bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide, Organ-delimited gene regulatory networks (OD-GRNs) provide high accuracy in candidate TF selection across diverse processes
Authors: Ranjan Rajeev , Srijan Sonali , Balekuttira Somaiah , Agarwal Tina , Ramey Melissa , Dobbins Madison , Wang Xiaojin , Hudson Karen , Li Ying , Varala Kranthi 
Published: June 2023

AbstractConstruction of organ-specific gene expression datasets that include hundreds to thousands of experiments would greatly aid reconstruction of gene regulatory networks with organ-level spatial resolution. However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, seed, seedling, silique, and stem in the model plantArabidopsis thaliana. In the leaf, root, flower, seed and, a gene regulatory network (GRN) inference approach was used to determine:i. influential transcription factors (TFs) in that organ and,ii. the most influential TFs for specific biological processes in the organ. These genome-wide, organ-delimited GRNs (OD-GRNs), identifiedde novomany known regulators of organ development and processes operating in those organs. Moreover, many previously unknown TF regulators were highly ranked as potential master regulators of organ development or organ-specific processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, with relevance to food and biofuel production. Of the top twenty candidate TFs, eight (e.g., WRI1, LEC1, and FUS3) are known regulators of seed oil content. Importantly, we validated that seven more candidate TFs, whose role was previously unknown in seed lipid biosynthesis, indeed affect this process by genetics and physiological approaches, thus yielding a net accuracy rate of >75% for thede novoTF predictions. The general approach developed here could be extended to any species with sufficiently large gene expression datasets to speed up hypothesis generation and testing for constructing gene regulatory networks at a high spatial resolution.Significance StatementOur study develops a machine-learning framework for building extremely large gene expression datasets for each organ, and to infer organ-delimited gene regulatory networks. We show that this approach is very successful at predicting which transcription factors are going to regulate processes at an organ level. We validated the accuracy of the predictions for transcription factor regulators using the seed lipid synthesis pathway as a case study. We demonstrated a very high success rate for uncovering both known and novel transcription factor regulators for the seed lipid biosynthesis pathway. The approach described in this study is broadly applicable across any organism (plant or animal) that has a large body of public gene expression data.
Enantioselectivity in the Enzymatic Dehydration of Malate and Tartrate: Mirror Image Specificities of Structurally Similar Dehydratases
Authors: Bellur Asutosh , Mukherjee Souradip , Sharma Pragya , Jayaraman Vijay , Balaram Hemalatha 
Published: June 2023

AbstractMalate (2-hydroxysuccinic acid) and tartrate (2,3-dihydroxysuccinic acid) are chiral substrates; the former existing in two enantiomeric forms (R and S) while the latter exists as three stereoisomers (R,R; S,S; and R,S). Dehydration by stereospecific hydrogen abstraction andanti-elimination of the hydroxyl group yield the achiral products fumarate and oxaloacetate, respectively. Class-I fumarate hydratase (FH) and L-tartrate dehydratase (L-TTD) are two highly conserved enzymes belonging to the iron-sulfur cluster hydrolyase family of enzymes that catalyze reactions on specific stereoisomers of malate and tartrate. FH fromMethanocaldococcus jannaschiiaccepts only S-malate and S,S-tartrate as substrates while the structurally similar L-TTD fromEscherichia coliaccepts only R-malate and R,R-tartrate as substrates. Phylogenetic analysis reveals a common evolutionary origin of L-TTDs and two-subunit archaeal FHs suggesting a divergence during evolution that may have led to the switch in substrate stereospecificity preference. Due to the high conservation of their sequences, a molecular basis for switch in stereospecificity is not evident from analysis of crystal structures of FH and predicted structure of L-TTD. The switch in enantiomer preference may be rationalised by invoking conformational plasticity of the amino acids interacting with the substrate, together with substrate reorientation and conformer selection about the C2-C3 bond of the dicarboxylic acid substrates. Although classical models of enzyme-substrate binding are insufficient to explain such a phenomenon, the enantiomer superposition model suggests that a minor reorientation in the active site residues could lead to the switch in substrate stereospecificity.
Fluctuating selection facilitates the discovery of broadly effective but difficult to reach adaptive outcomes in yeast
Authors: Fasanello Vincent J. , Liu Ping , Fay Justin C. , Botero Carlos A. 
Published: June 2023

ABSTRACTEvolutionary compromises are thought to be common under fluctuating selection because the mutations that best enable adaptation to one environmental context can often be detrimental in others. Yet, prior experimental work has shown that generalists can sometimes perform as well as specialists in their own environments. Here we use a highly replicated evolutionary experiment (N = 448 asexual lineages of the brewer’s yeast) to show that even though fluctuation between two environmental conditions often induces evolutionary compromises (at least early on), it can also help reveal difficult to reach adaptive outcomes that ultimately improve performance in both environments. Specifically, we begin by showing that yeast adaptation to chemical stress can involve fitness tradeoffs with stress-free environments and that, accordingly, lineages that are repeatedly exposed to occasional stress tend to respond by trading performance for breadth of adaptation. We then show that on rare occasions, fluctuating selection leads to the evolution of no-cost generalists that can even outcompete constant selection specialists in their own environments. We propose that the discovery of these broader and more effective adaptive outcomes under fluctuating selection could be partially facilitated by changes in the adaptive landscape that result from having to deal with fitness tradeoffs across different environmental conditions. Overall, our findings indicate that reconciling the short- and long-term evolutionary consequences of fluctuating selection could significantly improve our understanding of the evolution of specialization and generalism.
When offspring outsmarting parents: Neuronal genes expression in two generations of marine parasitic worm
Authors: Tolstenkov Oleg , Chatzigeorgiou Marios , Gorbushin Alexander 
Published: June 2023

AbstractTrematodes, or flukes, cause disease in millions of people, impact animal health, and alter the functional organization of biological communities. During the transition from the intramolluscan redia to the free-living cercaria stage in a complex life cycle of trematodes, extensive anatomical and behavioral modifications occur, enabling the cercaria to locate and infect the next host in the complex water environment. However, the functional changes that occur in the nervous system during this shift are not well understood.We used ade novotranscriptome to characterize the molecular building blocks of the trematode nervous system and identify pathways that may underlie differences in nervous system function between the rediae and cercariae stages of theCryptocotyle lingua, marine trematode species causing problems for fisheries. Our results confirmed the streamlined molecular toolkit of these parasitic trematodes, including the absence of certain key signaling pathways and ion channels. We documented the loss of nitric oxide synthase not only inC. linguabut also in the entire phylum Platyhelminthes. We identified several neuronal genes upregulated in dispersal larvae, including genes involved in synaptic vesicle trafficking, TRPA channels, G-protein coupled receptors, and surprisingly nitric oxide receptors soluble guanylate cyclase. Validation of these findings using neuronal markers andin situhybridization allowed us to hypothesize the protein function in relation to the adaptations and host-finding strategy of the dispersal larva. Our results and established behavior quantification toolkit for cercaria motility provide a foundation for future research on the behavior and physiology of parasitic flatworms, with potential implications for developing antiparasitic measures.HighlightsWe utilized a behavior quantification toolkit and described essential neuronal genes in a handy model species, enabling the study of fluke neurobiology at the systems level.We characterized and validated neuronal gene expression profiles in cercarial embryos within rediae and swimming host-searching cercariae.The streamlined molecular toolkit of parasites reveals the absence of important signaling pathways and ion channels in their nervous system.We documented loss of nitric oxide synthase in flatworms.The expression pattern of nitric oxide receptors, soluble guanylate cyclases, upregulated in swimming larvae, emphasizes their crucial involvement in the dispersal process.Two upregulated TRPA channels in cercaria are primarily expressed in cilia and peripheral neurons, emphasizing their importance in host finding.
TheCandida albicansreference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates biofilm formation and oral commensalism
Authors: Glazier Virginia E. , Kramara Juraj , Ollinger Tomye , Solis Norma V. , Zarnowski Robert , Wakade Rohan S. , Kim Min-Ju , Weigel Gabriel J. , Liang Shen-Huan , Bennett Richard J. , Wellington Melanie , Andes David R. , Stamnes Mark A. , Filler Scott G. , Krysan Damian J. 
Published: June 2023

AbstractCandida albicansis a diploid human fungal pathogen that displays significant genomic and phenotypic heterogeneity over a range of virulence traits and in the context of a variety of environmental niches. Here, we show that the effects of Rob1 on biofilm and filamentation virulence traits is dependent on both the specific environmental condition and the clinical strain ofC. albicans. TheC. albicansreference strain SC5314 is aROB1heterozygote with two alleles that differ by a single nucleotide polymorphism at position 946 resulting in a serine or proline containing isoform. An analysis of 224 sequencedC. albicansgenomes indicates that SC5314 is the onlyROB1heterozygote documented to date and that the dominant allele contains a proline at position 946. Remarkably, theROB1alleles are functionally distinct and the rareROB1946Sallele supports increased filamentation in vitro and increased biofilm formation in vitro and in vivo, suggesting it is a phenotypic gain-of-function allele. SC5314 is amongst the most highly filamentous and invasive strains characterized to date. Introduction of theROB1946Sallele into a poorly filamenting clinical isolate increases filamentation and conversion of an SC5314 laboratory strain to aROB1946Shomozygote increases in vitro filamentation and biofilm formation. In a mouse model of oropharyngeal infection, the predominantROB1946Pallele establishes a commensal state while theROB1946Sphenocopies the parent strain and invades into the mucosae. These observations provide an explanation for the distinct phenotypes of SC5314 and highlight the role of heterozygosity as a driver ofC. albicansphenotypic heterogeneity.ImportanceCandida albicansis a commensal fungus that colonizes human oral cavity and gastrointestinal tracts but also causes mucosal as well as invasive disease. The expression of virulence traits inC. albicansclinical isolates is heterogenous and the genetic basis of this heterogeneity is of high interest. TheC. albicansreference strain SC5314 is highly invasive and expresses robust filamentation and biofilm formation relative to many other clinical isolates. Here, we show that SC5314 derivatives are heterozygous for the transcription factor Rob1 and contain an allele with a rare gain-of-function SNP that drives filamentation, biofilm formation, and virulence in a model of oropharyngeal candidiasis. These finding explain, in part, the outlier phenotype of the reference strain and highlight the role of heterozygosity plays in the strain-to-strain variation of diploid fungal pathogens.
Single-cell sequencing of tumor-associated macrophages in aDrosophilamodel
Authors: Khalili Dilan , Mohammed Mubasher , Kunc Martin , Ankarklev Johan , Theopold Ulrich 
Published: June 2023

AbstractIntroductionTumor-associated macrophages may act to either limit or promote tumor growth, yet the molecular basis for either path is poorly characterized.MethodsWe use a larvalDrosophilamodel that expresses a dominant-active version of the Rasoncogene (RasV12) to study dysplastic growth during early tumor progression. We performed single-cell RNA-sequencing of macrophage-like hemocytes to characterize these cells in tumor-compared to wild type larvae. Hemocytes included manually extracted tumor-associated-as well as circulating cells.Results and discussionWe identified 5 distinct hemocyte clusters. In addition to RasV12larvae we included a tumor model where the activation of effector caspases was inhibited, mimicking an apoptosis-resistant setting. Circulating hemocytes from both tumor models differ qualitatively from control wild-type cells – they display an enrichment for genes involved in cell division, which was confirmed using proliferation assays. Split analysis of the tumor models further reveals that proliferation is strongest in the caspase-deficient setting. Similarly, depending on the tumor model, hemocytes that attach to tumors activate different sets of immune effectors – antimicrobial peptides dominate the response against the tumor alone, while caspase inhibition induces a shift toward members of proteolytic cascades. Finally, we provide evidence for transcript transfer between hemocytes and possibly other tissues. Taken together, our data support the usefulness ofDrosophilato study the response against tumors at the organismic level.
The Janelia Atalanta plasmids provide a simple and efficient CRISPR/Cas9-mediated homology directed repair platform forDrosophila
Authors: Stern David L. , Kim Elizabeth , Behrman Emily L. 
Published: June 2023

AbstractHomology-directed repair (HDR) is a powerful tool for modifying genomes in precise ways to address many biological questions. Use of Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)-Cas9 induced targeted DNA double-strand breakage has substantially simplified use of homology-directed repair to introduce specific perturbations inDrosophila, but existing platforms for CRISPR-Cas9-mediated HDR inDrosophilainvolve multiple cloning steps and have low efficiency. To simplify cloning of HDR plasmids, we designed a new plasmid platform, the Janelia Atalanta (pJAT) series, that exploits recent advances in dsDNA synthesis to facilitate Gateway cloning of gRNA sequences and homology arms in one step. Surprisingly, the pJAT plasmids yielded considerably higher HDR efficiency (approximately 25%) than we have observed with other approaches. pJAT plasmids work in multipleDrosophilaspecies and exhibited such high efficiency that previously impossible experiments inDrosophila, such as driving targeted chromosomal inversions, were made possible. We provide pJAT plasmids for a range of commonly performed experiments including targeted insertional mutagenesis, insertion of phiC31-mediated attP landing sites, generation of strains carrying a germ-line source of Cas9, and induction of chromosomal rearrangements. We also provide “empty” pJAT plasmids with multiple cloning sites to simplify construction of plasmids with new functionality. The pJAT platform is generic and may facilitate improved efficiency CRISPR-Cas9 HDR in a wide range of model and non-model organisms.
Confined environment facilitates stacked conformations in Holliday Junction
Authors: Agarwal Priya , Kabir Sahil Hasan , Pal Nibedita 
Published: June 2023

ABSTRACTHolliday Junction (HJ) is an important intermediate for homologous recombination and is involved in DNA break repair. It is a highly dynamic structure and transitions between two stacked isomers through an intermediate open conformer. In a constrained cellular environment, HJ is expected to behave differently than in vitro. This can affect target recognition by junction-binding proteins and their subsequent functions. However, the studies on the effect of the confined environment on HJ is extremely scanty. In this work, by employing fluorescence-based techniques we investigated the effect of confinement on HJ conformation using reverse micelle encapsulation as a model for confined space. We observed that inside reverse micelle, HJ prefers to adopt stacked conformation. Most strikingly, even at lower divalent cation concentrations, the preference for stacked conformation is prevalent over an open conformation. Our finding suggests that such confinement-induced changes in the conformer population might affect the interaction and activity of the HJ-recognizing proteins in the cellular environment.
Unveiling consistency in flexibility: the role of reward and cognitive control in moral decisions
Authors: Xu Xinyi Julia , Yang Guochun , Huang Jiamin , Wang Ruien , Wu Haiyan 
Published: June 2023

ABSTRACTMoral decisions are multifaceted with two essential aspects, flexibility and consistency. However, the interaction between these two and the underlying mechanisms is rarely studied. Here, we combined mouse-tracking and functional magnetic resonance imaging (fMRI) together in a value-based moral decision task, which allows us to quantify accumulative history responses as self-consistency. Using a multi-attribute time-dependent drift-diffusion model (tDDM), we disentangled the role of consistency and self-interest, highlighting the dominant role of cognitive-control-related regions. The drift rate of self-consistency was directly associated with the brain activity responsible for cognitive control, while the relationship between the reward and the activity of the related brain regions was mediated by the mouse-tracking index area under the curve(AUC). Dorsolateral prefrontal cortex was revealed as a hub connecting prACC and ventral striatum, whose functional connectivity was correlated with consistency drift rate and reward drift rate respectively. Furthermore, decision flexibility was quantified by choice entropy, which links to mouse tracking indices and the activity of cognitive -control related regions. Together, our study uncovers the interplay between self-consistency and reward in behavior, and highlights the key role of cognitive control in modulating these two attributes, thereby deepening our understanding of consistency and flexibility in moral decisions.
Proteasome-dependent degradation of histone H1 subtypes is mediated by its C-terminal domain
Authors: García-Gomis D , López J , Calderón A , Andrés M , Ponte I , Roque A 
Published: June 2023

AbstractHistone H1 is involved in chromatin compaction and dynamics. In human cells, the H1 complement is formed by different amounts of somatic H1 subtypes, H1.0-H1.5 and H1X. The amount of each variant depends on the cell type, the cell cycle phase, and the time of development and can be altered in disease. However, the mechanisms regulating H1 protein levels have not been described. We have analyzed the contribution of the proteasome to the degradation of H1 subtypes in human cells using two different inhibitors: MG132 and bortezomib. H1 subtypes accumulate upon treatment with both drugs, indicating that the proteasome is involved in the regulation of H1 protein levels.Proteasome inhibition caused a global increase in cytoplasmatic H1, with slight changes in the composition of H1 bound to chromatin and chromatin accessibility and no alterations in the nucleosome repeat length. The analysis of the proteasome degradation pathway showed that H1 degradation is ubiquitin-independent, whereas the whole protein and its C-terminal domain can be degraded directly by the 20S proteasome. Our study shows that histone H1 protein levels are under tight regulation preventing its accumulation in the nucleus. We revealed a new regulatory mechanism for histone H1 degradation, where the C-terminal disordered domain is responsible for its targeting and degradation by the 20S proteasome.StatementHistone H1 subtypes are a family of proteins involved in the regulation of chromatin structure. This work describes the degradation mechanism controlling the levels of histone H1 subtypes and the region within these proteins involved in the initial recognition. This regulatory mechanism protects the cell nucleus from the damaging effects of its accumulation.
Self-assembly of Grb2 meshworks revealed by Grb2-Gab1497-528complex structure
Authors: Breithaupt Constanze , Gruber Tobias , Mandel Katharina , Lewitzky Marc , Meister Annette , Jochen Balbach , Feller Stephan M. , Stubbs Milton T. 
Published: June 2023

AbstractThe ubiquitously expressed adaptor protein Growth factor receptor bound protein 2 (Grb2) plays an essential role in signal transduction by binding to activated receptor tyrosine kinases through its SH2 domain and to downstream effectors via its N- and C-terminal SH3 domains (nSH3, cSH3). Here we present the first structure of ligand-bound full length Grb2. The crystal structure of Grb2 in complex with a bidentate nSH3-cSH3-binding peptide, derived from the multi-site docking protein Grb2- associated binder-1 (Gab1), provides molecular insight into effector recognition by Grb2 and reveals the assembly of a two-dimensional meshwork, consisting of multimeric filament-like Grb2 chains linked to each other by the bivalent bound Gab1497-528peptide. Dominant contacts between Grb2 molecules in the multimer are provided by an intermolecular SH2/cSH3 domain interface that is also present in the closed dimer of ligand-free Grb2. We further show that Grb2 is able to self-assemble to form phase-separated condensates in solution. The Grb2 SH2 domain phosphotyrosine binding site is freely accessible in the multimeric assembly, and phase separation is fostered by addition of Gab1497- 528, as expected from the crystal structure. Multimeric assembly is also observed using a Grb2 SH2- cSH3 didomain construct, and suppressed using a Grb2 Tyr60Glu mutant, a mimic of thein vivophosphorylated Tyr160 central to the SH2/cSH3 interface, demonstrating that an intact SH2/cSH3 interface is needed for Grb2 assembly in solution.