bluuebunny/crossref_metadata_2025 huggingface dataset:
GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion
Authors: Feng Xinyu A. , Yamadi Maryam , Fu Yiben , Ness Kaitlin M. , Liu Celina , Ahmed Ishtiyaq , Bowman Gregory D. , Johnson Margaret E , Ha Taekjip , Wu Carl
Published: July 2023

To elucidate how eukaryotic sequence-specific transcription factors (TFs) search for gene targets on chromatin, we used multi-color smFRET and single-particle imaging to track the diffusion of purified GAGA-Associated Factor (GAF) on DNA and nucleosomes. Monomeric GAF DNA-binding domain (DBD) bearing one zinc finger finds its cognate site by 1D or 3D diffusion on bare DNA and rapidly slides back-and-forth between naturally clustered motifs for seconds before escape. Multimeric, full-length GAF also finds clustered motifs on DNA by 1D-3D diffusion, but remains locked on target for longer periods. Nucleosome architecture effectively blocks GAF-DBD 1D-sliding into the histone core but favors retention of GAF-DBD when targeting solvent-exposed sites by 3D-diffusion. Despite the occlusive power of nucleosomes, 1D-3D facilitated diffusion enables GAF to effectively search for clustered cognate motifs in chromatin, providing a mechanism for navigation to nucleosome and nucleosome-free sites by a member of the largest TF family.
Totally tubular: ASO-mediated knock-down ofG2019S-Lrrk2 modulates lysosomal tubule-associated antigen presentation in macrophages
Authors: Wallings Rebecca L. , Mark Julian R. , Staley Hannah A. , Gillett Drew A. , Neighbarger Noelle , Kordasiewicz Holly , Hirst Warren D. , Tansey Malú Gámez
Published: July 2023

Genetic variation around theLRRK2gene affects risk of both familial and sporadic Parkinson’s disease (PD). LRRK2 levels have become an appealing target for potential PD-therapeutics with LRRK2 antisense oligonucleotides (ASOs) now in clinical trials. However, LRRK2 has been suggested to play a fundamental role in peripheral immunity, and it is currently unknown if targeting increased LRRK2 levels in peripheral immune cells will be beneficial or deleterious. Furthermore, the precise role of LRRK2 in immune cells is currently unknown, although it has been suggested that LRRK2-mediated lysosomal function may be crucial to immune responses. Here, it was observed thatG2019Smacrophages exhibited increased stimulation-dependent lysosomal tubule formation (LTF) and MHC-II trafficking from the perinuclear lysosome to the plasma membrane in an mTOR dependent manner with concomitant increases in pro-inflammatory cytokine release. Both ASO-mediated knock down of mutantLrrk2 and LRRK2 kinase inhibition ameliorated this phenotype and decreased these immune responses in control cells. Given the critical role of antigen presentation, lysosomal function, and cytokine release in macrophages, it is likely LRRK2-targetting therapies may have therapeutic value with regards to mutantLRRK2but deleterious effects on the peripheral immune system, such as altered pathogen control and infection resolution.
From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability
Authors: Seal Srijit , Carreras-Puigvert Jordi , Carpenter Anne E , Spjuth Ola , Bender Andreas
Published: July 2023

Cell Painting assays generate morphological profiles that are versatile descriptors of biological systems and have been used to predictin vitroandin vivodrug effects. However, Cell Painting features are based on image statistics, and are, therefore, often not readily biologically interpretable. In this study, we introduce an approach that maps specific Cell Painting features into the BioMorph space using readouts from comprehensive Cell Health assays. We validated that the resulting BioMorph space effectively connected compounds not only with the morphological features associated with their bioactivity but with deeper insights into phenotypic characteristics and cellular processes associated with the given bioactivity. The BioMorph space revealed the mechanism of action for individual compounds, including dual-acting compounds such as emetine, an inhibitor of both protein synthesis and DNA replication. In summary, BioMorph space offers a more biologically relevant way to interpret cell morphological features from the Cell Painting assays and to generate hypotheses for experimental validation.

GRAPHICAL ABSTRACT

IN BRIEF

Seal et al. used machine learning models and feature selection approaches to group cell morphological features from Cell Painting assays and to describe the shared role of these morphological features in various cell health phenotypes. The resulting BioMorph space improves the ability to understand the mechanism of action and toxicity of compounds and to generate hypotheses to guide future experiments.

HIGHLIGHTS

Combining Cell Painting and Cell Health imaging data defines the BioMorph space.

BioMorph space allows detecting less common mechanisms for bioactive compounds.

BioMorph space can generate MOA hypotheses to guide experimental validation.

BioMorph space is more biologically relevant and interpretable than Cell Painting features.
Integrative and comparative genomic analyses of mammalian macrophage responses to intracellular mycobacterial pathogens
Authors: Hall Thomas J. , McHugo Gillian P. , Mullen Michael P. , Ward James A. , Killick Kate E. , Browne John A. , Gordon Stephen V. , MacHugh David E.
Published: July 2023

Mycobacterium tuberculosis, the causative agent of human tuberculosis (hTB), is currently classed as the thirteenth leading cause of death worldwide.Mycobacterium bovis, a close evolutionary relative ofM. tuberculosis, causes bovine tuberculosis (bTB) and is one of the most damaging infectious diseases to livestock agriculture. Previous studies have shown that the pathogenesis of bTB disease is comparable to hTB disease, and that the bovine and human alveolar macrophage (bAM and hAM, respectively) transcriptomes are extensively reprogrammed in response to infection with these intracellular mycobacterial pathogens. However, althoughM. bovisandM. tuberculosisshare over 99% identity at the genome level, the innate immune responses to these pathogens have been shown to be different in human or cattle hosts.

In this study, a multi-omics integrative approach was applied to encompass functional genomics and GWAS data sets across the two primary hosts (Bos taurusandHomo sapiens) and both pathogens (M. bovisandM. tuberculosis). Four different experimental infection groups were used, each with parallel non-infected control cells: 1) bAM infected withM. bovis, 2) bAM infected withM. tuberculosis, 3) hAM infected withM. tuberculosis, and 4) human monocyte-derived macrophages (hMDM) infected withM. tuberculosis. RNA-seq data from these experiments 24 hours post-infection (24 hpi) was analysed using three separate computational pipelines: 1) differentially expressed genes, 2) differential gene expression interaction networks, and 3) combined pathway analysis. The results of these analyses were then integrated with high-resolution bovine and human GWAS data sets to detect novel quantitative trait loci (QTLs) for resistance to mycobacterial infection and resilience to disease. Results from this study revealed common and unique response macrophage pathways for both pathogens and identified 32 genes (12 bovine and 20 human) significantly enriched for SNPs associated with disease resistance, the majority of which encode key components of the NF-κB signalling pathway and that also drive formation of the granuloma.
Co-adaptation improves performance in a dynamic human-machine interface
Authors: Yamagami Momona , Madduri Maneeshika M. , Chasnov Benjamin J. , Chou Amber H.Y. , Peterson Lauren N. , Burden Samuel A.
Published: July 2023

Despite the growing prevalence of adaptive systems in daily life, methods for analysis and synthesis of these systems are limited. Here we find theoretical obstacles to creating optimization-based algorithms that co-adapt with people in the presence of dynamic machines. These theoretical limitations motivate us to conduct human subjects experiments with adaptive interfaces, where we find an interface that decreases human effort while improving closed-loop system performance during interaction with a machine that has complex dynamics. Finally, we conduct computational simulations and find a parsimonious model for the human’s adaptation strategy in our experiments, providing a hypothesis that can be tested in future studies. Our results highlight major gaps in understanding of co-adaptation in dynamic human-machine interfaces that warrant further investigation. New theory and algorithms are needed to ensure interfaces are safe, accessible, and useful.
Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types
Authors: Dincer Tevfik Umut , Ernst Jason
Published: July 2023

We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization datasets. ChromActivity generates genomewide predictions of regulatory activity associated with each functional characterization dataset across many cell types based on available epigenomic data. It then for each cell type produces (1) ChromScoreHMM genome annotations based on the combinatorial and spatial patterns within these predictions and (2) ChromScore tracks of overall predicted regulatory activity. ChromActivity provides a resource for analyzing and interpreting the human regulatory genome across diverse cell types.
TriTan: An efficient triple non-negative matrix factorisation method for integrative analysis of single-cell multiomics data
Authors: Ma Xin , Lin Lijing , Zhao Qian , Iqbal Mudassar
Published: July 2023

Motivation

Single-cell multi-omics have opened up tremendous opportunities for understanding gene regulatory networks underlying cell states by simultaneously profiling transcriptomes, epigenomes and proteomes of the same cell. However, existing computational methods for integrative analysis of these high-dimensional multi-modal data are either computationally expensive or limited in interpretation ans scope. These limitations pose challenges in the implementation of these methods in large-scale studies and hinder a more in-depth understanding of the underlying regulatory mechanisms.

Results

Here, we propose TriTan (Triple inTegrative fast non-negative matrix factorisation), an efficient joint factorisation method for single-cell multiomics data. TriTan implements a highly efficient triple non-negative matrix factorisation algorithm which greatly enhances its computational speed, and facilitates interpretation by clustering both the cells and features simultaneously as well as identifying signature feature sets for each cell cluster. Additionally, three matrix factorisation produced by TriTan helps in finding associations of features across modalities, facilitating the prediction of cell type specific regulatory networks. We applied TriTan to single-cell multi-modal data obtained from different technologies and benchmarked it against the state-of-the-art methods where it shows highly competitive performance. Furthermore, we showed a range of downstream analyses that can be conducted utilising the outputs from TriTan.

Availability

https://github.com/maxxxxxxxin/TriTanonline.
Rewiring the carbon cycle: a theoretical framework for animal-driven ecosystem carbon sequestration
Authors: Rizzuto Matteo , Leroux Shawn J. , Schmitz Oswald J.
Published: July 2023

Most carbon cycle models do not consider animal-mediated effects, focusing instead on carbon exchanges among plants, microbes, and the atmosphere. Yet, a growing body of empirical evidence from diverse ecosystems points to pervasive animal effects on ecosystem carbon cycling and shows that ignoring them could lead to misrepresentation of an ecosystem’s carbon cycle. We develop a new theoretical framework to account for animal effects on ecosystem carbon cycling. We combine a classic ecosystem compartment modeling approach with a classic carbon model to account for carbon flux and storage among plant, animal, and soil microbial trophic compartments. We show, by way of numerical analyses of steady state conditions, that herbivore presence alters the dominant pathways of control over carbon storage and capture. This altered control arises via direct, consumptive effects and especially via indirect, non-consumptive pathways by instigating faster nutrient recycling. This leads to a quantitative change in the ecosystem’s carbon balance, increasing the amount of carbon captured and stored in the ecosystem by 2–3 fold. The modeling shows that animals could play a larger role in ecosystem carbon cycle than previously thought. Our framework provides further guidance for empirical research aimed at quantifying animal-mediated control of carbon cycling and to inform the development of nature-based climate change solutions that leverage animal influence on the carbon cycle to help mitigate climate change.
Tissue tension permits β-catenin phosphorylation to drive mesoderm specification in human embryonic stem cells
Authors: Ayad Nadia M.E. , Lakins Johnathon N. , Ghagre Ajinkya , Ehrlicher Allen J. , Weaver Valerie M.
Published: July 2023

The role of morphogenetic forces in cell fate specification is an area of intense interest. Our prior studies suggested that the development of high cell-cell tension in human embryonic stem cells (hESC) colonies permits the Src-mediated phosphorylation of junctional β-catenin that accelerates its release to potentiate Wnt-dependent signaling critical for initiating mesoderm specification. Using an ectopically expressed nonphosphorylatable mutant of β-catenin (Y654F), we now provide direct evidence that impeding tension-dependent Src-mediated β-catenin phosphorylation impedes the expression of Brachyury (T) and the epithelial-to-mesenchymal transition (EMT) necessary for mesoderm specification. Addition of exogenous Wnt3a or inhibiting GSK3β activity rescued mesoderm expression, emphasizing the importance of force dependent Wnt signaling in regulating mechanomorphogenesis. Our work provides a framework for understanding tension-dependent β-catenin/Wnt signaling in the self-organization of tissues during developmental processes including gastrulation.
Oral immunization with rVSV bivalent vaccine elicits protective immune responses, including ADCC, against both SARS-CoV-2 and Influenza A viruses
Authors: Ouyang Maggie Jing , Ao Zhujun , Olukitibi Titus A. , Lawrynuik Peter , Shieh Christopher , Kung Sam , Fowke Keith , Kobasa Darwyn , Yao Xiaojian
Published: July 2023

COVID-19 and influenza both cause enormous disease burdens, and vaccines are the primary measures for their control. Since these viral diseases are transmitted through the mucosal surface of the respiratory tract, developing an effective and convenient mucosal vaccine should be a high priority. We previously reported a recombinant vesicular stomatitis virus (rVSV)-based bivalent vaccine (v-EM2/SPΔC1Delta) that protects animals from both SARS-CoV-2 and influenza viruses via intramuscular and intranasal immunization. Here, we further investigated the immune response induced by oral immunization with this vaccine and its protective efficacy in mice. The results demonstrated that the oral cavity delivery, like the intranasal route, elicited strong and protective systemic immune responses against SARS-CoV-2 and influenza A virus. This included high levels of neutralizing antibodies (NAbs) against SARS-CoV-2, as well as strong anti-SARS-CoV-2 spike protein (SP) antibody-dependent cellular cytotoxicity (ADCC) and anti-influenza M2 ADCC responses in mice sera. Furthermore, it provided efficient protection against challenge with influenza H1N1 virus in a mouse model, with a 100% survival rate and a significant low lung viral load of influenza virus. All these findings provide substantial evidence for the effectiveness of oral immunization with the rVSV bivalent vaccine.
Absence of SARS-CoV-2 in Wildlife of Northeastern Minnesota and Isle Royale National Park
Authors: Castañeda David , Isaac Edmund J. , Kautz Todd , Romanski Mark C. , Moore Seth A. , Aliota Matthew T.
Published: July 2023

We investigated the presence of SARS-CoV-2 in free-ranging wildlife populations in Northeastern Minnesota on the Grand Portage Indian Reservation and Isle Royale National Park. 120 nasal samples were collected from white-tailed deer, moose, gray wolves, and black bears monitored for conservation efforts during 2022-2023. Samples were tested for viral RNA by RT-qPCR using the CDC N1/N2 primer set. Our data indicate that no wildlife samples were positive for SARS-CoV-2 RNA. Continued surveillance is therefore crucial to better understand the changing landscape of zoonotic SARS-CoV-2 in the Upper Midwest.
Crystal Structure of the 4-Hydroxybutyryl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus
Authors: Johnson Jerome , Tolar Bradley B. , Tosun Bilge , Yoshikuni Yasuo , Francis Christopher A. , Wakatsuki Soichi , DeMirci Hasan
Published: July 2023

The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. TheNitrosopumilus maritimus4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 fromNitrosopumilus maritimusSCM1, which reveals a highly conserved interdomain linker loop between the CoA-binding and ATP-grasp domains. Phylogenetic analysis suggests the widespread prevalence of this loop and highlights both its underrepresentation within the PDB and structural importance within the (ATP-forming) acyl- CoA synthetase (ACD) superfamily. This linker is shown to have a possible influence on conserved interface interactions between domains, thereby influencing homodimer stability. These results provide a structural basis for the energy efficiency of this key enzyme in the modified 3HP/4HB cycle of Thaumarchaeota.
Rescue of FTLD-associated TDP-43 pathology and neurodegeneration by peripheral AAV-mediated expression of brain-penetrant progranulin
Authors: Reich Marvin , Simon Matthew J. , Polke Beate , Werner Georg , Schrader Christian , Paris Iñaki , Robinson Sophie , Davis Sonnet S. , de Melo Gabrielly Lunkes , Schlaphoff Lennart , Spieth Lena , Berghoff Stefan , Logan Todd , Nuscher Brigitte , Buschmann Katrin , Edbauer Dieter , Simons Mikael , Suh Jung H. , Sandmann Thomas , Kariolis Mihalis S. , DeVos Sarah L. , Lewcock Joseph W. , Paquet Dominik , Capell Anja , Paolo Gilbert Di , Haass Christian
Published: July 2023

Progranulin (PGRN) haploinsufficiency is a major risk factor for frontotemporal lobar degeneration with TDP-43 pathology (FTLD-GRN). Multiple therapeutic strategies are in clinical development to restore PGRN levels in the CNS, including gene therapy. However, a limitation of current gene therapy approaches aimed to alleviate FTLD-associated pathologies may be their inefficient brain exposure and biodistribution. We therefore developed an adeno-associated virus (AAV) targeting the liver (L) to achieve sustained peripheral expression of a transferrin receptor (TfR) binding, brain-penetrant (b) PGRN variant (AAV(L):bPGRN) in two mouse models of FTLD-GRN, namelyGrnknockout andGrnxTmem106bdouble knockout mice. This therapeutic strategy avoids potential safety and biodistribution issues of CNS-administered AAVs while maintaining sustained levels of PGRN in the brain following a single dose. AAV(L):bPGRN treatment reduced several FTLD-GRNassociated disease pathologies including severe motor function deficits, aberrant TDP-43 solubility and phosphorylation, dysfunctional protein degradation, lipid metabolism, gliosis and neurodegeneration in the brain. Translatability of our findings was confirmed in a novel humanin vitromodel using co-cultured human induced pluripotent stem cell (hiPSC)-derived microglia lacking PGRN and TMEM106B and wild-type hiPSC-derived neurons. As in mice, aberrant TDP-43, lysosomal dysfunction and neuronal loss were ameliorated after treatment with exogenous TfR-binding protein transport vehicle fused to PGRN (PTV:PGRN). Together, our studies suggest that peripherally administered brain-penetrant PGRN replacement strategies can ameliorate FTLD-GRNrelevant phenotypes including TDP-43 pathology, neurodegeneration and behavioral deficits. Our data provide preclinical proof of concept for the use of this AAV platform for treatment of FTLD-GRNand potentially other CNS disorders.

One sentence summary

Peripheral AAV-mediated delivery of brain-penetrant PGRN rescues TDP-43 pathology, neurodegeneration and motor phenotypes in FTLD-GRNmodels.
Recurrent chromosome destabilization through repeat-mediated rearrangements in a fungal pathogen
Authors: Fouché Simone , Oggenfuss Ursula , McDonald Bruce A. , Croll Daniel
Published: July 2023

Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines. The triggers of destabilized chromosomes remain poorly understood but are often assumed to be associated with fragile sites. Here, we retrace a runaway chromosomal degeneration process observed in a fungal pathogen using telomere-to-telomere assemblies across an experimental pedigree. We show that the same fragile sites triggered reproducible, large-scale rearrangements through non-allelic recombination. Across the four-generation pedigree, chromosomal rearrangements were accompanied by non-disjunction events and caused aneuploid progeny to carry up to four chromosomal copies. We identify a specific transposable element as the most likely trigger for the repeated chromosomal degeneration. The element is associated with higher virulence of the pathogen and has undergone a burst increasing copy numbers across the genome. Chromosome sequences are also targeted by a genome defense mechanism active on duplicated sequences, which may contribute to decay. Our work identifies the exact sequence triggers initiating chromosome instability and perpetuating degenerative cycles. Dissecting proximate causes leading to run-away chromosomal degeneration expands our understanding of chromosomal evolution beyond cancer lines.
Strong Positive Selection Biases Identity-By-Descent-Based Inferences of Recent Demography and Population Structure inPlasmodium falciparum
Authors: Guo Bing , Borda Victor , Laboulaye Roland , Spring Michele D. , Wojnarski Mariusz , Vesely Brian A. , Silva Joana C. , Waters Norman C. , O’Connor Timothy D. , Takala-Harrison Shannon
Published: July 2023

Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD). Yet, strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we utilized simulations, a true IBD inference algorithm, and empirical datasets from different malaria transmission settings to investigate the extent of such bias and explore potential correction strategies. We analyzed whole genome sequence data generated from 640 new and 4,026 publicly availablePlasmodium falciparumclinical isolates. Our findings demonstrated that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discovered that the removal of IBD peak regions partially restored the accuracy of IBD-based inferences, with this effect contingent on the population’s background genetic relatedness. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.
Divergent evolution of head morphology between marine and freshwater sticklebacks
Authors: Fraimout Antoine , Chen Ying , Reid Kerry , Merilä Juha
Published: July 2023

Abstract

Intraspecific phenotypic differentiation is of common place occurrence, but the degree to which it reflects phenotypic plasticity or local adaptation remains often unclear. To be considered as adaptive, the differentiation must be genetically based and exceed what could be expected by neutral processes only. Using laboratory reared full-sib family data from replicate nine-spined stickleback (Pungitius pungitius) populations, we show that freshwater and marine fish display genetically based adaptive differentiation in head size and shape. Utilising identity-by-descent relationships among full-sibs as estimated with the aid of molecular markers, we further show that the studied traits are also highly heritable in all populations indicating and that they can respond to future episodes of natural selection. The head shape and size of pond fish suggests that observed adaptive differentiation has been driven by selection favoring limnetic feeding strategy among the pond fish. Analyses of gill-raker morphology were less conclusive: genetic differentiation was found in gill-raker length (pond > marine) and number, but the degree of divergence in these traits did not exceed neutral expectations. Yet, the direction of divergence in gill raker traits are suggestive of the limnetic feeding mode of pond fish, aligning with the inference from the head morphology analyses.
Microstructure-Based Modeling of Primary Cilia Mechanics
Authors: Mostafazadeh Nima , Resnick Andrew , Young Y.-N. , Peng Zhangli
Published: July 2023

A primary cilium, made of nine microtubule doublets enclosed in a cilium membrane, is a mechanosensing organelle that bends under an external mechanical load and sends an intracellular signal through transmembrane proteins activated by cilium bending. The nine microtubule doublets are the main load-bearing structural component, while the transmembrane proteins on the cilium membrane are the main sensing component. No distinction was made between these two components in all existing models, where the stress calculated from the structural component (nine microtubule doublets) was used to explain the sensing location, which may be totally misleading. For the first time, we developed a microstructure-based primary cilium model by considering these two components separately. First, we refined the analytical solution of bending an orthotropic cylindrical shell for individual microtubule, and obtained excellent agreement between finite element simulations and the theoretical predictions of a microtubule bending as a validation of the structural component in the model. Second, by integrating the cilium membrane with nine microtubule doublets, we found that the microtubule doublets may twist significantly as the whole cilium bends. Third, besides being cilium-length-dependent, we found the mechanical properties of the cilium are also highly deformation-dependent. More important, we found that the cilium membrane near the base is not under pure in-plane tension or compression as previously thought, but has significant local bending stress. This challenges the traditional model of cilium mechanosensing, indicating that transmembrane proteins may be activated more by membrane curvature than membrane stretching. Finally, we incorporated imaging data of primary cilia into our microstructure-based cilium model, and found that comparing to the ideal model with uniform microtubule length, the imaging-informed model shows the nine microtubule doublets interact more evenly with the cilium membrane, and their contact locations can cause even higher bending curvature in the cilium membrane than near the base.

SIGNIFICANCE

Factors regulating the mechanical response of a primary cilium to fluid flow remain unclear. Modeling the microtubule doublet as a composite of two orthotropic shells and the ciliary axoneme as an elastic shell enclosing nine such microtubule doublets, we found that the length distribution of microtubule doublets (inferred from cryogenic electron tomography images) is the primary determining factor in the bending stiffness of primary cilia, rather than just the ciliary length. This implies ciliary-associated transmembrane proteins may be activated by membrane curvature changes rather than just membrane stretching. These insights challenge the traditional view of ciliary mechanosensation and expands our understanding of the different ways in which cells perceive and respond to mechanical stimuli.
Structural basis for ssDNA-activated NADase activity of the prokaryotic SPARTA immune system
Authors: Zhang Jun-Tao , Wei Xin-Yang , Cui Ning , Tian Ruilin , Jia Ning
Published: July 2023

Argonaute proteins (Agos), which use small RNAs or DNAs as guides to recognize complementary nucleic acid targets, mediate RNA silencing in eukaryotes. In prokaryotes, Agos are involved in immunity: the short prokaryotic Ago/TIR-APAZ (SPARTA) immune system triggers cell death by degrading NAD+in response to invading plasmids, but its molecular mechanisms remain unknown. Here, we used cryogenic electron microscopy to determine the structures of inactive monomeric and active tetramericCrenotalea thermophilaSPARTA complexes, revealing mechanisms underlying SPARTA assembly, RNA-guided recognition of target single-stranded DNA (ssDNA) and subsequent SPARTA tetramerization, as well as tetramerization-dependent NADase activation. The small RNA guides Ago to recognize its ssDNA target, inducing SPARTA tetramerization via both Ago- and TIR-mediated interactions and resulting in a two-stranded, parallel, head-to-tail TIR rearrangement primed for NAD+hydrolysis. Our findings thus identify the molecular basis for target ssDNA-mediated SPARTA activation, which will facilitate the development of SPARTA-based biotechnological tools.
De novoand inherited variants inDDX39Bcause a Novel Syndrome Characterized by Neurodevelopmental Delay, Short Stature, and Congenital Hypotonia
Authors: Booth Kevin T.A. , Jangam Sharayu V. , Chui Martin M.C. , Treat Kayla , Graziani Lorenzo , Soldano Alessia , White Kerry , Christensen Celanie K. , Lynnes Ty , Yamamoto Shinya , Kanca Oguz , Tsang Mandy H.Y. , Lynch Sally A. , Mullegama Sureni V. , Batista Julia , Iancu Daniela , Joss Shelag K. , Mak Christopher C.Y. , Kwong Anna Y. , Bellen Hugo J. ,   BCM Center for Precision Medicine Models, Conboy Erin , Sanges Remo , Wangler Michael F. , Chung Brian H.Y. , Vetrini Francesco
Published: July 2023

DDX39Bis a member of the DEAD-box family of ATP-dependent RNA helicases. DEAD-box proteins are ubiquitously expressed from yeast to humans and perform essential functions associated with mRNA metabolism.DDX39Bis also a crucial component of the TRanscription-EXport (TREX) super protein complex, which recent studies have highlighted the important role of its subunits in neurodevelopmental disorders. Here, we describe six individuals from five families, four with novelde novomissense variants inDDX39B,and one carrying an inherited splicing variant, all presenting with mild to severe global developmental delay, congenital hypotonia, epilepsy, short stature, skeletal abnormalities and variable dysmorphic features. 3D molecular modeling predicts these variants would alter protein structure.DDX39Bis a conserved gene andDrosophila melanogaster(fruit flies) studies were conducted. We generated a new Hel25E Kozak-GAL4 allele which disrupts the fly gene and allows expression of transgenes. We also generated transgenicDDX39B-reference and variant flies. However, human referenceDDX39Bwhen overexpressed ubiquitously leads to lethality but the variants found in the patients do not recapitulate the lethality suggesting that the mutants are loss of function alleles. Blood transcriptomics revealed a significant excess of aberrant splicing events, indicating a disrupted mRNA processing as anticipated from the role ofDDX39Bin mRNA metabolism. Our human genetic data, coupled within silicoandin vivodata supports thatDDX39Bis a novel candidate gene in a potential group of disorders named TREX-complex-related neurodevelopmental syndrome.
Brain mechanisms explaining postural imbalance in traumatic brain injury: a systematic review
Authors: Hadi Zaeem , Mahmud Mohammad , Seemungal Barry M
Published: July 2023

Persisting imbalance and falls in community-dwelling traumatic brain injury (TBI) survivors – typically related to vestibular dysfunction - are linked to reduced long-term survival and re-employment rates. However, a detailed understanding of the impact of TBI upon the brain mechanisms mediating imbalance is lacking. To understand the state of the art concerning the brain mechanisms mediating imbalance in TBI, we performed a systematic review of the literature.

PubMed, Web of Science, and Scopus were searched and peer-reviewed research articles in humans, with any severity of TBI (mild, moderate, severe, or concussion), that linked a postural balance assessment (objective or subjective) with brain imaging (via CT, MRI, MRS, SPECT, EEG, MEG, NIRS, and evoked potentials) were included. Out of 1940 articles, 60 were retrieved and screened, and 25 were included in the systematic review. 17 of those were MRI-based studies (e.g., DTI, fMRI), 4 EEG studies, 3 fNIRS studies, and 1 study used both MRI and EEG.

The most consistent MRI finding was the link between imbalance and cerebellum, however, the regions within the cerebellum were not consistent. Functional changes in EEG studies were non-specific as all frequency bands were reportedly linked with balance. The findings from fNIRS studies were concentrated in frontal regions as these studies only used ROI analysis. Notably, only one study reported performing clinical vestibular assessment to exclude peripheral vestibular dysfunction.

In conclusion, the lack of consistent findings could reflect that imbalance in TBI is due to a brain network dysfunction in contrast to focal cortical damage. Notably, the inconsistency in the reported findings may be attributed to heterogeneity of methodology e.g., data analytical techniques, small sample sizes, and choice of control groups. Future studies should include a detailed clinical phenotyping of vestibular function in TBI patients, ideally in an acute prospective manner, to exclude peripheral disorders. Choosing the appropriate control groups (i.e., well characterized patient subgroups as controls) would ensure that the findings are specific to imbalance rather than being non-specifically linked to TBI. Moreover, a whole-brain imaging analysis (vs ROI) is recommended to reduce selection bias and is also important since TBI affects the brain in a widespread manner.
Computed Tomography-Based Analysis of Foramen Magnum and Occipital Condyles in adult Nigerians: An Anatomical Study
Authors: Muhammad Fatima , Ahmad Umar , ZYOUD Tawfiq Yousef Tawfiq , Jibril Murtala Muhammad , Kwairanga Suleiman Hamidu
Published: July 2023

Background

Precise identification of craniometric points is pivotal in forensic and anthropological research for reliable and accurate gender determination. The foramen magnum and occipital condyles’ morphology offers valuable data for this purpose.

Aim

The study aimed to determine variations in the morphology of the foramen magnum and occipital condyles among a population of 100 individuals, using advanced Computed Tomography (CT) scan technology.

Methods

We assessed a prospective cohort of 100 individuals who underwent cranial CT scans. The study focused on the morphological variations of the foramen magnum and occipital condyles, recording shapes such as oval, round, egg, tetragon, pentagon, hexagon, and irregular for the foramen magnum, and kidney-type, oval, S-like, 8-like, ring-like, and triangular for the occipital condyles.

Results

Notably, males demonstrated higher measurement values for most parameters, with the exception of the width of the occipital condyle, where females presented larger dimensions. Furthermore, a strong positive correlation was observed between the measurements of the foramen magnum (length and width) and specific parameters of the occipital condyles.

Conclusions

The study underscores the utility of foramen magnum dimensions, especially length, as a determinant in gender identification, with a success rate of 68% in the studied population. This research enhances our understanding of cranial morphology and its applications in forensic and anthropological investigations.
Phytohemagglutinin-Activated CAR-T Cells: Prolonged Persistence and Enhanced Anti-Tumor Response in CD19-Specific Acute Lymphoblastic Leukemia
Authors: Sert Berranur , Gulden Gamze , Teymur Tarik , Ay Yasin , Turan Raife Dilek , Unaldi Onur Mert , Güzenge Elanur , Erdil Hamza Emir , Isik Sevim , Oz Pınar , Bozkurt Ilknur , Arpacı Tahire , Kamalı Osman , Ovalı Ercüment , Tarhan Nevzat , Tastan Cihan
Published: July 2023

In recent times, chimeric antigen receptor (CAR)-T cell therapy has shown rapid advancements and gained clinical approval for use in cancer immunotherapy. CAR, a synthetic receptor integrated into autologous T cells, has yielded highly successful results in patients with leukemia. The significant potential of CAR-T cells has been validated through clinical trials in adult and pediatric cancer treatments. Our therapy developed specifically for CD19-specific Acute Lymphoblastic Leukemia (ALL) has shown promising results in in vitro and in vivo tests. To enhance the response against cancer, provide a bistimulatory effect, and increase stability, we designed two different CAR structures specific to CD19. These designs incorporate the CD28 and 41BB costimulatory domains. Through in vitro analysis, we evaluated the population ratios and cytotoxic activities of Central Memory T cells (TCM) and Stem Cell Memory T cells (TSCM) in CAR-T (CAR1928-T and CAR19BB-T) cells. Our initial design, CAR1928-T, produced an effective anti-tumor response. With our second design, CAR19BB-T, we not only achieved an anti-tumor effect but also conferred memory capabilities, leading to a comprehensive treatment approach. We demonstrated that CAR-T cells produced using Phytohemagglutinin (PHA) exhibited increased persistence in vitro and in vivo compared to anti-CD3 and anti-CD28 stimulation. The use of PHA to activate CAR19BB-T cells developed a long-lasting and effective CAR-T cell production method in vivo using cancerous animal models. CAR-T cell-treated mice survived tumor-free for up to 60 days, surpassing the survival of mice that received tumors only. Additionally, CAR19BB-T cell production with PHA remained stable over time. These results highlight a novel CAR-T cell production approach with a high-memory T cell profile capable of delaying or preventing cancer relapse. We optimized the method for the production of long-term and effective CAR-T cells and tested it in preclinical experiments. As a result, it was demonstrated that CAR-T cells generated with PHA, when administered as a co-stimulatory dose, can provide continuous proliferation and long-term persistence without compromising their anti-cancer efficacy. Preclinical studies have been completed to obtain valuable data for enhancing the long-term effectiveness of CAR-T therapy in clinical trials and transitioning to clinical applications.
Alterations in the gut microbiome of whiteleg shrimp (Penaeus vannamei) postlarvae following exposure to an AHPND-causing strain ofVibrio parahaemolyticus
Authors: Beltrán Manuel J. , Quimi Mujica Juan , Diringer Benoit , Barahona Sergio P.
Published: July 2023

Acute Hepatopancreatic Necrosis Disease (AHPND), attributed to the production of PirA/PirB toxins by certain Vibrio parahaemolyticus strains, poses a significant threat to global shrimp aquaculture, causing substantial mortality and economic losses. To enhance our understanding of this disease within a closed culture system on the northern coast of Peru, we conducted a comparative analysis of the gut microbiomes between healthy and diseased postlarvae. Diseased postlarvae were obtained through exposure to an AHPND-causing strain of V. parahaemolyticus. Five healthy and five diseased postlarvae were randomly sampled from experimental rearing tanks, and their medial guts were extracted. High-throughput sequencing targeting the V4 region of the 16S rRNA gene was employed for amplicon library construction, and assessments of alpha and beta diversities, as well as taxonomic composition, were conducted. Our results revealed reduced diversity and distinct compositional profiles in the gut microbiomes of diseased postlarvae. The order Rhodobacteriales was dominant in the gut microbiomes of healthy postlarvae, while the order Vibrionales (including an unassigned genus within Vibrionales, Vibrio, and Pseudoalteromonas) exhibited the highest abundance in diseased postlarvae. In conclusion, exposure to an AHPND-causing strain of V. parahaemolyticus induces significant dysbiosis in the gut microbiome of whiteleg shrimp postlarvae.
Refrigerated storage and cryopreservation of hormone induced sperm in a threatened frog
Authors: Upton Rose , Calatayud Natalie E. , Clulow Simon , Brett Darcie , Burton Alana L. , Colyvas Kim , Mahony Michael , Clulow John
Published: July 2023

There are strong potential benefits of incorporating assisted reproductive technologies (ARTs) into conservation programs for the management of threatened amphibians as the global amphibian decline continues. As sperm cryopreservation and other ARTs advance in common species, focus on non-lethal sperm collection methods for threatened amphibians is imperative. We aimed to realise this goal by testing various doses of exogenous hormones for non-lethal induction of spermiation in a threatened frog (Litoria aurea) and develop cold storage and cryopreservation protocols following the recovery of urinic sperm. Our major findings include: (1) that sperm release could be induced in high concentrations with 20 IU/g bodyweight of human chorionic gonadotrophin (hCG); (2) high levels (>50%) of live, motile sperm could be recovered post-cryopreservation by treating the sperm with 15% v/v DMSO and 1% w/v sucrose pre-freeze; and (3) urinic sperm stored at 5°C retained motility over a 14-day period. Our findings demonstrate that it is possible to obtain and store large quantities of quality sperm from a threatened amphibian via non-lethal means, representing an important step forward for the use of ARTs in conservation programs for rare and threatened species.

Lay Summary

Amphibians are undergoing an extinction crisis unparalleled in any other taxa. The development of assisted reproductive technologies, such as sperm cryopreservation and IVF have an important role to play in the conservation management of amphibians globally. Here we report non-lethal methods of sperm collection and storage in a highly threatened amphibian. Major findings include successfully induced sperm release in high concentrations, retention of ∼50% live, motile sperm after 7 days storing it at 5°C, and successful recovery of of more than 50% live, motile sperm following cryopreservation. Our results demonstrate the viability of obtaining and storing sperm from rare and threatened species via non-lethal means, providing an important step forward for the use of ARTs in conservation programs around the globe.
In silico characterization and phylogenetic analysis of Elaeocarpus ganitrus based on ITS2 barcode sequence
Authors: Kushwaha Jyotsana , Joshi Alpana
Published: July 2023

Plant molecular systematics relies on using DNA barcodes for studying the evolutionary relationship between species Sequences of the nuclear internal transcribed spacer (ITS) regions have been used widely in molecular phylogenetic studies because of their high variability compared to plastid sequences. Elaeocarpus is a diverse genus within the family Elaeocarpaceae and is widely distributed worldwide among tropical and subtropical climatic zones. Elaeocarpus ganitrus has important medicinal and religious values in India. However, Elaeocarpus ganitrus evolutionary relationship with other Elaeocarpus species is not much explored, especially at the molecular and phylogenetic levels. The present research successfully amplified the nuclear gene ITS2, sequenced and submitted it to NCBI Genbank after using Basic Local Alignment Search Tool (BLAST). Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP) resulted in different numbers of molecular operational taxonomic units (MOTUs). The lowest score of ASAP (4.5) segregated the sequences into 31 MOTUs with the Threshold dist. value of 0.003524. This study establishes an evolutionary relationship between Elaeocarpus ganitrus and other species belonging to the same genus through the neighbor-joining method. The 38 Elaeocarpus samples were clustered into seven major groups based on ITS2 sequence: Group I is represented by Elaeocarpus ganitrus along with Elaeocarpus sylvestris, Elaeocarpus glabripetalus, Elaeocarpus duclouxii, Elaeocarpus decipiens, and Elaeocarpus zollingeri. Group II is characterized by Elaeocarpus austroyunnanensis and Elaeocarpus glaber. Group III comprises Elaeocarpus sphaericus, Elaeocarpus angustifolius, Elaeocarpus grandis, Elaeocarpus ptilanthus, and Elaeocarpus sphaerocarpus. Three accessions of Elaeocarpus hookerianus are placed in group IV. Elaeocarpus largiflorens and Elaeocarpus thelmae represent group V. Groupr VI contains three species: Elaeocarpus sylvestris, Elaeocarpus dubius, and Elaeocarpus johnsonii. Group VII comprises five species which include Elaeocarpus glabripetalus, Elaeocarpus rugosus, Elaeocarpus tuberculatus, Elaeocarpus hainanensis, and Elaeocarpus angustifolius. The study concludes with the possibility of correctly using the ITS2 gene to identify, discriminate, and documentation of Elaeocarpus ganitrus and other species of the same genus.
Neuroendocrine Gene Expression Coupling of Interoceptive Bacterial Food Cues to Foraging Behavior ofC. elegans
Authors: Boor Sonia A. , Meisel Joshua D. , Kim Dennis H.
Published: July 2023

Animal internal state is modulated by nutrient intake, resulting in behavioral responses to changing food conditions. The neural mechanisms by which internal states are generated and maintained are not well understood. Here, we show that in the nematodeCaenorhabditis elegans,distinct cues from bacterial food – interoceptive signals from the ingestion of bacteria and gustatory molecules sensed from nearby bacteria – act antagonistically on the expression of the neuroendocrine TGF-beta ligand DAF-7 from the ASJ pair of sensory neurons to modulate foraging behavior. A positive-feedback loop dependent on the expression ofdaf-7from the ASJ neurons acts to promote transitions between roaming and dwelling foraging states and influence the persistence of roaming states. SCD-2, theC. elegansortholog of mammalian Anaplastic Lymphoma Kinase (ALK), which has been implicated in the central control of metabolism of mammals, functions in the AIA interneurons to regulate foraging behavior and cell-non-autonomously control the expression of DAF-7 from the ASJ neurons. Our data establish how a dynamic neuroendocrinedaf-7expression feedback loop regulated by SCD-2 functions to couple sensing and ingestion of bacterial food to foraging behavior. We further suggest that this neuroendocrine feedback loop underlies previously characterized exploratory behaviors inC. elegans. Our data suggest that the expression ofdaf-7from the ASJ neurons contributes to and is correlated with an internal state of “unmet need” that regulates exploratory foraging behavior in response to bacterial cues in diverse physiological contexts.