedABCEgene copies through more recent duplication events. Deeper analysis ofAtABCE2and its paralogueAtABCE1from 1135Arabidopsis thalianaecotypes revealed 4 and 35 non-synonymous SNPs, respectively. The lower natural variation inAtABCE2compared toAtABCE1is in consistence with its crucial role for plant viability. Overall, while the sequence of the ABCE protein family is highly conserved in the plant kingdom, many plants have evolved to have more than one copy of this essential translational factor.

Significance statement

In most eukaryotes there is a single ABCE protein, which is involved in many vital processes in cells. However, less is known about ABCEs specifically in plants. Here we show that while the sequence of ABCE proteins is highly conserved in plants, they have evolved to often have multiple copies of this essential translational factor. By studying 76 species from the entire plant kingdom, we observed as many as eightABCEgenes being present at a time, although most species have less. SomeABCEcopies appeared earlier than others and were found in multiple species. Thus, our findings indicate that ABCE genes in plants are not a single-copy gene family and should instead be re-classified as a low-copy gene family.
Human eukaryotic initiation factor 4G directly binds the 40S ribosomal subunit to promote efficient translation
Authors: Villa Nancy , Fraser Christopher S.
Published: October 2023

Messenger RNA (mRNA) recruitment to the 40S ribosomal subunit is mediated by eukaryotic initiation factor 4F (eIF4F). This complex includes 3 subunits: eIF4E (m7G cap binding protein), eIF4A (DEAD box helicase), and eIF4G. Mammalian eIF4G is a scaffold that coordinates the activities of eIF4E and eIF4A and provides a bridge to connect the mRNA and 40S ribosomal subunit through its interaction with eIF3. While the roles of many eIF4G binding domains are relatively clear, the precise function of RNA binding by eIF4G remains to be elucidated. In this work, we used an eIF4G-dependent translation assay to reveal that the RNA binding domain (eIF4G-RBD; amino acids 682–720) stimulates translation. This stimulating activity is observed when eIF4G is independently tethered to an internal region of the mRNA, suggesting that the eIF4G-RBD promotes translation by a mechanism that is independent of the m7G cap and mRNA tethering. Using a kinetic helicase assay, we show that the eIF4G-RBD has a minimal effect on eIF4A helicase activity, demonstrating that the eIF4G-RBD is not required to coordinate eIF4F-dependent duplex unwinding. Unexpectedly, native gel electrophoresis and fluorescence polarization assays reveal a previously unidentified direct interaction between eIF4G and the 40S subunit. Using binding assays, our data show that this 40S subunit interaction is separate from the previously characterized interaction between eIF4G and eIF3. Thus, our work reveals how eIF4F can bind to the 40S subunit using eIF3-dependent and eIF3-independent binding domains to promote translation initiation.
An updated model of shoot apical meristem regulation by ERECTA family and CLAVATA3 signaling pathways
Authors: Uzair Muhammad , Urquidi Camacho Ricardo Andres , Liu Ziyi , Overholt Alex M. , DeGennaro Daniel , Zhang Liang , Herron Brittani S. , Hong Tian , Shpak Elena D.
Published: October 2023

The shoot apical meristem (SAM) gives rise to above-ground organs. The size of the SAM is relatively constant due to the balance of stem cell replenishment versus cell recruitment into developing organs. In angiosperms, the transcription factor WUSCHEL (WUS) promotes stem cell identity in the central zone of the SAM. WUS forms a negative feedback loop with a signaling pathway activated by CLAVATA3 (CLV3). In the periphery of the SAM, the ERECTA family (ERf) receptors promote cell differentiation and constrain the expression ofWUSandCLV3. Here, we show that four ligands of ERfs redundantly inhibitCLV3andWUSexpression. Transcriptome analysis confirmed thatWUSandCLV3are the main targets of ERf signaling and uncovered several new ones. Analysis of promoter reporters indicated that in the vegetative meristem, theWUSexpression domain mostly overlapped with theCLV3domain and did not shift along the apical-basal axis inclv3. A 3D mathematical model reproduced the experimentally observedCLV3andWUSexpression patterns with fewer assumptions than earlier models. Based on these findings, we propose that CLV3 regulates cellular levels ofWUSexpression through autocrine signaling, while ERfs regulateWUSspatial expression, preventing its encroachment into the peripheral zone.

One Sentence Summary

Through autocrine signaling, CLV3 regulates the level ofWUSexpression in the vegetative SAM but not its location, while ERfs regulate theWUSspatial pattern, preventing its expansion into the peripheral zone.
BiP/GRP78 is a pro-viral factor for diverse dsDNA viruses that promotes the survival and proliferation of cells upon KSHV infection
Authors: Najarro Guillermo , Brackett Kevin , Woosley Hunter , Faeldonea Catya , Moreno Osvaldo Kevin , Negron Adriana Ramirez , Love Christina , Ward Ryan , Langelier Charles , Gardner Brooke M. , Arias Carolina
Published: October 2023

The Endoplasmic Reticulum (ER)-resident HSP70 chaperone BiP (HSPA5) plays a crucial role in maintaining and restoring protein folding homeostasis in the ER. BiP’s function is often dysregulated in cancer and virus-infected cells, conferring pro-oncogenic and pro-viral advantages. We explored BiP’s functions during infection by the Kaposi’s sarcoma-associated herpesvirus (KSHV), an oncogenic gamma-herpesvirus associated with cancers of immunocompromised patients. Our findings reveal that BiP protein levels are upregulated in infected epithelial cells during the lytic phase of KSHV infection. This upregulation occurs independently of the unfolded protein response (UPR), a major signaling pathway that regulates BiP availability. Genetic and pharmacological inhibition of BiP halts KSHV viral replication and reduces the proliferation and survival of KSHV-infected cells. Notably, inhibition of BiP limits the spread of other alpha- and beta-herpesviruses and poxviruses with minimal toxicity for normal cells. Our work suggests that BiP is a potential target for developing broad-spectrum antiviral therapies against double-stranded DNA viruses and a promising candidate for therapeutic intervention in KSHV-related malignancies.
Spatial Patterning of Laminin and N-Cadherin for Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes (hiPSC-CMs)
Authors: Lane Kerry V. , Dow Liam P. , Castilloa Erica A. , Boros Rémi , Feinstein Sam D. , Pardon Gaspard , Pruitt Beth L.
Published: October 2023

Controlling cellular shape with protein micropatterning can mimic physiological morphologies and has been shown to improve reproducibility, enhancing our ability to collect statistics on single-cell behaviors. It has also advanced efforts in developing human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) as a promising human model for studies of heart structure and function. hiPSC-CMs have key physiological differences from primary human cardiomyocytes (CMs), including lower sarcomere alignment and contractility, smaller area and lower aspect ratio, and lower force production. Protein micropatterning has been demonstrated to make hiPSC-CMs behave more like primary human CMs across these metrics. However, these micropatterned models typically use only extracellular matrix (ECM) proteins and have not investigated whether providing a protein associated with CM-CM interactions, such as N-cadherin, further enhances hiPSC-CM structure and function. Here, we developed a novel dual-protein patterning process to geometrically control single-cell CM placement on deformable hydrogels suitable for traction force microscopy (TFM). The patterns were comprised of rectangular laminin islands for attachment across the majority of the cell area, with N-cadherin “end-caps” imitating cell-cell interactions. We first photopatterned two proteins on a glass coverslip using a two-step process with photomolecular adsorption of proteins. After both photopatterning steps were complete, we transferred the pattern from the coverslip to a physiologically relevant ∼10-kPa polyacrylamide hydrogel. We seeded α-actinin-tagged hiPSC-CMs on the dual-protein-patterned hydrogels and verified interaction between the hiPSC-CMs and the N-cadherin end-caps via immunofluorescent staining. We found hiPSC-CMs on dual-protein patterns have a higher cell area and contractility in the direction of sarcomere organization than those on laminin-only patterns, but no difference in sarcomere organization or force production. While N-cadherin modestly improves the single-cell patterned hiPSC-CM model, it is not sufficient to replicate the role of cell-cell contacts in CM development for in vitro hiPSC-CM systems.
Eccentricity strongly modulates visual processing delays
Authors: Burge Johannes , Dyer Callista M.
Published: October 2023

The temporal dynamics of visual information processing varies with the stimulus being processed and with the retinal location that initiates the processing. Here, we present psychophysical data with sub-millisecond precision showing that increasing eccentricity decreases the delay with which stimuli are processed. We show that, even within the central +/-6º of the visual field, processing delays change by a factor of up to three times. A simple model, grounded in retinal physiology, provides a good account of the data. The relative delays are on the order of only milliseconds. But if later processing leaves the delays unresolved, they can cause dramatic misperceptions of motion and 3D layout. We discuss the implications for how the human visual system solves the temporal binding problem across eccentricity. The results highlight the severe computational challenge of obtaining accurate, temporally-unified percepts of the environment with spatiotemporally-staggered processing across the visual field.
Decoding Phospho-Regulation and Flanking Regions in Autophagy-Associated Short Linear Motifs: A Case Study of Optineurin-LC3B Interaction
Authors: Antonescu Oana N. , Utichi Mattia , Sora Valentina , Tiberti Matteo , Maiani Emiliano , Lambrughi Matteo , Papaleo Elena
Published: October 2023

Short Linear Motifs (SLiMs) play a pivotal role in mediating interactions between intrinsically disordered proteins and their binding partners. SLiMs exhibit sequence degeneracy and undergo regulation through post-translational modifications, including phosphorylation. The flanking regions surrounding the core motifs also exert a crucial role in shaping the modes of interaction. In this study, we aimed to integrate biomolecular simulations, in silico high-throughput mutational scans, and biophysical experiments to elucidate the structural details of phospho-regulation in a class of SLiMs crucial for autophagy, known as LC3 interacting regions (LIRs). As a case study, we investigated the interaction between optineurin and LC3B. Optineurin LIR perfectly exemplify a class of LIR where there is a complex interplay of different phosphorylations and a N-terminal helical flanking region to be disentangled. Our work unveils the unexplored role of the N-terminal flanking region upstream of the LIR core motif in contributing to the interaction interface. The results offer an atom-level perspective on the structural mechanisms and conformational alterations induced by phosphorylation in optineurin and LC3B recognition, along with of effects of mutations on the background of the phosphorylated form of the protein. Additionally, we assessed the impact of disease-related mutations on optineurin, accounting for different functional features.

Notably, we established an approach based on Microfluidic Diffusional Sizing as a novel method to investigate the binding affinity of SLiMs to target proteins, enabling precise measurements of the dissociation constant for a selection of variants identified in the in silico mutational screening. Overall, our work provides a versatile toolkit to characterize other LIR-containing proteins and their modulation by phosphorylation or other phospho-regulated SLiMs, thereby advancing the understanding of important cellular processes.
Successive responses of three coral holobiont components (coral hosts, symbiotic algae, and bacteria) to daily temperature fluctuations
Authors: Hsieh Yunli Eric , Lu Chih-Ying , Liu Po-Yu , Kao Jia-Min , Yang Sung-Yin , Wu Chien-Yi , Wong Jing-Wen Michelle , Shikina Shinya , Fan Tung-Yung , Yang Shan-Hua
Published: October 2023

Coral reef ecosystems support over a quarter of the world’s marine life and play important ecological and economic roles. However, the increasingly severe weather events associated with ocean warming and climate change are believed to be rapidly altering the functions of coral reefs and their ecosystems. Corals and their associated microbiota form a “holobiont,” which includes symbiotic algae and other associated microbiota dominated by bacteria. These microbiota have a direct relationship with the health of the coral host. Their composition is influenced by various environmental factors, such as increasing sea water temperatures. Previous studies of the effects of temperature changes on coral physiology and associated bacterial communities have been conducted based on stable water temperatures set by mean temperatures, or by slowly increasing/decreasing temperatures. However, the daily temperature fluctuations that corals experience in nature are not stable. Rather, there may be significant differences of up to 6°C in a single day. The current understanding of the effects of large daily temperature fluctuations on coral and associated bacterial community dynamics is limited. Hence, in this study, we conducted a four-week tank experiment using different large daily temperature fluctuations accompanied by continuous warming conditions to investigate the effects on two common reef-building corals,Stylophora pistillataandPocillopora acuta, in Taiwan. During the experiment, the activity of coral host catalase was measured, the photosynthetic ability of symbiotic algae was recorded, and the variation in bacterial communities was analyzed using the V6-V8 region of 16S rDNA. According to the results, different parts of the holobionts of different coral species exhibited varying response rates to the continuous warming conditions and diurnal temperature fluctuations. Additionally, it was found that diurnal temperature fluctuations may mitigate the heat stress on the host and reduce the changes in bacterial response to warming. Furthermore, the holobionts of different coral species may adopt different adaptation and survival strategies in response to diurnal temperature fluctuations and warming. Finally, based on the response of these two coral species under the conditions of diurnal temperature fluctuations and continuous warming,AcinetobacterandRhodobacteraceaewere identified as potential indicator coral-associated bacteria. This is the first study to investigate the tripartite dynamic response of coral, symbiotic algae and bacteria to daily temperature fluctuations.
Multichannel bioelectronic sensing using engineeredEscherichia coli
Authors: Zhang Xu , Ajo-Franklin Caroline
Published: October 2023

By engineering extracellular electron transfer (EET) to be dependent on an analyte, researchers have developed whole cell bioelectronic sensors that sense hazards to human and environmental health1. However, these sensors regulate a single electron transfer pathway as an electrochemical channel, limiting the sensing information to a single analyte. To increase information content, we developed a multichannel bioelectronic sensor through which different chemicals regulate distinct extracellular electron transfer pathways within a singleEscherichia colicell. One channel utilizes the flavin synthesis pathway fromBacillus subtilis2and the other a set of cytochromes constructing the Mtr pathway fromShewanella oneidensis3. We demonstrate an arsenite responsive promoter can control the Mtr pathway through activation of cytochrome CymA expression and a cadmium responsive promoter can control the flavin synthesis pathway4,5. The redox potential of flavin-mediated EET is different from that of CymA-mediated one6. This allowed for development of a redox-potential-dependent algorithm that distinguishes variable input signals of each analyte mediated by two EET pathways in vivo. This approach enables a 2-bit binary signal readout for real-time tracking throughout the entire sensing duration. Our multichannel bioelectronic sensor was able to accurately sense and distinguish different heavy metals in Brays Bayou water samples with a response time comparable to that in clean water. This multichannel bioelectronic sensors allow for simultaneous detection of different chemicals, significantly expanding information transmission and helping to safeguard human and environmental health.
Wolbachiaenhances the survival ofDrosophilainfected with fungal pathogens
Authors: Perlmutter Jessamyn I. , Atadurdyyeva Aylar , Schedl Margaret E. , Unckless Robert L.
Published: October 2023

Wolbachiabacteria of arthropods are at the forefront of basic and translational research on multipartite host-symbiont-pathogen interactions. These microbes are vertically inherited from mother to offspring via the cytoplasm. They are the most widespread endosymbionts on the planet due to their infamous ability to manipulate the reproduction of their hosts to spread themselves in a population, and to provide a variety of fitness benefits to their hosts. Importantly, some strains ofWolbachiacan inhibit viral pathogenesis within and between arthropod hosts. Mosquitoes carrying thewMelWolbachiastrain ofDrosophila melanogasterhave a greatly reduced capacity to spread viruses like dengue and Zika to humans. Therefore,Wolbachiaare the basis of several global vector control initiatives. While significant research efforts have focused on viruses, relatively little attention has been given toWolbachia-fungal interactions despite the ubiquity of fungal entomopathogens in nature. Here, we demonstrate thatWolbachiaincrease the longevity of theirDrosophila melanogasterhosts when challenged with a spectrum of yeast and filamentous fungal pathogens. We find that this pattern can vary based on host genotype, sex, and fungal species. Further,Wolbachiacorrelates with higher fertility and reduced pathogen titers during initial fungal infection, indicating a significant fitness benefit. This study demonstratesWolbachia’s role in diverse fungal pathogen interactions and determines that the phenotype is broad, but with several variables that influence both the presence and strength of the phenotype. These results enhance our knowledge of the strategiesWolbachiauses that likely contribute to such a high global symbiont prevalence.

Importance

Wolbachiabacteria of arthropods are at the forefront of global initiatives to fight arthropod-borne viruses. Despite great success in using the symbiont to fight viruses, little research has focused onWolbachia-fungal interactions. Here, we find thatWolbachiaofDrosophila melanogaster, the same strain widely used in antiviral initiatives, can also increase the longevity of flies systemically infected with a panel of yeast and filamentous fungal pathogens. The symbiont also partially increases host fertility and reduces fungal titers during early infection, indicating a significant fitness benefit. This represents a major step forward inWolbachiaresearch since its pathogen blocking abilities can now be extended to a broad diversity of another major branch of microbial life. This discovery may inform basic research on pathogen blocking and has potential translational applications in areas including biocontrol in agriculture.
Transcriptional coupling of telomeric retrotransposons with the cell cycle
Authors: Liu Mengmeng , Xie Xiao-Jun , Li Xiao , Ren Xingjie , Sun Jasmine , Lin Zhen , Hemba-Waduge Rajitha-Udakara-Sampath , Ji Jun-Yuan
Published: October 2023

Instead of employing telomerases to safeguard chromosome ends, dipteran species maintain their telomeres by transposition of telomeric-specific retrotransposons (TRs): inDrosophila, these areHeT-A,TART, andTAHRE. Previous studies have shown how these TRs create tandem repeats at chromosome ends, but the exact mechanism controlling TR transcription has remained unclear. Here we report the identification of multiple subunits of the transcription cofactor Mediator complex and transcriptional factors Scalloped (Sd, the TEAD homolog in flies) and E2F1-Dp as novel regulators of TR transcription and telomere length inDrosophila. Depletion of multiple Mediator subunits, Dp, or Sd increased TR expression and telomere length, while over-expressing E2F1-Dp or knocking down the E2F1 regulator Rbf1 (Retinoblastoma-family protein 1) stimulated TR transcription, with Mediator and Sd affecting TR expression through E2F1-Dp. The CUT&RUN analysis revealed direct binding of CDK8, Dp, and Sd to telomeric repeats. These findings highlight the essential role of the Mediator complex in maintaining telomere homeostasis by regulating TR transcription through E2F1-Dp and Sd, revealing the intricate coupling of TR transcription with the host cell-cycle machinery, thereby ensuring chromosome end protection and genomic stability during cell division.
Phylogenetic Distribution of Prokaryotic Non-Homologous End Joining DNA Repair Systems in Bacteria and Archaea
Authors: Manoj Femila , Kuhlman Thomas E.
Published: October 2023

Nonhomologous end-joining (NHEJ) is a repair mechanism for double strand breaks (DSBs) of DNA. This mechanism is ubiquitously observed within the eukaryotic domain; however, its presence is not as pervasive among prokaryotes and archaea. Notably, in prokaryotes, it has been discerned that multiple distinct NHEJ pathways have evolved in contrast to the singular NHEJ pathway prevalent in eukaryotes. We performed phylogenetic analysis to gain deeper insights into the distribution of these prokaryotic NHEJ pathways. Concurrently, components of the prokaryotic NHEJ pathways were used to find if any archaea carry the genes required and may be able to carry out NHEJ. The results show that few prokaryotes carry the components required for NHEJ, but multiple pathways may be active in a single species. In the context of Archaea, the analysis revealed that a substantial number of species contain fragments or segments of prokaryotic NHEJ elements. Nevertheless, the presence of all the necessary components for the complete execution of the NHEJ pathway remains relatively rare within the archaeal domain.
Beyond the “resprouter versus non‐resprouter” dichotomy: On the prevalence and evolutionary fingerprint of resprouting in tropical dry forest trees
Authors: de Souza Cléber Rodrigo , de Coelho de Souza Fernanda , Dexter Kyle G. , Maia Vinícius A. , de Aguiar‐Campos Natália , Farrapo Camila L. , Santos Alisson B. M. , Paula Gabriela G. P. , Morel Jean D. , Fagundes Nathalle C. A. , Santos Paola F. , Coelho Polyanne Aparecida , Silva Wilder B. , Santos Rubens M.
Published: October 2023

Resprouting is a plant persistence strategy in response to disturbance or stressful environmental conditions. Resprouters can dominate in stressful environments such as tropical dry forests (TDFs), but our knowledge of resprouting in TDFs is limited. Here, using a dataset of forest inventories in 16 TDF fragments (covering 15,642 trees and 321 species), we investigated patterns of resprouting in ecosystems subject to substantial seasonal water stress. We focused on two resprouting metrics: the proportion of trees that are multistemmed (resprouting frequency) and the number of stems per tree. In addition, we investigated the relative importance of environmental factors, taxonomic identity, and evolutionary history in resprouting response. Taxa with low to medium resprouting frequencies (17.19%–40.2%) are the most prevalent in TDF, compared to non‐resprouters and high‐frequency resprouters. Overall, resprouting ability appears to be an intrinsic trait that varies in response to environmental conditions but only within a range constrained by taxonomic identity. However, we found no phylogenetic signal above the genus level for any resprouting variables. Thus, the variation in resprouting across TDF lineages likely has been shaped by divergence between closely related taxa and convergence between distantly related ones, reflecting the specific environmental and disturbance factors to which they have been subjected.
Re‐tribalization in the 21st century, part 1
Authors: Ahmed Akbar , Martin Frankie , Ahmed Hoti Amineh
Published: October 2023

This exploratory study presents ‘re‐tribalization’ as a framework for comprehending contemporary global patterns and phenomena. It posits a link between the erosion of modernity's traits and a resurgence of tribal behaviour – the more elements that we associate with modernity diminish, the more we see the emergence of group formations akin to anthropological notions of tribes. This trend manifests not only in societies where tribal and lineage affiliations remain central to identity but also – perhaps more notably, considering modernity's promises – in developed nations, including global powerhouses like the USA, India and China. ‘Re‐tribalization’ signifies a modern‐day recourse to a so‐called tribal past, fortifying intra‐group cohesion and creating a distinction from other groups, thus delineating ‘us’ and ‘them’. This process highlights the drawing of boundaries between communities, positing that such delineations were more apparent in the past and need to be re‐established to navigate today's challenges and crises. The study traces the historical lineage of re‐tribalization appeals and their ties to nationalism, citing instances from Johann Gottfried Herder's works. This argument leverages the authors’ nearly two decades of ethnographic fieldwork, a collection of four studies and initial insights from their soon‐to‐be‐published book.
‘Hustlers vs dynasties’: Confronting patrimonial capitalism in Kenya's 2022 elections
Authors: Lockwood Peter
Published: October 2023

During Kenya's 2022 presidential race, William Samoei Ruto, the country's ex‐Deputy President, successfully leveraged his ‘Hustler Nation’ campaign to clinch victory. This campaign played on the struggles of the informal economy labourers, pledging a ‘hustler’ government dedicated to their cause. However, Ruto's campaign also utilized rhetoric against the deeply rooted ‘dynasties’ of Kenya's patrimonial capitalism, exploiting widespread dissatisfaction with the political and economic dominance of the Kenyatta family, including the incumbent President Uhuru Kenyatta. Throughout the campaign, voters debated the acceptable extent of wealth held by the country's affluent families and the potential of such wealth to manipulate democratic politics. This concise article unpacks the moral undertones of Kenyan disillusionment with Kenyatta supremacy, calling for reinvigorated anthropological scrutiny of the confrontations against modern patrimonial capital and the emerging resistances framed in the discourse of economic justice.
Fisherfolk and football: An ethnographic tale of loss in a changing climate
Authors: Haneefa Muhammed
Published: October 2023

Sea level rise is dramatically altering the daily lives of fisherfolk in the Ottummal coastal region of Malabar, India. This article draws on ethnographic fieldwork to explore the erosion of subaerial beaches, which have traditionally served as vital social and cultural touchstones for the community. It examines the profound impact of this erosion on the community's leisure activities, particularly their beloved pastime of football. It also analyses the local government's proposed strategy of managed retreat, which involves relocating vulnerable communities away from threatened areas. It considers its limitations in light of the fisherfolk's deep emotional and cultural connections with their lands and non‐material culture. The article posits that while climatologists and satellites can give a bird's eye view, anthropologists and ethnographers can give a worm's eye view of climate change.
Navigating uncertainty: The interplay of ‘magical football’ and ‘football magic’ in Cameroonian football
Authors: Umeya Kiyoshi , Yosimbom Hassan M.
Published: October 2023

Cameroon's Indomitable Lions (a nickname for the Cameroon national football team) are renowned for their ‘magical football’, a term that embodies their extraordinary performances. This article delves into the intertwining concepts of ‘magical football’ and ‘football magic’, seeking to understand how these elements contribute to the Lions’ success. The study reviews historical instances of the Lions’ participation in the Africa Cup of Nations and FIFA World Cup competitions, analyzing how natural football abilities interweave with supernatural enhancement to influence game outcomes. The findings suggest that talent alone does not guarantee victory, and the uncertainty of elements beyond our rational comprehension can significantly impact the game.
Gut microbiome as a biomarker for predicting early recurrence of HBV‐related hepatocellular carcinoma
Authors: Zheng Chongming , Lu Fei , Chen Bo , Yang Jinhuan , Yu Haitao , Wang Daojie , Xie Haonan , Chen Kaiwen , Xie Yitong , Li Jiacheng , Bo Zhiyuan , Wang Yi , Chen Gang , Deng Tuo
Published: October 2023

To investigate the potential of the gut microbiome as a biomarker for predicting the early recurrence of HBV‐related hepatocellular carcinoma (HCC), we enrolled 124 patients diagnosed with HBV‐associated HCC and 82 HBV‐related hepatitis, and 86 healthy volunteers in our study, collecting 292 stool samples for 16S rRNA sequencing and 35 tumor tissue samples for targeted metabolomics. We performed an integrated bioinformatics analysis of gut microbiome and tissue metabolome data to explore the gut microbial–liver metabolite axis associated with the early recurrence of HCC. We constructed a predictive model based on the gut microbiota and validated its efficacy in the temporal validation cohort. Dialister, Veillonella, the Eubacterium coprostanoligenes group, and Lactobacillus genera, as well as the Streptococcus pneumoniae and Bifidobacterium faecale species, were associated with an early recurrence of HCC. We also found that 23 metabolites, including acetic acid, glutamate, and arachidonic acid, were associated with the early recurrence of HCC. A comprehensive analysis of the gut microbiome and tissue metabolome revealed that the entry of gut microbe‐derived acetic acid into the liver to supply energy for tumor growth and proliferation may be a potential mechanism for the recurrence of HCC mediated by gut microbe. We constructed a nomogram to predict early recurrence by combining differential microbial species and clinical indicators, achieving an AUC of 78.0%. Our study suggested that gut microbes may serve as effective biomarkers for predicting early recurrence of HCC, and the gut microbial–tumor metabolite axis may explain the potential mechanism by which gut microbes promote the early recurrence of HCC.
2‐Hydroxyethyl methacrylate (HEMA): A clinical review of contact allergy and allergic contact dermatitis. Part 2. Cross‐ and co‐sensitization, other skin reactions to HEMA, position of HEMA among (meth)acrylates, sensitivity as screening agent, presence of HEMA in commercial products and practical information on patch test procedures
Authors: de Groot Anton C. , Rustemeyer Thomas
Published: October 2023

This is the second part of a literature review of the clinical aspects of contact allergy to and allergic contact dermatitis from 2‐hydroxyethyl methacrylate (HEMA). Topics include cross‐ and co‐sensitization, atypical manifestations of contact allergy, frequency of positive patch tests to HEMA compared with other (meth)acrylates, sensitivity of HEMA as a screening agent, the presence of HEMA in commercial products, and practical information on patch testing procedures. Primary sensitization to methacrylates including HEMA may result in methacrylate and acrylate cross‐sensitization. There is a strong cross‐allergy between HEMA, ethylene glycol dimethacrylate (EGDMA), and hydroxypropyl methacrylate; many reactions to EGDMA are cross‐reactions to primary HEMA sensitization. Rare atypical manifestations of HEMA‐allergy include lichen planus, lymphomatoid papulosis, systemic contact dermatitis, leukoderma after positive patch tests, and systemic side effects such as nausea, diarrhoea, malaise, and palpitations. The occurrence of respiratory disease caused by methacrylates such as asthma is not infrequent. HEMA is the most frequently patch test‐positive methacrylate. It is a good screening agent for allergy to other (meth)acrylates. Patch test sensitization to HEMA 2% pet. is extremely rare. There are (some) indications that HEMA is frequently used in dental products and nail cosmetics.
Two models of mind blanking
Authors: Kaufmann Angelica , Parmigiani Sara , Kawagoe Toshikazu , Zabaroff Elliot , Wells Barnaby
Published: October 2023

Mind blanking is a mental state in which attention does not bring any perceptual input into conscious awareness. As this state is still largely unexplored, we suggest that a comprehensive understanding of mind blanking can be achieved through a multifaceted approach combining self‐assessment methods, neuroimaging and neuromodulation. In this article, we explain how electroencephalography and transcranial magnetic stimulation could be combined to help determine whether mind blanking is associated with a lack of mental content or a lack of linguistically or conceptually determinable mental content. We also question whether mind blanking occurs spontaneously or intentionally and whether these two forms are instantiated by the same or different neural correlates.