bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome sequences ofAegilopsspecies of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement
Authors: Avni Raz , Lux Thomas , Minz-Dub Anna , Millet Eitan , Sela Hanan , Distelfeld Assaf , Deek Jasline , Yu Guotai , Steuernagel Burkhard , Pozniak Curtis , Ens Jennifer , Gundlach Heidrun , Mayer Klaus F. X. , Himmelbach Axel , Stein Nils , Mascher Martin , Spannagl Manuel , Wulff Brande B. H. , Sharon Amir
Published: August 2021

Aegilopsis a close relative of wheat (Triticumspp.), andAegilopsspecies in the section Sitopsis represent a rich reservoir of genetic diversity for improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies ofAe. longissimaandAe. speltoides. Whole-genome comparative analysis, along with the recently sequencedAe. sharonensisgenome, showed that theAe. longissimaandAe. sharonensisgenomes are highly similar and most closely related to the wheat D subgenome. By contrast, theAe. speltoidesgenome is more closely related to the B subgenome. Haplotype block analysis supported the idea thatAe. speltoidesis the closest ancestor of the wheat B subgenome and highlighted variable and similar genomic regions between the threeAegilopsspecies and wheat. Genome-wide analysis of nucleotide-binding site leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential ofAegilopsgenomes for wheat improvement.

Teaser

Genome sequences of Aegilops species provides a key for efficient exploitation of this rich genetic resource in wheat improvement.
The miR-430 locus with extreme promoter density is a transcription body organizer, which facilitates long range regulation in zygotic genome activation
Authors: Hadzhiev Yavor , Wheatley Lucy , Cooper Ledean , Ansaloni Federico , Whalley Celina , Chen Zelin , Gustincich Stefano , Sanges Remo , Burgess Shawn , Beggs Andrew , Müller Ferenc
Published: August 2021

In anamniote embryos the major wave of zygotic genome activation (ZGA) starts during the mid-blastula transition. This major wave of ZGA is facilitated by several mechanisms, including dilution of repressive maternal factors and accumulation of activating transcription factors during the fast cell division cycles preceding the mid-blastula transition. However, a set of genes escape global genome repression and are activated substantially earlier, during what is called, the minor wave of genome activation. While the mechanisms underlying the major wave of genome activation have been studied extensively, the minor wave of genome activation is little understood. In zebrafish the earliest expressed RNA polymerase II (Pol II) transcribed genes are activated in a pair of large transcription bodies depleted of chromatin, abundant in elongating Pol II and nascent RNAs (Hadzhiev et al., 2019; Hilbert et al., 2021). This transcription body includes the miR-430 gene cluster required for maternal mRNA clearance. Here we explored the genomic, chromatin organisation and cis-regulatory mechanisms of the minor wave of genome activation occurring in the transcription body. By long read genome sequencing we identified a remarkable cluster of miR-430 genes with over 300 promoters and spanning 0.6 Mb, which represent the highest promoter density of the genome. We demonstrate that the miR-430 gene cluster is required for the formation of the transcription body and acts as a transcription organiser for minor wave activation of a set of zinc finger genes scattered on the same chromosome arm, which share promoter features with the miR-430 cluster. These promoter features are shared among minor wave genes overall and include the TATA-box and sharp transcription start site profile. Single copy miR-430 promoter transgene reporter experiments indicate the importance of promoter-autonomous mechanisms regulating escape from global repression of the early embryo. These results together suggest that formation of the transcription body in the early embryo is the result of high promoter density coupled to a minor wave-specific core promoter code for transcribing key minor wave ZGA genes, which are required for the overhaul of the transcriptome during early embryonic development.
Blocking cell fusion inhibits age-induced polyploidy and maintains epithelial organization in Drosophila
Authors: Dehn Ari S. , Gogna Navdeep , Nishina Patsy M. , Losick Vicki P.
Published: August 2021

A characteristic of normal aging and age-related diseases is the remodeling of a tissue’s cellular organization through polyploid cell growth. Polyploidy arises from an increase in nuclear ploidy or the number of nuclei per cell. However, it is not known whether age-induced polyploidy is an adaption to stressors or a precursor to degeneration. Here, we find that the adult fruit fly’s abdominal epithelium becomes polyploid with age through generation of large multinucleated cells that make up more than 40% of the tissue area. The syncytia arise by cell fusion, not endomitosis. Epithelial multinucleation is also a characteristic of macular degeneration, including Ctnna1tvrm5, a mouse model for pattern dystrophy. Similarly, we find that the knockdown of alpha-catenin enhances multinucleation in the fly epithelium. We further show that age-induced polyploidy can be suppressed by inhibiting cell fusion revealing a means to maintain tissue organization in older animals.
piRNAs regulate a Hedgehog germline-to-soma pro-aging signal
Authors: Shi Cheng , Murphy Coleen T.
Published: August 2021

The reproductive system regulates the aging of the soma through competing anti- and pro-aging signals. Germline removal extends somatic lifespan through conserved pathways including Insulin, mTOR, and steroid signaling, while germline hyperactivity cuts lifespan short through mechanisms that remain elusive. Here, we show that mating-induced germline hyperactivity leads to the dramatic downregulation of piRNAs, which in turn releases silencing of their targets, including the Hedgehog-like ligand encoding genes wrt-1 and wrt-10, ultimately causing somatic collapse and early death. Germline-produced Hedgehog signals require PTR-6 and PTR-16 receptors for mating-induced body shrinking and lifespan shortening. Our results reveal an unconventional role of the piRNA pathway in transcriptional regulation of Hedgehog signaling, as well as a new role of Hedgehog signaling in the regulation of longevity and somatic maintenance. Our data suggest that Hedgehog signaling is controlled by the tunable piRNA pathway to encode the previously unknown germline-to-soma pro-aging signal. Mating-induced downregulation of piRNAs in the germline and subsequent signaling to the soma via the Hedgehog pathway enables the animal to tune its somatic resource allocation in response to germline needs to optimize reproductive timing and survival.
The human inactive X chromosome modulates expression of the active X chromosome
Authors: San Roman Adrianna K. , Godfrey Alexander K. , Skaletsky Helen , Bellott Daniel W. , Groff Abigail F. , Harris Hannah L. , Blanton Laura V. , Hughes Jennifer F. , Brown Laura , Phou Sidaly , Buscetta Ashley , Kruszka Paul , Banks Nicole , Dutra Amalia , Pak Evgenia , Lasutschinkow Patricia C. , Keen Colleen , Davis Shanlee M. , Tartaglia Nicole R. , Samango-Sprouse Carole , Muenke Maximilian , Page David C.
Published: August 2021

Researchers have presumed that the “inactive” X chromosome (Xi) has little impact, in trans, on the “active” X (Xa). To test this, we quantified Xi and Xa gene expression in individuals with one Xa and zero to three Xi’s. Our linear modeling revealed modular Xi and Xa transcriptomes and significant Xi-driven expression changes for 38% (162/423) of expressed X-chromosome genes. By integrating allele-specific analyses, we found that modulation of Xa transcript levels by Xi contributes to many of these Xi-driven changes (≥ 121 genes). By incorporating metrics of evolutionary constraint, we identified 10 X-chromosome genes most likely to drive sex differences in common disease, and sex chromosome aneuploidy syndromes. We conclude that human X chromosomes are regulated both in cis, through Xi-wide transcriptional attenuation, and in trans, through positive or negative modulation of individual Xa genes by Xi. The sum of cis and trans effects differs widely among genes.
The Mismatch Between Neuroscience Graduate Training and Professional Skill Sets
Authors: Shah S. , Juavinett A.L.
Published: August 2021

Understanding the skill sets required for career paths is a prerequisite for preparing students for those careers. Neuroscience career paths are rapidly changing as the field expands and increasingly overlaps with computational and data-heavy job sectors. With the steady growth in neuroscience trainees and the diversification of jobs for those trainees, it is important to assess whether or not our training is matching the skill sets required in the workforce. Here, we surveyed hundreds of neuroscience professionals and graduate students to assess their use and valuation of a range of skills, from bench skills to communication and management. We find that professionals with neuroscience degrees can be clustered into three main groups based on their skill sets: academic research, industry research and technical work, and non-research. Further, we find that while graduate students do not use or highly value management and communication skills, almost all neuroscience professionals report strongly needing those skills. Finally, coding and data analysis skills are widely used in academic and industry research and predict higher salaries. Our findings can help trainees assess their own skill sets as well as encourage educational leaders to offer training in management and communication–skills which may help catapult trainees into the next stages of their careers.
Transcriptome profiling of Candidatus Liberibacter asiaticus in citrus and psyllids
Authors: De Francesco Agustina , Lovelace Amelia H. , Shaw Dipan , Qiu Min , Wang Yuanchao , Gurung Fatta , Ancona Veronica , Wang Chunxia , Levy Amit , Jiang Tao , Ma Wenbo
Published: August 2021

Candidatus Liberibacter asiaticus (Las) is an emergent bacterial pathogen that is associated with the devastating citrus Huanglongbing (HLB). Vectored by the Asian citrus psyllid, Las colonizes the phloem tissue of citrus, causing severe damage to infected trees. So far, cultivating pure Las culture in axenic media has not been successful and dual-transcriptome analyses aiming to profile gene expression in both Las and its host(s) have a low coverage of the Las genome due to the low abundance of bacterial RNA in total RNA extracts from infected tissues. Therefore, the lack of a Las transcriptome remains as a significant knowledge gap. Here, we used a bacterial cell enrichment procedure and confidently determined the expression profiles of approximately 84% of the Las genes. Genes that exhibited the highest expression levels in citrus include ion transporters, ferritin, outer membrane porins, and genes involved in phage-related functions, pilus formation, cell wall modification, and stress responses. One hundred and six genes were found to be differentially expressed in citrus vs psyllids. Genes related to transcription/translation and resilience to host defense response were upregulated in citrus; whereas genes involved in energy generation and the flagella system were expressed to higher levels in psyllids. We also determined the relative expression levels of potential Sec-dependent effectors, which are considered as key virulence factors of Las. This work advances our understanding of HLB biology and offers novel insight into the interactions of Las with its plant host and insect vector.
H3-K27M-Mutant Nucleosomes Interact with MLL1 to Shape the Glioma Epigenetic Landscape
Authors: Furth Noa , Algranati Danielle , Dassa Bareket , Beresh Olga , Fedyuk Vadim , Morris Natasha , Kasper Lawryn H. , Jones Dan , Monje Michelle , Baker Suzanne J. , Shema Efrat
Published: August 2021

Cancer-associated mutations in genes encoding histones dramatically reshape chromatin and support tumorigenesis. Lysine to methionine substitution of residue 27 on histone H3 (K27M) is a driver mutation in high-grade pediatric gliomas, known to abrogate Polycomb Repressive Complex 2 (PRC2) activity. We applied single-molecule systems to image individual nucleosomes and delineate the combinatorial epigenetic patterns associated with H3-K27M expression. We found that chromatin marks on H3-K27M-mutant nucleosomes are dictated both by their incorporation preferences and by intrinsic properties of the mutation. Mutant nucleosomes not only preferentially bind PRC2, but also directly interact with MLL1, thus leading to genome-wide redistribution of H3K4me3. H3-K27M-mediated deregulation of both repressive and active chromatin marks leads to unbalanced ‘bivalent’ chromatin, which may support a poorly differentiated cellular state. This study provides evidence for a direct effect of H3-K27M oncohistone on the MLL1-H3K4me3 pathway and highlights the capability of single-molecule tools to reveal mechanisms of chromatin deregulation in cancer.
The obesity-linked human lncRNA AATBC regulates adipocyte plasticity by stimulating mitochondrial dynamics and respiration
Authors: Giroud Maude , Kotschi Stefan , Kwon Yun , Le Thuc Ophélia , Hoffmann Anne , Gil-Lozano Manuel , Karbiener Michael , Higareda-Almaraz Juan Carlos , Khani Sajjad , Tews Daniel , Fischer-Posovszky Pamela , Sun Wenfei , Dong Hua , Ghosh Adhideb , Wolfrum Christian , Wabitsch Martin , Virtanen Kirsi A. , Blüher Matthias , Nielsen Søren , Zeigerer Anja , García-Cáceres Cristina , Scheideler Marcel , Herzig Stephan , Bartelt Alexander
Published: August 2021

Adipocytes are critical regulators of metabolism and energy balance. While white adipocyte dysfunction is a hallmark of obesity-associated disorders, the activation of thermogenic brown and beige adipocytes is linked to improved cardiometabolic health. As adipocytes dynamically adapt to environmental cues by functionally switching between white and thermogenic phenotypes, a molecular understanding of this adipocyte plasticity could help improving energy balance and weight loss. Here, we show that the long non-coding RNA (lncRNA) Apoptosis associated transcript in bladder cancer (AATBC) is a human-specific regulator of adipocyte plasticity. Searching for new human lncRNAs implicated in adipocyte biology we compared transcriptional profiles of human adipose tissues and cultured adipocytes and discovered that AATBC was enriched in thermogenic conditions. Using primary human adipocytes and immortalized human adipocytes we found that gain-of-function of AATBC enhanced the thermogenic phenotype whereas loss-of-function diminished this effect. The AATBC-mediated increase in mitochondrial respiration was linked to a more fragmented mitochondrial network and vice versa. While we found that AATBC is predominantly located in the nucleus, its effect on global transcription was only marginal. As AATBC is specific to humans, we expressed AATBC in adipose tissue of mice to study its systemic impact, which led to lower plasma leptin levels. Interestingly, this association was also present in human subjects, as AATBC in adipose tissue was inversely correlated with plasma leptin levels, body mass index and other measures of metabolic health. In conclusion, AATBC is a novel obesity-linked regulator of adipocyte plasticity and mitochondrial function in humans.
Inhibiting retinoic acid mitigates vision loss in a mouse model of retinal degeneration
Authors: Telias Michael , Sit Kevin , Frozenfar Daniel , Smith Benjamin , Misra Arjit , Goard Michael J , Kramer Richard H
Published: August 2021

In degenerative retinal disorders, rod and cone photoreceptors die, causing vision impairment and blindness. Downstream neurons survive but undergo morphological and physiological remodeling, with some retinal ganglion cells (RGC) exhibiting heightened spontaneous firing. Retinoic acid (RA) has been implicated as the key signaling molecule that induces RGC hyperactivity, obscuring RGC light responses and reducing light avoidance behaviors triggered by residual rods and cones. However, evidence that RA-dependent remodeling corrupts image-forming vision has been lacking. Here we show that disulfiram, an FDA-approved drug that inhibits RA synthesis, and BMS 493, an RA receptor (RAR) inhibitor, reduce RGC hyperactivity and augment image detection in visually impaired mice. Functional imaging of visual cortical neurons shows that disulfiram and BMS 493 sharpen orientation-tuning and strengthen response fidelity to naturalistic scenes. These findings establish a causal link between RA-induced retinal hyperactivity and vision impairment and define molecular targets and candidate drugs for boosting image-forming vision in retinal degeneration.
Planar aggregation of the influenza viral fusion peptide alters membrane structure and hydration, promoting poration
Authors: Rice Amy , Haldar Sourav , Wang Eric , Blank Paul S. , Akimov Sergey A. , Galimzyanov Timur R. , Pastor Richard W. , Zimmerberg Joshua
Published: August 2021

To infect, enveloped viruses employ spike protein, spearheaded by its amphipathic fusion peptide (FP), that upon activation extends out from the viral surface to embed into the target cellular membrane. Here we report that synthesized influenza virus FP are membrane active, generating pores in giant unilamellar vesicles (GUV), and thus potentially explain both influenza virus’ hemolytic activity and the liposome poration seen in cryo-electron tomography. Experimentally, FP were heterogeneously distributed on the GUV at the time of poration. Consistent with this heterogeneous distribution, molecular dynamics (MD) simulations of asymmetric bilayers with different numbers of FP in one leaflet show FP aggregation. At the center of FP aggregates, a profound change in the membrane structure results in thinning, higher water permeability, and curvature. Ultimately, a hybrid bilayer nanodomain can form with one lipidic leaflet and one peptidic leaflet. Membrane elastic theory predicts a reduced barrier to water pore formation when even a dimer of FP thins the membrane as above, and the FP of that dimer tilts, to continue the leaflet bending initiated by the hydrophobic mismatch between the FP dimer and the surrounding lipid.
TNFa and IL-6 promote ex-vivo proliferation of lineage-committed human regulatory T cells
Authors: Skartsis Nikolaos , Peng Yani , Ferreira Leonardo M.R. , Nguyen Vinh , Muller Yannick , Vincenti Flavio , Tang Qizhi
Published: August 2021

Treg therapy is being tested in clinical trials in transplantation and autoimmune diseases, however, the impact of inflammation on Tregs is unclear. In this study, we challenged human Tregs ex-vivo with pro-inflammatory cytokines, TNFα and IL-6. These cytokines enhanced Treg proliferation induced by anti-CD3 and anti-CD28 or CD28 superagonist (CD28SA) while maintaining high expression of FOXP3 and HELIOS, demethylated FOXP3 enhancer, and low expression of cytokines IFNg, IL-4 and IL-17. Blocking TNF receptor signaling using etanercept or deletion of TNF receptor 2 using CRISPR/Cas9 blunted Treg proliferation and attenuated FOXP3 and HELIOS expression, revealing the importance of TNFR2 signaling in Treg proliferation and lineage stability. The robust proliferation induced by CD28SA with IL-6 and TNFα may be adopted for the expansion of therapeutic Tregs. Metabolomics analysis showed that Tregs expanded with CD28SA plus cytokines had more active glycolysis and oxidative phosphorylation, increased energy production, and higher antioxidant potential. Finally, CD28SA plus cytokine-expanded Tregs had comparable suppressive activity in vitro and in vivo in a humanized mouse model of graft-versus-host-disease when compared to Tregs expanded using the conventional protocol. These results demonstrate that human Tregs positively respond to proinflammatory cytokines with enhanced proliferation without compromising their lineage identity or function.
NAD kinase promotes Staphylococcus aureus pathogenesis by supporting production of virulence factors and protective enzymes
Authors: Leseigneur Clarisse , Boucontet Laurent , Duchateau Magalie , Pizarro-Cerda Javier , Matondo Mariette , Colucci-Guyon Emma , Dussurget Olivier
Published: August 2021

Nicotinamide adenine dinucleotide phosphate (NADPH) is the primary electron donor for reductive reactions that are essential for the biosynthesis of major cell components in all organisms. Nicotinamide adenine dinucleotide kinase (NADK) is the only enzyme that catalyzes synthesis of NADP(H) from NAD(H). While the enzymatic properties and physiological functions of NADK have been thoroughly studied, the role of NADK in bacterial pathogenesis remains unknown. Here, we used CRISPR interference to knockdown NADK gene expression to address the role of this enzyme in Staphylococcus aureus pathogenic potential. We find that NADK inhibition drastically decreases mortality of zebrafish infected with S. aureus. Further, we show that NADK promotes S. aureus survival in infected macrophages by protecting bacteria from antimicrobial defense mechanisms. Proteome-wide data analysis revealed that production of major virulence associated factors is sustained by NADK. We demonstrate that NADK is required for expression of the quorum-sensing response regulator AgrA, which controls critical S. aureus virulence determinants. These findings support a key role for NADK in bacteria survival within innate immune cells and the host during infection.
Cell-to-cell variations in subcellular localisation of V2R are independent of its expression level
Authors: Koers Eline J. , Morgan Bradley A. , Heydenreich Franziska M. , Plouffe Bianca , Styles Iain B. , Veprintsev Dmitry B.
Published: August 2021

G protein coupled receptors (GPCRs) translate the actions of hormones into intracellular signalling events. Mutations in GPCRs can prevent their correct expression and trafficking to the cell surface and cause disease. We use single cell measurements in HEK293 cells to show that the balance between endoplasmic reticulum (ER) and cell surface localisation of the Vasopressin 2 receptor (V2R) varies significantly from cell to cell. We find that mutations in the V2R affect the proportion of cells able to send this GPCR to the cell surface but do not prevent all cells in the population from correctly trafficking the mutant receptors. These findings reveal that the ability of cells to correctly traffic V2R to the cell surface depends not only on the expressed V2R mutant but also on the individual cell environment.

Significance statement

Missense mutations in the Vasopressin 2 Receptor (V2R) cause Nephrogenic Diabetes Insipidus. Some of these mutations prevent correct expression and trafficking of V2R to the cell surface resulting in a loss-of-function. We show -using single cell measurements-that the balance between endoplasmic reticulum and cell surface localisation of the V2R varies significantly from cell to cell, independent from its expression level. Mutations affect the proportion of cells able to send V2R to the cell surface but do not prevent all cells in the population from correctly trafficking the mutant receptors. Hence, the ability of cells to correctly traffic V2R to the cell surface depends not only on expressed V2R mutant but also on the cell environment.
Ability of nucleoside-modified mRNA to encode HIV-1 envelope trimer nanoparticles
Authors: Mu Zekun , Wiehe Kevin , Saunders Kevin O. , Henderson Rory , Cain Derek W. , Parks Robert , Martik Diana , Mansouri Katayoun , Edwards Robert J. , Newman Amanda , Lu Xiaozhi , Xia Shi-Mao , Bonsignori Mattia , Montefiori David , Han Qifeng , Venkatayogi Sravani , Evangelous Tyler , Wang Yunfei , Rountree Wes , Tam Ying , Barbosa Christopher , Munir Alam S. , Williams Wilton B. , Pardi Norbert , Weissman Drew , Haynes Barton F.
Published: August 2021

The success of nucleoside-modified mRNAs in lipid nanoparticles (mRNA-LNP) as COVID-19 vaccines heralded a new era of vaccine development. For HIV-1, multivalent envelope (Env) trimer protein nanoparticles are superior immunogens compared to trimers alone for priming of broadly neutralizing antibody (bnAb) B cell lineages. The successful expression of complex multivalent nanoparticle immunogens with mRNAs has not been demonstrated. Here we show that mRNAs can encode antigenic Env trimers on ferritin nanoparticles that initiate bnAb precursor B cell expansion and induce serum autologous tier 2 neutralizing activity in bnAb precursor VH + VL knock-in mice. Next generation sequencing demonstrated acquisition of critical mutations, and monoclonal antibodies that neutralized heterologous HIV-1 isolates were isolated. Thus, mRNA- LNP can encode complex immunogens and are of use in design of germline-targeting and sequential boosting immunogens for HIV-1 vaccine development.
Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)
Authors: Wu Xudong , Rapoport Tom A.
Published: August 2021

We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: (1) a Fab-fragment of an antibody directed against the nanobody, and (2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ∼120 kDa, called Legobody, does not perturb the nanobody-target interaction and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23 kDa membrane protein, resulting in a map at 3.2Å overall resolution with density sufficient forde novomodel building, and for the 22 kDa RBD of SARS-CoV2 spike protein, resulting in a map at 3.6 Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.
Deterministic shifts in molecular evolution correlate with convergence to annualism in killifishes
Authors: Thompson Andrew W. , Black Amanda C. , Huang Yu , Shi Qiong , Furness Andrew I. , Braasch Ingo , Hoffmann Federico G. , Ortí Guillermo
Published: August 2021

The repeated evolution of novel life histories correlating with ecological variables offer opportunities to test scenarios of convergence and determinism in genetic, developmental, and metabolic features. Here we leverage the diversity of aplocheiloid killifishes, a clade of teleost fishes that contains over 750 species on three continents. Nearly half of these are “annual” or seasonal species that inhabit bodies of water that desiccate and are unfeasible for growth, reproduction, or survival for weeks to months at a time. We present a large-scale phylogenomic reconstruction of aplocheiloid killifish evolution using newly sequenced transcriptomes from all major clades. We show that developmental dormancy (diapause) and annualism have up to seven independent origins in Africa and America. We then measure evolutionary rates of orthologous genes and show that annual life history is correlated with higher dN/dSratios. Many of these fast-evolving genes in annual species constitute key developmental genes and nuclear-encoded metabolic genes that control oxidative phosphorylation. Lastly, we compare these fast-evolving genes to genes associated with developmental dormancy and metabolic shifts in killifishes and other vertebrates and thereby identify molecular evolutionary signatures of repeated evolutionary transitions to extreme environments.
Complex feline disease mapping using a dense genotyping array
Authors: Hernandez Isabel , Hayward Jessica J. , Brockman Jeff A. , White Michelle E. , Mouttham Lara , Wilcox Elizabeth A. , Garrison Susan , Castelhano Marta G. , Loftus John P. , Gomes Filipe Espinheira , Balkman Cheryl , Brooks Marjory B. , Fiani Nadine , Forman Marnin , Kern Tom , Kornreich Bruce , Ledbetter Eric , Peralta Santiago , Struble Angela M. , Caligiuri Lisa , Corey Elizabeth , Lin Lin , Jordan Julie , Sack Danny , Boyko Adam R. , Lyons Leslie A. , Todhunter Rory J.
Published: August 2021

The current feline genotyping array of 63k single nucleotide polymorphisms has proven its utility within breeds, and its use has led to the identification of variants associated with Mendelian traits in purebred cats. However, compared to single gene disorders, association studies of complex diseases, especially with the inclusion of random bred cats with relatively low linkage disequilibrium, require a denser genotyping array and an increased sample size to provide statistically significant associations. Here, we undertook a multi-breed study of 1,122 cats, most of which were admitted and phenotyped for nine common complex feline diseases at the Cornell University Hospital for Animals. Using a proprietary 340k single nucleotide polymorphism mapping array, we identified significant genome-wide associations with hyperthyroidism, diabetes mellitus, and eosinophilic keratoconjunctivitis. These results provide genomic locations for variant discovery and candidate gene screening for these important complex feline diseases, which are relevant not only to feline health, but also to the development of disease models for comparative studies.
Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition
Authors: Ibiapino Amalia , Báez Mariana , García Miguel A. , Costea Mihai , Stefanović Saša , Pedrosa-Harand Andrea
Published: August 2021

Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 89-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta.

Highlights

Cuscuta subgenus Pachystigma contains species with strikingly bimodal karyotypes. The emergence of these karyotypes is linked to the enrichment of varied repetitive sequences in the largest chromosomal pairs.
The Epithelial and Stromal Immune Microenvironment in Gastric Cancer: A Comprehensive Analysis Reveals Prognostic Factors with Digital Cytometry
Authors: Shen Wenjun , Wang Guoyun , Cooper Georgia R. , Jiang Yuming , Zhou Xin
Published: August 2021

Background

Gastric cancer (GC) is the third leading cause of cancer-related deaths worldwide. Tumor heterogeneity continues to confound researchers’ understanding of tumor growth and the development of an effective therapy. Digital cytometry allows interpretation of heterogeneous bulk tissue transcriptomes at the cellular level.

Methods

We built a novel signature matrix to dissect epithelium and stroma signals using a scRNA-seq data set for GC. We applied cell mixture deconvolution to estimate diverse epithelial, stromal, and immune cell proportions from bulk transcriptome data in four independent GC cohorts. Robust computational methods were applied to identify strong prognostic factors for GC.

Results

We identified an EMEC population whose proportions were significantly higher in patients with stage I cancer than other stages, and it was predominantly present in tumor samples but not typically found in normal samples. We found that the ratio of EMECs to stromal cells and the ratio of adaptive T cells to monocytes were the most significant prognostic factors within the non-immune and immune factors, respectively. The STEM score, which unifies these two prognostic factors was an independent prognostic factor of overall survival (HR=0.92, 95% CI=0.89-0.94,p= 2.05 × 10−9). The entire GC cohort was stratified into three risk groups (high-, moderate-, and low-risk) which yielded incremental survival times (p< 0.0001). For stage III disease, patients in the moderate- and low-risk groups experienced better survival benefits from radiation therapy ((HR=0.16, 95% CI=0.06-0.4,p< 0.0001), whereas those in the high-risk group did not (HR=0.49, 95% CI=0.14-1.72,p= 0.25).

Conclusions

We conclude that the STEM score is a promising prognostic factor for gastric cancer.
Immuno-proteomic profiling reveals abundant airway CD8 T cells and ongoing epithelial injury in prolonged post-COVID19 respiratory disease
Authors: Vijayakumar Bavithra , Boustani Karim , Ogger Patricia P. , Papadaki Artermis , Tonkin James , Orton Christopher M. , Ghai Poonam , Suveizdyte Kornelija , Hewitt Richard J. , Snelgrove Robert J. , Molyneaux Philip L. , Garner Justin L. , Peters James E. , Shah Pallav L. , Lloyd Clare M. , Harker James A.
Published: August 2021

Some patients hospitalized with acute COVID19 suffer respiratory symptoms that persist for many months. To characterize the local and systemic immune responses associated with this form of ‘Long COVID’, we delineated the immune and proteomic landscape in the airway and peripheral blood of normal volunteers and patients from 3 to 6 months after hospital discharge. The bronchoalveolar lavage (but not peripheral blood) proteome was abnormal in patients with post-COVID19 lung disease with significantly elevated concentration of proteins associated with apoptosis, tissue repair and epithelial injury. This correlated with an increase in cytotoxic lymphocytes (especially tissue resident CD8+T cells), lactate dehydrogenase and albumin (biomarkers of cell death and barrier integrity). Follow-up of a subset of these patients greater than 1-year post-COVID19 indicated these abnormalities resolved over time. Collectively, these data indicate that COVID-19 results in a prolonged change to the airway immune landscape in those with persistent lung disease, with evidence of cell death and tissue repair linked to ongoing activation of cytotoxic T cells.

Highlights

The post-COVID19 airway is characterized by increased cytotoxic lymphocytes.

Distinct airway proteomes are associated with the airway immune cell landscape.

The peripheral blood does not predict immune-proteome alterations in the airway post-COVID19.

Persistent abnormalities in the airway immune-proteome post-COVID19 airways correlate with ongoing epithelial damage.
Spectral inference reveals principal cone-integration rules of the zebrafish inner retina
Authors: Bartel Philipp , Yoshimatsu Takeshi , Janiak Filip K , Baden Tom
Published: August 2021

In the vertebrate retina, bipolar cells integrate the signals from different cone types at two main sites: directly, via dendritic inputs in the outer retina, and indirectly, via axonal inputs in the inner retina. Of these, the functional wiring of the indirect route, involving diverse amacrine cell circuits, remains largely uncharted. However, because cone-photoreceptor types differ in their spectral sensitivities, insights into the total functional cone-integration logic of bipolar cell might be gained by linking spectral responses across these two populations of neurons. To explore the feasibility of such a “spectral-circuit-mapping” approach, we here recordedin vivoresponses of bipolar cell presynaptic terminals in larval zebrafish to widefield but spectrally resolved flashes of light. We then mapped the results onto the previously established spectral sensitivity functions of the four cones.

We find that this approach could explain ∼95% of the spectral and temporal variance of bipolar cell responses by way of a simple linear model that combined weighted inputs from the cones with four stereotyped temporal components. This in turn revealed several notable integration rules of the inner retina. Overall, bipolar cells were dominated by red-cone inputs, often alongside equal sign inputs from blue- and green-cones. In contrast, UV-cone inputs were uncorrelated with those of the remaining cones. This led to a new axis of spectral opponency which was mainly set-up by red-/green-/blue-cone “Off” circuits connecting to “natively-On” UV-cone circuits in the outermost fraction of the inner plexiform layer – much as how key colour opponent circuits are established in mammals. Beyond this, and despite substantial temporal diversity that was not present in the cones, bipolar cell spectral tunings were surprisingly simple. They either approximately resembled both opponent and non-opponent spectral motifs already present in the cones or exhibited a stereotyped non-opponent broadband response. In this way, bipolar cells not only preserved the efficient spectral representations in the cones, but also diversified them to set up a total of six dominant spectral motifs which included three axes of spectral opponency. More generally, our results contribute to an emerging understanding of how retinal circuits for colour vision in ancestral cone-tetrachromats such as zebrafish may be linked to those found in mammals.
ACE2 Pathway Regulates Thermogenesis and Energy Metabolism
Authors: Cao Xi , Shi Tingting , Zhang Chuanhai , Jin Wanzhu , Song Lini , Zhang Yichen , Liu Jingyi , Yang Fangyuan , Rotimi Charles N , Xu Amin , Yang Jinkui
Published: August 2021

Identification of key regulators of energy homeostasis holds important therapeutic promise for metabolic disorders, such as obesity and diabetes. ACE2 cleaves angiotensin II (Ang II) to generate Ang-(1-7) which acts mainly through the Mas receptor. Here, we identify ACE2 pathway as a critical regulator in the maintenance of thermogenesis and energy expenditure. We found that ACE2 is highly expressed in brown adipose tissue (BAT) and that cold stimulation increases ACE2 and Ang-(1-7) levels in BAT and serum. ACE2 knockout mice (ACE2-/y), Mas knockout mice (Mas-/-), and the mice transplanted with brown adipose tissue from Mas-/- mice displayed impaired thermogenesis. In contrast, impaired thermogenesis of db/db obese diabetic mice and high-fat diet-induced obese mice were ameliorated by overexpression of ACE2 or continuous infusion of Ang-(1-7). Activation of ACE2 pathway was associated with improvement of metabolic parameters, including blood glucose, lipids and energy expenditure in multiple animal models. Consistently, ACE2 pathway remarkably enhanced the browning of white adipose tissue. Mechanistically, we showed that ACE2 pathway activated Akt/FoxO1 and PKA pathway, leading to induction of UCP1 and activation of mitochondrial function. Our data propose that adaptive thermogenesis requires regulation of ACE2 pathway and highlight novel therapeutic targets for the treatment of metabolic disorders.
A SAXS-based approach to rationally evaluate radical scavengers – toward eliminating radiation damage in solution and crystallographic studies
Authors: Stachowski Timothy R. , Snell Mary E. , Snell Edward H.
Published: August 2021

X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a successful mitigation strategy but also has its limitations including the trapping of non-biological structural states. Crystallographic and solution studies performed at physiological temperatures can reveal otherwise hidden but relevant conformations, but are limited by their increased susceptibility to radiation damage. In this case, chemical additives that scavenge the species generated by radiation can mitigate damage but are not always successful and the mechanisms are often unclear. Using a protein designed to undergo a large-scale structural change from breakage of a disulfide bond, radiation damage can be monitored with small-angle X-ray scattering. Using this, we have quantitatively evaluated how three scavengers commonly used in crystallographic experiments – sodium nitrate, cysteine, and ascorbic acid – perform in solution at 10°C. Sodium nitrate was the most effective scavenger and completely inhibited fragmentation of the disulfide bond at a lower concentration (500 µM) compared with cysteine (∼5 mM) while ascorbic acid performed best at 5 mM but could only reduce fragmentation by ∼75% after a total accumulated dose of 792 Gy. The relative effectiveness of each scavenger matches their reported affinities for solvated electrons. Saturating concentrations of each scavenger shifted fragmentation from first order to a zeroth-order process, perhaps indicating the direct contribution of photoabsorption. The SAXS-based method can detect damage at X-ray doses far lower than those accessible crystallographically, thereby providing a detailed picture of scavenger processes. The solution results are also in close agreement with what is known about scavenger performance and mechanism in a crystallographic setting and suggest that a link can be made between the damage phenomenon in the two scenarios. Therefore, our engineered approach might provide a platform for more systematic and comprehensive screening of radioprotectants that can directly inform mitigation strategies for both solution and crystallographic experiments, while also clarifying fundamental radiation damage mechanisms.
Comparative analysis of XANES and EXAFS for local structural characterization of disordered metal oxides
Authors: Li Junying , Li Yuanyuan , Routh Prahlad K. , Makagon Evgeniy , Lubomirsky Igor , Frenkel Anatoly I.
Published: August 2021

In functional materials, the local environment around active species that may contain just a few nearest-neighboring atomic shells often changes in response to external conditions. Strong disorder in the local environment poses a challenge to commonly used extended X-ray absorption fine structure (EXAFS) analysis. Furthermore, the dilute concentrations of absorbing atoms, small sample size and the constraints of the experimental setup often limit the utility of EXAFS for structural analysis. X-ray absorption near-edge structure (XANES) has been established as a good alternative method to provide local electronic and geometric information of materials. The pre-edge region in the XANES spectra of metal compounds is a useful but relatively under-utilized resource of information of the chemical composition and structural disorder in nano-materials. This study explores two examples of materials in which the transition metal environment is either relatively symmetric or strongly asymmetric. In the former case, EXAFS results agree with those obtained from the pre-edge XANES analysis, whereas in the latter case they are in a seeming contradiction. The two observations are reconciled by revisiting the limitations of EXAFS in the case of a strong, asymmetric bond length disorder, expected for mixed-valence oxides, and emphasize the utility of the pre-edge XANES analysis for detecting local heterogeneities in structural and compositional motifs.
Exploiting spatio-spectral aberrations for rapid synchrotron infrared imaging
Authors: Anand Vijayakumar , Ng Soon Hock , Katkus Tomas , Maksimovic Jovan , Klein Annaleise R , Vongsvivut Jitraporn , Bambery Keith R , Tobin Mark J , Juodkazis Saulius
Published: August 2021

The Infrared Microspectroscopy Beamline at the Australian Synchrotron is equipped with a Fourier transform infrared (FTIR) spectrometer, which is coupled with an infrared (IR) microscope and a choice of two detectors: a single-point narrow-band mercury cadmium telluride (MCT) detector and a 64 × 64 multi-pixel focal plane array (FPA) imaging detector. A scanning-based point-by-point mapping method is commonly used with a tightly focused synchrotron IR beam at the sample plane, using an MCT detector and a matching 36× IR reflecting objective and condenser (NA = 0.5), which is time consuming. In this study, the beam size at the sample plane was increased using a 15× objective and the spatio-spectral aberrations were investigated. A correlation-based semi-synthetic computational optical approach was applied to assess the possibilities of exploiting the aberrations to perform rapid imaging rather than a mapping approach.
Crystal structures of phosphine-supported (η5-cyclopentadienyl)molybdenum(II) propionyl complexes
Authors: Whited Matthew T. , Ball Margaret A. , Block Alison , Brewster Benjamin A. , Ferrer LouLou , Jin-Lee Helen J. , King Colby J. , North Jamie D. , Shelton Inger L. , Wilson David G.
Published: August 2021

Three cyclopentadienylmolybdenum(II) propionyl complexes featuring triarylphosphine ligands with different para substituents, namely, dicarbonyl(η5-cyclopentadienyl)propionyl(triphenylphosphane-κP)molybdenum(II), [Mo(C5H5)(C3H5O)(C18H15P)(CO)2], (1), dicarbonyl(η5-cyclopentadienyl)propionyl[tris(4-fluorophenyl)phosphane-κP]molybdenum(II), [Mo(C5H5)(C3H5O)(C18H12F3P)(CO)2], (2), and dicarbonyl(η5-cyclopentadienyl)propionyl[tris(4-methoxyphenyl)phosphane-κP]molybdenum(II) dichloromethane solvate, [Mo(C5H5)(C3H5O)(C21H21O3P)(CO)2]·CH2Cl2, (3), have been prepared from the corresponding ethyl complexes via phosphine-induced migratory insertion. These complexes exhibit four-legged piano-stool geometries with molecular structures quite similar to each other and to related acetyl complexes. The extended structures of the three complexes differ somewhat, with the para substituent of the triarylphosphine of (2) (fluoro) or (3) (methoxy) engaging in non-classical C—H...F or C—H...O hydrogen-bonding interactions. The structure of (3) exhibits modest disorder in the position of one Cl atom of the dichloromethane solvent, which was modeled with two sites showing approximately equivalent occupancies [0.532 (15) and 0.478 (15)].
Do high-resolution satellite indices at field level reduce basis risk of satellite-based weather index insurance?
Authors: Kölle Wienand , Buchholz Matthias , Musshoff Oliver
Published: August 2021

Purpose

Satellite-based weather index insurance has recently been considered in order to reduce the high basis risk of station-based weather index insurance. However, the use of satellite data with a relatively low spatial resolution has not yet made it possible to determine the satellite indices free of disturbing landscape elements such as mountains, forests and lakes.

Design/methodology/approach

In this context, the Normalized Difference Vegetation Index (NDVI) was used based on both Moderate Resolution Imaging Spectroradiometer (MODIS) (250 × 250 m) and high-resolution Landsat 5/8 (30 × 30 m) images to investigate the effect of a higher spatial resolution of satellite-based weather index contracts for hedging winter wheat yields. For three farms in north-east Germany, insurance contracts both at field and farm level were designed.

Findings

The results indicate that with an increasing spatial resolution of satellite data, the basis risk of satellite-based weather index insurance contracts can be reduced. However, the results also show that the design of NDVI-based insurance contracts at farm level also reduces the basis risk compared to field level. The study shows that higher-resolution satellite data are advantageous, whereas satellite indices at field level do not reduce the basis risk.

Originality/value

To the best of the author’s knowledge, the effect of increasing spatial resolution of satellite images for satellite-based weather index insurance is investigated for the first time at the field level compared to the farm level.