bluuebunny/crossref_metadata_2025 huggingface dataset:
Fossil calibrations for molecular analyses and divergence time estimation for true crabs (Decapoda: Brachyura)
Authors: Luque Javier , Bracken-Grissom Heather D. , Ortega-Hernández Javier , Wolfe Joanna M.
Published: April 2023

True crabs, or Brachyura, comprise over 7,600 known species and are among the most ecologically dominant, economically significant, and popularly recognized group of extant crustaceans. There are over 3,000 fossil brachyuran species known from mid and upper Jurassic, Cretaceous, and Cenozoic deposits across the globe, many of them preserved in exquisite detail, but the origins and early evolution of true crabs remain unresolved. This uncertainty hinders the identification of the stratigraphically earliest occurrence of major brachyuran groups in the fossil record, obscuring our understanding of their phylogenetic relationships and thus the ability to estimate divergence times to answer large scale macroevolutionary questions. Here, we present 36 vetted fossil node calibration points for molecular phylogenetic analysis of crabs (one Anomura and 35 Brachyura) and reassess the earliest occurrences of several key clades based on recent fossil discoveries or re-examination of previous studies. For each calibrated node, we provide the minimum and tip maximum ages for the stratigraphically oldest fossil that can be reliably assigned to the group. Disentangling the anatomical disparity of fossil forms and their phylogenetic relationships is crucial to recognize the earliest branching members among brachyuran groups. This represents a critical first step understanding the evolution of carcinization and decarcinization in true crabs, the appearance of key adaptations, and the transition from sea to land and freshwater. The identification of reliable fossils for deep time calibrations, both as tips and nodes, is pivotal to ensure not only precise but more accurate divergence time estimations when reconstructing the crab tree of life.

PLAIN LANGUAGE SUMMARY

We present 36 vetted fossil calibration points for molecular phylogenetic analysis of crabs (one Anomura and 35 Brachyura) and reassess the earliest occurrences of several key groups based on recent fossil discoveries or re-examination of previous studies, together with discussions for each taxon. We also provide some general observations and recommendations on fossil age selection and stratigraphic considerations. The identification of reliable fossils for deep time calibrations, both as tips and nodes, is pivotal to ensure not only precise but more accurate divergence time estimations when reconstructing phylogenetic trees.
Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples
Authors: Chen Qingwang , Guo Xiaorou , Wang Haiyan , Sun Shanyue , Jiang He , Zhang Peipei , Shang Erfei , Zhang Ruolan , Cao Zehui , Niu Quanne , Zhang Chao , Liu Yaqing , Zheng Yuanting , Yu Ying , Hou Wanwan , Shi Leming
Published: April 2023

RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the viability of employing PFB or SFB samples as substitute RNA sources in transcriptomic analysis and performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples in terms of protein-coding gene expression patterns, differential expression gene profiling, and immunological characterizations, suggesting that PFB can be a viable alternative for transcriptomic analysis. This contributes to the optimization of blood sample utilization and the advancement of precision medicine research.
A benchmark study on current GWAS models in admixed populations
Authors: Yang Zikun , Huaman Basilio Cieza , Reyes-Dumeyer Dolly , Montesinos Rosa , Soto-Añari Marcio , Custodio Nilton , Tosto Giuseppe
Published: April 2023

Objective

The performances of popular Genome-wide association study (GWAS) models haven’t been examined yet in a consistent manner under the scenario of genetic admixture, which introduces several challenging aspects such as heterogeneity of minor allele frequency (MAF), a wide spectrum of case-control ratio, and varying effect sizes etc.

Methods

We generated a cohort of synthetic individuals (N=19,234) that simulates 1) a large sample size; 2) two-way admixture [Native American-European ancestry] and 3) a binary phenotype. We then examined the inflation factors produced by three popular GWAS tools: GMMAT, SAIGE, and Tractor. We also computed power calculations under different MAFs, case-control ratios, and varying ancestry percentages. Then, we employed a cohort of Peruvians (N=249) to further examine the performances of the testing models on 1) real genetic data and 2) small sample sizes. Finally, we validated these findings using an independent Peruvian cohort (N=109) included in 1000 Genome project (1000G).

Result

In the synthetic cohort, SAIGE performed better than GMMAT and Tractor in terms of type-I error rate, especially under severe unbalanced case-control ratio. On the contrary, power analysis identified Tractor as the best method to pinpoint ancestry-specific causal variants, but showed decreased power when no adequate heterogeneity of the true effect sizes was simulated between ancestries. The real Peruvian data showed that Tractor is severely affected by small sample sizes, and produced severely inflated statistics, which we replicated in the 1000G Peruvian cohort.

Discussion

The current study illustrates the limitations of available GWAS tools under different scenarios of genetic admixture. We urge caution when interpreting results under complex population scenarios.
Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs
Authors: Brümmer Anneke , Bergmann Sven
Published: April 2023

Expression quantitative trait loci (eQTL) studies typically consider exon expression of genes and discard intronic RNA sequencing reads despite their information on RNA metabolism. Here, we quantified genetic effects on exon and intron levels of genes and their ratio in lymphoblastoid cell lines, revealing thousands of cis-QTLs of each type. Genetic effects were often shared between cis-QTL types, but 6084 (41%) were not detectable at exon levels. We show that exon levels preferentially capture genetic effects on transcriptional regulation, while exon-intron-ratios better detect those on co- and post-transcriptional processes. Considering all cis-QTL types substantially increased the number of colocalizing GWAS variants (by 61%). It further allowed dissecting the potential gene regulatory processes underlying GWAS associations, suggesting comparable contributions by transcriptional (48%) and co- and post-transcriptional regulation (42%) to complex traits. Overall, integrating intronic RNA sequencing reads in eQTL studies expands our understanding of genetic effects on gene regulatory processes.
5-hydroxymethylcytosine profiling of cell-free DNA identifies bivalent genes that are prognostic of survival in high-risk neuroblastoma
Authors: Chennakesavalu Mohansrinivas , Moore Kelley , Chaves Gepoliano , Veeravalli Sahil , TerHaar Rachel , Wu Tong , Lyu Ruitu , Chlenski Alexandre , He Chuan , Piunti Andrea , Applebaum Mark A.
Published: April 2023

Neuroblastoma is the most common extra-cranial solid tumor in childhood and epigenetic dysregulation is a key driver of this embryonal disease. In cell-free DNA from neuroblastoma patients with high-risk disease, we found increased 5-hydroxymethylcytosine (5-hmC) deposition on Polycomb Repressive Complex 2 (PRC2) target genes, a finding previously described in the context of bivalent genes. As bivalent genes, defined as genes bearing both activating (H3K4me3) and repressive (H3K27me3) chromatin modifications, have been shown to play an important role in development and cancer, we investigated the potential role of bivalent genes in maintaining a de-differentiated state in neuroblastoma and their potential use as a biomarker. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogenous neuroblastoma cell lines. Through gene set variance analysis, we developed a clinically implementable bivalent signature. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in high-risk neuroblastoma patients. Thus, low expression of bivalent genes is a biomarker of ultra-high-risk disease and may represent a therapeutic opportunity in neuroblastoma.
Identification of disease mechanisms and novel disease genes using clinical concept embeddings learned from massive amounts of biomedical data
Authors: Bugrim Andrej
Published: April 2023

Motivation

Knowledge of relationship and similarity among human diseases can be leveraged in many biomedical applications such as drug repositioning, biomarker discovery, differential diagnostics, and understanding of disease mechanisms. Recently developedcui2vecresource provides embeddings of approximately 109 thousand biomedical terms and allows computing novel measures of disease similarity, directly related to patterns in real-world data. We investigate whether disease embeddings fromcui2veccan be utilized to identify functional relations among diseases, to uncover their molecular mechanisms, and to generate hypotheses about novel gene-disease associations and potential drug targets.

Methods and results

We focus on a subset of 3,568cui2vecterms corresponding to human diseases annotated in DisGeNET database. Disease-disease distance matrix is computed for this set of diseases based on their embedding vectors. Clustering of this matrix reveals a well-defined structure with good correspondence between disease clusters and the top MeSH disease categories. Using pulmonary embolism as an example we show how disease clustering is related to known mechanistic relations among diseases. Next, we combine disease embeddings with annotated gene-disease associations from DisGeNET to generate joint gene-disease co-embeddings. From these we identify molecular pathways most characteristic for each disease group and show that they are highly relevant to known disease physiology. Finally, we leverage disease similarity to generate and rank hypothesis for gene-disease associations and demonstrate that this method generates highly accurate results and can suggest relevant drug targets.

Conclusions

We show that combination of disease embeddings learned from massive amounts of biomedical records with curated data on gene-disease associations can reliably reveal groups of functionally related diseases and their molecular mechanisms and predict novel gene-disease associations. Importantly, our analysis does not require knowledge of associated genes for every disease to identify patterns in the embedding space, therefore it can be used to suggest mechanisms for conditions that have not been functionally understood. In this respect our analysis can be applied to identify potential markers and drug targets for poorly characterized orphan and rare diseases. It can also reveal unexpected novel connections among diseases and between diseases and molecular pathways.
Inference of population genetics parameters using discriminator neural networks: an adversarial Monte Carlo approach
Authors: Gower Graham , Picazo Pablo Iáñez , Lindgren Finn , Racimo Fernando
Published: April 2023

Accurately estimating biological variables of interest, such as parameters of demographic models, is a key problem in evolutionary genetics. Likelihood-based and likelihood-free methods both typically use only limited genetic information, such as carefully chosen summary statistics. Deep convolutional neural networks (CNNs) trained on genotype matrices can incorporate a great deal more information, and have been shown to have high accuracy for inferring parameters such as recombination rates and population sizes, when evaluated using simulations. However these methods are typically framed as regression or classification problems, and it is not straightforward to ensure that the training data adequately model the empirical data on which they are subsequently applied. It has recently been shown that generative adversarial networks (GANs) can be used to iteratively tune parameter values until simulations match a given target dataset. Here, we investigate an adversarial architecture for discriminator-based inference, which iteratively improves the sampling distribution for training the discriminator CNN via Monte Carlo density estimation. We show that this method produces parameter estimates with excellent agreement to simulated data. We developeddinf, a modular Python package for discriminator-based inference that incorporates this method, and is available fromhttps://github.com/RacimoLab/dinf/.
BRCA2-HSF2BP Oligomeric Ring Disassembly by BRME1 Promotes Homologous Recombination
Authors: Ghouil Rania , Miron Simona , Sato Koichi , Ristic Dejan , van Rossum-Fikkert Sari E. , Legrand Pierre , Ouldali Malika , Winter Jean-Marie , Ropars Virginie , David Gabriel , Arteni Ana-Andreea , Wyman Claire , Knipscheer Puck , Kanaar Roland , Zelensky Alex N. , Zinn-Justin Sophie
Published: April 2023

In meiotic homologous recombination (HR), BRCA2 facilitates loading of the recombinases RAD51 and DMC1 at the sites of double-strand breaks. The HSF2BP-BRME1 complex interacts with BRCA2 to support its function in meiotic HR. In somatic cancer cells ectopically producing HSF2BP, DNA damage can trigger HSF2BP-dependent degradation of BRCA2, which prevents HR. Here we show that, upon binding to BRCA2, HSF2BP assembles into a large ring-shaped 24-mer consisting of three interlocked octameric rings. Addition of BRME1 leads to dissociation of this ring structure, and cancels the disruptive effect of HSF2BP on cancer cell resistance to DNA damage. It also prevents BRCA2 degradation during inter-strand DNA crosslink repair inXenopusegg extracts. We propose that the control of HSF2BP-BRCA2 oligomerization by BRME1 ensures timely assembly of the ring complex that concentrates BRCA2 and controls its turnover, thus promoting meiotic HR.
Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae
Authors: Benito Joseph B. , Porter Megan L. , Niemiller Matthew L.
Published: April 2023

Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length ofrrnLand intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwellingCrangonyx forbesiexhibited a unique gene order, a longnad5locus, longerrrnLandrrnSloci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.
A high-quality pseudo-phased genome forMelaleuca quinquenerviashows allelic diversity of NLR-type resistance genes
Authors: Chen Stephanie H , Martino Alyssa M , Luo Zhenyan , Schwessinger Benjamin , Jones Ashley , Tolessa Tamene , Bragg Jason G , Tobias Peri A , Edwards Richard J
Published: April 2023

Background

The coastal wetland tree speciesMelaleuca quinquenervia(Cav.) S.T.Blake (Myrtaceae), commonly named the broad-leaved paperbark, is a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. The species has been widely grown as an ornamental, becoming invasive in areas such as Florida in the United States. Long-lived trees must respond to a wide range pests and pathogens throughout their lifespan, and immune receptors encoded by the nucleotide- binding domain and leucine-rich repeat containing (NLR) gene family play a key role in plant stress responses. Expansion of this gene family is driven largely by tandem duplication, resulting in a clustering arrangement on chromosomes. Due to this clustering and their highly repetitive domain structure, comprehensive annotation of NLR encoding genes within genomes has been difficult. Additionally, as many genomes are still presented in their haploid, collapsed state, the full allelic diversity of the NLR gene family has not been widely published for outcrossing tree species.

Results

We assembled a chromosome-level pseudo-phased genome forM.quinquenerviaand describe the full allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, differences in clusters and in the types and numbers of novel integrated domains.

Conclusions

We anticipate that the high quality of the genome forM. quinquenerviawill provide a new framework for functional and evolutionary studies into this important tree species. Our results indicate a likely role for maintenance of NLR allelic diversity to enable response to environmental stress, and we suggest that this allelic diversity may be even more important for long-lived plants.
High-fat diet in early life triggers both reversible and persistent epigenetic changes in the medaka fish (Oryzias latipes)
Authors: Inoue Yusuke , Suzuki Yuta , Kunishima Yoshimi , Washio Terumi , Morishita Shinichi , Takeda Hiroyuki
Published: April 2023

The nutritional status during early life can have enduring effects on an animal’s metabolism, although the mechanisms underlying these long-term effects are still unclear. Epigenetic modifications are considered a prime candidate mechanism for encoding early-life nutritional memories during this critical developmental period. However, the extent to which these epigenetic changes occur and persist over time remains uncertain, in part due to challenges associated with directly stimulating the fetus with specific nutrients in viviparous mammalian systems. In this study, we used medaka as an oviparous vertebrate model to establish an early-life high-fat diet (HFD) model. Larvae were fed with HFD from the hatching stages (one week after fertilization) for six weeks, followed by normal chow (NC) for eight weeks until the adult stage. We examined the changes in the transcriptomic and epigenetic state of the liver over this period. We found that HFD induces fatty liver phenotypes, accompanied by drastic changes in the hepatic transcriptome, chromatin accessibility, and histone modifications, especially in metabolic genes. These changes were largely reversed after the long-term NC, demonstrating the high plasticity of the epigenetic state in hepatocytes. However, we found a certain number of genomic loci showing non-reversible epigenetic changes, especially around genes related to cell signaling, liver fibrosis, and hepatocellular carcinoma, implying persistent changes in the cellular state of the liver triggered by early-life HFD feeding. Our data provide novel insights into the epigenetic mechanism of nutritional programming and a comprehensive atlas of the long-term epigenetic state in an early-life HFD model of non-mammalian vertebrates.
Holocene climate change promoted allopatric divergence and disjunct geographic distribution in a bee orchid species
Authors: Gibert Anais , Buscail Roselyne , Baguette Michel , Fraisse Christelle , Roux Camille , Schatz Bertrand , Bertrand Joris A. M.
Published: April 2023

Aim: Species with disjunct geographic distributions provide natural opportunities to investigate incipient or recent allopatric divergence. The combination of both genetic and ecological data may be fruitful to decipher the causes of such pattern: i) actual vicariance, ii) successful colonization from one source range to a new range (dispersal, biological introduction) or iii) parallel convergent evolution. Location: Southern France and Northern Spain. Taxon: The bee orchid Ophrys aveyronensis (and its two recognized subspecies O. a. subsp. aveyronensis and O. a. subsp. vitorica) displays a disjunct geographic distribution with two subranges separated by 600 km on both sides of the Pyrenees Mountains. Methods: Through a combination of population genomics and Ecological Niche Modelling (ENM), we investigated the causes of this intriguing biogeographic pattern. Results: The population genomic data demonstrate that all the studied populations exhibit similar patterns of genetic diversity and dramatic decrease in effective size compared to the ancestral population. Significant genetic differentiation and reciprocal monophyly exist between populations of the two subranges of O. aveyronensis, despite a very recent divergence time as young as ca. 1500 generations ago. Moreover, (paleo-)ecological Niche Modelling analyses support that the disjunct geographic distribution of the O. aveyronensis is consistent with a range split of a broad ancestral range, contraction and distinct longitudinal and latitudinal shifts in response to climate warming during the Holocene. Main Conclusion: The congruence of the results obtained from both population genomics and ENM approaches documents how very recent continental allopatric divergence initiated speciation in this system. Ophrys aveyronensis provides a promising opportunity to study the onset of reproductive isolation and parallel evolution following an initial stage of geographic separation in a group with high diversification rate.
Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution
Authors: Zabaikina Iryna , Bokes Pavol , Singh Abhyudai
Published: April 2023

We consider a protein that negatively regulates the rate with which a cell grows. Since less growth means less protein dilution, this mechanism forms a positive feedback loop on the protein concentration. We couple the feedback model with a simple description of the cell cycle, in which a division event is triggered when the cell volume reaches a critical threshold. Following the division we either track only one of the daughter cells (single cell framework) or both cells (population frame-work). For both frameworks, we find an exact time-independent distribution of protein concentration and cell volume. We explore the consequences of dilution feedback on ergodicity, population growth rate, and the bias of the population distribution towards faster growing cells with less protein.
Essential roles of the ANKRD31-REC114 interaction in meiotic recombination and mouse spermatogenesis
Authors: Xu Jiaqi , Li Tao , Kim Soonjoung , Boekhout Michiel , Keeney Scott
Published: April 2023

Meiotic DNA double-strand breaks (DSBs) initiate homologous recombination and are crucial for ensuring proper chromosome segregation. In mice, ANKRD31 recently emerged as a regulator of DSB timing, number, and location, with a particularly important role in targeting DSBs to the pseudoautosomal regions (PARs) of sex chromosomes. ANKRD31 interacts with multiple proteins, including the conserved and essential DSB-promoting factor REC114, so it was hypothesized to be a modular scaffold that “anchors” other proteins together and to meiotic chromosomes. To determine if and why the REC114 interaction is important for ANKRD31 function, we generated mice withAnkrd31mutations that either reduced (missense mutation) or eliminated (C-terminal truncation) the ANKRD31– REC114 interaction without diminishing contacts with other known partners. A complete lack of the ANKRD31–REC114 interaction mimicked anAnkrd31null, with delayed DSB formation and recombination, defects in DSB repair, and altered DSB locations including failure to target DSBs to the PARs. In contrast, when the ANKRD31– REC114 interaction was substantially but not completely disrupted, spermatocytes again showed delayed DSB formation globally, but recombination and repair were hardly affected and DSB locations were similar to control mice. The missenseAnkrd31allele showed a dosage effect, wherein combining it with the null or C-terminal truncation allele resulted in intermediate phenotypes for DSB formation, recombination, and DSB locations. Our results show that ANKRD31 function is critically dependent on its interaction with REC114, and that defects in ANKRD31 activity correlate with the severity of the disruption of the interaction.

Significance

Homologous recombination initiated by double-strand breaks (DSBs) during meiosis is a nearly universal feature of eukaryotic lifecycles, but is also dangerous because DSBs are potentially toxic or mutagenic. The vertebrate-specific protein ANKRD31 is an important regulator of DSB formation, proposed to be a scaffold protein that coordinates the activities of multiple DSB-promoting factors, including the widely conserved REC114. We test this hypothesis here through generation of targetedAnkrd31mutations that specifically attenuate or eliminate the ANKRD31-REC114 interaction. Analysis of this allelic series demonstrates that the ANKRD31-REC114 interaction is essential for all ANKRD31 activities in vivo, providing insight into how ANKRD31 controls DSB locations, timing, and number.
The missing fraction problem as an episodes of selection problem
Authors: Mittell Elizabeth A. , Morrissey Michael B.
Published: April 2023

In evolutionary quantitative genetics, the missing fraction problem refers to the case where phenotypes seen later in life are biased because a non-random subset of those phenotypes are missing from the population due to prior viability selection on correlated traits. As any such missing fraction will bias our estimates of selection, and therefore, responses to selection, it is one potential explanation for the paradox of stasis seen in wild populations. The two components required for the missing fraction problem to arise are: (1) viability selection; and (2) correlation between later-life traits and those important for early-life survival. Although it is plausible that these conditions are widespread in wild populations, this problem has received very little attention since it was first discussed (Grafen 1988; Hadfield 2008). It is impossible to know what phenotypes would have been expressed later in life by individuals who died during an earlier episode of viability selection, which has probably put researchers off. Here we show that we can break the problem down into episodes of selection and recover either (a) true estimates of phenotypic selection for later-life traits, or (b) adjusted estimates of the response to selection, depending on the data available. Implementation of complex statistics should uncover how prevalent the problem may be across many existing datasets (the latter approach). Whereas overall, we hope that viewing the missing fraction problem as an episodes of selection problem increases motivation, and provides justification, for a shift in focus to directly studying early-life viability selection.

“…what a correlation with [lifetime reproductive success] or its components tells you depends on the causes of the natural variation in the character. It will not always be easy to discover those causes.”

— Grafen (1988)

“It is surprising that the problem of missing data has received so little attention given that viability selection is central to evolutionary biology.”

— Hadfield (2008)
Characterization of the smallArabidopsis thalianaGTPase and ADP-ribosylation factor-like 2 protein TITAN 5
Authors: Mohr Inga , Mirzaiebadizi Amin , Sanyal Sibaji K. , Chuenban Pichaporn , Ahmadian Mohammad R. , Ivanov Rumen , Bauer Petra
Published: April 2023

Small GTPases function by conformational switching ability between GDP- and GTP-bound states in rapid cell signaling events. The ADP-ribosylation factor (ARF) family is involved in vesicle trafficking. Though evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. Here, we characterized biochemical properties and cellular localization of the essential small ARF-like GTPase TITAN 5/HALLIMASCH/ARL2/ARLC1 (hereafter termed TTN5) fromArabidopsis thaliana. Two TTN5 variants were included in the study with point mutations at conserved residues, suspected to be functional for nucleotide exchange and GTP hydrolysis, TTN5T30Nand TTN5Q70L. We found that TTN5 had a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanism. TTN5 acted as a non-classical small GTPase with a remarkably low GTP hydrolysis activity, suggesting it is likely present in GTP-loaded active form in the cell. We analyzed signals from yellow fluorescent protein (YFP)-tagged TTN5 and fromin situimmunolocalization of hemagglutine-tagged HA3-TTN5 in Arabidopsis seedlings and in a transient expression system. Together with colocalization using endomembrane markers and pharmacological treatments the microscopic analysis suggests that TTN5 can be present at the plasma membrane and dynamically associated with membranes of vesicles, Golgi stacks and multivesicular bodies. While the TTN5Q70Lvariant showed similar GTPase activities and localization behavior as wild-type TTN5, the TTN5T30Nmutant differed in some aspects.

Hence, the unusual capacity of rapid nucleotide exchange activity of TTN5 is linked with cell membrane dynamics, likely associated with vesicle transport pathways in the endomembrane system.

Highlights

The small ARF-like GTPase TTN5 has a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanism

Biochemical data classified TTN5 as a non-classical small GTPase, likely present in GTP-loaded active form in the cell

YFP-TTN5 is dynamically associated with vesicle transport and different processes of the endomembrane system, requiring the active form of TTN5
Small ARF-like 2 GTPase TITAN 5 is linked with the dynamic regulation of IRON-REGULATED TRANSPORTER 1
Authors: Mohr Inga , Eutebach Monique , Knopf Marie C. , Schommen Naima , Gratz Regina , Angrand Kalina , Genders Lara , Brumbarova Tzvetina , Bauer Petra , Ivanov Rumen
Published: April 2023

Iron acquisition is crucial for plants. The abundance of IRON-REGULATED TRANSPORTER 1 (IRT1) at the plasma membrane is controlled through endomembrane trafficking. Vesicular trafficking requires small ARF-like GTPases, one of them is TITAN 5 (TTN5). Its physiological functions during the life cycle and cellular targets remain unknown. Little is known how the vesicular trafficking mechanism affects IRT1 localization.

We show that TTN5 interacts with the large cytoplasmic variable region and protein-regulatory platform of IRT1.ttn5-1+/-plants have a reduced activity of root iron reductase, needed for iron uptake via IRT1. Fluorescent fusion proteins of TTN5 and IRT1 colocalize at the plasma membrane and in endosomes/multivesicular bodies, where IRT1 sorting and cycling between the plasma membrane and the vacuole are coordinated. Colocalization at the plasma membrane depends partly on the interaction ability of TTN5. TTN5 can also interact with peripheral membrane proteins that are components of the IRT1 regulation machinery, like the trafficking factor SNX1, the C2 domain protein EHB1 and the SEC14-GOLD protein PATL2. Hence, this work links iron acquisition and vesicular trafficking involving a small GTPase of the ARF family. This opens up the possibility to study the involvement of TTN5 in nutritional cell biology in the endomembrane system.

Highlights

TTN5 interacts with the large intracellular loop and variable region of IRON-REGULATED TRANSPORTER 1 (IRT1)

TTN5 has a positive effect on root iron (Fe) reductase activity.

TTN5 and IRT1 colocalize at the plasma membrane and in the endomembrane system related to vesicle transport

TTN5 can interact with peripheral membrane proteins of the IRT1 interactome, EHB1, PATL2 and SNX1 suggesting a coordinating role in IRT1 regulation

One-sentence summary

TTN5, a small ARF-like GTPase, is connected to the dynamic regulation of IRON-REGULATED TRANSPORTER 1 (IRT1) in the vesicular trafficking system through direct protein interaction and colocalization, linking with various peripheral membrane proteins of the IRT1 interactome and iron reductase activity.
Yield and agronomic performance of sweet corn in response to inoculation withAzospirillumsp. in arid land conditions
Authors: Contreras-Liza Sergio , Villadeza Christofer , Grados Pedro Rodriguez , Palomares Edison Goethe , Arbizu Carlos Irwin
Published: April 2023

Nitrogen is the most common limiting factor for crop productivity and most maize cultivars require fertilizing. Here we report the possibility of partially replacing the nitrogenous fertilizer in sweet corn inoculated with a native strain of Azospirillum in arid land on the coast of Peru. We examined an agronomic experiment in a crop field of arid soils under drip irrigation in Huacho (Peru) using a commercial variety of sweet corn. The treatments were two levels of nitrogen (90 and 180 kg N ha-1), one or two applications to the foliage of a native strain ofAzospirillumsp. (1 × 108CFU/mL) and a control treatment only with nitrogen fertilizer. Eleven agronomic variables related to productive aspects were evaluated, performing statistical analysis and the comparison of treatment means. The inoculation withAzospirillumsp. did not significantly (p> 0.05) affect the total weight of ears, the number of ears per plant and the number of male flowers, but it significantly (p< 0.05) influenced the grain yield per hectare, survival of plants, the weight of grain per plant, diameter and length of the cob. In some productive characteristics of sweet corn cv“Pardo”, a significant effect was found by inoculation withAzospirillumsp., surpassing in grain yield the control only with nitrogen fertilization, suggesting that it is possible to complement the application of nitrogen to the soil through the inoculation of this strain, replacing up to 50% of the levels of fertilizer application since the B/C ratio increased.
Workflows for detecting fungicide resistance in net form and spot form net blotch pathogens
Authors: Knight N. L. , Adhikari K. C. , Dodhia K. , Mair W. J. , Lopez-Ruiz F. J.
Published: April 2023

Fungicide resistance inPyrenophora teresf.maculataandP. teresf.tereshas become an important disease management issue. Control of the associated barley foliar diseases, spot form and net form net blotch, respectively, relies on three major groups of fungicides, demethylation inhibitors (DMI), succinate dehydrogenase inhibitors (SDHI) and quinone outside inhibitors (QoI). However, resistance has been reported for the DMI and SDHI fungicides in Australia. To enhance detection of different resistance levels, phenotyping and genotyping workflows were designed. The phenotyping workflow generated cultures directly from lesions and compared growth on discriminatory doses of tebuconazole (DMI) and fluxapyroxad (SDHI). Genotyping real-time PCR assays were based on alleles associated with sensitivity or resistance to the DMI and SDHI fungicides. These workflows were applied to a net blotch collection from 2019 consisting predominantly ofP. teresf.teresfrom South Australia andP. teresf.maculatafrom Western Australia. For South Australia theCyp51AL489-3 andSdhC-R134 alleles, associated with resistance to tebuconazole and fluxapyroxad, respectively, were the most prevalent. These alleles were frequently found in single isolates with dual resistance. This study also reports the first detection of a 134 base pair insertion located at position −66 (PtTi-6) in theCyp51Apromoter ofP. teresf.maculatafrom South Australia. For Western Australia, the PtTi-1 insertion was the most common allele associated with resistance to tebuconazole. These workflows will be valuable for screeningP. terespopulations for fungicide resistance, and informing appropriate management strategies.
Listening with generative models
Authors: Cusimano Maddie , Hewitt Luke B. , McDermott Josh H.
Published: April 2023

Perception has long been envisioned to use an internal model of the world to explain the causes of sensory signals. However, such accounts have historically not been testable, typically requiring intractable search through the space of possible explanations. Using auditory scenes as a case study, we leveraged contemporary computational tools to infer explanations of sounds in a candidate internal model of the auditory world (ecologically inspired audio synthesizers). Model inferences accounted for many classic illusions. Unlike traditional accounts of auditory illusions, the model is applicable to any sound, and exhibited human-like perceptual organization for real world sound mixtures. The combination of stimulus-computability and interpretable model structure enabled ‘rich falsification’, revealing additional assumptions about sound generation needed to account for perception. The results show how generative models can account for the perception of both classic illusions and everyday sensory signals, and provide the basis on which to build theories of perception.
Attraction of female house mice to male ultrasonic courtship vocalizations depends on their social experience and estrous stage
Authors: Beck Jakob , Wernisch Bettina , Klaus Teresa , Penn Dustin J. , Zala Sarah M.
Published: April 2023

Male house mice (Mus musculus) produce complex ultrasonic vocalizations (USVs), especially during courtship and mating. Playback experiments suggest that female attraction towards recordings of male USVs depends on their social experience, paternal exposure, and estrous stage. We conducted a playback experiment with wild-derived female house mice(M. musculus musculus)and compared their attraction to male USVs versus the same recording without USVs (background noise). We tested whether female attraction to USVs is influenced by the following factors: (1) social housing (two versus one female per cage); (2) neonatal paternal exposure (rearing females with versus without father); and (3) sexual receptivity (pro-estrous and estrous stages versus non-receptive metestrous and diestrous stages). We found that females showed a significant attraction to male USVs but only if females were housed with another female. Individually housed females showed the opposite response. We found no evidence that pre-weaning exposure to a father influenced females’ preferences, whereas sexual receptivity influenced females’ attraction to male USVs: non-receptive females showed preferences towards male USVs but receptive females did not. Finally, we found that individually housed females were more likely to be in sexually receptive estrous stages than those housed socially, and that attraction to male USVs was most pronounced amongst non-receptive females that were socially housed. Our findings indicate that the attraction of female mice to male USVs depends upon their social experience and estrous stage, though not paternal exposure. They contribute to the growing number of studies showing that social housing and estrous stage influence the behavior of house mice and we show how such unreported variables can contribute to the replication crisis.
Computer Vision Estimation of Stress and Anxiety Using a Gamified Mobile-based Ecological Momentary Assessment and Deep Learning: Research Protocol
Authors: Kargarandehkordi Ali , Washington Peter
Published: April 2023

Stress and anxiety can contribute to the development of major health problems such as heart disease, depression, and obesity. Due to its subjective nature, it is challenging to precisely measure human affect by relying on automated approaches. We therefore propose a personalized prediction framework fine-tuned for each participant in lieu of the traditional “one-size-fits-all” machine learning approach. We aim to collect such individualized data via two distinct procedures: 1) a smartphone-based ecological momentary assessment of stress, and 2) Zoom calls. The data collected from these periodic self-reports will include selfie photographs and ecological momentary assessments of affect. To enhance user engagement during the data collection process, we propose the use of gamification, an emerging trend which involves influencing user behavior and lifestyle by incorporating fun and engaging game elements into non-game contexts (e.g., health-related tasks). In addition to developing a standardized platform to achieve more accurate recognition of stress and anxiety, we plan to conduct a concurrent study in which we will capture videos of our subjects undertaking the Stroop Color Word and Amygdala Test and analyze the footage to identify additional significant characteristics that relate to anxiety. This could include features such as head and mouth movements, lip and cheek deformations, eye gaze, and blinking rates. The final results will provide a comparative evaluation of both objective measures of stress. This research project was approved by the University of Hawaii Institutional Review Board.
Clinical, genomic, and neurophysiological correlates of lifetime suicide attempts among individuals with an alcohol use disorder
Authors: Barr Peter B. , Neale Zoe , Chatzinakos Chris , Schulman Jessica , Mullins Niamh , Zhang Jian , Chorlian David B. , Kamarajan Chella , Kinreich Sivan , Pandey Ashwini K. , Pandey Gayathri , de Viteri Stacey Saenz , Acion Laura , Bauer Lance , Bucholz Kathleen K. , Chan Grace , Dick Danielle M. , Edenberg Howard J. , Foroud Tatiana , Goate Alison , Hesselbrock Victor , Johnson Emma C. , Kramer John , Lai Dongbing , Plawecki Martin H. , Salvatore Jessica E. , Wetherill Leah , Agrawal Arpana , Porjesz Bernice , Meyers Jacquelyn L.
Published: April 2023

Research has identified clinical, genomic, and neurophysiological markers associated with suicide attempts (SA) among individuals with psychiatric illness. However, there is limited research among those with an alcohol use disorder (AUD), despite their disproportionately higher rates of SA. We examined lifetime SA in 4,068 individuals with DSM-IV alcohol dependence from the Collaborative Study on the Genetics of Alcoholism (23% lifetime suicide attempt; 53% female; mean age: 38). Within participants with an AUD diagnosis, we explored risk across other clinical conditions, polygenic scores (PGS) for comorbid psychiatric problems, and neurocognitive functioning for lifetime suicide attempt. Participants with an AUD who had attempted suicide had greater rates of trauma exposure, major depressive disorder, post-traumatic stress disorder, and other substance use disorders compared to those who had not attempted suicide. Polygenic scores for suicide attempt, depression, and PTSD were associated with reporting a suicide attempt (ORs = 1.22 – 1.44). Participants who reported a SA also had decreased right hemispheric frontal-parietal theta and decreased interhemispheric temporal-parietal alpha electroencephalogram resting-state coherences relative to those who did not, but differences were small. Overall, individuals with an AUD who report a lifetime suicide attempt appear to experience greater levels of trauma, have more severe comorbidities, and carry polygenic risk for a variety of psychiatric problems. Our results demonstrate the need to further investigate suicide attempts in the presence of substance use disorders.
Deep Learning Utilizing Suboptimal Spirometry Data to Improve Lung Function and Mortality Prediction in the UK Biobank
Authors: Hill Davin , Torop Max , Masoomi Aria , Castaldi Peter J. , Silverman Edwin K. , Bodduluri Sandeep , Bhatt Surya P. , Yun Taedong , McLean Cory Y. , Hormozdiari Farhad , Dy Jennifer , Cho Michael H. , Hobbs Brian D.
Published: April 2023

Background

Spirometry measures lung function by selecting the best of multiple efforts meeting pre-specified quality control (QC), and reporting two key metrics: forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC). We hypothesize that discarded submaximal and QC-failing data meaningfully contribute to the prediction of airflow obstruction and all-cause mortality.

Methods

We evaluated volume-time spirometry data from the UK Biobank. We identified “best” spirometry efforts as those passing QC with the maximum FVC. “Discarded” efforts were either submaximal or failed QC. To create a combined representation of lung function we implemented a contrastive learning approach,Spirogram-basedContrastiveLearningFramework (Spiro-CLF), which utilized all recorded volume-time curves per participant and applied different transformations (e.g. flow-volume, flow-time). In a held-out 20% testing subset we applied the Spiro-CLF representation of a participant’s overall lung function to 1) binary predictions of FEV1/FVC < 0.7 and FEV1Percent Predicted (FEV1PP) < 80%, indicative of airflow obstruction, and 2) Cox regression for all-cause mortality.

Findings

We included 940,705 volume-time curves from 352,684 UK Biobank participants with 2-3 spirometry efforts per individual (66.7% with 3 efforts) and at least one QC-passing spirometry effort. Of all spirometry efforts, 24.1% failed QC and 37.5% were submaximal. Spiro-CLF prediction of FEV1/FVC < 0.7 utilizing discarded spirometry efforts had an Area under the Receiver Operating Characteristics (AUROC) of 0.981 (0.863 for FEV1PP prediction). Incorporating discarded spirometry efforts in all-cause mortality prediction was associated with a concordance index (c-index) of 0.654, which exceeded the c-indices from FEV1(0.590), FVC (0.559), or FEV1/FVC (0.599) from each participant’s single best effort.

Interpretation

A contrastive learning model using raw spirometry curves can accurately predict lung function using submaximal and QC-failing efforts. This model also has superior prediction of all-cause mortality compared to standard lung function measurements.

Funding

MHC is supported by NIH R01HL137927, R01HL135142, HL147148, and HL089856.

BDH is supported by NIH K08HL136928, U01 HL089856, and an Alpha-1 Foundation Research Grant.

DH is supported by NIH 2T32HL007427-41

EKS is supported by NIH R01 HL152728, R01 HL147148, U01 HL089856, R01 HL133135, P01 HL132825, and P01 HL114501.

PJC is supported by NIH R01HL124233 and R01HL147326.

SPB is supported by NIH R01HL151421 and UH3HL155806.

TY, FH, and CYM are employees of Google LLC