bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-parametric thrombus profiling microfluidics detects intensified biomechanical thrombogenesis associated with hypertension and aging
Authors: Din Misbahud , Paul Souvik , Ullah Sana , Yang Haoyi , Xu Rong-Guang , Abidin Nurul Aisha Zainal , Sun Allan , Chen Yiyao Catherine , Gao Rui , Chowdhury Bari , Zhou Fangyuan , Rogers Stephenie , Miller Mariel , Biswas Atreyee , Hu Liang , Fan Zhichao , Zahner Christopher , Fan Jin , Chen Zi , Berman Megan , Xue Lingzhou , Ju Lining Arnold , Chen Yunfeng
Published: June 2024

Arterial thrombosis, which represents a critical complication of cardiovascular diseases, is a leading cause of death and disability worldwide with no effective bioassay for clinical prediction. As a symbolic feature of arterial thrombosis, severe stenosis in the blood vessel creates a high-shear, high-gradient flow environment that effectively facilitates platelet aggregation towards vessel occlusion even with platelet amplification loops inhibited. However, no approach is currently available to comprehensively characterize the size, composition and platelet activation status of thrombi forming under this biorheological condition. Here, we present a thrombus profiling assay that monitors the multi-dimensional attributes of thrombi forming in conditions mimicking the physiological scenario of arterial thrombosis. Using this platform, we demonstrate that different receptor-ligand interactions contribute distinctively to the composition and activation status of the thrombus. Our investigation into hypertensive and older individuals reveals intensified biomechanical thrombogenesis and multi-dimensional thrombus profile abnormalities, demonstrating a direct contribution of mechanobiology to arterial thrombosis and endorsing the diagnostic potential of the assay. Furthermore, we identify the hyperactivity of GPIbalpha-integrin alphaIIbbeta3 mechanosensing axis as a molecular mechanism that contributes to hypertension-associated arterial thrombosis. By studying the interactions between anti-thrombotic inhibitors and hypertension, and the inter-individual variability in personal thrombus profiles, our work reveals a critical need for personalized anti-thrombotic drug selection that accommodates each patient's pathological profile.
Comprehensive profiling of transcriptional regulation in cartilage reveals pathogenesis of osteoarthritis
Authors: Tian Wen , Dong Shan-Shan , Jiang Feng , Zhang Jun-Qi , Wang Chen , He Chang-Yi , Hu Shou-Ye , Hao Ruo-Han , Song Hui-Miao , Gao Hui-Wu , An Ke , Zhu Dong-Li , Yang Zhi , Guo Yan , Yang Tie-Lin
Published: June 2024

Cartilage damage is a leading cause of osteoarthritis (OA) etiology, however, the underlying mechanism governing gene expression regulation in this progress is poorly understood. Here, we described a comprehensive profiling of transcriptional regulation of 235 primary human cartilage samples. We identified 3,352 independent significant expression quantitative trait loci (eQTLs) for 3,109 genes. We explored the candidate casual SNP and its underlying regulatory mechanism using our established functional fine-mapping pipeline by integrating the cartilage-specific ATAC-seq data. We identified 117 causal eQTLs that display allele-specific open chromatin (ASoC) and 547 transcription factor binding-disruption (TBD) eQTLs. We conducted cell type-interaction eQTL (ci-eQTL) analyses based on speculated chondrocyte subtype proportions and revealed the regulation relationship of 120 eQTL-gene pairs showed cell type dependency. Further, by integrating with genome-wide association studies (GWASs) data of OA, we nominated 43 candidate effector genes for OA risk loci. We verified that the T allele of the OA risk variant rs11750646 increased the AR binding affinity to an open chromatin region and promoted the expression of an OA-related gene PIK3R1. Altogether, our findings provide new insights into the unique regulatory landscape of cartilage and elucidate potential mechanisms underlying the OA pathogenesis.
Massively Parallel Reporter Assays identify enhancer elements in Oesophageal Adenocarcinoma
Authors: Yang SH , Ahmed I , Li Y , Bleaney CW , Sharrocks AD
Published: June 2024

Cancer is a disease underpinned by aberrant gene expression. Enhancers are regulatory elements that play a major role in transcriptional control and changes in active enhancer function are likely critical in the pathogenesis of oesophageal adenocarcinoma (OAC). Here, we utilise STARR-seq to profile the genome-wide enhancer landscape in OAC and identify hundreds of high-confidence enhancer elements. These regions are enriched in enhancer-associated chromatin marks, are actively transcribed and exhibit high levels of associated gene activity in OAC cells. These characteristics are maintained in human patient samples, demonstrating their disease relevance. This relevance is further underlined by their responsiveness to oncogenic ERBB2 inhibition and increased activity compared to the pre-cancerous Barrett’s state. Mechanistically, these enhancers are linked to the core OAC transcriptional network and in particular KLF5 binding is associated with high level activity, providing further support for a role of this transcription factor in defining the OAC transcriptome. Our results therefore uncover a set of enhancer elements with physiological significance, that widen our understanding of the molecular alterations in OAC and point to mechanisms through which response to targeted therapy may occur.
Echo-locate: Cerebellar activity predicts vocalization in fruit-eating bats
Authors: Hariharan Shivani , González Palomares Eugenia , Hechavarria Julio C.
Published: June 2024

Echolocating bats exhibit remarkable auditory behaviors, enabled by adaptations within and outside their auditory system. Yet, research in echolocating bats has focused mostly on brain areas that belong to the classic ascending auditory pathway. This study provides direct evidence linking the cerebellum, an evolutionarily ancient and non-classic auditory structure, to vocalization and hearing. We report that in the fruit-eating batCarollia perspicillata, external sounds can evoke cerebellar responses with latencies below 20 ms. Such fast responses are indicative of early inputs to the bat cerebellum. In vocalizing bats, distinct spike train patterns allow the prediction with over 85% accuracy of the sound they are about to produce, or have just produced, i.e., communication calls or echolocation pulses. Taken together, our findings provide evidence of specializations for vocalization and hearing in the cerebellum of an auditory specialist.

Teaser

The cerebellum of fruit-eating bats responds to sounds and predicts future and past vocalizations
Palytoxin Evokes Reversible Spreading Depolarization in the Locust CNS
Authors: Wang Yuyang , Van Dusen Rachel A. , McGuire Catherine , Andrew R. David , Robertson R. Meldrum
Published: June 2024

Spreading depolarization (SD) describes the near-complete depolarization of CNS neural cells as a consequence of chemical, electrical, and metabolic perturbations. It is well-established as the central mechanism underlying insect coma and various mammalian neurological dysfunctions. Despite significant progress in our understanding, the question remains: which cation channel, if any, generates SD in the CNS?

Previously, we speculated that the sodium-potassium ATPase (NKA) might function as a large-conductance ion channel to initiate SD in insects, potentially mediated by a palytoxin (PLTX)-like endogenous activator. In the current study, we evaluate the effectiveness and properties of PLTX as an SD initiator inL. migratoria. Whereas bath-applied PLTX failed to ignite SD, direct injection into the neuropil triggered SD in 57% of the preparations. Notably, PLTX-induced SD onset was significantly more rapid compared to ouabain injection and azide controls, though their electrophysiological features remained similar. Furthermore, PLTX-induced SD was recoverable and resulted in a greater frequency of repetitive SD events compared to ouabain.

Surprisingly, prior PLTX treatment disrupted the onset and recovery of subsequent SD evoked by other means. PLTX injection could attenuate the amplitude and hasten the onset time of azide-induced SD. Such an effect is associated with a complete inhibition at higher doses of subsequent anoxic SD induced through azide treatment or submersion.

These results show that PLTX can trigger repetitive and reversible SD-like events in locusts and simultaneously interfere with anoxic SD occurrence. We suggest that the well-documented NKA pump conversion into an open non-selective cationic channel is a plausible mechanism of SD activation in the locust CNS, warranting additional investigations.
MultiGreen: A multiplexing architecture for GreenGate cloning
Authors: Pennetti Vincent J. , LaFayette Peter R. , Parrott Wayne Allen
Published: June 2024

Genetic modification of plants fundamentally relies upon customized vector designs. The ever-increasing complexity of transgenic constructs has led to increased adoption of modular cloning systems for their ease of use, cost effectiveness, and rapid prototyping. GreenGate is a modular cloning system catered specifically to designing bespoke, single transcriptional unit vectors for plant transformation— which is also its greatest flaw. MultiGreen seeks to address GreenGate’s limitations while maintaining the syntax of the original GreenGate kit. The primary limitations MultiGreen addresses are 1) multiplexing in series, 2) multiplexing in parallel, and 3) repeated cycling of transcriptional unit assembly through binary intermediates. MultiGreen efficiently concatenates bespoke transcriptional units using an additional suite of level 1acceptor vectors which serve as an assembly point for individual transcriptional units prior to final, level 2, condensation of multiple transcriptional units. Assembly with MultiGreen level 1 vectors scales at a maximal rate of 2*⌈log6n⌉+3 days per assembly, wherenrepresents the number of transcriptional units. Further, MultiGreen level 1 acceptor vectors are binary vectors and can be used directly for plant transformation to further maximize prototyping speed. MultiGreen is a 1:1 expansion of the original GreenGate architecture’s grammar and has been demonstrated to efficiently assemble plasmids with multiple transcriptional units. MultiGreen has been validated by using a truncated violacein operon fromChromobacterium violaceumin bacteria and by deconstructing the RUBY reporter forin plantafunctional validation. MultiGreen currently supports many of our in-house multi transcriptional unit assemblies and will be a valuable strategy for more complex cloning projects.
Vertical transmission of fungus-growing ant microbiota is species-specific and constrained by queens
Authors: Sadowski Victoria A. , Sapountzis Panagiotis , Kooij Pepijn W. , Boomsma Jacobus J. , Adams Rachelle M.M.
Published: June 2024

Multipartite symbioses are inherently complex, involving dynamic ecological interactions between organisms with intertwined yet distinct evolutionary histories. The fungus-growing (attine) ants facilitate maintenance of a symbiotic species network through maternal vertical transmission of an obligate fungal symbiont. While the gut microbiomes of fungus-growing ant species are remarkably simple, their fungal gardens support diverse microbial communities. Here, we focus on an understudied transmission bottleneck: the fungal garden pellet that nest-founding queens transfer to inoculate a new fungal garden. We used 16S rRNA metagenomic sequencing to reconstruct the extent of vertical transmission of bacteria to new gardens via queen pellets in four sympatric fungus-growing ant species (Atta sexdens,Atta cephalotes,Acromyrmex echinatior, andMycetomoellerius mikromelanos) from Central Panama. We also characterized the bacterial communities associated with queen eggs and somatic tissues (mesosomas, guts and ovaries) to assess whether queens are likely to transmit symbiotic bacteria of workers, such as cuticular Actinobacteria and endosymbionts (Wolbachia,Mesoplasma, andSpiroplasma). Our results suggest that garden-associated bacteria are mainly horizontally acquired as the bacterial communities of pellets shared few bacterial taxa with the mature gardens of the four ant species investigated. While the bacterial communities of garden pellets showed some species-specificity, a subset of prevalent bacterial taxa were shared across ant species. Further, our findings provide evidence for vertical transmission of species-specific endosymbiotic bacteria through a transovarial route and/or via fecal droplets. Overall, while we found mixed evidence for vertical transmission of garden bacteria, our results support maternal transmission as a primary route for gut-associated symbionts. While our results suggest that vertical transmission of fungus-growing ant bacterial associates is mediated by the ant hosts, the mechanism behind this host control is not yet understood.
Tracking tree demography and forest dynamics at scale using remote sensing
Authors: Battison Robin , Prober Suzanne M. , Zdunic Katherine , Jackson Toby D. , Fischer Fabian Jörg , Jucker Tommaso
Published: June 2024

Capturing how tree growth and survival vary through space and time is critical to understanding the structure and dynamics of tree-dominated ecosystems. However, characterising demographic processes at scale is inherently challenging, as trees are slow-growing, long-lived, and cover vast expanses of land.

We used repeat airborne laser scanning data acquired over 25 km2of semi-arid, old-growth temperate woodland in Western Australia to track the height growth, crown expansion and mortality of 42,810 individual trees over nine years.

We found that demographic rates are constrained by a combination of tree size, competition and topography. After initially investing in height growth, trees progressively shifted to crown expansion as they grew larger, while mortality risk decreased considerably with size. Across the landscape, both tree growth and survival increased with topographic wetness, resulting in vegetation patterns that are strongly spatially structured. Moreover, biomass gains from woody growth generally outpaced losses from mortality, suggesting these old-growth woodlands remain a net carbon sink in the absence of wildfires.

Our study sheds new light on the processes that shape the dynamics and spatial structure of semi-arid woody ecosystems and provides a roadmap for using emerging remote sensing technologies to track tree demography at scale.
Grapevine vigour: a critical factor driving Trunk Disease expression
Authors: Claverie Marion , Audras Maïko , Berud François , Richy Didier
Published: June 2024

Esca and Black Dead Arm (EBDA) are complex grapevine trunk diseases (GTD) that are major causes of mortality and production decline in French vineyards. Unravelling the different factors that determine symptom expression is crucial in mitigating the impact on growers. While cultivar, climate, age, and pruning system are known contributors, they do not fully explain the variability in EBDA occurrence. This study investigates the role of grapevine vigour as a determinant factor in EBDA expression.

In 2022 and 2023, three vineyard networks were monitored, each consisting of approximately 30 vineyard plots of Grenache Noir, uniform in age. To minimize climate variation the selected vineyards were located within small geographical areas. We evaluated grapevine vigour and its primary drivers—water and nitrogen status, weed cover, production, and vegetation biomass—and correlated these factors with EBDA occurrence.

Results show that current-year vigour is positively correlated with the EBDA incidence rate in all network*year scenarios. The relationship curve suggests that, while low to moderate vigour is consistently associated with reduced symptom expression, high vigour can be correlated with either high or low expression and implies the involvement of additional factors. In one instance, previous year water stress, of all tested variables, was most correlated with current year EBDA incidence, though vigour was also influential. In that case, EBDA expression seems to be maximal when water stress the year before is combined with a substantial current year spring vigour. While these results need to be confirmed over a longer period, in more regions and with other cultivars, they open new perspectives of applications for growers. They suggest a wider implication of grapevine physiology than just vigour.
Unveiling Vertebrate Development Dynamics in FrogXenopus laevisusing Micro-CT Imaging
Authors: Jakub Laznovsky , Michaela Kavkova , Alice Reis , Pavla Robovska-Havelkova , Jan Krivanek , Tomas Zikmund , Jozef Kaiser , Marcela Buchtova , Jakub Harnos
Published: June 2024

Background

Xenopus laevis, the African clawed frog, is a versatile vertebrate model organism employed across various biological disciplines, prominently in developmental biology to elucidate the intricate processes underpinning body plan reorganization during metamorphosis. Despite its widespread utility, a notable gap exists in the availability of comprehensive datasets encompassingXenopus’late developmental stages.

Findings

In the present study, we harnessed micro-computed tomography (micro-CT), a non-invasive 3D imaging technique utilizing X-rays to examine structures at a micrometer scale, to investigate the developmental dynamics and morphological changes of this crucial vertebrate model. Our approach involved generating high-resolution images and computed 3D models of developingXenopusspecimens, spanning from premetamorphosis tadpoles to fully mature adult frogs. This extensive dataset enhances our understanding of vertebrate development and is adaptable for various analyses. For instance, we conducted a thorough examination, analyzing body size, shape, and morphological features, with a specific emphasis on skeletogenesis, teeth, and organs like the brain at different stages. Our analysis yielded valuable insights into the morphological changes and structure dynamics in 3D space duringXenopus’development, some of which were not previously documented in such meticulous detail. This implies that our datasets effectively capture and thoroughly examineXenopusspecimens. Thus, these datasets hold the solid potential for additional morphological and morphometric analyses, including individual segmentation of both hard and soft tissue elements withinXenopus.

Conclusions

Our repository of micro-CT scans represents a significant resource that can enhance our understanding ofXenopus’development and the associated morphological changes. The widespread utility of this amphibian species, coupled with the exceptional quality of our scans, which encompass a comprehensive series of developmental stages, opens up extensive opportunities for their broader research application. Moreover, these scans have the potential for use in virtual reality, 3D printing, and educational contexts, further expanding their value and impact.

Graphical abstract & lay summary

3D images of selected developmental stages ofX. laevisin a comparison (scale bar = 10 mm).

Lay summary

X-ray tomography was used to examine the African clawed frog (Xenopus laevis). An extensive data set of specimens from tadpoles to adult frogs provides novel insights into the changes and developmental dynamics of selected structures, which opens avenues to an improved understanding of this crucial animal model.
UsingGalleria mellonellato study pathogen dissemination and anti-infective surface coatings
Authors: Maslova Evgenia , Staber Ciaram , McCarthy Ronan R
Published: June 2024

Hospital associated infections and localised hospital outbreaks are a major challenge for infection control teams (ICTs) in hospitals around the world. Advances in artificial intelligence and infection modelling have enabled ICT teams to better predict and trace infection spread. However, it is notoriously difficult to replicate bacterial dissemination or validate prediction models in a laboratory setting due to a lack of effectivein vivomodels. In this work, we sought to developGalleria mellonellaas a model organism to replicate the dissemination of pathogens in a hospital intensive care unit (ICU). By combining this model organism with 3D printed models of a real hospital ICU, we are able to demonstrate that larvae do disseminate the multidrug resistant pathogenAcinetobacter baumanniiwithin this ICU model and that it is possible to use this model to identify infection hotspots. Importantly, this model can also be used for intervention strategy testing as we also show that bacterial dissemination can be significantly mitigated by the introduction of antimicrobial wall surface coatings. This model provides a robust platform for the testing of antimicrobial surface coatings as well as the study of genetic determinants with a role in pathogen dissemination.
Gcn2 rescues reprogramming in the absence of Hog1/p38 signaling inC. neoformansduring thermal stress
Authors: Goich David , Bloom Amanda L. M. , Duffy Sean R. , Ventura Maritza N. , Panepinto John C.
Published: June 2024

The fungusCryptococcus neoformansis an opportunistic pathogen of people that reprograms its translatome to facilitate adaptation and virulence within the host. We studied the role of Hog1/p38 in reprogramming translation during thermal stress adaptation, and found that this pathway acts on translation via crosstalk with the Gcn2 pathway, a well-studied regulator of general translation control. Using a combination of molecular assays and phenotypic analysis, we show that increased output from the Gcn2 pathway in a Hog1 deletion mutant is associated with rescue of thermal stress adaptation at both molecular and phenotypic scales. We characterize known outputs of the Hog1 pathway during thermal stress as either Gcn2-dependent or Gcn2-independent, and demonstrate that Hog1 activation regulates the Gcn2 pathway even in the absence of thermal stress. Finally, we implicate this phenomenon in another Hog1-regulated process, morphogenesis, and recapitulate Hog1-Gcn2 crosstalk in the distantly related fungal pathogen,Candida albicans.Our results point to an important link between the stress response machinery and translation control, and clarify the etiology of phenotypes associated with Hog1 deletion. More broadly, this study highlights complex interplay between core conserved signal transduction pathways and the utility of molecular assays to better understand how these pathways are connected.

Importance

Cryptococcus neoformansis an opportunistic pathogen of people that causes deadly cryptococcal meningitis, which is is responsible for an estimated 19% of AIDS-related mortality. When left untreated, cryptococcal meningitis is uniformly fatal, and in patients receiving the most effective antifungal regimens, mortality remains high. Thus, there is a critical need to identify additional targets that play a role in adaptation to the human host and virulence. This study explores the role of the stress response kinases Hog1 and Gcn2 in thermoadaptation, which is pre-requisite for virulence. Our results show that compensatory signaling occurs via the Gcn2 pathway when Hog1 is deleted, and that disruption of both pathways increases sensitivity to thermal stress. Importantly, our study highlights the insufficiency of using single gene deletion mutants to study gene function, since many phenotypes associated with Hog1 deletion were driven by Gcn2 signaling in this background, rather than loss of direct Hog1 activity.
Intestinal tissue response to Shiga toxin exposure
Authors: Hanson Kendal L. , Weiss Alison Ann
Published: June 2024

Shiga toxin (Stx) is produced by some pathogenic strains ofE. coli. To study the impact of Stx on the human intestine we utilized human intestinal organoids (HIOs) and human intestinal enteroids (HIEs) grown as human intestinal enteroid monolayers (HIEMs) in transwells. To establish optimal experimental conditions, HIEMs were grown with or without mesenchymal cells added to the basolateral wells to recapitulate the interactions between the intestinal epithelium and underlying mesenchyme. Monolayer barrier integrity was determined through transepithelial electrical resistance (TEER) readings. Apical saline was used on the apical surface since growth medium caused uneven development of the TEER. Medium used for epithelial cells contains added growth factors, while mesenchymal medium lacks these growth factors. We have shown that mesenchymal cells can maintain the epithelial monolayer in medium lacking growth factors suggesting they produce these factors. Furthermore, growth factors produced by mesenchymal cells need to buildup in the medium over time, since daily medium changes were not as effective as medium changes performed every three days. We have also shown that addition of growth factors is toxic to mesenchymal cells. Epithelial cells were more resistant to Stx2 than the mesenchymal cells, and mesenchymal cells contributed to epithelial cell death. Epithelial cells tolerated luminal exposure better than basolateral exposure. These studies demonstrate the importance of understanding tissue interactions in a disease state when using in vitro and in vitro models.

Importance

These studies have cemented the need for complex cell culture models when studying host-pathogen interactions. Common animal models such as mice are resistant toE. coliO157:H7 infections and intestinal delivery of Stx2, while humans appear to be sensitive to both. It has been proposed that in humans, STEC-mediated intestinal damage destroys the intestinal barrier and allows basolateral access to Stx2. In mice, there is no epithelial damage, therefore they are resistant to epithelial delivery of Stx2, while remaining sensitive to Stx2 injection. Our studies show that like mice, the human epithelial layer is quite resistant to Stx2, and it is the sensitivity of the mesenchymal cells that kills the epithelial cells. We have shown that Stx2 is transported through the intact epithelium without causing damage to the resistant epithelial layer. Understanding tissue interactions during infections is therefore critical in determining the effects of pathogens on human tissues.
Microglia replacement effectively attenuates the disease progress of ALSP in the mouse model and human patient
Authors: Wu Jingying , Wang Yafei , Li Xiaoyu , Cai Yuanyuan , Ouyang Pei , He Yang , Zhang Mengyuan , Luan Xinghua , Jin Yuxiao , Liu Taohui , Li Yuxin , Huang Xiaojun , Mao Ying , Rao Yanxia , Cao Li , Peng Bo
Published: June 2024

Microglia play critical roles in the brain physiology and pathology. CSF1R is primarily expressed in microglia. The mono-allelicCSF1Rmutation causes adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP), a lethal neurological disease and no rational cure in clinical trials. There are no animal models mimicking human ALSP. In this study, we first developed mouse models based on human ALSP hotspot mutations. We then utilized microglia replacement by bone marrow transplantation (Mr BMT) to replace theCsf1r-deficient microglia in ALSP mice byCsf1r-normal donor cells. With pathogenic gene correction, Mr BMT efficiently attenuated the pathologies. Previously, an ALSP patient received traditional bone marrow transplantation (tBMT) due to a misdiagnosis of metachromatic leukodystrophy. The disease progress was halted for 15 years with unknown reasons. We demonstrated that tBMT in ALSP is equivalent to or close to Mr BMT, achieving efficient microglia replacement and therefore attenuating the ALSP progress in the mouse model. Next, we applied tBMT to replaceCSF1R-deficient microglia in human patients. Our clinical results show that after microglia replacement, the ALSP course is effectively halted. Together, microglia replacement corrects the pathogenic gene and thus halts the disease progress in the mouse model and human patients. This study strongly demonstrates clinical potentials of microglia replacement in neurological disease treatments.
Identifying factors that contribute to collision avoidance behaviours while walking in a natural environment
Authors: Nikmanesh Mohammadamin , Cinelli Michael E. , Marigold Daniel S.
Published: June 2024

Busy walking paths, like in a park, a sidewalk in a city centre, or a shopping mall, frequently necessitate collision avoidance behaviour. Lab-based research has shown how a variety of situation-specific factors (e.g., distraction, object/pedestrian proximity) and person-specific factors (e.g., pedestrian size, age), typically studied independently, affect avoidance behaviour. What happens in the real world is unclear. Thus, we filmed unscripted pedestrian walking behaviours on a busy ∼3.5 m urban path adjacent to the water. We leveraged deep learning algorithms to identify and extract walking trajectories of pedestrians and had unbiased raters characterize interaction details. Here we analyzed over 500 situations where two pedestrians approached each other from opposite ends (i.e., one-on-one pedestrian interactions). We found that smaller medial-lateral distance between approaching pedestrians and a lower number of surrounding pedestrians (i.e., smaller crowd size) predicted an increase in the likelihood of a subsequent path deviation. Furthermore, we found that whether a pedestrian looked distracted or held, pushed, or pulled something while walking predicted the medial-lateral distance between pedestrians at the time of crossing. Although pedestrians maintained a larger personal space boundary compared to lab settings, this is likely because of the outdoor path’s width. Overall, our results suggest that collision avoidance behaviours in lab and real-world environments share similarities and offer insights relevant to developing more accurate computational models for realistic pedestrian movement.
Culture-dependent identification of rare marine sediment bacteria from the Gulf of Mexico and Antarctica
Authors: Kennedy Sarah J. , Atkinson Celine Grace F. , Tubbs Tristan J. , Baker Bill J. , Shaw Lindsey N.
Published: June 2024

Laboratory-viable cultivars of previously uncultured bacteria further taxonomic understanding. Despite many years of modern microbiological investigations, the vast majority of bacterial taxonomy remains uncharacterized. While many attempts have been made to decrease this knowledge gap, culture-based approaches parse away at the unknown and are critical for improvement of both culturing techniques and computational prediction efficacy. To this end of providing culture-based approaches, we present a multi-faceted approach to recovering marine environmental bacteria. We employ combinations of nutritional availability, inoculation techniques, and incubation parameters in our recovery of marine sediment-associated bacteria from the Gulf of Mexico and Antarctica. The recovered biodiversity spans several taxa, with 16S-ITS-23S rRNA gene-based identification of multiple isolates belonging to rarer genera increasingly undergoing phylogenetic rearrangements. Our modifications to traditional culturing techniques have not only recovered rarer taxa, but also resulted in the recovery of biotechnologically promising bacteria. Together, we propose our stepwise combinations of recovery parameters as a viable approach to decreasing the bacterial knowledge gap.
New Insights into Neuromuscular Contracture Reveals Myotendinous-SMAD4 Signaling Underlies Contracture Formation
Authors: Arvind Varun , Shyu Peter Timothy , Hyman Joshua E. , Huang Alice H.
Published: June 2024

Neuromuscular contractures (NC) are a prevalent cause of joint deformity in children suffering from neuromuscular disorders or nerve damage, leading to persistent disability. The role of tendon in the development of NC remains poorly understood, with current treatments predominantly targeting muscle. Here, we establish a surgical model of NC in the hindlimb that recapitulates functional deformity and transcriptomic changes observed in human disease. Our findings indicate that in NC, tendons dramatically elongate, undergoing changes in matrix and structural composition that reduce tensile stiffness. Contrary to expectations, we find that tendon elongation was principally driven by increased myotendon infiltration into muscle which restricted muscle elongation contributing to NC. Using lineage tracing, we show that myotendon elongation was due to increased infiltration of intrinsically derived tenocytes. Transcriptional profiling revealed BMP signaling as a key factor in myotendon elongation, corroborated by elevated myotendinous Smad4 activity in both our mouse model and in human NC tissues. Crucially, administration of a small molecule inhibitor of BMP-mediated Smad4 signaling not only restored joint mobility but also prevented myotendon elongation. These insights establish of a clinically relevant mouse model of NC and unveil a novel role for myotendon elongation in NC progression. Excitingly, our results suggest that targeting myotendon signaling could represent a new direction for tendon-focused therapies in NC management.
An algicidal bacterium shapes the microbiome during outdoor diatom cultivation collapse
Authors: Gilbert Naomi E. , Kimbrel Jeffery A. , Samo Ty J. , Siccardi Anthony J. , Stuart Rhona K. , Mayali Xavier
Published: June 2024

Biogeochemistry and productivity of algae-dominated environments is fundamentally influenced by the diversity and activity of bacteria. Namely, algicidal bacteria that prey on algal hosts can control elemental cycling and host populations within outdoor algal ponds used for biofuel production. In this study, we describe the genomic and proteomic signatures of a putative algicidal bacterium,Kordiasp. (familyFlavobacteriaceae), that bloomed during a population-wide crash of the biofuel diatom,Phaeodactylum tricornutum. ThisKordiasp. bloom occurred after 29 days of cultivation in outdoor algal raceway ponds inoculated withP. tricornutum, but not in parallel ponds inoculated withMicrochloropsis salina. Several signatures of antagonism expressed byKordiaduring diatom demise highlights previously unexplored mechanisms that may aid in algicidal activity or bacterial competition, including the type VI secretion system and hydrogen peroxide production. Analysis of accompanying downstream microbiota (primarily of theRhodobacteraceaefamily) provides evidence that cross-feeding is important in supporting microbial diversity during algal demise. Specifically,in situand laboratory data suggest thatKordiaacts as a primary degrader of biopolymers during algal demise, and co-occurringRhodobacteraceaeexploit degradation molecules or scavenge metabolic byproducts for carbon. Further, targeted analysis of 30Rhodobacteraceaemetagenome assembled genomes suggest algal pondRhodobacteraceaecommonly harbor pathways for carbon monoxide oxidation, a potential strategy to persist under competition. Collectively, these observations further constrain the role of algicidal bacteria in the aquatic ecosystem.
Exploring metabolic changes in gout – Insights from a genetic study
Authors: Salo Ville , Kettunen Johannes ,   FinnGen,   Estonian Biobank Research Team, Sliz Eeva
Published: June 2024

Gout is the most common inflammatory joint disease caused by the crystallization of urate inside the joints. Patients with gout typically have abnormal blood lipid and sugar levels, which are associated with cardiovascular diseases. However, the relationship between gout and metabolic changes is unclear. Our goal was two-fold: to identify new gout risk factors using genome-wide association analysis and subsequently to investigate the effects of the identified risk alleles on metabolic measures in the bloodstream. We performed a genome-wide meta-analysis for gout in the FinnGen project, the Estonian Biobank, and the UK Biobank, encompassing a total of 992,583 individuals, including 17,972 gout cases. Given that gout is commonly recognized as a disease affecting the elderly, and males specifically, we further explored age- and sex-stratified genetic associations in FinnGen (10,885 cases and 366,392 controls). Finally, we determined the metabolomic consequences of the gout risk-increasing alleles using data from a large metabolomics GWAS. In the meta-analysis, we observed 32 genome-wide significant (P<5×10−8) loci, one of which was novel. In the age- and sex-stratified analyses, we additionally identified one novel gout-associated locus in the male subgroup. The metabolomic findings suggested that the majority of the gout risk alleles primarily affected urate concentration in the bloodstream but not the concentrations of lipids and other metabolites. Therefore, it appears that the associations between gout and metabolic factors at the population level are likely explained by shared lifestyle risk factors. In conclusion, our study sheds new light on the genetic architecture of gout and adds to the growing body of evidence supporting the role of urate, but not other metabolic measures, including lipoprotein lipids and glucose, as a key risk factor for developing gout.
Blockchain based clinical trial management system: A scoping review and conceptual framework
Authors: Arjun M. C. , Ahamed Ashikh , Kurpad Anura V. , Thomas Tinku
Published: June 2024

Objective

The primary objective of the study was to map the real-world evidence of using Blockchain technology in clinical trial management systems and to create a novel conceptual framework for a Blockchain based digital ecosystem. As a first step towards validation of this conceptual framework, we aimed to create a blockchain simulation in Python programming language.

Methods

We did a scoping review of research articles which demonstrated a proof-of-concept or real-world application of Blockchain technology in clinical trial management. We searched in the PubMed, Web of Science, and IEEE Xplore to retrieve original articles published in English till April 2023. A novel conceptual framework was developed for a Blockchain based digital ecosystem with all the stakeholders involved in the conduct of clinical trial. We coded a simulation of clinical trial specific blockchain in Python using Django framework and the codes are made publicly available in GitHub.

Results

We retrieved 960 abstracts and included 21 full text articles in the review. Private blockchains like Hyperledger fabric and Ethereum are the most popular choice of platform. Smart contracts act as a key functionality in the Blockchain system to control specific activities. Clinical trial data was mostly stored outside the Blockchain, but Interplanetary File System is a popular choice for decentralized storage of data.

Conclusions

The scoping review, conceptual framework and the open-source Python codes would act as a guiding map for future research and product development in Blockchain based clinical trial management system and advancement in clinical research informatics.
Structure and physiological investigation of arginylated actin
Authors: Pinto Clyde Savio , Bakker Saskia E. , Suchenko Andrejus , Hussain Hamdi , Hatano Tomoyuki , Sampath Karuna , Chinthalapudi Krishna , Mishima Masanori , Balasubramanian Mohan
Published: June 2024

Actin is an evolutionarily conserved cytoskeletal protein with crucial roles in cell polarity, division, migration, and muscle contraction. Actin function is regulated in part by posttranslational modifications. One such modification in non-muscle cells is arginylation, in which an arginine residue is added to the N-terminus of β-actin. What is the structure of arginylated β-actin (R-β-actin), are its interactions with other proteins altered and what phenotypes result when R-β-actin is the sole actin isoform present in the cell? Here we report the 4.2 Å structure of ADP-bound human R-β-actin filaments, the overall structure of which is nearly identical to the filaments made of non-arginylated actin.In vitrofunctional assays using isoform-pure actins with defined post-translational modifications reveal that the interaction between myosin-II and actin is altered upon actin arginylation, due to frequent detachment of myosin-II from R-actin filaments.In vivo, we find that replacement of the only actin gene inSchizosaccharomyces pombewith a synthetic gene encoding R-Sp-actin reduces Arp2/3-based actin patches while thickening the formin-induced actin. Furthermore, consistent with altered interactions between myosin-II and R-actin filaments, the assembly and constriction of cytokinetic actomyosin ring are perturbed in the R-Sp-actin cells. Thus, despite the overall structural similarity of arginylated and non-arginylated actin filaments, actin arginylation affects actin filament assortment into distinct subcellular structures and its interaction with myosin II.
Genome organization regulates nuclear pore complex formation and promotes differentiation duringDrosophilaoogenesis
Authors: Kotb Noor M. , Ulukaya Gulay , Chavan Ankita , Nguyen Son C. , Proskauer Lydia , Joyce Eric F. , Hasson Dan , Jagannathan Madhav , Rangan Prashanth
Published: June 2024

Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes inDrosophilainvolves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ cell genes during differentiation, and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we found that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ cell genes into a silenced state and activating a group of oocyte genes and nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, cross-talk between genome architecture and NPCs is essential for successful cell fate transitions.
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
Authors: Gabriel Lars , Brůna Tomáš , Hoff Katharina J. , Ebel Matthis , Lomsadze Alexandre , Borodovsky Mark , Stanke Mario
Published: June 2024

Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes, and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both. A further significant performance improvement integrating all three data types was made by the recently released GeneMark-ETP. We here present the BRAKER3 pipeline that builds on GeneMark-ETP and AUGUSTUS, and further improves accuracy using the TSEBRA combiner. BRAKER3 annotates protein-coding genes in eukaryotic genomes using both short-read RNA-seq and a large protein database, along with statistical models learned iteratively and specifically for the target genome. We benchmarked the new pipeline on genomes of 11 species under an assumed level of relatedness of the target species proteome to available proteomes. BRAKER3 outperforms BRAKER1 and BRAKER2. The average transcript-level F1-score is increased by about 20 percentage points on average, whereas the difference is most pronounced for species with large and complex genomes. BRAKER3 also outperforms other existing tools, MAKER2, Funannotate, and FINDER. The code of BRAKER3 is available on GitHub and as a ready-to-run Docker container for execution with Docker or Singularity. Overall, BRAKER3 is an accurate, easy-to-use tool for eukaryotic genome annotation.
GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
Authors: Brůna Tomáš , Lomsadze Alexandre , Borodovsky Mark
Published: June 2024

Large-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic genome annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating genomic-, transcriptomic-, and protein-derived evidence that has been developed with a focus on large plant and animal genomes. GeneMark-ETP first identifies genomic loci where extrinsic data are sufficient for making gene predictions with “high confidence.” The genes situated in the genomic space between the high-confidence genes are predicted in the next stage. The set of high-confidence genes serves as an initial training set for the statistical model. Further on, the model parameters are iteratively updated in the rounds of gene prediction and parameter re-estimation. Upon reaching convergence, GeneMark-ETP makes the final predictions and delivers the whole complement of predicted genes. GeneMark-ETP outperforms gene finders using a single type of extrinsic evidence. Comparisons with gene finders MAKER2 and TSEBRA, those that use both transcript- and protein-derived extrinsic evidence, show that GeneMark-ETP delivers state-of-the-art gene-prediction accuracy, with the margin of outperforming existing approaches increasing in its application to larger and more complex eukaryotic genomes.
Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
Authors: Lv Pengfei , Yang Xingzhuo , Zhao Xianguo , Zhao Zhangwu , Du Juan
Published: June 2024

Diapause represents a crucial adaptive strategy used by insects to cope with changing environmental conditions. In North China, the Asian corn borer (Ostrinia furnacalis) enters a winter larval diapause stage. Although there is growing evidence implicating epigenetic mechanisms in diapause regulation, it remains unclear whether dynamic genome-wide profiles of epigenetic modifications exist during this process. By investigating multiple histone modifications, we have discovered the essential roles of H3K9me3 and H3K27me3 during diapause of the Asian corn borer. Building upon previous findings in vertebrates highlighting the connection between DNA methylation and repressive histone methylations, we have examined changes in the genome-wide profile of H3K9me3, H3K27me3, and DNA methylation at the nondiapause, prediapause, and diapause stages. Data analysis reveals significant alterations in these three modifications during diapause. Moreover, we observe a correlation between the H3K9me3 and H3K27me3 modification sites during diapause, whereas DNA modifications show little association with either H3K9me3 or H3K27me3. Integrative analysis of epigenome and expression data unveils the relationship between these epigenetic modifications and gene expression levels at corresponding diapause stages. Furthermore, by studying the function of histone modifications on genes known to be important in diapause, especially those involved in the juvenile pathway, we discover that the juvenile hormone pathway lies downstream from H3K9me3 and H3K27me3 histone modifications. Finally, the analysis of gene loci with modified modifications unreported in diapause uncovers novel pathways potentially crucial in diapause regulation. This study provides a valuable resource for future investigations aiming to elucidate the underlying mechanisms of diapause.