bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic basis of expression and splicing underlying spike architecture in wheat (Triticum aestivumL.)
Authors: Yang Guang , Pan Yan , Cui Licao , Chen Mingxun , Zeng Qingdong , Pan Wenqiu , Liang Zhe , Edwards Dave , Batley Jacqueline , Han Dejun , Deng Pingcheng , Yu Hao , Henry Robert J , Song Weining , Nie Xiaojun
Published: May 2023

Introduction

Wheat is one of the most important staple crops worldwide, and an important source of human protein and mineral element intake. Continuously increasing stable production of wheat is critical for global food security under the challenge of population growth and limited resource input.

Objective

Spike architecture determines the potential grain yield of wheat. However, the mechanisms of transcriptional regulation of spike architecture in wheat remain largely unknown, limiting further genetic improvement of wheat yield. In this study we explored the genetic basis of spike architecture in wheat.

Methods

Population RNA-seq methods were used to identify the eQTLs and sQTLs associated with spike architecture and applied this to dissection of the genetic basis of gene expression and splicing controlling these complex yield-related traits.

Results

In total, 4,143 expression quantitative trait loci (eQTLs) and 12,933 splice QTLs (sQTLs) were identified in wheat based on 178 RNA-seq samples, revealing 774 cis-eQTLs and 321 cis-sQTLs for 86 eGenes and 73 sGenes, respectively. Integration of eQTLs and sQTLs with genome-wide association study (GWAS) identified dozens of additional novel candidate genes that may contribute to spike-related traits. Gene network analysis showed that eQTLs and sQTLs were widely involved in the co-expression modules that regulate wheat spike architecture. Notably, the eQTL locusAX-108754757regulated the expression of 5 eGenes that negatively controled grain number per spike.AX-111592099regulated both the splicing and expression ofTraesCS7B02G442100,encoding an E3 ubiquitin ligase, and playing a central role in regulating spike length.

Conclusion

This study provides new insights into the genetic basis of spike architecture. This improved understanding of spike-related traits in wheat will contribute to more rapid genetic improvement.
Active and Allosteric Site Binding MOLECULAR MECHANICS-QUANTUM MECHANICS studies of STEVIOSIDE Derivative in PCSK9 Protein Intended to provide a safe Antilipidemic agent
Authors: Irfan N , Vaithyanathan Prakash , Anandaram Harishchander , Zaidh S Mohammed , Varshini S Priya , Puratchikody A
Published: May 2023

Interaction of low-density lipoprotein receptors with proprotein convertase subtilisin/ kexin type 9 (PCSK9) plays a vital role in causing atherosclerosis. It is the hidden precursor of clinical myocardial infarction (MI), stroke, CVD and estimates 60% of deaths worldwide. The current need is to design small molecules to prevent the interaction between PCSK9 with LDL receptors. This study aims to evaluate the PCSK9 antagonistic effect of a derivative of Stevioside (also referred as Methylidene tetracyclo derivative) and atorvastatin. Also, a comparative study was performed to analyze the binding interaction of molecules inside the active and allosteric sites of PCSK9. The RCSB downloaded protein 7S5H and above said ligands were optimized to the local minima energy level and docked inside the active and allosteric sites. The stability of non-bonded interaction of complex was analyzed using Desmond MD simulation studies. The results of docking showed that the Methylidene tetracyclo molecule possesses a two-fold higher affinity of -10.159 kcal/mol in the active site and -10.824 kcal/mol in the allosteric site. The Phe377 amino acid made the Methylidene tetracyclo molecule orient inside the active site. Nine H-bonds with 5 amino acids of allosteric site increase the binding affinity compared to Atorvastatin. The MD simulation studies exposed that the nonbonded interaction of Methylidene tetracyclo molecule was stable throughout 100ns. This confirms the Methylidene tetracyclo molecule will be the better hit as well as the lead molecule to inhibit PCSK9 protein.
Broad-Spectrum Heavily Mutated Monoclonal Antibody Isolated from COVID-19 Convalescent Vaccinee with Capacity to Neutralize SARS-CoV2 Variants Ranging from B.1 to BQ.1.1
Authors: Choudhary Alok K , Calianese David , Honnen William , Kolloli Afsal , Dikdan Ryan J , Jaijyan Dabbu , Song Ge , Capozzola Tazio , Akkaraju Vikash , Mattappallil Arun , Rosania Anthony , Khan Salman , Lerman Mark , Afzal Nikaein , Subbian Selvakumar , Chou Ting Chao , Andrabi Raiees , Burton Dennis , Pinter Abraham
Published: May 2023

The increasing prevalence of the highly antibody-evasive Omicron sublineages increases the risk of breakthrough infections and leaves high-risk and vulnerable immunocompromised individuals with no effective options for prophylactic or therapeutic antibody treatments. Here, we report a heavily mutated anti-RBD monoclonal antibody, Acovimab, directed against a site in the receptor-binding motif (RBM) region of the CoV2 receptor-binding domain (RBD), that possesses very broad and highly potent neutralizing activity against CoV2 variants, including many Omicron variants. This antibody is derived from the IGHV1-58*01 germline sequence and possesses a relatively high level of mutation (15.5% of the VH aa sequence), which is unusual for anti-RBD antibodies. Neutralizing activity was very potent (IC50s range of 1-9 ng/ml) for early Omicron subvariants that possess an unmutated F486 residue and is retained but less potent (IC50s of 200-650 ng/ml) for more resistant Omicron subvariants which contain the F486V mutation (BA4/5, BA4.6, and BQ1.1), but is lost for the later ultra-resistant variants that contain F486S (XBB) or F486P (XBB.1.5) mutations. Based on these specificities, it is predicted that Acovimab by itself should protect against CoV2 infections other than those caused by the XBB/XBB.1.5 family. Acovimab also shows strong synergy in neutralization when combined with Sotrovimab, which neutralizes all Omicron variants, including XBB.1.5. Plasma from subjects with hybrid immunity (induced by vaccination + infection) possessed low levels of XBB.1.5 RBM-targeting plasma-neutralizing antibodies, and these also neutralized synergistically when combined with Sotrovimab. These results suggest potentially novel immunotherapeutic options for treating most of the CoV2 variants responsible for current infections.
Sea-ice melt determines seasonal phytoplankton dynamics and delimits the habitat of temperate Atlantic taxa as the Arctic Ocean atlantifies
Authors: Oldenburg Ellen , Popa Ovidiu , Wietz Matthias , von Appen Wilken-Jon , Torres-Valdes Sinhue , Bienhold Christina , Ebenhöh Oliver , Metfies Katja
Published: May 2023

The Arctic Ocean is one of the regions where anthropogenic environmental change is progressing most rapidly and drastically. The impact of rising temperatures and decreasing sea ice on Arctic marine microbial communities is yet not well understood. Microbes form the basis of food webs in the Arctic Ocean, providing energy for larger organisms. Previous studies have shown that Atlantic taxa associated with low light are robust to more polar conditions. In this study, we compared to which extent sea ice melt influences light-associated phytoplankton dynamics and biodiversity over two years at two mooring locations in the Fram Strait. One mooring is deployed in pure Atlantic water, and the second in the intermittently ice-covered Marginal Ice Zone. Time-series analysis of amplicon sequence variants abundance over a two-year period, allowed us to identify communities of co-occurring taxa that exhibit similar patterns throughout the annual cycle. We then examined how alterations in environmental conditions affect the prevalence of species. During high abundance periods of diatoms, polar phytoplankton populations dominated, while temperate taxa were weakly represented. Generally, polar pelagic and ice-associated taxa (such asFragilariopsis cylindrusorMelosira arctica) were more prevalent in Atlantic conditions whereas temperate taxa (such asOdontella auritaorProboscia alata) have limited potential to persist in colder ice-impacted waters. In contrast to previous assumptions, we think that sea-ice melt acts as a barrier to the horizontal extent of temperate diatoms by preventing their succession at places strongly influenced by polar conditions such as the melting sea ice.
FOXM1 expression reverts aging chromatin profiles through repression of the senescence-associated pioneer factor AP-1
Authors: Ferreira Fábio J. , Galhardo Mafalda , Teixeira Joana , Logarinho Elsa , Bessa José
Published: May 2023

Aging is characterized by changes in gene expression that drive deleterious cellular phenotypes leading to senescence. The transcriptional activation of senescence genes has been mainly attributed to epigenetic shifts, but the changes in chromatin accessibility and its underling mechanisms remain largely elusive in natural aging. Here, we profiled chromatin accessibility in human dermal fibroblasts (HDFs) from neonatal and octogenarian individuals. We found that AP-1 binding motifs are prevalent in elderly specific accessible regions of the chromatin while neonatal-specific regions are highly enriched for TEAD binding motifs. We further show thatTEAD4andFOXM1share a conserved transcriptional regulatory landscape controlled by an age-dependent enhancer that closes with aging and drives senescence when deleted. Finally, we demonstrate thatFOXM1ectopic expression in elderly cells partially resets chromatin accessibility to a youthful state due to FOXM1 repressive function in the promoters of several members of the AP-1 complex. These results placeFOXM1at a top hierarchical level in chromatin remodeling required to prevent senescence.
Can motional dynamics account for the cytotoxicity of beta amyloid oligomers?
Authors: Yeh Chen-Tsen , Chang Han-Wen , Hsu Wen-Hsin , Huang Shing-Jong , Wu Meng-Hsin , Tu Ling-Hsien , Lee Ming-Che , Chung Chan Jerry Chun
Published: May 2023

The underlying biophysical principle governing the cytotoxicity of the oligomeric aggregates of β-amyloid (Aβ) peptides has long been an enigma. Here we show that the size of Aβ40oligomers can be actively controlled by incubating the peptides in reverse micelles. Our approach allowed for the first time a detailed comparison of the structures and dynamics of two Aβ40oligomers of different size, viz., 10 and 23 nm, by solid-state NMR. From the chemical shift data, we infer that the conformation of the residues from K16 to K28 are different between the 10-nm and 23-nm oligomers. We find that the 10-nm oligomers are more cytotoxic, and the molecular motions of their charged residues are more dynamic. Interestingly, the residue A21 exhibits an unusually high structural rigidity. Our data raise the interesting possibility that the cytotoxicity of Aβ40oligomers could also be correlated to the motional dynamics of the charged residues.
Evolution of irreversible differentiation under stage-dependent cell differentiation
Authors: Gao Yuanxiao , Zapién-Campos Román , Pichugin Yuriy , Traulsen Arne
Published: May 2023

The specialization of cells is a hallmark of complex multicellularity. Cell differentiation enables the emergence of specialized cell types that carry out separate functions previously executed by a multifunctional ancestor cell. One view is that initial cell differentiation occurred randomly, especially for genetically identical cells, exposed to the same life history environment. How such a change in differentiation probabilities can affect the evolution of differentiation patterns is still unclear. We develop a theoretical model to investigate the effect of stage-dependent cell differentiation -- cells change their developmental trajectories during a single round of development via cell divisions -- on the evolution of optimal differentiation patterns. We found that irreversible differentiation -- a cell type gradually losing its differentiation capability to produce other cell types -- is more favored under stage-dependent than stage-independent cell differentiation in relatively small organisms with limited differentiation probability variations. Furthermore, we discovered that irreversible differentiation of germ cells, which is the gradual loss of germ cells' ability to differentiate, is a prominent pattern among irreversible differentiation patterns under stage-dependent cell differentiation. In addition, large variations in differentiation probabilities prohibit irreversible differentiation from being the optimal differentiation pattern.
EXTRANEURAL RABIES VIRUS INFECTION LEADS TO TISSUE DAMAGE AND CELL DEATH IN MICE
Authors: Leal Rodrigues Érika D. , Pacheco da Silva Vinicius , Bastos Chaves Victor G. , de Sousa Moraes Cássia N. , de Souza Pereira Sara , Nogueira Lima André L. , Fernandes Barbosa Coelho Taciana , da Costa Vasconcelos Pedro F. , Ribeiro Cruz Ana C. , Medeiros Neves Casseb Livia
Published: May 2023

Rabies, a fatal neurological disease caused byLyssavirus rabies(RABV), poses a significant threat to public health globally. Despite extensive studies on RABV-induced neuropathology, the involvement of extraneural organs during rabies pathogenesis and the tropisms of wild-type strains to different organs remain largely unknown. Here, we investigated the tropism of a dog and bat RABV variant to three different extraneural tissues (kidneys, lungs and liver) and characterized cellular and tissue damage associated with infection in mice over 30 days. Our results reveal that RABV may have a tropism for the kidneys and cause tissue-specific cellular damage. Furthermore, we propose that RABV spreads to extraneural tissues simultaneously with central nervous system (CNS) infection. Understanding the involvement of extraneural organs in rabies pathogenesis may contribute to the development of effective treatment strategies of this fatal disease.

AUTHOR SUMMARY

Rabies is a lethal viral infection that targets the nervous system and generally can be transmitted to humans by bites of infected animals. While there has been significant research focused on how the virus damages the brain, little is known about how the infection affects other organs in the periphery. To address this knowledge gap, we conducted an experimental study to investigate the effects of two distinct wild strains of the virus, one isolated from dogs and the other from bats, on the lungs, liver, and kidneys in mice model of infection. Our findings suggest that the rabies virus infection leads to cell death and produces specific lesions in each of these organs, and we hypothesize that rabies virus may spread to these tissues at the same time as the brain, which possible contributes to the disease outcome. These findings enhance our understanding on how rabies virus targets organs outside the nervous system and its pathology in these different systems.
The salt-and-pepper pattern in mouse blastocysts is compatible with signalling beyond the nearest neighbours
Authors: Fischer Sabine C. , Schardt Simon , Lilao-Garzón Joaquín , Descalzo Silvia Muñoz
Published: May 2023

Embryos develop in a concerted sequence of spatio-temporal arrangements of cells. In the preimplantation mouse embryo, the distribution of the cells in the inner cell mass evolves from a salt-and-pepper pattern to spatial segregation of two distinct cell types. The exact properties of the salt-and-pepper pattern have not been analysed so far. We investigate the spatio-temporal distribution of NANOG and GATA6 expressing cells in the ICM of the mouse blastocysts with quantitative three-dimensional single cell-based neighbourhood analyses. A combination of spatial statistics and agent-based modelling reveals that the cell fate distribution follows a local clustering pattern. Using ordinary differential equations modelling, we show that this pattern can be established by a distance-based signalling mechanism enabling cells to integrate information from the whole inner cell mass into their cell fate decision. Our work highlights the importance of longer-range signalling to ensure coordinated decisions in groups of cells to successfully build embryos.
3D imaging reveals apical stem cell responses to ambient temperature
Authors: Wenzl Christian , Lohmann Jan U.
Published: May 2023

Plant growth is driven by apical meristems at the shoot and root growth points, which comprise continuously active stem cell populations. While many of the key factors involved in homeostasis of the shoot apical meristem (SAM) have been extensively studied under artificial constant growth conditions, only little is known how variations in the environment affect the underlying regulatory network. To shed light on the responses of the SAM to ambient temperature, we combined 3D live imaging of fluorescent reporter lines that allowed us to monitor the activity of two key regulators of stem cell homeostasis in the SAM namelyCLAVATA3(CLV3)andWUSCHEL (WUS),with computational image analysis to derive morphological and cellular parameters of the SAM. WhereasCLV3expression marks the stem cell population,WUSpromoter activity is confined to the organizing center (OC), the niche cells adjacent to the stem cells, hence allowing us to record on the two central cell populations of the SAM. Applying an integrated computational analysis of our data we found that variations in ambient temperature not only led to specific changes in spatial expression patterns of key regulators of SAM homeostasis, but also correlated with modifications in overall cellular organization and shoot meristem morphology.
Novel regulatory variant in ABO intronic RUNX1 binding site inducing A3phenotype
Authors: Thun Gian Andri , Gueuning Morgan , Sigurdardottir Sonja , Meyer Eduardo , Gourri Elise , Schneider Linda , Merki Yvonne , Trost Nadine , Neuenschwander Kathrin , Engström Charlotte , Frey Beat M. , Meyer Stefan , Mattle-Greminger Maja P.
Published: May 2023

Background and Objectives

Mixed-field agglutination in ABO phenotyping (A3, B3) has been linked to genetically different blood cell populations like in chimerism, or to rare variants in eitherABOexon 7 or regulatory regions. Clarification of such cases is challenging and would greatly benefit from sequencing technologies that allow resolving full-gene haplotypes at high resolution.

Materials and Methods

We used long-read sequencing by Oxford Nanopore Technologies to sequence the entireABOgene, amplified in two overlapping long-range PCR fragments, in a blood donor presented with A3B phenotype. Confirmation analyses were carried out by Sanger sequencing and included samples from other family members.

Results

Our data revealed a novel heterozygous g.10924C>A variant on theABO*A-allele located in the transcription factor binding site for RUNX1 in intron 1 (+5.8 kb site). Inheritance was shown by the results of the donor’s mother, who shared the novel variant and the anti-A specific mixed-field agglutination.

Conclusion

We discovered a regulatory variant in the 8-bp RUNX1 motif ofABO, which extends current knowledge of three other variants affecting the same motif and also leading to A3or B3phenotypes. Overall, long-range PCR combined with nanopore sequencing proved powerful and showed great potential as emerging strategy for resolving cases with cryptic ABO phenotypes.
JLOH: Inferring Loss of Heterozygosity Blocks from Sequencing Data
Authors: Schiavinato Matteo , del Olmo Valentina , Muya Victor Njenga , Gabaldón Toni
Published: May 2023

Heterozygosity is a genetic condition in which two or more alleles are found at a genomic locus. Among the organisms that are more prone to heterozygosity are hybrids, i.e. organisms that are the offspring of genetically divergent yet still interfertile individuals. One of the most studied aspects is the loss of heterozygosity (LOH) within genomes, where multi-allelic sites lose one of their two alleles by converting it to the other, or by remaining hemizygous at that site. LOH is deeply interconnected with adaptation, especially in hybrids, but thein silicotechniques to infer LOH blocks are hardly standardized, and a general tool to infer and analyse them in most genomic contexts and species is missing. Here, we present JLOH, a computational toolkit for the inference and exploration of LOH blocks which only requires commonly available genomic data as input. Starting from mapped reads, called variants and a reference genome sequence, JLOH infers candidate LOH blocks based on single-nucleotide polymorphism density (SNPs/kbp) and read coverage per position. If working with a hybrid organism of known parentals, JLOH is also able to assign each LOH block to its subgenome of origin.
Intercellular interaction between FAP fibroblasts and CD150 inflammatory monocytes mediates fibro-stenosis in Crohn’s disease
Authors: Ke Bo-Jun , Abdurahiman Saeed , Biscu Francesca , Dragoni Gabriele , Santhosh Sneha , De Simone Veronica , Zouzaf Anissa , van Baarle Lies , Stakenborg Michelle , Bosáková Veronika , Van Rymenant Yentl , Verhulst Emile , Verstockt Sare , Bislenghi Gabriele , Wolthuis Albert , Frič Jan , Breynaert Christine , D’Hoore Andre , Van Der Veken Pieter , De Meester Ingrid , Verstockt Bram , de Hertogh Gert , Vermeire Séverine , Matteoli Gianluca
Published: May 2023

Crohn’s disease (CD) is marked by recurring intestinal inflammation and tissue injury, often resulting in fibro-stenosis and bowel obstruction, necessitating surgical intervention with high recurrence rates. To elucidate complex intercellular interactions leading to fibro-stenosis in CD, we analysed the transcriptome of cells isolated from the transmural ileum of CD patients, including a trio of lesions from each patient: non-affected, inflamed, and stenotic ileum samples, and compared them with samples from non-CD patients. Our computational analysis revealed that pro-fibrotic signals from a subset of monocyte-derived cells expressing CD150 induce a disease-specific fibroblast population, resulting in chronic inflammation and tissue fibrosis. The transcription factor TWIST1 was identified as a key modulator of fibroblast activation and extracellular matrix (ECM) production. Therapeutic inhibition of TWIST1 inhibits fibroblast activation, reducing ECM production and deposition. These findings suggest that the myeloid-stromal axis may offer a promising therapeutic target to prevent fibro-stenosis in CD.
Genetic control of the error-prone repair of a chromosomal double-strand break with 5’ overhangs in yeast
Authors: Shaltz Samantha , Jinks-Robertson Sue
Published: May 2023

A targeted double-strand break introduced into the genome ofSaccharomyces cerevisiaeis repaired by the relatively error-prone nonhomologous-end joining (NHEJ) pathway when homologous recombination is not an option. A ZFN cleavage site was inserted out-of-frame into theLYS2locus of a haploid yeast strain to study the genetic control of NHEJ when the ends contain 5′ overhangs. Repair events that destroyed the cleavage site were identified either as Lys+colonies on selective medium or as surviving colonies on rich medium. Junction sequences in Lys+events solely reflected NHEJ and were influenced by the nuclease activity of Mre11 as well as by the presence/absence of the NHEJ-specific polymerase Pol4 and the translesion-synthesis DNA polymerases Pol σ and Pol 11. Although most NHEJ events were dependent on Pol4, a 29-bp deletion with endpoints in 3-bp repeats was an exception. The Pol4-independent deletion required TLS polymerases as well as the exonuclease activity of the replicative Pol DNA polymerase. Survivors were equally split between NHEJ events and 1 kb or 11 kb deletions that reflected microhomology-mediated end joining (MMEJ). MMEJ events required the processive resection activity of Exo1/Sgs1, but there unexpectedly was no dependence on the Rad1-Rad10 endonuclease for the removal of presumptive 3′ tails. Finally, NHEJ was more efficient in non-growing than in growing cells and was most efficient in G0 cells. These studies provide novel insight into the flexibility and complexity of error-prone DSB repair in yeast.
VERY LONG-CHAIN ACYL-CoA SYNTHETASE-3 (ACSVL3) PROMOTES THE MALIGNANT GROWTH BEHAVIOR OF U87 GLIOMA CELLS VIA CHANGES IN CELL CYCLE WITHOUT AFFECTING APOPTOSIS
Authors: Yang Haiyan , Shi Xiaohai , Kolar Elizabeth A. , Clay Emily M. , Xia Shuli , Pei Zhengtong , Watkins Paul A.
Published: May 2023

Decreasing the expression of very long-chain acyl-CoA synthetase 3 (ACSVL3) in U87MG glioblastoma cells by either RNA interference or genomic knockout (KO) significantly decreased their growth rate in culture, as well as their ability to form rapidly growing tumors in mice. U87-KO cells grew at a 9-fold slower rate than U87MG cells. When injected subcutaneously in nude mice, the tumor initiation frequency of U87-KO cells was 70% of that of U87MG cells, and the average growth rate of tumors that did form was decreased by 9-fold. Two hypotheses to explain the decreased growth rate of KO cells were investigated. Lack of ACSVL3 could reduce cell growth either by increasing apoptosis, or via effects on the cell cycle. We examined intrinsic, extrinsic, and caspase-independent apoptosis pathways; none were affected by lack of ACSVL3. However, significant differences in the cell cycle were seen in KO cells, suggesting arrest in S-phase. Levels of cyclin-dependent kinases 1, 2, and 4 were elevated in U87-KO cells, as were regulatory proteins p21 and p53 that promote cell cycle arrest. In contrast, lack of ACSVL3 reduced the level of the inhibitory regulatory protein p27. γ-H2AX, a marker of DNA double strand breaks, was elevated in U87-KO cells, while pH3, a mitotic index marker, was reduced. Previously reported alterations in sphingolipid metabolism in ACSVL3-depleted U87 cells may explain the effect of KO on cell cycle. These studies reinforce the notion that ACSVL3 is a promising therapeutic target in glioblastoma.
Local Genetic Sex Differences in Quantitative Traits
Authors: Uffelmann Emil , de Leeuw Christiaan , Posthuma Danielle
Published: May 2023

Introductory Paragraph

Recently, large-scale sex-stratified Genome-Wide Association Studies (GWASs) have been conducted that compare heritabilities and estimate global genetic correlations between males and females1–5. These studies have identified a small number of traits that show genetic sex differences on a global level. However, such global analyses cannot elucidate the local architecture of genetic sex differences6. To address this gap and gain insight into local (dis-)similarities in genetic signal between males and females, we estimated local genetic correlations and tested whether these differ from one, compared local heritability estimates, and tested for equality of local genetic effects in 157 quantitative traits. While the vast majority of loci do not significantly differ between males and females, almost every trait we studied had at least one locus that did. We show that these loci can highlight trait-relevant biology and may partly explain observed phenotypic sex differences.
Self-assembly of DNA nanostructures in different cations
Authors: Rodriguez Arlin , Gandavadi Dhanush , Mathivanan Johnsi , Song Tingjie , Madhanagopal Bharath Raj , Talbot Hannah , Sheng Jia , Wang Xing , Chandrasekaran Arun Richard
Published: May 2023

The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions which restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions have been used so far (typically Mg2+and Na+). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (∼134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca2+, Ba2+, Na+, K+and Li+and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na+, K+and Li+) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg2+, Ca2+and Ba2+). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.
Visualizing the chaperone-mediated folding trajectory of the G protein β5 β-propeller
Authors: Wang Shuxin , Sass Mikaila I. , Kwon Yujin , Ludlam W. Grant , Smith Theresa M. , Carter Ethan J. , Gladden Nathan E. , Riggi Margot , Iwasa Janet H. , Willardson Barry M. , Shen Peter S.
Published: May 2023

The cytosolic Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with β- propeller domains. Here, we determined structures of CCT in complex with its accessory co chaperone, phosducin-like protein 1 (PhLP1), in the process of folding Gβ5, a component of Regulator of G protein Signaling (RGS) complexes. Cryo-EM and image processing revealed an ensemble of distinct snapshots that represent the folding trajectory of Gβ5from an unfolded molten globule to a fully folded β-propeller. These structures reveal the mechanism by which CCT directs Gβ5folding through initiating specific intermolecular contacts that facilitate the sequential folding of individual β-sheets until the propeller closes into its native structure. This work directly visualizes chaperone-mediated protein folding and establishes that CCT directs folding by stabilizing intermediates through interactions with surface residues that permit the hydrophobic core to coalesce into its folded state.
Ab initioprediction of specific phospholipid complexes and membrane association of HIV-1 MPER antibodies by multi-scale simulations
Authors: Maillie Colleen , Golden Jay , Wilson Ian A. , Ward Andrew B. , Mravic Marco
Published: May 2023

A potent class of HIV-1 broadly neutralizing antibodies (bnAbs) targets the envelope glycoprotein’s membrane proximal exposed region (MPER) through a proposed mechanism where hypervariable loops embed into lipid bilayers and engage headgroup moieties alongside the epitope. We address the feasibility and determinant molecular features of this mechanism using multi-scale modeling. All-atom simulations of 4E10, PGZL1, 10E8 and LN01 docked onto HIV-like membranes consistently form phospholipid complexes at key complementarity-determining region loop sites, solidifying that stable and specific lipid interactions anchor bnAbs to membrane surfaces. Ancillary protein-lipid contacts reveal surprising contributions from antibody framework regions. Coarse-grained simulations effectively capture antibodies embedding into membranes. Simulations estimating protein-membrane interaction strength for PGZL1 variants along an inferred maturation pathway show bilayer affinity is evolved and correlates with neutralization potency. The modeling demonstrated here uncovers insights into lipid participation in antibodies’ recognition of membrane proteins and highlights antibody features to prioritize in vaccine design.
Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall
Authors: Harvey William T. , Ebert Peter , Ebler Jana , Audano Peter A. , Munson Katherine M. , Hoekzema Kendra , Porubsky David , Beck Christine R. , Marschall Tobias , Garimella Kiran , Eichler Evan E.
Published: May 2023

Advances in long-read sequencing (LRS) technology continue to make whole-genome sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phasedde novogenome assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs) associated with disease. Limitations remain with respect to cost, scalability, and platform-dependent read accuracy and the tradeoffs between sequence coverage and sensitivity of variant discovery are important experimental considerations for the application of LRS. We compare the genetic variant calling precision and recall of Oxford Nanopore Technologies (ONT) and PacBio HiFi platforms over a range of sequence coverages. For read-based applications, LRS sensitivity begins to plateau around 12-fold coverage with a majority of variants called with reasonable accuracy (F1 score above 0.5), and both platforms perform well for SV detection. Genome assembly increases variant calling precision and recall of SVs and indels in HiFi datasets with HiFi outperforming ONT in quality as measured by the F1 score of assembly-based variant callsets. While both technologies continue to evolve, our work offers guidance to design cost-effective experimental strategies that do not compromise on discovering novel biology.
The microbiota ofAmblyomma americanumreflects known westward expansion
Authors: Martinez-Villegas Luis , Lado Paula , Klompen Hans , Wang Selena , Cummings Caleb , Pesapane Risa , Short Sarah M.
Published: May 2023

Abstract

Amblyomma americanum, a known vector of multiple tick-borne pathogens, has expanded its geographic distribution across the United States in the past decades. Tick microbiomes may play a role shaping their host’s life history and vectorial capacity. Bacterial communities associated withA. americanummay reflect, or enable, geographic expansion and studying the microbiota will improve understanding of tick- borne disease ecology. We examined the microbiota structure of 189 adult ticks collected in four regions encompassing their historical and current geographic distribution. Both geographic region of origin and sex were significant predictors of alpha diversity. As in other tick models, within-sample diversity was low and uneven given the presence of dominant endosymbionts. Beta diversity analyses revealed that bacterial profiles of ticks of both sexes collected in the West were significantly different from those of the Historic range. Biomarkers were identified for all regions except the historical range. In addition, Bray-Curtis dissimilarities overall increased with distance between sites. Relative quantification of ecological processes showed that, for females and males, respectively, drift and dispersal limitation were the primary drivers of community assembly. Collectively, our findings highlight how microbiota structural variance discriminates the western-expanded populations ofA. americanumticks from the Historical range. Spatial autocorrelation, and particularly the detection of non- selective ecological processes, are indicative of geographic isolation. Our conclusions demonstrate the value of synergistic analysis of biogeographic and microbial ecology data in investigating range expansion inA. americanumand potentially other tick vectors as well.

Importance

The incidence of tick-borne diseases is on the rise worldwide, including in the United States. This increase in cases is in large part due to the geographic expansion of tick vectors. Among them is the Lone Star tick,Amblyomma americanum, and understanding the factors driving its recent expansion is important for risk assessment and tick population control. Climate change and human activities have previously been posited to be main driving forces for their expansion. New sources of relevant biological data can further our understanding of this phenomenon. Microbial communities associated with ticks include bacteria that affect pathogen transmission and tick behaviors. Here, we investigated whether bacterial community and geographic location data could be combined to better understand the expansion ofA. americanumpopulations. It’s not clear whether differences in the microbiota are reflective of or facilitating expansion, but our findings suggest this approach is promising and warrants further investigation.
Graded and sharp transitions in semantic function in left temporal lobe
Authors: Krieger-Redwood Katya , Wang Xiuyi , Souter Nicholas , Alam Tirso Rene del Jesus Gonzalez , Smallwood Jonathan , Jackson Rebecca L. , Jefferies Elizabeth
Published: May 2023

Recent work has focussed on how patterns of functional change within the temporal lobe relate to whole-brain dimensions of intrinsic connectivity variation (Margulies et al., 2016). We examined two such ‘connectivity gradients’ reflecting the separation of (i) unimodal versus heteromodal and (ii) visual versus auditory-motor cortex, examining visually presented verbal associative and feature judgments, plus picture-based context and emotion generation. Functional responses along the first dimension sometimes showed graded change between modality-tuned and heteromodal cortex (in the verbal matching task), and other times showed sharp functional transitions, with deactivation at the extremes and activation in the middle of this gradient (internal generation). The second gradient revealed more visual than auditory-motor activation, regardless of content (associative, feature, context, emotion) or task process (matching/generation). We also uncovered subtle differences across each gradient for content type, which predominantly manifested as differences in relative magnitude of activation or deactivation.
Atomistic ensemble of active SHP2 phosphatase
Authors: Anselmi Massimiliano , Hub Jochen S.
Published: May 2023

SHP2 phosphatase plays an important role in regulating several intracellular signaling pathways. Pathogenic mutations of SHP2 cause developmental disorders and are linked to hematological malignancies and cancer. SHP2 comprises two tandemly-arranged SH2 domains, a catalytic PTP domain, and a disordered C-terminal tail. Under physiological, non-stimulating conditions, the catalytic site of PTP is occluded by the N-SH2 domain, so that the basal activity of SHP2 is low. Whereas the autoinhibited structure of SHP2 has been known for two decades, its active, open structure still represents a conundrum. Since the oncogenic mutant SHP2E76Kalmost completely populates the active, open state, this mutant has been extensively studied as a model for activated SHP2. By molecular dynamics simulations and accurate explicit-solvent SAXS curve predictions, we present the heterogeneous atomistic ensemble of constitutively active SHP2E76Kin solution, encompassing a set of conformational arrangements and radii of gyration in agreement with experimental SAXS data.
Isolated loss of the AUTS2 long isoform, brain-wide or targeted toCalbindin-lineage cells, generates a specific suite of brain, behavioral and molecular pathologies
Authors: Song Yunshu , Seward Christopher H. , Chen Chih-Ying , LeBlanc Amber , Leddy Analise M. , Stubbs Lisa
Published: May 2023

Rearrangements within theAUTS2region are associated with a rare syndromic disorder with intellectual disability, developmental delay and behavioral abnormalities as core features. In addition, smaller regional variants are linked to wide range of neuropsychiatric disorders, underscoring the gene’s essential role in brain development. Like many essential neurodevelopmental genes,AUTS2is large and complex, generating distinct long (AUTS2-l) and short (AUTS2-s) protein isoforms from alternative promoters. Although evidence suggests unique isoform functions, the contributions of each isoform to specificAUTS2-linked phenotypes have not been clearly resolved. Furthermore,Auts2is widely expressed across the developing brain, but cell populations most central to disease presentation have not been determined. In this study, we focused on the specific roles of AUTS2-l in brain development, behavior, and postnatal brain gene expression, showing that brain-wide AUTS2-l ablation leads to specific subsets of the recessive pathologies associated with C-terminal mutations that disrupt both isoforms. We identify downstream genes that could explain expressed phenotypes including hundreds of putative direct AUTS2- l target genes. Furthermore, in contrast to C-terminalAuts2mutations which lead to dominant hypoactivity, AUTS2-l loss-of-function is associated with dominant hyperactivity, a phenotype exhibited by many human patients. Finally, we show that AUTS2-l ablation inCalbindin 1-expressing cell lineages is sufficient to yield learning/memory deficits and hyperactivity with abnormal dentate gyrus granule cell maturation, but not other phenotypic effects. These data provide new clues toin vivoAUTS2-l functions and novel information relevant to genotype-phenotype correlations in the humanAUTS2region.
Revealing Heavy Metal Resistances in the Yanomami Microbiome
Authors: Conteville Liliane Costa , Oliveira-Ferreira Joseli , Vicente Ana Carolina P
Published: May 2023

BACKGROUND

The Amazon hosts invaluable and unique biodiversity as well as mineral resources. As a consequence, there are large illegal and artisanal gold mining areas in indigenous territories. Mercury has been used in gold mining, and some are released into the environment and atmosphere, primarily affecting indigenous as the Yanomami. In addition, other heavy metals have been associated with gold mining and other metal-dispersing activities in the region.

OBJECTIVE

Investigation of the Yanomami gut microbiome focusing on metal resistance.

METHODS

Metagenomic data from the Yanomami gut microbiome were assembled into contigs, and their putative proteins were matched to a database of metal resistance proteins.

FINDINGS

Most identified proteins have the potential to confer resistance to multiple metals (two or more), followed by mercury, copper, zinc, chromium, arsenic, and others. Operons with potential resistance to mercury, arsenic, chromium, nickel, zinc, copper, copper/silver, and cobalt/nickel were identified. Mercury resistance operon was the most abundant, even though a diversity of operons in the Yanomami microbiome was observed to have the potential to confer resistance to various metals

CONCLUSION

The Yanomami gut microbiome gene composition shows that these people have been exposed directly or indirectly to mercury and other heavy metals.

Sponsorships

This study was partly financed by the Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ); and PAEF (IOC-023-FIO-18-2-47).
Molecular basis for Gβγ-mediated activation of phosphoinositide 3-kinase γ
Authors: Chen Chun-Liang , Syahirah Ramizah , Ravala Sandeep K. , Yen Yu-Chen , Klose Thomas , Deng Qing , Tesmer John J. G.
Published: May 2023

The conversion of PIP2 to PIP3 by phosphoinositide 3-kinase γ (PI3Kγ) is a critical step in neutrophil chemotaxis and is essential for metastasis in many types of cancer. PI3Kγ is activated via directed interaction with Gβγ heterodimers released from cell-surface G protein-coupled receptors (GPCRs) responding to extracellular signals. To resolve how Gβγ activates PI3Kγ, we determined cryo-EM reconstructions of PI3Kγ–Gβγ complexes in the presence of various substrates/analogs, revealing two distinct Gβγ binding sites, one on the p110γ helical domain and one on the C-terminal domain of the p101 subunit. Comparison of these complexes with structures of PI3Kγ alone demonstrates conformational changes in the kinase domain upon Gβγ binding similar to those induced by Ras·GTP. Assays of variants perturbing the two Gβγ binding sites and interdomain contacts that change upon Gβγ binding suggest that Gβγ not only recruits the enzyme to membranes but also allosterically controls activity via both sites. Studies in a zebrafish model examining neutrophil migration are consistent with these results. These findings set the stage for future detailed investigation of Gβγ-mediated activation mechanisms in this enzyme family and will aid in developing drugs selective for PI3Kγ.
Macrophages allocate independent of apoptosis and produce reactive oxygen species during interdigital phagocytosis
Authors: Hernández-García David , García-Meléndrez Celina , Hernández-Martínez Rocío , Collazo-Navarrete Omar , Covarrubias Luis
Published: May 2023

During programmed cell death (PCD), it is commonly accepted that macrophages are recruited by apoptotic cells to complete cell degradation. Interdigital cell death, a classical model of PCD, contributes to digit individualization in limbs of mammals and other vertebrates. Here we show that macrophages are present in interdigits before significant cell death occurs and remain after apoptosis inhibition. The typical interdigital phagocytic activity was not observed after a partial depletion of macrophages and was markedly reduced by engulfment/phagosome maturation inhibition, as detected by its association with high lysosomal activity. β-galactosidase activity in this region was also coupled with phagocytosis, against its relationship with cellular senescence. Interdigital phagocytosis correlated with high levels of reactive oxygen species (ROS), common in embryo regions carrying abundant cell death, suggesting that macrophages are the major source of ROS. ROS generation was dependent on NADPH oxidases and blood vessel integrity, but not directly associated with lysosomal activity. Therefore, macrophages prepattern regions where abundant cell death is going to occur, and high lysosomal activity and the generation of ROS by an oxidative burst-like phenomenon are activities of phagocytosis.

Summary statement

Recruitment of macrophages to the interdigital regions is not linked to apoptosis initiation and they phagocytize by a mechanism involving high lysosomal activity and an oxidative burst-like phenomenon.
Freezing of gait assessment with inertial measurement units and deep learning: effect of tasks, medication states, and stops
Authors: Yang Po-Kai , Filtjens Benjamin , Ginis Pieter , Goris Maaike , Nieuwboer Alice , Gilat Moran , Slaets Peter , Vanrumste Bart
Published: May 2023

Abstract

Background

Freezing of gait (FOG) is an episodic and highly disabling symptom of Parkinson’s Disease (PD). Traditionally, FOG assessment relies on time-consuming visual inspection of camera footage. Therefore, previous studies have proposed portable and automated solutions to annotate FOG. However, automated FOG assessment is challenging due to gait variability caused by medication effects and varying FOG-provoking tasks. Moreover, whether automated approaches can differentiate FOG from typical everyday movements, such as volitional stops, remains to be determined. To address these questions, we evaluated an automated FOG assessment model with deep learning (DL) based on inertial measurement units (IMUs). We assessed its performance trained on all standardized FOG-provoking tasks and medication states, as well as on specific tasks and medication states. Furthermore, we examined the effect of adding stopping periods on FOG detection performance.

Methods

Twelve PD patients with self-reported FOG (mean age 69.33 ± 6.28 years) completed a FOG-provoking protocol, including timed-up-and-go and 360-degree turning-in-place tasks in On/Off dopaminergic medication states with/without volitional stopping. IMUs were attached to the pelvis and both sides of the tibia and talus. A multi-stage temporal convolutional network was developed to detect FOG episodes. FOG severity was quantified by the percentage of time frozen (%TF) and the number of freezing episodes (#FOG). The agreement between the model-generated outcomes and the gold standard experts’ video annotation was assessed by the intra-class correlation coefficient (ICC).

Results

For FOG assessment in trials without stopping, the agreement of our model was strong (ICC(%TF) = 0.92 [0.68, 0.98]; ICC(#FOG) = 0.95 [0.72, 0.99]). Models trained on a specific FOG-provoking task could not generalize to unseen tasks, while models trained on a specific medication state could generalize to unseen states. For assessment in trials with stopping, the model trained on stopping trials made fewer false positives than the model trained without stopping (ICC(%TF) = 0.95 [0.73, 0.99]; ICC(#FOG) = 0.79 [0.46, 0.94]).

Conclusion

A DL model trained on IMU signals allows valid FOG assessment in trials with/without stops containing different medication states and FOG-provoking tasks. These results are encouraging and enable future work investigating automated FOG assessment during everyday life.