bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-range alteration of the physical environment mediates cooperation betweenPseudomonas aeruginosaswarming colonies
Authors: Deforet Maxime 
Published: July 2022

AbstractPseudomonas aeruginosamakes and secretes massive amounts of rhamnolipid surfactants that enable swarming motility over biogel surfaces. But how this rhamnolipids interact with biogels to assist swarming remains unclear. Here I use a combination of optical techniques across scales and genetically-engineered strains to demonstrate that rhamnolipids can induce agar gel swelling over distances > 10,000x the body size of an individual cell. The swelling front is on the micrometric scale, and is easily visible using shadowgraphy. Rhamnolipid transport is not restricted to the surface of the gel, but occurs through the whole thickness of the plate and, consequently, the spreading dynamics depends on the local thickness. Surprisingly, rhamnolipids can cross the whole gel and induce swelling on the opposite side of a two-face Petri dish. The swelling front delimits an area where the mechanical properties of the surface properties are modified: water wets the surface more easily, which increases the motility of individual bacteria and enables collective motility. A genetically-engineered mutant unable to secrete rhamnolipids (DrhlA), and therefore unable to swarm, is rescued from afar with rhamnolipids produced by a remote colony. These results exemplify the remarkable capacity of bacteria to change the physical environment around them and its ecological consequences.Significance statementLiving organisms have the ability to interact mechanically with their environment.Pseudomonas aeruginosa, a motile bacterium, can spread collectively on biogels, a behavior called swarming. Rhamnolipids, surfactant moleculesP. aeruginosamake and secrete, are required for swarming. Here, I demonstrate rhamnolipids not only physically alter the biogel in the vicinity of the secreting cells, but also over distances much greater than the bacterial cell size, through gel swelling. This long-distance physical alteration can even rescue a remote colony which would not produce rhamnolipids. This work illustrates the remarkable ability of bacteria to change the mechanical property of the world surrounding them.
Gait, physical activity, and tibiofemoral cartilage damage: A longitudinal machine learning analysis in the Multicenter Osteoarthritis Study
Authors: Costello Kerry E. , Felson David T. , Jafarzadeh S. Reza , Guermazi Ali , Roemer Frank W. , Segal Neil A. , Lewis Cora E. , Nevitt Michael C. , Lewis Cara L. , Kolachalama Vijaya B. , Kumar Deepak 
Published: July 2022

ABSTRACTObjectiveTo 1) develop and evaluate a machine learning model incorporating gait and physical activity to predict medial tibiofemoral cartilage worsening over two years in individuals without or with early knee osteoarthritis and 2) identify influential predictors in the model and quantify their effect on cartilage worsening.DesignAn ensemble machine learning model was developed to predict worsened cartilage MRI Osteoarthritis Knee Score at follow-up from gait, physical activity, clinical and demographic data from the Multicenter Osteoarthritis Study. Model performance was evaluated in repeated cross-validations. The top 10 predictors of the outcome across 100 held-out test sets were identified by a variable importance measure statistic, and their marginal effect on the outcome was quantified by g-computation.ResultsOf 947 legs in the analysis, 14% experienced medial cartilage worsening at follow-up. The median (2.5th-97.5thpercentile) AUC across the 100 held-out test sets was 0.73 (0.65-0.79). Presence of baseline cartilage damage, higher Kellgren-Lawrence grade, greater pain during walking, higher lateral ground reaction force impulse, greater time spent lying, and lower vertical ground reaction force unloading rate were associated with greater risk of cartilage worsening.ConclusionsAn ensemble machine learning approach incorporating gait, physical activity, and clinical/demographic features showed good performance for predicting cartilage worsening over two years. While identifying potential intervention targets from the model is challenging, these results suggest that lateral ground reaction force impulse, time spent lying, and vertical ground reaction force unloading rate should be investigated further as potential early intervention targets to reduce medial tibiofemoral cartilage worsening.Summary boxWhat are the findings?Machine learning models predicted cartilage worsening in persons without or with early knee osteoarthritis from gait, physical activity, and clinical and demographic characteristics with a median AUC of 0.73 across 100 held-out test sets.High lateral ground reaction force impulse, more time spent lying, and low vertical ground reaction force unloading rate were associated with increased risk of cartilage worsening over two years.How might it impact on clinical practice in the future?Gait and physical activity are some of the only modifiable risk factors for knee osteoarthritis; this study identified three potential intervention targets to slow early knee osteoarthritis progression.
Development of allosteric, selective cyclin-dependent kinase 2 (CDK2) inhibitors that are negatively cooperative with cyclin binding and show potential as contraceptive agents
Authors: Faber Erik B. , Tang Jian , Roberts Emily , Ganeshkumar Sornakala , Sun Luxin , Wang Nan , Rasmussen Damien , Majumdar Abir , John Kristen , Yang An , Khalid Hira , Hawkinson Jon E. , Levinson Nicholas M. , Schönbrunn Ernst , Chennathukuzhi Vargheese , Harki Daniel A. , Georg Gunda I. 
Published: July 2022

AbstractCompared to most ATP-site kinase inhibitors, small molecules that target an allosteric pocket have the potential for improved selectivity due to the often observed lower structural similarity at these distal sites. Despite their promise, relatively few examples of structurally confirmed, high-affinity allosteric kinase inhibitors exist. Cyclin-dependent kinase 2 (CDK2) is a target for many therapeutic indications, including non-hormonal contraception.1 However, an inhibitor against this kinase with exquisite selectivity has not reached the market because of the structural similarity between CDKs.1-2 In this paper, we describe the development and mechanism of action of new type III inhibitors that bind CDK2 with nanomolar affinity, making them the highest affinity, structurally confirmed allosteric CDK inhibitors reported. Notably, these anthranilic acid inhibitors exhibit a strong negative cooperative relationship with cyclin binding, which remains an underexplored mechanism for CDK2 inhibition. Furthermore, the binding profile of these compounds in both biophysical and cellular assays demonstrate the promise of this series for further development into a therapeutic selective for CDK2 over highly similar kinases like CDK1. The potential of these inhibitors as efficacious contraceptive agents is seen by incubation with mouse testicular explants, where they recapitulate Cdk2-/- and Spdya-/- phenotypes.
Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding
Authors: Mitsi Konstantina , Richter Daniel J. , Arroyo Alicia S. , López-Escardó David , Antó Meritxell , Guillén Antonio , Ruiz-Trillo Iñaki 
Published: July 2022

AbstractMicrobial eukaryotes are diverse and ecologically important organisms, yet sampling constraints have hindered the understanding of their distribution and diversity in freshwater ecosystems. Metabarcoding has provided a powerful complement to traditional limnological studies, revealing an unprecedented diversity of protists in freshwater environments. Here, we aim to expand our knowledge of the ecology and diversity of protists in lacustrine ecosystems by targeting the V4 hypervariable region of the 18S rRNA gene in water column, sediment and biofilm samples collected from Sanabria Lake (Spain) and surrounding freshwater ecosystems. Sanabria is a temperate lake, which are relatively understudied by metabarcoding in comparison to alpine and polar lakes. The phylogenetic diversity of microbial eukaryotes detected in Sanabria span all currently recognized eukaryotic supergroups, with Stramenopiles being the most abundant and diverse supergroup in all sampling sites. Parasitic microeukaryotes account for 21% of the total protist ASVs identified in our study and were dominated by Chytridiomycota, both in terms of richness and abundance in all sampling sites. Sediments, biofilms and water column samples harbour distinct microbial communities. Phylogenetic placement of poorly assigned and abundant ASVs indicates molecular novelty inside Rhodophyta, Bigyra, early-branching Nucletmycea and Apusomonadida. In addition, we report the first freshwater incidence of the previously exclusively marine genera Abeoforma and Sphaeroforma. Our results contribute to a deeper understanding of microeukaryotic communities in freshwater ecosystems, and provide the first molecular reference for future biomonitoring surveys in Sanabria Lake.
Sediment substrate size influences fish diversity in tributary mouth areas in impounded boreal rivers in Sweden
Authors: Näslund J. , Bowes R. , Sandin L. , Bergman E. , Greenberg L. 
Published: July 2022

ABSTRACTLarge boreal rivers in Sweden are generally impounded by hydropower dams and a large proportion of their main stem shallow flowing habitats have been lost. Tributaries often contain relatively undisturbed habitats and could be important for the conservation of species diversity. Tributary mouth areas could be biodiversity hot-spots, due to the vicinity to the main stem and favorable environmental conditions. In this study, we investigate whether tributary mouth areas in two impounded boreal rivers (Ume- and Lule River) could be regarded as biodiversity hot spots for fish. Based on electrofishing in 20 tributary mouths, we found that overall fish diversity is generally low. The highest species richness and diversity was found in mouth areas dominated by intermediate substrate sizes (gravel – cobble). Few, if any, species were found in association with fine sediment substrates (smaller than sand). The tributary mouth areas had similar species richness and diversity as areas in the tributaries located 1-km upstream of the mouth, but the fish community composition often differed between these sites. Management action favoring fish diversity in the tributary mouth areas could include protection or rehabilitation of areas dominated by medium sized substrate and reduction of erosion and transport of fine sediments in the tributaries. Overall, we find no support for tributary mouths being hot-spots for fish biodiversity and while some patterns in diversity gives hints on suitable management action, it is important to further understand impacts in tributaries and their mouths especially in relation to temporal dynamics of the fish community.
Stromal transdifferentiation drives lymph node lipomatosis and induces extensive vascular remodeling
Authors: Bekkhus Tove , Olofsson Anna , Sun Ying , Magnusson Peetra , Ulvmar Maria H. 
Published: July 2022

AbstractLymph node (LN) lipomatosis is a common, but rarely discussed phenomenon, associated with aging, involving a gradual exchange of the LN parenchyma into adipose tissue. The mechanisms behind these changes and the effects on the LN have been unknown. We show that LN lipomatosis starts in the medullary regions of the human LN and link the initiation of lipomatosis to transdifferentiation of LN medullary fibroblasts into adipocytes. The latter is associated with a downregulation of lymphotoxin beta expression. We also show that, medullary fibroblasts, in contrast to the reticular cells in the T-cell zone, display an inherent higher sensitivity for adipogenesis. Progression of lipomatosis leads to a gradual loss of the medullary lymphatic network, but at later stages, collecting-like lymphatic vessels, are found inside the adipose tissue. The stromal dysregulation includes a dramatic remodeling and dilation of the high endothelial venules associated with reduced density of naïve T-cells. Abnormal clustering of plasma cells is also observed. Thus, LN lipomatosis causes widespread stromal dysfunction with consequences for the immune contexture of the human LN. Our data warrant an increased awareness of LN lipomatosis as a factor contributing to decreased immune functions in the elderly and in disease.Graphical abstractIn lymph nodes (LNs) of young patients there is a normal lymph flow, normal and functioning high endothelial venules (HEVs) with a high density of surrounding naïve T-cells. With aging lymphotoxin beta (LTB) is downregulated in the medulla of the LN and the fibroblasts of the medulla, namely the medullary reticular cells (MedRCs), transdifferentiate into adipocytes inducing LN lipomatosis. LN lipomatosis leads to loss of lymphoid tissue, medullary sinuses and can be predicted to result in a shortcut of the lymph flow based on the presence of collecting-like vessels in the adipose tissue in late stage lipomatosis. Lipomatosis also induce extensive vascular remodeling with loss of medullary lymphatic vessels and dysfunctional, highly dilated HEVs with lower density of naïve T-cells and trapped plasma cells.
A Versatile Agrobacterium-Based Transformation System for Genetic Engineering of Diverse Citrus Cultivars
Authors: Dominguez Michelle M. , Padilla Carmen S. , Mandadi Kranthi K. 
Published: July 2022

ABSTRACTDeveloping an efficient transformation system is vital in genetically engineering recalcitrant crops, particularly trees. Here, we outline an Agrobacterium tumefaciens-based transformation methodology for citrus genetic engineering. The process was optimized to suit the requirements of fourteen citrus varieties by establishing appropriate infection, co-cultivation, selection, and culture media conditions. The procedure includes transforming seedling-derived epicotyl segments with an A. tumefaciens strain, then selecting and regenerating transformed tissues. Transgenic shoots were further identified by a visual reporter (e.g., β-glucuronidase) and confirmed by Northern and Southern blot analysis. Transgene integrations among the transgenic lines ranged between one to four. The methodology can yield transformation efficiencies of up to 11%, and transgenic plants can be recovered as early as six months, depending on the variety. In addition, we show that incorporating A. tumefaciens helper virulence genes (virG and virE), spermidine, and lipoic acid in the resuspension buffer before transformation improved the transformation efficiency of specific recalcitrant cultivars, presumably by enhancing T-DNA integration and alleviating oxidative stress on the explant tissues. In conclusion, the optimized methodology can be utilized to engineer diverse recalcitrant citrus varieties towards trait improvement or functional genetics applications.
The genetic architecture of local adaptation in a cline
Authors: Laroche Fabien , Lenormand Thomas 
Published: July 2022

AbstractLocal adaptation is pervasive. It occurs whenever selection favors different phenotypes in different environments, provided that there is genetic variation for the corresponding traits and that the effect of selection is greater than the effect of drift and migration. In many cases, ecologically relevant traits are quantitative and controlled by many genes. It has been repeatedly proposed that the localization of these genes in the genome may not be random, but could be an evolved feature. In particular, the clustering of local adaptation genes may be theoretically expected and has been observed in several situations. Previous theory has focused on two-patch or continent-island models to investigate this phenomenon, reaching the conclusion that such clustering could evolve, but in relatively limited conditions. In particular, it required that migration rate was neither too low nor too large and that the full optimization of trait values could not be eventually achieved by a mutation at a single locus. Here, we investigate this question in a spatially-explicit model, considering two contiguous habitats with distinct trait optima on a circular stepping-stone. We find that clustering of local-adaptation genes is pervasive within clines during both the establishment phase of local adaptation and the subsequent “reconfiguration” phase where different genetic architectures compete with each other. We also show that changing the fitness function relating trait to fitness has a strong impact on the overall evolutionary dynamics and resulting architecture.
H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements
Authors: Tafessu Amanuel , O’Hara Ryan , Martire Sara , Dube Altair L. , Saha Purbita , Banaszynski Laura A. 
Published: July 2022

AbstractBackgroundThe histone variant H3.3 is enriched at active regulatory elements such as promoters and enhancers in mammalian genomes. These regions are highly accessible, creating an environment that is permissive to transcription factor binding and the recruitment of transcriptional coactivators that establish a unique chromatin post-translational landscape. How H3.3 contributes to the establishment and function of chromatin states at these regions is poorly understood.ResultsWe performed genomic analyses of features associated with active promoter chromatin in mouse embryonic stem cells (ESCs) and found evidence of subtle yet widespread promoter dysregulation in the absence of H3.3. Loss of H3.3 deposition at promoters reduces chromatin accessibility and transcription factor (TF) footprinting for nearly all TFs expressed in ESCs. H3.3 deletion leads to reduced promoter enrichment of the transcriptional coactivator and histone acetyltransferase, p300. Subsequently, histone H3 acetylation at lysine 27 (H3K27ac) is reduced at promoters in the absence of H3.3, along with reduced enrichment of the bromodomain-containing protein BRD4, an acetyl lysine reader. Despite the observed chromatin dysregulation, H3.3 KO ESCs maintain transcription from ESC-specific genes. However, upon undirected differentiation, H3.3 KO cells retain footprinting of ESC-specific TFs motifs and fail to generate footprints of lineage-specific TF motifs, in line with their diminished capacity to differentiate.ConclusionsH3.3 facilitates DNA accessibility, TF binding, and histone post-translational modification at active promoters. While H3.3 is not required for maintaining transcription in ESCs, it is required for TF binding at new promoters during differentiation.
Cavity geometry shapes overall ant colony organization through spatial limits but workers maintain fidelity zones
Authors: Chism Greg T. , Nichols William , Dornhaus Anna 
Published: July 2022

AbstractMany animals inhabit nests that protect them from adverse environments. However, the effects of living in a built or found structure are not limited to protection: the physical space can shape and organize behavior, particularly in self-organized collective systems. In addition, the geometry of nest space may not be under the animal’s control, raising the question whether animals can compensate for the effects that unexpected or suboptimal geometries may have. Here we examine how the shape of a nest cavity affects spatial organization of colonies in the antTemnothorax rugatulus, a species that adapted to nest cavities of unmodifiable internal dimensions, since they inhabit rock crevices with rigid walls. We show that the emerging spatial relationships of workers, brood, queens, and young alates, as well as their relationships and distances to significant points in the nest, are all significantly influenced by nest shape, with the brood distributions most affected. However, we also found that the size of worker spatial fidelity zones, i.e. the areas in the nest that individual workers occupy and that may be key regulators of division of labor, are overall not affected by nest shape. These findings indicate that ants may actively regulate which areas of a nest they occupy, and that they may compensate for effects of nest architecture constraints. Physical properties of nests can thus influence the organization of ant colonies, highlighting the need to explore spatial constraints as a direct influence on the organization, movement, and communication of evolved or engineered self-organized systems.
Functional analysis of recurrent non-coding variants in human melanoma
Authors: Godoy Paula M. , Zarov Anna P. , Kaufman Charles K. 
Published: July 2022

ABSTRACTSmall nucleotide variants in non-coding regions of the genome can alter transcriptional regulation, leading to changes in gene expression which can activate oncogenic gene regulatory networks. Melanoma is heavily burdened by non-coding variants, representing over 99% of total genetic variation, including the well-characterized TERT promoter mutation. However, the compendium of regulatory non-coding variants is likely still functionally under-characterized. We developed a pipeline to identify hotspots, i.e. recurrently mutated regions, in melanoma containing putatively functional non-coding somatic variants that are located within predicted melanoma-specific regulatory regions. We identified hundreds of statistically significant hotspots, including the hotspot containing the TERT promoter variants, and focused in on a hotspot in the promoter of CDC20. We found that variants in the promoter of CDC20, which putatively disrupt an ETS motif, lead to lower transcriptional activity in reporter assays. Using CRISPR/Cas9, we generated an indel in the CDC20 promoter in a human A375 melanoma cell line and observed decreased expression of CDC20, changes in migration capabilities, and an altered transcriptional state previously associated with neural crest transcriptional programs and melanoma initiation. Overall, our analysis prioritized several recurrent functional non-coding variants that, through downregulation of CDC20, led to perturbation of key melanoma phenotypes.
Pitfalls of genotyping microbial communities with rapidly growing genome collections
Authors: Zhao Chunyu , Shi Zhou Jason , Pollard Katherine S. 
Published: July 2022

SUMMARYDetecting genetic variants in metagenomic data is a priority for understanding the evolution, ecology, and functional characteristics of microbial communities. Many recent tools that perform this metagenotyping rely on aligning reads of unknown origin to a reference database of sequences from many species before calling variants. Using simulations designed to represent a wide range of scenarios, we demonstrate that diverse and closely related species both reduce the power and accuracy of reference-based metagenotyping. We identify multi-mapping reads as a prevalent source of errors and illustrate a tradeoff between retaining correct alignments versus limiting incorrect alignments, many of which map reads to the wrong species. Then we quantitatively evaluate several actionable mitigation strategies and review emerging methods with promise to further improve metagenotyping. These findings document a critical challenge that has come to light through the rapid growth of genome collections that push the limits of current alignment algorithms. Our results have implications beyond metagenotyping to the many tools in microbial genomics that depend upon accurate read mapping.HIGHLIGHTSMost microbial species are genetically diverse. Their single nucleotide variants can be genotyped using metagenomic data aligned to databases constructed from genome collections (“metagenotyping”).Microbial genome collections have grown and now contain many pairs of closely related species.Closely related species produce high-scoring but incorrect alignments while also reducing the uniqueness of correct alignments. Both cause metagenotype errors.This dilemma can be mitigated by leveraging paired-end reads, customizing databases to species detected in the sample, and adjusting post-alignment filters.