bluuebunny/crossref_metadata_2025 huggingface dataset:
Agreement between the ventilated capsule and the KuduSmart® device for measuring sweating responses to passive heat stress and exercise
Authors: Ravanelli Nicholas , Newhouse Douglas , Foster Fergus , Caldwell Aaron R.
Published: April 2023

The present study assessed agreement between the KuduSmart® device and the ventilated capsule (VC) technique for measuring: i) minute-averaged local sweat rate (LSR); ii) sweating onset; iii) thermosensitivity; and iv) steady-state LSR, during passive heat stress and exercise. On two separate occasions for each heat stress intervention, participants were either passively heated by recirculating hot water (49°C) through a tube-lined garment until rectal temperature increased 1°C over baseline (n=8), or walked on a treadmill for 60 minutes at a fixed rate of heat production (n=9). LSR of the forearm was concurrently measured with a VC and the KuduSmart® device secured within ∼2 cm. Mean body temperature was calculated as the weighted average between rectal (80%) and mean skin (20%) temperature. Using a ratio scale Bland-Altman analysis with the VC as the reference, the KuduSmart® device demonstrated systematic bias for minute-averaged LSR (1.19 [1.09, 1.28]) and steady-state LSR (1.16 [1.09,1.23]), however no bias for thermosensitivity (1.08 [1.00, 1.16]) or sweating onset (1.00 [1.00, 1.00]). Although poor agreement was observed for minute-averaged LSR (CV = 43.3%), more than 73% of all observations with the KuduSmart® device (n=2795) were within an absolute error of < 0.2 mg/cm2/min to the VC. The KuduSmart® device demonstrated acceptable agreement for steady-state LSR (CV = 19.5%) and thermosensitivity (CV = 21.7%), and almost perfect agreement for sweating onset (CV = 0.14%). Collectively, the KuduSmart® device may be a satisfactory in-field solution for assessing the sweating response to heat stress.
Fatty acid amide hydrolase drives adult mammary gland development by promoting luminal cell differentiation
Authors: Tundidor Isabel , Seijo-Vila Marta , Blasco-Benito Sandra , Rubert-Hernández María , Moreno-Bueno Gema , Bindila Laura , Fernández de la Rosa Rubén , Guzmán Manuel , Sánchez Cristina , Pérez-Gómez Eduardo
Published: April 2023

Mammary gland development occurs primarily in adulthood, undergoing extensive expansion during puberty followed by cycles of functional specialization and regression with every round of pregnancy/lactation/involution. This process is ultimately driven by the coordinated proliferation and differentiation of mammary epithelial cells. However, the endogenous molecular factors regulating these developmental dynamics are still poorly defined. Endocannabinoid signaling is known to determine cell fate-related events during the development of different organs in the central nervous system and the periphery. Here, we report that the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH) plays a pivotal role in adult mammary gland development. Specifically, it is required for luminal lineage specification in the mammary gland, and it promotes hormone-driven secretory differentiation of mammary epithelial cells by controlling the endogenous levels of anandamide and the subsequent activation of cannabinoid CB1receptors. Together, our findings shed light on the role of the endocannabinoid system in breast development and point to FAAH as a therapeutic target in milk-production deficits.
Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning
Authors: Zirak Bahar , Naghipourfar Mohsen , Saberi Ali , Pouyabahar Delaram , Zarezadeh Amirhossein , Luo Lixi , Fish Lisa , Huh Doowon , Navickas Albertas , Sharifi-Zarchi Ali , Goodarzi Hani
Published: April 2023

Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes1,2. However, the mechanisms that govern their sorting and secretion are still not well understood. In this study, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequence. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis, and confirmed that primary RNA sequence is a major determinant in small RNA secretion. Additionally, we used ExoGRU to revealcisandtransfactors that underlie small RNA secretion, including known and novel RNA-binding proteins, e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. We used exoCLIP to reveal the RNA interactome of HNRNPA2B1 and RBM24 in extracellular vesicles. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into complex processes such as small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.
A diffusion-driven switch specifies rhizoid precursor cells inMarchantia polymorpha
Authors: Mercadal Josep , Ferreira-Guerra Mar , Caño-Delgado Ana I. , Ibañes Marta
Published: April 2023

The specification of rhizoid precursor cells in the epidermis ofMarchantia polymorphagemmae has been shown to involve lateral inhibition mediated by the microRNA FRH1, which represses its activator RSL1, a rhizoidspecific transcription factor. However, how inhibition is conferred to adjacent cells and which is the mechanism underlying the emergence of rhizoid precursors remain unknown. In this paper, we use mathematical and computational modeling to show that the previously reported rhizoid patterns in WT, gain-of-function and lossof-function mutants ofFRH1andRSL1are consistent with lateral inhibition mediated by a mobile FRH1. Our modeling results suggest that cells inMarchantiawildtype gemmae reside close to a critical state, where diffusion of FRH1 drives a switch of RSL1 expression that specifies rhizoid precursors. This process involves an initially random trigger and subsequent lateral inhibition, leading to cellular patterns consisting of small and filamentous clusters of rhizoid precursors. We confirm these predictions with new data on WT rhizoid distributions. Our findings highlight a novel mechanism of cellular pattern formation, opening new research directions for understanding cellular differentiation and tissue morphogenesis, with potential implications for a broad range of biological systems.
Multiomics Approach to Understanding Olaparib Resistance and Predicting Drug Response
Authors: Lim Won-Jun , Kim Hyunjin M. , Oh YongHo , Pyo Junhee
Published: April 2023

We aimed to uncover genetic factors affecting resistance to the cancer drug olaparib. To do this, we utilized multiomics matrix factorization (MOFA), a multiomics approach, to explore omic-based features that might become biomarker candidates. Our results showed that 17 damaging mutations, 6 gene expression signatures, 17 DNA methylations, and 26 transcription-factor activities can impact the refractory response to olaparib.

To verify the potential utility of the identified biomarker candidates, we generated a predictive model to differentiate between olaparib responding and nonresponding cell lines using machine learning techniques, including support vector machine algorithms, random forest algorithms, and Siamese neural networks. The model was centered around six gene-expression biomarker candidates and validated using the Genomics of Drug Sensitivity in Cancer database.

Our findings suggest that using a multiomics approach with machine learning methods can lead to a better understanding of the mechanism of drug resistance and identify biomarkers, which will ultimately facilitate the appropriate administration of drugs to patients. The source codes can be found athttps://github.com/wjlim/DrugResistance.
Both CD8 and CD4 T cells contribute to immunosurveillance preventing the development of neoantigen-expressing autochthonous sarcomas
Authors: Himes Jonathon E. , Wisdom Amy J. , Wang Laura , Shepard Sam J. , Daniel Andrea R. , Williams Nerissa , Luo Lixia , Ma Yan , Mowery Yvonne M. , Kirsch David G.
Published: April 2023

The adaptive immune system plays an essential anti-tumor role through immunosurveillance and response to immunotherapies. Characterizing phenotypic features and mechanisms of dysfunction of tumor-specific T cell populations may uncover novel immunotherapeutic targets and biomarkers of response. To study tumor-specific T cell responsesin vivo, a tumor model must express a known neoantigen. While transplant models with known neoantigen expression are widely available, autochthonous tumor models in which the tumor coevolves with the immune system are limited. In this study, we combined CRISPR/Cas9 and sleeping beauty transposase technology to develop an autochthonous orthotopic murine sarcoma model with oncogenic KrasG12D, functionally impaired p53, and expression of known MHCI and MHCII sarcoma neoantigens. Using MHC tetramer flow cytometry, we identified a tumor-specific immune response in the peripheral blood as early as 10 days after tumor induction leading to tumor clearance. Tumors developed at high penetrance after co-depletion of CD8 and CD4 T cells, but depletion of either CD8 or CD4 T cells alone was insufficient to permit tumor growth. These results suggest that CD8 and CD4 T cells can independently contribute to immunosurveillance leading to clearance of sarcomas expressing MHCI and MHCII neoantigens.
A soybean pattern recognition receptor conferring broad-spectrum pathogen and pest resistance regulates expression of several NLR receptor proteins
Authors: Ngaki Micheline N. , Srivastava Subodh K. , Feifei Wang , Bhattacharyya Madan K.
Published: April 2023

Overexpressors ofGlycine max disease resistant 1(GmDR1) exhibits broad-spectrum resistance againstFusarium virguliforme, soybean cyst nematode (SCN), spider mites, and soybean aphids in soybean. To understand the mechanisms of broad-spectrum immunity mediated byGmDR1, we investigated the transcriptomes of a strong and a weakGmDR1-overexpressors following treatment with chitin, a pathogen- and pest-associated molecular pattern (PAMP) found in these organisms. The strong and weakGmDR1-overexpressors exhibited altered expression of 6,098 and 992 genes, respectively, as compared to the nontransgenic control following chitin treatment. However, only 192 of these genes exhibited over two-fold changes in expression levels in both strong and weakGmDR1-overexpressors as compared to the control. MapMan analysis of the 192 genes revealed 64 biotic stress-related genes, of which 53 were induced and 11 repressed as compared to the control. The 53 chitin-induced genes include nine that encode receptor kinases, 13 encodenucleotide-binding leucine-richrepeat (NLR) receptor proteins, seven encoding WRKY transcription factors, four ethylene response factors, and three MYB-like transcription factors. Investigation of a subset of these genes revealed three receptor protein kinases, seven NLR proteins, and one WRKY transcription factor genes that are induced followingF. virguliformeand SCN infection. The integral plasma membrane GmDR1 protein most likely recognizes PAMPs including chitin and activates transcription of genes encoding receptor kinases and NLR proteins. GmDR1 could be a pattern recognition receptor that regulates the expression of several NLRs for expression of PAMP-triggered immunity and/or priming the effector triggered immunity.
Impaired centrosome biogenesis in kidney stromal progenitors reduces abundance of interstitial lineages and accelerates injury-induced fibrosis
Authors: Langner Ewa , Cheng Tao , Kefaloyianni Eirini , Gluck Charles , Wang Baolin , Mahjoub Moe R.
Published: April 2023

Defective centrosome function can disrupt embryonic kidney development, by causing changes to the renal interstitium that leads to fibrocystic disease pathologies. Yet, it remains unknown how mutations in centrosome genes impact kidney interstitial cells. Here, we examined the consequences of defective centrosome biogenesis on stromal progenitor cell growth, differentiation and fate. Conditional deletion ofCep120, a ciliopathy gene essential for centrosome duplication, in the stromal mesenchyme resulted in reduced abundance of pericytes, interstitial fibroblasts and mesangial cells. This was due to delayed mitosis, increased apoptosis, and changes in Wnt and Hedgehog signaling essential for differentiation of stromal lineages.Cep120ablation resulted in hypoplastic kidneys with medullary atrophy and delayed nephron maturation. Finally, centrosome loss in the interstitium sensitized kidneys of adult mice, causing rapid fibrosis via enhanced TGF-β/Smad3-Gli2 signaling after renal injury. Our study defines the cellular and developmental defects caused by centrosome dysfunction in embryonic kidney stroma.

Graphical Abstract

Highlights

Defective centrosome biogenesis in kidney stroma causes:

Reduced abundance of stromal progenitors, interstitial and mesangial cell populations

Defects in cell-autonomous and paracrine signaling

Abnormal/delayed nephrogenesis and tubular dilations

Accelerates injury-induced fibrosis via defective TGF-β/Smad3-Gli2 signaling axis
Adventitial macrophage accumulation impairs perivascular nerve function in mesenteric arteries with inflammatory bowel disease
Authors: Grunz Elizabeth A. , Jones Benjamin W. , Lateef Olubodun , Sen Sidharth , Wilkenson Katie , Joshi Trupti , Boerman Erika M.
Published: April 2023

1.

Introduction:Inflammatory bowel disease (IBD) involves aberrant immune responses and is associated with both cardiovascular disease risk and altered intestinal blood flow. However, little is known about how IBD affects regulation of perivascular nerves that mediate blood flow. Previous work found perivascular nerve function is impaired in mesenteric arteries with IBD. The purpose of this study was to determine the mechanism of impaired perivascular nerve function.

Methods:RNA sequencing was performed on mesenteric arteries from IL10-/-mice treated withH.hepaticusto induce disease (IBD) or left non-gavaged (Control). For all other studies, Control and IBD mice received either saline or clodronate liposome injections to study the effect of macrophage depletion. Perivascular nerve function was assessed using pressure myography and electrical field stimulation. Leukocyte populations, and perivascular nerves, and adventitial neurotransmitter receptors were labeled using fluorescent immunolabeling.

Results:IBD was associated with increased in macrophage-associated gene expression, and immunolabeling showed accumulation of adventitial macrophages. Clodronate liposome injection eliminated adventitial macrophages, which reversed significant attenuation of sensory vasodilation, sympathetic vasoconstriction and sensory inhibition of sympathetic constriction in IBD. Acetylcholine-mediated dilation was impaired in IBD and restored after macrophage depletion, but sensory dilation remained nitric oxide independent regardless of disease and/or macrophage presence.

Conclusion:Altered neuro-immune signaling between macrophages and perivascular nerves in the arterial adventitia contributes to impaired vasodilation, particularly via dilatory sensory nerves. Targeting the adventitial macrophage population may help preserve intestinal blood flow in IBD patients.
SARS-CoV-2 Spike Protein Accumulation in the Skull-Meninges-Brain Axis: Potential Implications for Long-Term Neurological Complications in post-COVID-19
Authors: Rong Zhouyi , Mai Hongcheng , Kapoor Saketh , Puelles Victor G. , Czogalla Jan , Schädler Julia , Vering Jessica , Delbridge Claire , Steinke Hanno , Frenzel Hannah , Schmidt Katja , Caliskan Özüm Sehnaz , Wettengel Jochen Martin , Cherif Fatma , Ali Mayar , Kolabas Zeynep Ilgin , Ulukaya Selin , Horvath Izabela , Zhao Shan , Krahmer Natalie , Tahirovic Sabina , Yildirim Ali Önder , Huber Tobias B. , Ondruschka Benjamin , Bechmann Ingo , Ebert Gregor , Protzer Ulrike , Bhatia Harsharan Singh , Hellal Farida , Ertürk Ali
Published: April 2023

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has been associated mainly with a range of neurological symptoms, including brain fog and brain tissue loss, raising concerns about the virus’s acute and potential chronic impact on the central nervous system. In this study, we utilized mouse models and human post-mortem tissues to investigate the presence and distribution of the SARS-CoV-2 spike protein in the skull-meninges-brain axis. Our results revealed the accumulation of the spike protein in the skull marrow, brain meninges, and brain parenchyma. The injection of the spike protein alone caused cell death in the brain, highlighting a direct effect on brain tissue. Furthermore, we observed the presence of spike protein in the skull of deceased long after their COVID-19 infection, suggesting that the spike’s persistence may contribute to long-term neurological symptoms. The spike protein was associated with neutrophil-related pathways and dysregulation of the proteins involved in the PI3K-AKT as well as complement and coagulation pathway. Overall, our findings suggest that SARS-CoV-2 spike protein trafficking from CNS borders into the brain parenchyma and identified differentially regulated pathways may present insights into mechanisms underlying immediate and long-term consequences of SARS-CoV-2 and present diagnostic and therapeutic opportunities.

Graphical Summary

Short Summary

The accumulation of SARS-CoV-2 spike protein in the skull-meninges-brain axis presents potential molecular mechanisms and therapeutic targets for neurological complications in long-COVID-19 patients.
RSim: A Reference-Based Normalization Method via Rank Similarity
Authors: Yuan Bo , Wang Shulei
Published: April 2023

Microbiome sequencing data normalization is crucial for eliminating technical bias and ensuring accurate downstream analysis. However, this process can be challenging due to the high frequency of zero counts in microbiome data. We propose a novel reference-based normalization method called normalization via rank similarity (RSim) that corrects sample-specific biases, even in the presence of many zero counts. Unlike other normalization methods, RSim does not require additional assumptions or treatments for the high prevalence of zero counts. This makes it robust and minimizes potential bias resulting from procedures that address zero counts, such as pseudo-counts. Our numerical experiments demonstrate that RSim reduces false discoveries, improves detection power, and reveals true biological signals in downstream tasks such as PCoA plotting, association analysis, and differential abundance analysis.
Erythropoietic, hematinic and leucocytic activities of the aqueous extracts of the fruits and leaves ofSolanum torvum
Authors: Ibrahim Ilyas , Bardoe Denis , Hayford Daniel
Published: April 2023

The Turkey berry(Solanum torvum)plant is globally exploited for its medicinal and pharmacological benefits. This study was conducted to investigate the erythropoietic, hemanitic and leucocytic activities of the aqueous extracts of the fruits and leaves ofSolanum torvum. Three groups of rabbits with five replicates each (aged 6-8 weeks) where either given the aqueous extracts of fresh turkey berry fruits, fresh turkey berry leafs, or distilled water at a dose of 0.5ml and a concentration of 100g of leaf or fruit against 100ml of distilled water (1g per 1ml of distilled water) per day over a six-week period. The rabbits were fedad libitumwith concentrate and water throughout the experimental period. A full blood count (FBC) using a BC 2600 hematology analyzer was conducted on the collected blood samples of the experimental animals at the end of the sixth week of extract administration. The blood samples of the rabbits given the aqueous extracts of the fruit and leaf of turkey berry at the end of the six weeks of treatment administration showed a significant (p<0.05) increase in red blood cell count, hemoglobin level, white blood cell count and hematocrit. The results indicated thatSolanum torvumhad a positive erythropoietic, hemanitic and leucocytic properties. This implies thatSolanum torvumis effective in improving the quality of blood and hence can prevent some hematological disorders.
GENI: a web server to identify gene set enrichments in tumor samples
Authors: Hayashi Arata , Ruppo Shmuel , Heilbrun Elisheva E. , Mazzoni Chiara , Adar Sheera , Yassour Moran , Rmaileh Areej Abu , Shaul Yoav D.
Published: April 2023

The Cancer Genome Atlas (TCGA) and other projects provide informative tumor-associated genomic data for the broad research community. Hence, several useful web-based tools have been generated to ease non-expert users with the analysis and characterization of a specific gene behavior in selected tumors. However, none of the existing tools offer the user the means to evaluate the expression profile of a given gene in the context of the whole transcriptome. Currently, such analyses require prior bioinformatic knowledge and expertise. Therefore, we developed GENI (Gene ENrichment Identifier) as a fast, user-friendly tool to analyze the TCGA expression data for gene set enrichments. GENI analyzes large-scale tumor-associated gene expression datasets and evaluates biological relevance, thus offering researchers a simplified means to analyze cancer patient-derived data.

Availability and implementation

GENI is a freely available fast web-based tool developed using the R programming language. It is accessible via the URL:https://yoavshaul-lab.shinyapps.io/gsea-geni/. The complete script can be found athttps://github.com/ArataHayashi/GENI-Gene-ENrichment-Identifier.
Arsenite methyltransferase 3 regulates hepatic energy metabolism which dictates the hepatic response to arsenic exposure
Authors: Delaney Patrice , Khan Nouf , O’Connor Matthew J. , Ambrosio Elizabeth Mayela , Garcia-Sabaté Anna , M. Teo Jeremy C. , Pergantis Spiros A. , Ober Elke , Sadler Kirsten C.
Published: April 2023

Inorganic arsenic (iAs(III)) is among the most pervasive environmental toxicants in the world. The iAs metabolizing enzyme, arsenite methyltransferase (AS3MT), is a key mediator of iAs(III) toxicity and has been almost exclusively investigated in the context of iAs(III) exposure. We use functional genomics approach with zebrafishas3mtmutants which lack arsenite methyltransferase activity to uncover novel, arsenic-independent functions for As3mt. Transcriptomic analysis of untreated whole larvae, and the larval and adult livers fromas3mtmutants revealed thousands of differentially expressed genes (DEGs) compared to wild-type controls. These were enriched for genes functioning in the ribosome or mitochondria. Nearly all genes in the citric acid cycle and mitochondrial transport were downregulated inas3mtmutant livers. This resulted in reduction in reactive oxygen species levels by half and fatty liver in 81% ofas3mtmutant larvae. An inverse expression pattern was detected for over 2,000 of the As3mt regulated DEGs in the liver of larvae with transgenic overexpression of As3mt in hepatocytes. Replacingas3mtexpression in hepatocytes ofas3mtmutants prevented fatty liver, demonstrating that As3mt has novel, cell-autonomous and arsenic-independent functions regulating mitochondrial metabolism. We suggest that these functions contribute to iAs toxicity, as the mitochondrial function genes that were downregulated in the liver of unexposedas3mtmutants were further downregulated upon iAs exposure andas3mtmutants were sensitized to iAs. This indicates that As3mt regulates hepatic energy metabolism and demonstrates that, in addition to its role in iAs detoxification, the physiological functions of As3mt contribute to arsenic toxicity.

SIGNIFICANCE

Arsenic is an endemic environmental toxicant, and the current paradigm is that susceptibility to arsenic toxicity is dictated by levels of expression of the arsenite 3 methyltransferase gene (As3mt), which is dedicated enzyme involved in arsenic detoxification. Our data showing that As3mt serves arsenic-independent functions in energy metabolism challenge this paradigm. We show that zebrafishas3mtmutants have loss of mitochondrial function and develop fatty liver and suggest thatas3mtmutants are sensitized to arsenic toxicity due, in part, to impaired mitochondrial function. This finding opens an entirely new area of study to identify the cellular function of As3mt and further advances the understanding of how genetic variants in As3mt confer sensitivity arsenic toxicology.
Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56
Authors: Yang Yingying , Ritzenhofen Kira , Otrzonsek Jessica , Schallenberg-Rüdinger Mareike , Knoop Volker
Published: April 2023

The mitochondrial C-to-U RNA editing factor PPR56 of the mossPhyscomitrium patensis an RNA-binding pentatricopeptide repeat protein equipped with a terminal DYW-type cytidine deaminase domain. Transferred intoEscherichia coli,PPR56 works faithfully on its two native RNA editing targets, nad3eU230SL and nad4eU272SL, and also converts cytidines into uridines at over 100 off-targets in the bacterial transcriptome. Accordingly, PPR56 is attractive for detailed mechanistic studies in the heterologous bacterial setup, allowing for scoring differential RNA editing activities of many target and protein variants in reasonable time. Here, we report (i) on the effects of numerous individual and combined PPR56 protein and target modifications, (ii) on the spectrum of off-target C-to-U editing in the bacterial background transcriptome for PPR56 and two variants engineered for target re-direction and (iii) on combinations of targets in tandem or separately at the 5’- and 3’-ends of large mRNAs. The latter experimentation finds enhancement of RNA editing at weak targets in many cases, including cox3eU290SF as a new candidate mitogenome target. We conclude that C-to-U RNA editing can be much enhanced by transcript features also outside the region ultimately targeted by PPRs of a plant editing factor, possibly facilitated by its enrichment or scanning along transcripts.
Whole-genome sequencing confirms multiple species of Galapagos giant tortoises
Authors: Gaughran Stephen J. , Gray Rachel , Jones Menna , Fusco Nicole , Ochoa Alexander , Miller Joshua M. , Poulakakis Nikos , de Queiroz Kevin , Caccone Adalgisa , Jensen Evelyn L.
Published: April 2023

Galapagos giant tortoises are endemic to the Galapagos Archipelago, where they are found in isolated populations. While these populations are widely considered distinguishable in morphology, behavior, and genetics, the recent divergence of these taxa has made their status as species controversial. Here, we apply multispecies coalescent methods for species delimitation to whole genome resequencing data from 38 tortoises across all 13 extant taxa to assess support for delimiting these taxa as species. In contrast to previous studies based solely on divergence time, we find strong evidence to reject the hypothesis that all Galapagos giant tortoises belong to a single species. Instead, a conservative interpretation of model-based and divergence-based results indicates that these taxa form a species complex consisting of a minimum of 9 species, with some analyses supporting as many as 13 species. There is mixed support for the species status of taxa living on the same island, with some methods delimiting them as separate species and others suggesting multiple populations of a single species per island. These results make clear that Galapagos giant tortoise taxa represent different stages in the process of speciation, with some taxa further along in that evolutionary process than others. A better understanding of the more complex parts of that process is urgently needed, given the threatened status of Galapagos giant tortoises.

Lay Summary

Species delimitation is a challenging problem in evolutionary biology, but one that is central to the field. Distinguishing species can affect conservation management practices, from conservation status assessments to strategies for breeding programs. More fundamentally, understanding species boundaries affects our ability to assess biodiversity and to study evolutionary processes. The Galapagos Archipelago presents several radiations of closely related taxa that inspired Charles Darwin to develop his theory of evolution by natural selection and later led to foundational case studies in speciation. The Galapagos giant tortoises were one such inspiration. Nearly two centuries later, there is still an ongoing debate about the taxonomic status of these tortoises, with opinions on their status ranging from barely differentiated populations to separate species. Here, we present the first genomic species delimitation of Galapagos giant tortoises and provide convincing evidence that this group is a complex consisting of between 9 and 13 species. These results provide valuable guidance to conservation stakeholders in the Galapagos, while also adding an important case study to the delimitation of island species.
AI-Guided Discovery of Novel SARS-CoV-2 PLpro Inhibitors: Accelerating Antiviral Drug Development in the Fight Against COVID-19
Authors: Spagnoli Will , Danter Wayne R
Published: April 2023

The global pandemic caused by SARS-CoV-2 has highlighted the urgent need for effective antiviral drugs. The papain-like protease (PLpro) is a key viral enzyme involved in the replication and immune evasion of SARS-CoV-2, making it a promising target for antiviral drug development. In this study, we employed an artificial intelligence (AI)-driven drug discovery platform, LIME, to generate novel inhibitors of the SARS-CoV-2 PLpro. LIME is based on generative language models that can generate diverse, valid, and synthetically accessible compounds. The LIME software was used to identify potential inhibitors with strong binding affinity and specificity to the target protein. The top 13 hit compounds were tested in vitro, and the top 5 inhibitors with strong binding affinity and specificity were selected for further analysis. A top candidate molecule, CSEMRS-1376, exhibited similar binding energies and structural similarities to the known SARS-CoV-2 PLpro inhibitor, XR8-89. Computational analysis of the absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles of the hit compounds and XR8-89 showed that both CSEMRS-1376 and XR8-89 demonstrated favorable ADMET profiles. Overall, the LIME software successfully identified several novel molecules, including CSEMRS-1376, with strong potential as a therapeutic agent against SARS-CoV-2. The study highlights the potential of AI-driven drug discovery platforms, such as LIME, to accelerate the drug development process and pave the way for more efficient and effective therapeutics.
Identification of a Rabenosyn-5 like protein and Rab5b in host cell cytosol uptake reveals conservation of endosomal transport in malaria parasites
Authors: Sabitzki Ricarda , Rossmann Anna-Lena , Schmitt Marius , Flemming Sven , Guillen-Samander Andres , Behrens Hannah Michaela , Jonscher Ernst , Hoehn Katharina , Froehlke Ulrike , Spielmann Tobias
Published: April 2023

Vesicular trafficking, including secretion and endocytosis, plays fundamental roles in the unique biology of P. falciparum blood-stage parasites. Endocytosis of host cell cytosol (HCC) provides nutrients and room for parasite growth and is critical for the action of antimalarial drugs and parasite drug resistance. Previous work showed that PfVPS45 functions in endosomal transport of HCC to the parasite's food vacuole, raising the possibility that malaria parasites possess a canonical endolysosomal system. However, the seeming absence of VPS45-typical functional interactors such as rabenosyn 5 (Rbsn5) and the re-purposing of Rab5 isoforms and other endolysosomal proteins for secretion in apicomplexans question this idea. Here we identified a parasite Rbsn5-like protein and show that it functions with VPS45 in the endosomal transport of HCC. We also show that PfRab5b but not PfRab5a is involved in the same process. Inactivation of PfRbsn5L resulted in PI3P and PfRab5b decorated HCC-filled vesicles, typical for endosomal compartments. Overall, this indicates that despite the low sequence conservation of PfRbsn5 and the unusual N-terminal modification of PfRab5b, principles of endosomal transport in malaria parasite are similar to that of model organisms. Using a conditional double protein inactivation system, we further provide evidence that the PfKelch13 compartment, an unusual apicomplexa-specific endocytosis structure at the parasite plasma membrane, is connected upstream of the Rbsn5/VPS45/Rab5b-dependent endosomal route. Altogether, this work indicates that HCC-uptake consists of a highly parasite-specific part that feeds endocytosed material into an endosomal system containing more canonical elements, leading to the delivery of HCC to the food vacuole.
Expansion of triplet nucleotide repeats in primates and other vertebrates: an evolutionary perspective
Authors: Murthy Saketh , Mishra Rakesh K
Published: April 2023

Triplet nucleotide repeat (TNR) expansion has been linked to more than 40 inheritable neurological, neuromuscular and neurodegenerative disorders. Increase in copy number beyond a threshold causes further rapid expansion of the repeats, leading to instability and disease via gain/loss of function, toxic RNA products or chromosome instability. An analysis of these repeat regions across vertebrates shows that these repeats have consistently either arisen late or have increased in copy number in vertebrates, most significantly in primates and particularly in humans. Many of the known diseases have neurological basis, suggests positive selection of these repeats for neuronal function. Late occurrence of the diseases implicates a lack of negative selection. This evolutionary trade-off, a higher neuronal capability at the cost of disease susceptibility, is further supported by the observation that most of the genes associated with TNR expansion diseases have neuronal function.
TcHRG plays a central role in orchestrating heme uptake inTrypanosoma cruziepimastigotes
Authors: Tevere Evelyn , Di Capua Cecilia Beatriz , Chasen Nathan Michael , Etheridge Ronald Drew , Cricco Julia Alejandra
Published: April 2023

Trypanosoma cruzi, a heme auxotrophic parasite, can control intracellular heme content by modulatingTcHRG expression when a free heme source is added to axenic culture. Herein, we explore the role ofTcHRG protein in regulating the uptake of heme derived from hemoglobin in epimastigotes. It was found that the parasite’s endogenousTcHRG (protein and mRNA) responds similarly to bound (hemoglobin) and free (hemin) heme. Additionally, the overexpression ofTcHRG leads to an increase in intracellular heme content. The localization ofTcHRG is also not affected in parasites supplemented with hemoglobin as the sole heme source. Endocytic null epimastigotes do not show a significant difference in growth profile, intracellular heme content andTcHRG protein accumulation compared to WT when feeding with hemoglobin or hemin as a source of heme. These results suggest that the uptake of hemoglobin-derived heme likely occurs through extracellular proteolysis of hemoglobinviathe flagellar pocket, and this process is governed byTcHRG. In sum,T. cruziepimastigotes controls heme homeostasis by modulatingTcHRG expression independently of the source of available heme.
Developmental plasticity and variability in the formation of egg-spots, a pigmentation ornament in the cichlidAstatotilapia calliptera
Authors: Clark Bethan , Hickey Aaron , Fischer Bettina , Elkin Joel , Santos M. Emília
Published: April 2023

Vertebrate pigmentation patterns are highly diverse, yet we have a limited understanding of how evolutionary changes to genetic, cellular, and developmental mechanisms generate variation. To address this, we examine the formation of a sexually-selected male ornament exhibiting inter- and intra-specific variation, the egg-spot pattern, consisting of circular yellow-orange markings on the male anal fins of haplochromine cichlid fishes. We focus onAstatotilapia calliptera, the ancestor-type species of the Malawi cichlid adaptive radiation of over 850 species. We identify a key role for iridophores in initialising egg-spot aggregations composed of iridophore-xanthophore associations. Despite adult sexual dimorphism, aggregations initially form in both males and females, with development only diverging between the sexes at later stages. Unexpectedly, we found that the timing of egg-spot initialisation is plastic. The earlier individuals establish their own territory the earlier the aggregations form, with iridophores being the cell type that responds to social conditions. Furthermore, we observe apparent competitive interactions between adjacent egg-spot aggregations, which strongly suggests that egg-spot patterning results mostly from cell-autonomous cellular interactions. Together, these results demonstrate thatA. callipteraegg-spot development is an exciting model for investigating pigment pattern formation at the cellular level in a system with developmental plasticity, sexual dimorphism, and intra-specific variation. AsA. callipterarepresents the ancestral bauplan for egg-spots, these findings provide a baseline for informed comparisons across the incredibly diverse Malawi cichlid radiation.
A fluorescent reporter model for the visualization and characterization of TDC
Authors: Fiore Alessandra , Sala Eleonora , Laura Chiara , Riba Michela , Nelli Maria , Fumagalli Valeria , Oberrauch Federico , Mangione Marta , Cristofani Claudia , Provero Paolo , Iannacone Matteo , Kuka Mirela
Published: April 2023

TDCare hematopoietic cells that combine dendritic cell (DC) and conventional T cell markers and functional properties. They were identified in secondary lymphoid organs (SLOs) of naïve mice as cells expressing CD11c, major histocompatibility molecule (MHC)-II, and the T cell receptor (TCR) β chain. Despite thorough characterization as to their potential functional properties, a physiological role for TDCremains to be determined. Unfortunately, using CD11c as a marker for TDChas the caveat of its upregulation on different cells, including T cells, upon activation. Therefore, a more specific marker is needed to further investigate TDCfunctions in peripheral organs in different pathological settings. Here we took advantage of Zbtb46-GFP reporter mice to explore the frequency and localization of TDCin peripheral tissues at steady state and upon viral infection. RNA sequencing analysis confirmed that TDCidentified with this reporter model have a gene signature that is distinct from conventional T cells and DC. In addition, frequency and total numbers of TDCin the SLOs recapitulated those found using CD11c as a marker. This reporter model allowed for identification of TDCin situ not only in SLOs but also in the liver and lung of naïve mice. Interestingly, we found that TDCnumbers in the SLOs increased upon viral infection, suggesting that TDCmight play a role during viral infections. In conclusion, we propose a visualization strategy that might shed light on the physiological role of TDCin several pathological contexts, including infection and cancer.
Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA-flexibility
Authors: Back Georg , Walther Dirk
Published: April 2023

Mechanical properties of DNA have been implied to influence many its biological functions. Recently, a new high-throughput method, called loop-seq, that allows measuring the intrinsic bendability of DNA fragments, has been developed. Using loop-seq data, we created a deep learning model to explore the biological significance of local DNA flexibility in a range of different species from different kingdoms. Consistently, we observed a characteristic and largely nucleotide-composition-driven change of local flexibility near transcription start sites. No evidence of a generally present region of lowered flexibility upstream of transcription start sites to facilitate transcription factor binding was found. Yet, depending on the actual transcription factor investigated, flanking-sequence-dependent DNA flexibility was identified as a potential factor influencing binding. Compared to randomized genomic sequences, depending on species and taxa, actual genomic sequences were observed both with increased and lowered flexibility. Furthermore, inArabidopsis thaliana, crossing-over and mutation rates, bothde novoand fixed, were found to be linked to rigid sequence regions. Our study presents a range of significant correlations between characteristic DNA mechanical properties and genomic features, the significance of which with regard to detailed molecular relevance awaits further experimental and theoretical exploration.
The interaction of hierarchical and socializing accountability and the emergence of intelligent accountability in a classroom – a critical analysis
Authors: Arikan Özlem
Published: April 2023

Purpose

This study aims to investigate the impact on organizational members of team marks and peer feedback in a classroom as an organizational setting, where equals were engaged in a hierarchical form of accountability. It uses Roberts’s framework of hierarchical, socializing, and intelligent forms of accountability and discusses the viability of intelligent accountability in higher education, given the accountability structure for academics.

Design/methodology/approach

Autoethnography based on excerpts from the lecturer’s diary.

Findings

The blurred boundaries of hierarchical and socializing forms of accountability create both tensions and kinships for students, and these two forms of accountability constantly impact on each other. Although the accounting tools have an individualizing effect on some students, several examples of intelligent accountability are uncovered. It is concluded that academia’s audit culture, which focuses on immediate outcomes, and academics’ ever-increasing workloads make successful innovations less likely.

Originality/value

This study contributes to the accountability literature in revealing a constant dynamic between hierarchical and socializing forms of accountability through examination of a unique setting in which the boundaries between the two are completely blurred. By empirically examining how accounting individualizes and how intelligent accountability emerges, this study contributes to the limited empirical literature on the impact of accountability on individuals, and particularly to studies of classrooms as organizations, with implications for education policies.
Organizational career development and retention of millennial employees: the role of job engagement and organizational engagement
Authors: Jena Lipsa , Nayak Umakanta
Published: April 2023

Purpose

The study examines the mediating mechanisms of job engagement (JE) and organizational engagement (OE) in the relationship between organizational career development (OCD) and retention of millennial employees.

Design/methodology/approach

Data from a total of 422 employees working in information technology organizations in India were collected through a structured questionnaire survey and subjected to analysis using structural equation modelling (SEM) with a confidence level of 95 percent. The convenience sampling technique for collecting data and descriptive research design was used in the study.

Findings

Results of SEM indicate that there is a positive relationship between OCD and employee retention (ER), which is mediated by JE and OE partially.

Originality/value

The study contributes by establishing the mediating role played by JE and OE in the relationship between OCD and ER.
Decoding a construction organisation's tendency to litigate: an understanding through financial statements
Authors: Jagannathan Murali , Delhi Venkata Santosh Kumar
Published: April 2023

Purpose

Despite the availability of amicable means to resolve construction disputes, litigation remains a mainstream dispute resolution process in some countries. This tendency to litigate (TTL) calls for research to develop appropriate precautions to encourage stakeholders to resolve most commercial disputes through alternate dispute resolution (ADR) techniques. While a claimant's TTL arise from the individual, project and organisation preferences, this study, which can benefit both potential claimants and employers by saving time and money on litigation, identifies a bidder's financial parameters that may increase its litigation propensities, as a first step towards aiding employers to incorporate precautions to discourage such tendencies.

Design/methodology/approach

After the literature review, the theoretical construct proposed by Rachlinski's “framing theory of litigation” (based on Kahneman and Tversky's Prospects Theory) is used to explain organisation-level litigation decision-making. The study sources data from the financial statements of Indian construction/real estate firms, followed by panel regression analysis to test the theoretical construct's validity.

Findings

The results show that the TTL (risk-seeking behaviour) generally increases with a lower value of sales, higher assets and profitability. Interestingly, organisation-level cash flow shows an insignificant influence on litigation tendencies.

Practical implications

Knowing which financial parameters may increase litigation tendencies could help employers evaluate a bidder's propensity to litigate project disputes.

Originality/value

Researchers use financial statements to explore correlations among financial variables. However, in the construction context, there are no empirical studies with data from construction firms to understand potential litigation expenses compared to specific financial ratios.
Gender and negotiation initiation during Covid-19: studying negotiations over salary, work-role and work-home balance and the pandemic's perceived effects
Authors: Nelson Noa , Doron Noa , Amdur Shachaf
Published: April 2023

Purpose

The study tested the effects of gender on negotiation initiation in three topics: salary, work-role and work-home balance; and on employee's perceptions of Covid-19 as inhibiting or enhancing negotiation initiation in these topics.

Design/methodology/approach

The authors employed a mixed-methods approach in a sample of 387 Israeli employees (189 female). Analyses of variance tested for gender differences in negotiation initiation and in Covid-19's perceived effects. Participants' additional written explanations, specifying how the pandemic inhibited or enhanced negotiation initiation, were inductively analyzed.

Findings

Compared to male, female employees were less inclined to initiate negotiation in all three topics, and more likely to perceive Covid-19 as inhibiting salary and work-role negotiations. Qualitative explanations demonstrated gender-role-consistent motives for avoiding or initiating salary negotiations during Covid-19. They also suggested that the pandemic increased the legitimacy and significance of work-home balance negotiations, across gender.

Originality/value

The study provides new evidence on gender differences in negotiation initiation, particularly over work-role and work-home balance, and is among the first to test these differences in Israel. Moreover, it sheds light on the effects that Covid-19, as a world-wide crisis, had on employees' negotiations in general, and gender equality in employees' negotiations in particular.