bluuebunny/crossref_metadata_2025 huggingface dataset:
OxoScan-MS: Oxonium ion scanning mass spectrometry facilitates plasma glycoproteomics in large scale
Authors: White Matthew E. H. , Jones D. Marc , de Folter Joost , Aulakh Simran Kaur , Flynn Helen R. , Krüger Lynn , Demichev Vadim , Tober-Lau Pinkus , Kurth Florian , Mülleder Michael , Blanchard Véronique , Messner Christoph B. , Ralser Markus
Published: June 2022

Protein glycosylation is a complex and heterogeneous post-translational modification. Specifically, the human plasma proteome is rich in glycoproteins, and as protein glycosylation is frequently dysregulated in disease, glycoproteomics is considered an underexplored resource for biomarker discovery. Here, we present OxoScan-MS, a data-independent mass spectrometric acquisition technology and data analysis software that facilitates sensitive, fast, and cost-effective glycoproteome profiling of plasma and serum samples in large cohort studies. OxoScan-MS quantifies glycosylated peptide features by exploiting a scanning quadrupole to assign precursors to oxonium ions, glycopeptide-specific fragments. OxoScan-MS reaches a high level of sensitivity and selectivity in untargeted glycopeptide profiling, such that it can be efficiently used with fast microflow chromatography without a need for experimental enrichment of glycopeptides from neat plasma. We apply OxoScan-MS to profile the plasma glycoproteomic in an inpatient cohort hospitalised due to severe COVID-19, and obtain precise quantities for 1,002 glycopeptide features. We reveal that severe COVID-19 induces differential glycosylation in disease-relevant plasma glycoproteins, including IgA, fibrinogen and alpha-1-antitrypsin. Thus, with OxoScan-MS we present a strategy for quantitatively mapping glycoproteomes that scales to hundreds and thousands of samples, and report glycoproteomic changes in severe COVID-19.
Increased α-ketoglutarate as a missing link from the C3-C4 intermediate state to C4 photosynthesis in the genus Flaveria
Authors: Tang Qiming , Huang Yuhui , Ni Xiaoxiang , Lyu Ming-Ju Amy , Chen Genyun , Sage Rowan , Zhu Xinguang
Published: June 2022

As a complex trait, C4 photosynthesis has multiple independent origins in evolution. Phylogenetic evidence and theoretical analysis suggest that C2 photosynthesis, which is driven by glycine decarboxylation in the bundle sheath cell, may function as a bridge from C3 towards C4 photosynthesis. However, the exact molecular mechanism underlying the transition between C2 photosynthesis towards C4 photosynthesis remains elusive. Here, we provide multiple evidence suggesting a role of higher α-ketoglutarate (AKG) concentration during this transition. Metabolomic data of 12 Flaveria species, including multiple photosynthetic types, show that AKG concentration initially increases in the C3-C4 intermediate with a further increase in C4 species. Petiole feeding of AKG increased the concentrations of C4 related metabolites in C3-C4 and C4 species but not the activity of C4 related enzymes. Sequence analysis shows that glutamate synthase (Fd-GOGAT), which catalyzes the generation of glutamate using AKG, was under strong positive selection during the evolution of C4 photosynthesis. Simulations with a constraint-based model for C3-C4 intermediate further show that decreasing the activity of Fd-GOGAT facilitates the transition from a C2-dominant to a C4-dominant CO2 concentrating mechanisms. All these provide an insight into the mechanistic switch from C3-C4 intermediate to C4 photosynthesis.
TDP 2 modulates the expression of estrogen-responsive oncogenes
Authors: Manguso Nicholas , Kim Minhyung , Joshi Neeraj , Al Mahmud Rasel , Aldaco Juan , Suzuki Ryusuke , Cortes-Ledesma Felipe , Cui Xiaojiang , Yamada Shintaro , Takeda Shunichi , Giuliano Armando , You Sungyong , Tanaka Hisashi
Published: June 2022

With its ligand estrogen, the estrogen receptor (ER) stimulates tumor cell growth by activating a global transcriptional program. This activation involves topoisomerase 2 (TOP2), which resolves topological problems by transiently creating and re-ligating DNA double-strand breaks (DSBs). Recent studies have uncovered the involvement of DNA repair proteins in the repair of TOP2-induced DSBs. These noncanonical repair pathways may serve as backup processes when TOP2 is halted and fails to re-ligate DSBs, but their impact on transcription remains elusive. In this study, we investigated the role of tyrosyl-DNA phosphodiesterase 2 (TDP2), an enzyme that acts for the removal of halted TOP2 from the 5’-end of the DNA, in the estrogen-induced transcriptome. Using TDP2-deficient ER-positive cells and mice, we showed that TDP2 regulates the expression of oncogeneMYC.MYCinduction by estrogen was a very early event (1 hour) and TOP2-dependent. In TDP2-deficient cells, the induction ofMYCby estrogen became prolonged and volatile. Bulk and single-cell RNA-seq identified the oncogenesMYCandCCND1as genes whose estrogen response was regulated by TDP2. These results suggest that TDP2 may play a role in the repair of TOP2-induced DSBs in specific genomic loci and tightly regulates the expression of oncogenes.
Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes
Authors: Kawahara Akito Y. , Storer Caroline G. , Markee Amanda , Heckenhauer Jacqueline , Powell Ashlyn , Plotkin David , Hotaling Scott , Cleland Timothy P. , Dikow Rebecca B. , Dikow Torsten , Kuranishi Ryoichi B. , Messcher Rebeccah , Pauls Steffen U. , Stewart Russell J. , Tojo Koji , Frandsen Paul B.
Published: June 2022

Insect silk is an incredibly versatile biomaterial. Lepidoptera and their sister lineage, Trichoptera, display some of the most diverse uses of silk with varying strength, adhesive qualities and elastic properties. It is well known that silk fibroin genes are long (> 20 kb) and have many repetitive motifs. These features make these genes challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (Plodia interpunctella) and genomic sequences for the caddisfly, Eubasilissa regina. Both genomes were highly contiguous (N50 = 9.7 Mbp/32.4 Mbp, L50 = 13/11) and complete (BUSCO Complete = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. This study demonstrates that HiFi long-read sequencing can significantly help our understanding of genes with highly contiguous, repetitive regions.
Beyond the Delay Neural Dynamics: a Decoding Strategy for Working Memory Error Reduction
Authors: Ye Zeyuan , Li Haoran , Tian Liang , Zhou Changsong
Published: June 2022

Understanding how the brain preserves information despite intrinsic noise is a fundamental question in working memory. Typical working memory tasks consist of delay phase for maintaining information, and decoding phase for retrieving information. While previous works have focused on the delay neural dynamics, it is poorly understood whether and how the neural process during decoding phase reduces memory error. We studied this question by training recurrent neural networks (RNNs) on a color delayed-response task. We found that the trained RNNs reduce the memory error of high-probability-occurring colors (common colors) by decoding/attributing a broader range of neural states to them during decoding phase. This decoding strategy can be further explained by a continuing converging neural dynamics following delay phase and a non-dynamic biased readout process. Our findings highlight the role of the decoding phase in working memory, suggesting that neural systems deploy multiple strategies across different phases to reduce memory errors.

Significance

Preserving information under noise is crucial in working memory. A typical working memory task consists of a delay phase for maintaining information, and a decoding phase for decoding the maintained into an output action. While the delay neural dynamics have been intensively studied, the impact of the decoding phase on memory error reduction remains unexplored. We trained recurrent neural networks (RNNs) on a color delayed-response task and found that RNNs reduce memory error of a color by decoding a larger portion of the neural state to that color. This strategy is supported both by a converging neural dynamic, and a non-dynamic readout process. Our results suggest that neural networks can utilize diverse strategies, beyond delay neural dynamics, to reduce memory errors.
Dynamin forms liquid-like condensates at synapses to support ultrafast endocytosis
Authors: Imoto Yuuta , Ma Ye , Itoh Kie , Blumrich Eva-Maria , Matsubayashi Hideaki T. , Liu Jian , Wu Bin , Cousin Michael A. , Ha Taekjip , Inoue Takanari , Watanabe Shigeki
Published: June 2022

Endocytosis at synapses is accelerated by the pre-accumulation of Dynamin 1xA at the endocytic zone by Syndapin 1. However, it is unclear how these proteins support the ultrafast kinetics of endocytosis. Here we report that these proteins phase separate at the presynaptic endocytic zone where ultrafast endocytosis takes place. Specifically, the proline-rich motif of Dynamin 1xA interacts with the Src-Homology 3 domain of Syndapin 1 and forms liquid-like condensates. Single-particle tracking of Dynamin 1xA molecules at synapses shows that their diffusion slows down substantially when they are in the condensates, indicating the presence of molecular crowding and intermolecular interaction. When Dynamin 1xA is mutated to disrupt its interaction with Syndapin 1 the condensates do not form. Thus, the liquid-like assembly of these endocytic proteins provides a catalytic platform for ultrafast endocytosis.
Cholecystokinin-expressing (CCK+) basket cells are key controllers of theta-gamma coupled rhythms in the hippocampus
Authors: Chatzikalymniou Alexandra P , Sengupta Spandan , Lefebvre Jeremie , Skinner Frances K
Published: June 2022

Various inhibitory cell types underlie cognitively important brain rhythms and their couplings. Precisely how this is manifest is unclear. Complex network interactions make an understanding of inhibitory cell contributions extremely difficult and using experiments alone is insufficient. Using detailed biophysical models, we obtain hypotheses of how theta and gamma rhythms in the hippocampus are generated and coupled. We find critical contributions by parvalbumin-expressing (PV+) basket cells (BCs), cholecystokinin-expressing (CCK+) BCs and bistratified cells. Based on this, we develop and explore a population rate model and predict that CCK+BCs exert more control relative to PV+BCs for theta-gamma coupling, and that theta frequencies are more strongly affected by PV+BC to CCK+BC coupling relative to CCK+BC to PV+BC. As specific inhibitory cell types can be targeted during behaviour, it is possible to test these predictions. Our work shows that combining models at different scales creates new insights that otherwise would not be revealed.
Ankyrin-B is lipid-modified by S-palmitoylation to promote dendritic membrane scaffolding of voltage-gated sodium channel Nav1.2 in neurons
Authors: Gupta Julie P. , Jenkins Paul M.
Published: June 2022

Neuronal ankyrin-B is an intracellular scaffolding protein that plays multiple roles in the axon. By contrast, relatively little is known about the function of ankyrin-B in dendrites, where ankyrin-B is also localized in mature neurons. Recently, we showed that ankyrin-B acts as a scaffold for the voltage-gated sodium channel, NaV1.2, in dendrites of neocortical pyramidal neurons. How ankyrin-B is itself targeted to the dendritic membrane is not well understood. Here, we report that ankyrin-B is lipid-modified by S-palmitoylation to promote dendritic localization of NaV1.2. We identify the palmitoyl acyl transferase zDHHC17 as a key mediator of ankyrin-B palmitoylation in heterologous cells and in neurons. Additionally, we find that zDHHC17 regulates ankyrin-B protein levels independently of its S-acylation function through a conserved binding mechanism between the ANK repeat domain of zDHHC17 and the zDHHC ankyrin-repeat binding motif of ankyrin-B. We subsequently identify five cysteines in the N-terminal ankyrin repeat domain of ankyrin-B that are necessary for ankyrin-B palmitoylation. Mutation of these five cysteines to alanines not only abolishes ankyrin-B palmitoylation, but also prevents ankyrin-B from scaffolding Nav1.2 at dendritic membranes of neurons due to ankyrin-B’s inability to localize properly at dendrites. Thus, we show palmitoylation is critical for localization and function of ankyrin-B at dendrites. Strikingly, loss of ankyrin-B palmitoylation does not affect ankyrin-B-mediated axonal cargo transport of synaptic vesicle synaptotagmin-1 in neurons. This is the first demonstration of S-palmitoylation of ankyrin-B as an underlying mechanism required for ankyrin-B localization and function in scaffolding Nav1.2 at dendrites.
Sentieon DNAscope LongRead – A highly Accurate, Fast, and Efficient Pipeline for Germline Variant Calling from PacBio HiFi reads
Authors: Freed Donald , Rowell William J. , Wenger Aaron M. , Li Zhipan
Published: June 2022

PacBio® HiFi sequencing is the first technology to offer economical and highly accurate long-read sequencing, with average read lengths greater than 10kb and average base accuracy of 99.8%1. Here, we present DNAscope LongRead, an accurate and efficient pipeline for germline variant calling from PacBio® HiFi reads. DNAscope LongRead is a modification and extension of Sentieon’s DNAscope tool, a precisionFDA award-winning variant caller. DNAscope LongRead is computationally efficient, calling variants from 30x HiFi samples in under 4 hours on a 16-core machine (120 virtual core-hours) and highly accurate, with precision and recall on the most recent GIAB benchmark dataset exceeding 99.83% for HiFi samples sequenced at 30x coverage, and robust to changes in benchmark dataset and upstream library preparation and sequencing.
Mystery of fatal ‘Staggering disease’ unravelled: Novel rustrela virus causes severe encephalomyelitis in domestic cats
Authors: Matiasek Kaspar , Pfaff Florian , Weissenböck Herbert , Wylezich Claudia , Kolodziejek Jolanta , Tengstrand Sofia , Ecke Frauke , Nippert Sina , Starcky Philip , Litz Benedikt , Nessler Jasmin , Wohlsein Peter , Baumbach Christina , Mundhenk Lars , Aebischer Andrea , Reiche Sven , Weidinger Pia , Olofsson Karin M. , Rohdin Cecilia , Weissenbacher-Lang Christiane , Matt Julia , Rosati Marco , Flegel Thomas , Hörnfeldt Birger , Höper Dirk , Ulrich Rainer G. , Nowotny Norbert , Beer Martin , Ley Cecilia , Rubbenstroth Dennis
Published: June 2022

‘Staggering disease’ is a neurological disorder considered a threat to European domestic cats (Felis catus) for almost five decades. However, its aetiology has remained obscure. Rustrela virus (RusV), a relative of rubella virus, has recently been shown to be associated with encephalitis in a broad range of mammalian hosts. Here, we report the detection of RusV RNA and antigen by metagenomic sequencing, RT-qPCR, in-situ hybridization and immunohistochemistry in brain tissues of 28 out of 29 cats with non-suppurative meningoencephalomyelitis and ‘staggering disease’-like neurological disorder from Sweden, Austria, and Germany, but not in non-affected control cats. Screening of possible reservoir hosts in Sweden revealed RusV infection in wood mice (Apodemus sylvaticus). Our work strongly indicates RusV as the long-sought cause of feline ‘staggering disease’. Given its broad host spectrum and considerable geographic range, RusV may be the aetiological agent of neuropathologies in further mammals, possibly even including humans.
Elemental diet enriched in amino acids alters gut microbial community and prevents colonic mucus degradation in mice with colitis
Authors: Zhang Bowei , Zhao Congying , Zhang Yunhui , Zhang Xuejiao , Li Xiang , Liu Xiaoxia , Yin Jia , Li Xinyang , Wang Jin , Wang Shuo
Published: June 2022

The role of dietary amino acids or intact proteins in the progression of colitis remains controversial, and the mechanism involving gut microbes is unclear. Here, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of DSS-induced colitis in mice. Our results showed that ED induced remission of colitis in mice. Notably, ED treatment reduced the abundance of the mucolytic bacteria Akkermansia and Bacteroides, which was attributed to the decreased colonic protein fermentation. Consistently, the activities of mucolytic enzymes were decreased, leading to the protection of mucus layer degradation and microbial invasion. The fecal microbiota transplantation of ED-fed mice reshaped microbial ecology and alleviated intestinal inflammation in recipient mice. ED failed to induce remission of colitis in pseudo-germ-free mice. Together, we convincingly demonstrated the critical role of gut microbiota in the prevention of ED on colitis.

Importance

The prevalence of inflammatory bowel disease is rapidly increasing and has become a global burden. Several specific amino acids have been shown to benefit mucosal healing and colitis remission. However, the role of amino acids or intact proteins in diets and enteral nutrition formulas is controversial, and the mechanisms involving gut microbes remain unclear. In this study, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of colitis in mice. The underlying mechanisms were explored by utilizing fecal microbiota transplantation and pseudo-germ-free mice. ED treatment reduced the abundance of mucolytic bacteria, thereby protecting the mucus layer from microbial invasion and degradation. For the first time, we convincingly demonstrated the critical role of gut microbiota in the effects of ED. This study may provide new insights into the gut microbiota-diet interaction in human health.
Plant signals anticipate the induction of the type III secretion system inPseudomonas syringaepv.actinidiaefacilitating efficient temperature-dependent effector translocation
Authors: Puttilli Maria Rita , Danzi Davide , Correia Cristiana , Brandi Jessica , Cecconi Daniela , Manfredi Marcello , Marengo Emilio , Santos Conceição , Spinelli Francesco , Polverari Annalisa , Vandelle Elodie
Published: June 2022

Disease resistance in plants depends on a molecular dialogue with microbes that involves many known chemical effectors, but the time course of the interaction and the influence of the environment are largely unknown. The outcome of host–pathogen interactions is thought to reflect the offensive and defensive capabilities of both players. When plants interact withPseudomonas syringae, several well-characterized virulence factors contribute to early bacterial pathogenicity, including the type III secretion system (T3SS), which must be activated by signals from the plant and environment to allow the secretion of virulence effectors. The manner in which these signals regulate T3SS activity is still unclear. Here, we strengthen the paradigm of the plant–pathogen molecular dialogue by addressing overlooked details concerning the timing of interactions, specifically the role of plant signals and temperature on the regulation of bacterial virulence during the first few hours of the interaction. Whole-genome expression profiling after 1 h revealed that the perception of plant signals from kiwifruit or tomato extracts anticipates T3SS expression inP. syringaepv.actinidiaecompared to apoplast-like conditions, facilitating more efficient effector transportin planta, as revealed by the induction of a temperature-dependent hypersensitive response in the non-host plantArabidopsis thalianaCol-0. Our results show that, in the arms race between plants and bacteria, the temperature-dependent timing of bacterial virulence versus the induction of plant defenses is probably one of the fundamental parameters governing the outcome of the interaction.

Abstract importance

Plant diseases– their occurrence and severity– result from the impact of three factors: the host, the pathogen, and the environmental conditions, interconnected in the disease triangle. Time was further included as a fourth factor accounting for plant disease, leading to a more realistic three-dimensional disease pyramid to represent the evolution of disease over time. However, this representation still considers time only as a parameter determining when and to which extent a disease will occur, at a scale from days to months. Here, we show that time is a factor regulating the arms race between plants and pathogens, at a scale from minutes to hours, and strictly depends on environmental factors. Thus, besides the arms possessed by pathogens and plants per se, the opportunity and the timing of arms mobilization should make the difference to determine the outcome of an interaction and thus the occurrence of plant disease.
Iron status and the risk of sepsis and severe COVID-19: A two-sample Mendelian randomization study
Authors: Mohus Randi Marie , Flatby Helene , Liyanarachi Kristin V. , DeWan Andrew T. , Solligård Erik , Damås Jan Kristian , Åsvold Bjørn Olav , Gustad Lise T. , Rogne Tormod
Published: June 2022

Introduction

Observational studies have indicated an association between iron status and risk of sepsis and severe COVID-19. However, these findings may be affected by residual confounding, reverse causation.

Methods

In a two-sample Mendelian randomization study using inverse variance weighted method, we estimated the effect of genetically-predicted iron biomarkers (serum iron, transferrin saturation (TSAT), total iron binding capacity (TIBC) and ferritin) on risk of sepsis and risk of being hospitalized with COVID-19. For the COVID-19 outcomes we additionally conducted sex-stratified analyses. Weighted median, Weighted mode and MR Egger were used as sensitivity analyses.

Results

For risk of sepsis, one standard deviation increase in genetically-predicted serum iron was associated with odds ratio (OR) of 1.14 (95% confidence interval [CI] 1.01 to 1.29,P=0.031). The findings were supported in the analyses for transferrin saturation and total iron binding capacity, while the estimate for ferritin was inconclusive. We found a tendency of higher risk of hospitalization with COVID-19 for serum iron; OR 1.29 (CI 0.97–1.72,P=0.08), where sex stratified analyses showed OR 1.63 (CI 0.94–2.86,P=0.09) for women and OR 1.21 (CI 0.92–1.62,P=0.17) for men. Sensitivity analyses supported the main findings and did not suggest bias due to pleiotropy.

Conclusions

Our findings suggest a causal effect of genetically-predicted higher iron status and risk of hospitalization due to sepsis and indications of an increased risk of being hospitalized with COVID-19. These findings warrant further studies to assess iron status in relation to severe infections, including the potential of improved management.
Superior prognostic value of three-dimensional echocardiography-derived right ventricular ejection fraction: a meta-analysis
Authors: Sayour Alex Ali , Tokodi Márton , Celeng Csilla , Takx Richard A. P. , Fábián Alexandra , Lakatos Bálint K. , Friebel Rocco , Surkova Elena , Merkely Béla , Kovács Attila
Published: June 2022

Aims

We aimed to confirm that three-dimensional echocardiography (3DE)-derived right ventricular (RV) ejection fraction (EF) is a more robust predictor of adverse cardiopulmonary outcomes than the conventional echocardiographic parameters.

Methods and Results

We performed a meta-analysis of studies reporting the impact of unit change of RVEF, tricuspid annular plane systolic excursion (TAPSE), fractional area change (FAC), and free-wall longitudinal strain (FWLS) on clinical outcomes (all-cause mortality and/or adverse cardiopulmonary outcomes). Hazard ratios (HR) were rescaled by the within-study standard deviations (SD) to represent standardized changes. Within each study, we calculated the ratio of HRs related to 1 SD reduction in RVEF versus TAPSE, or FAC, or FWLS, to quantify the predictive value of RVEF relative to the other metrics. These ratios of HRs were pooled using random-effects models.

Ten independent studies were identified as suitable, including data on 1,928 patients with various cardiopulmonary conditions. Overall, 1 SD reduction in RVEF was robustly associated with adverse outcomes (HR: 2.64 [95% CI: 2.18 to 3.20], p<0.001; heterogeneity: I2=65%, p=0.002). In studies reporting HRs for RVEF and TAPSE, FAC, or FWLS in the same cohort, RVEF had superior predictive value per SD reduction versus the other three parameters (vs. TAPSE, HR: 1.54 [95% CI: 1.04 to 2.28], p=0.031; vs. FAC, HR: 1.45 [95% CI: 1.15 to 1.81], p=0.001; vs. FWLS, HR: 1.44 [95% CI: 1.07 to 1.95], p=0.018).

Conclusion

3DE-derived RVEF has superior prognostic value compared with conventional RV indices, therefore, it might further refine the risk stratification of patients with cardiopulmonary diseases.

Graphical Abstract

Added predictive value of three-dimensional (3D) echocardiography-derived right ventricular ejection fraction (RVEF) versus conventional metrics of RV systolic function on clinical outcomes: a meta-analysis of 10 studies. FAC: fractional area change, FWLS: free-wall longitudinal strain, HR: hazard ratio, SD: standard deviation, TAPSE: tricuspid annular plane systolic excursion
Osmotic stress response in BetP: How lipids and K+ team up to overcome downregulation
Authors: Heinz Veronika , Güler Günnur , Leone Vanessa , Madej M. Gregor , Maksimov Stanislav , Gärtner Rebecca M. , Rudi Olga , Hamdi Farzad , Kastritis Panagiotis L. , Mäntele Werner , Krämer Reinhard , Forrest Lucy R. , Perez Camilo , Ziegler Christine
Published: June 2022

The trimeric betaine symporter BetP senses an osmotic upshift via its osmosensory C-terminal domain and responds rapidly with a steep increase in transport rate. Full activation requires both an elevated internal K+ concentration and a yet unknown membrane stimulus. Moreover, the molecular mechanisms of stress sensing and upregulation remain unclear. Here, we show that K+ binding to BetP in vivo is highly cooperative. Using X-ray crystallography, we identify four putative K+ interaction sites at the C-terminal domains of BetP. Single particle CryoEM on BetP reconstituted in amphipols (AMP-BetP), in the absence of K+, revealed that the three C-terminal domains are oriented symmetrically near the membrane surface, representing a new downregulated state. The presence of K+ resulted in asymmetric partial unfolding of the C-terminal domains, which was assigned as an intermediate between the downregulated state and the conformation observed in crystal structures. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy in 2D crystals of BetP reveal glutamate/aspartate and tyrosine responses to K+, in agreement with the identified K+ interaction sites, as well as specific unfolding events in the C-terminal domain upon activation. A rearrangement of the relative protomer orientations confers upregulation through key structural elements involved in the alternating access of BetP affecting sodium and betaine binding affinities. Although K+-specific regulation is unique to BetP we discuss unfolding/refolding of sensory domains as a unifying element in hyperosmotic stress response of osmoregulated transporters.
Inhibition of Tgfβ signaling enables durable ventricular pacing by TBX18 gene transfer
Authors: Fan Jinqi , Kim Nam Kyun , Fernandez Natasha , Kim Tae Yun , Li Jun , Wolfson David , Cho Hee Cheol
Published: June 2022

Implantable cardiac pacemaker devices are generally effective for patients with symptomatic bradyarrhythmia. However, device-dependent cardiac pacing is far from ideal and often inadequate, particularly for pediatric patients who need to go through invasive revision of the indwelling hardware. Biological pacemakers have been proposed as device-free alternatives to the current treatment, but sustained, unwavering biological pacing beyond days after the biologic delivery has not been demonstrated. We have previously demonstrated that re-expression of an embryonic transcription factor, TBX18, could reprogram ventricular cardiomyocytes into induced pacemaker myocytes (iPMs). Here, we report that exogenous expression of TBX18 per se leads to severe fibrosis in situ, impairing the iPMs’ ability to pace together. Acute fibrosis is accompanied with proliferation and activation of cardiac fibroblasts via Tgfβ-Smad2/3 pathway. Small molecule inhibition of Tgfβ signaling mitigated the interstitial remodeling, independent from TBX18-induced iPM reprogramming at the single-cell level. Direct and focal gene transfer of TBX18 into the left ventricular myocardium created ventricular pacing in a rat model of chronic atrioventricular block, but such activity began to wane in a week. In contrast, a combination therapy consisting of TBX18 gene transfer and Tgfβ inhibition enabled sustained biological pacing beyond the four-week study period. Our data demonstrate that inhibition of Tgfβ signaling suffices to achieve durable cardiac pacing by TBX18-induced biological pacemakers.
Spatial metabolomics reveal divergent cardenolide processing in the monarch butterfly (Danaus plexippus) and the common crow (Euploea core)
Authors: Dreisbach Domenic , Bhandari Dhaka R. , Betz Anja , Tenbusch Linda , Vilcinskas Andreas , Spengler Bernhard , Petschenka Georg
Published: June 2022

Although being famous for sequestering milkweed cardenolides, the mechanism of sequestration and where cardenolides are localized in caterpillars of the monarch butterfly (Danaus plexippus) is still unknown. While monarchs tolerate cardenolides by a resistant Na+/K+-ATPase, it is unclear how closely related species such as the non-sequestering common crow (Euploea core) cope with these toxins. Using novel atmospheric-pressure scanning microprobe matrix-assisted laser/desorption ionization mass spectrometry imaging, we compared the distribution of cardenolides in caterpillars ofD. plexippusandE. core. Specifically, we tested at which physiological scale quantitative differences between both species are mediated and how cardenolides distribute across body tissues. WhereasD. plexippussequestered most cardenolides from milkweed (Asclepias curassavica), no cardenolides were found in the tissues ofE. core. Remarkably, quantitative differences already manifest in the gut lumen: while monarchs retain and accumulate cardenolides above plant concentrations, the toxins are degraded in the gut lumen of crows. We visualized cardenolide transport over the monarch midgut epithelium and identified integument cells as the final site of storage where defenses might be perceived by predators. Our study provides molecular insight into cardenolide sequestration and highlights the great potential of mass spectrometry imaging for understanding the kinetics of multiple compounds including endogenous metabolites, plant toxins, or insecticides in insects.
Uncovering the evolutionary tail of GZMM: An NSP4 related protease
Authors: Hafeez Ahmer Bin , Ahmad Jamshaid
Published: June 2022

Serine proteases are the most predominant class performing a number of activities in organisms. Undergoing several mutations in their sequence over a span of a billion years yet S1 chymotrypsin/trypsin family has maintained a common fold. Granule Associated Serine Peptidases of Immune Defense (GASPIDS) belonging to the S1 class, found in the granules of immune cells are explicitly involved in the regulation of immune-related functions possessing a conserved catalytic triad Ser-Asp-His. The neutrophils along with other cells express four serine proteases (ELA2, PR3, CTSG and NSP4) sharing certain common characteristics. Similarly, CTLs and NK cells express a set of proteases, Granzymes. This study infers an evolutionary relationship among GASPIDs. We employed computational strategies and found that a higher degree of similarity existed between NSP4 and GZMM as compared to their members i.e. NSPs and granzymes, respectively. Similarly, GZMM a protease of NK cells and t cells lineage is found in the Met-ase locus consisting of NSPs genes i.e.,Ela2, Prtn3andCtsg. The evolutionary relationship ofPrss57/NSP4 andgzmm/GZMM was reconstructed through empirical phylogenetic analysis which revealedPrss57/NSP4 to be closely related togzmm/GZMM. Additional co-expression analysis was carried out to determine the regulatory role ofPrss57, inducingGzmm. From this work, we inferred thatPrss57/NSP4 is closely related toGzmm/GZMM.
A modular T7-based gene expression platform in Pseudomonas putida: Construction and in silico analysis
Authors: Beentjes Marleen , Löwe Hannes , Pflüger-Grau Katharina , Kremling Andreas
Published: June 2022

The T7 RNA polymerase is considered one of the most popular tools for heterologous gene expression in the gold standard biotechnological host Escherichia coli. However, the exploitation of this tool in other prospective biotechnological hosts is still very scarce. To this intent, we established and characterized a modular T7 RNA polymerase-based system for heterologous protein production in Pseudomonas putida, using the model protein eGFP as an easy-to-quantify reporter protein. We have effectively targeted the limitations associated with the initial genetic set-up of the system, such as slow growth and low protein production rates. By replacing the T7-phage inherent TΦ terminator downstream of the heterologous gene with the synthetic tZ terminator, growth and protein production rates improved drastically, and the T7 RNA polymerase system reached a productivity level comparable to that of an intrinsic RNA polymerase based system. Furthermore, we could show that the system is saturated with T7 RNA polymerase by applying a T7 RNA polymerase ribosome binding site library to tune heterologous protein production. The saturation points to an essential role for the ribosome binding sites of the T7 RNA polymerase since, in an oversaturated system, cellular resources are lost to the synthesis of unnecessary T7 RNA polymerase. Eventually, we combined the experimental data into a model that can predict the eGFP production rate with respect to the relative strength of the ribosome binding sites upstream of the T7 gene.

Abstract Figure
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms
Authors: Bordin Nicola , Sillitoe Ian , Nallapareddy Vamsi , Rauer Clemens , Lam Su Datt , Waman Vaishali P. , Sen Neeladri , Heinzinger Michael , Littmann Maria , Kim Stephanie , Velankar Sameer , Steinegger Martin , Rost Burkhard , Orengo Christine
Published: June 2022

Over the last year, there have been substantial improvements in protein structure prediction, particularly in methods like DeepMind’s AlphaFold2 (AF2) that exploit deep learning strategies. Here we report a new CATH-Assign protocol which is used to analyse the first tranche of AF2 models predicted for 21 model organisms and discuss insights these models bring on the nature of protein structure space. We analyse good quality models and those with no unusual structural characteristics, i.e., features rarely seen in experimental structures. For the ∼370,000 models that meet these criteria, we observe that 92% can be assigned to evolutionary superfamilies in CATH. The remaining domains cluster into 2,367 putative novel superfamilies. Detailed manual analysis on a subset of 618 of those which had at least one human relative revealed some extremely remote homologies and some further unusual features, but 26 could be confirmed as novel superfamilies and one of these has an alpha-beta propeller architectural arrangement never seen before. By clustering both experimental and predicted AF2 domain structures into distinct ‘global fold’ groups, we observe that the new AF2 models in CATH increase information on structural diversity by 36%. This expansion in structural diversity will help to reveal associated functional diversity not previously detected. Our novel CATH-Assign protocol scales well and will be able to harness the huge expansion (at least 100 million models) in structural data promised by DeepMind to provide more comprehensive coverage of even the most diverse superfamilies to help rationalise evolutionary changes in their functions.
massDatabase: utilities for the operation of the public compound and pathway database
Authors: Shen Xiaotao , Wang Chuchu , Snyder Michael P.
Published: June 2022

One of the major challenges in LC-MS data (metabolome, lipidome, and exposome) is converting many metabolic feature entries to biological function information, such as metabolite annotation and pathway enrichment, which are based on the compound and pathway databases. Multiple online databases have been developed, containing lots of information about compounds and pathways. However, there is still no tool developed for operating all these databases for biological analysis. Therefore, we developed massDatabase, an R package that operates the online public databases and combines with other tools for streamlined compound annotation and pathway enrichment analysis. massDatabase is a flexible, simple, and powerful tool that can be installed on all platforms, allowing the users to leverage all the online public databases for biological function mining. A detailed tutorial and a case study are provided in the Supplementary Materials.

Availability and implementation

https://massdatabase.tidymass.org/.

Contact

shenxt@stanford.edu and mpsnyder@stanford.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
Wheat pollen uptake of CRISPR/Cas9 RNP-PDMAEMA nanoassemblies results in targeted loss of gene function in progeny
Authors: Gogoi Neelam , Kanwal Mehwish , Norman Michael , Downs Jacob , Ahmad Nabil , Mago Rohit , Bariana Harbans , Müllner Markus , Bansal Urmil , Jones Brian
Published: June 2022

The utility of CRISPR in plants has remained limited by the dual difficulties of delivering the molecular machinery to target cells and the use of somatic cell techniques that require tissue culture-basedde novoorganogenesis. We developed 5-10 nm isodiametric polyplex nanoassemblies, comprising poly [2-(dimethylamino)ethylmethacrylate] PDMAEMA (PD) polycationic linear homopolymers and CRISPR/Cas9 ribonucleoproteins (RNPs), that enable endocytosis-driven RNP uptake into pollen grains. Pollen from wheat plants (genotype Gladius+Sr50), homozygous for monogenicSr50-mediated resistance to stem rust (Puccinia graminisf. sp. tritici -Pgt), were incubated with RNP/PD nanoassemblies targeting the dominant,Sr50rust resistance gene. The treated pollen grains were then used to fertilize Gladius+Sr50 florets and the resulting M1 plants were tested for loss ofSr50function via rust resistance screens. The identification of fully susceptible M1 seedlings indicated that theSr50RNPs acted on both alleles, indicating they were transferred via the treated pollen to the zygote. The ability to readily deliver CRISPR RNPs to reproductive cells via biodegradable, polymeric nanocomplexes has significant implications for the efficiency of gene editing in plants.
Confounding effects of heart rate, breathing rate, and frontal fNIRS on interoception
Authors: Candia-Rivera Diego , Sappia M. Sofía , Horschig Jörn M. , Colier Willy N. J. M. , Valenza Gaetano
Published: June 2022

Recent studies have established that cardiac and respiratory phases can modulate perception and related neural dynamics. While heart rate and respiratory sinus arrhythmia possibly affect interoception biomarkers, such as heartbeat-evoked potentials, the relative changes in heart rate and cardiorespiratory dynamics in interoceptive processes have not yet been investigated. In this study, we investigated the variation in heart and breathing rates, as well as higher functional dynamics including cardiorespiratory correlation and frontal hemodynamics measured with fNIRS, during a heartbeat counting task. To further investigate the functional physiology linked to changes in vagal activity caused by specific breathing rates, we performed the heartbeat counting task together with a controlled breathing rate task. The results demonstrate that focusing on heartbeats decreases breathing and heart rates in comparison, which may be part of the physiological mechanisms related to “listening” to the heart, the focus of attention, and self-awareness. Focusing on heartbeats was also observed to increase frontal connectivity, supporting the role of frontal structures in the neural monitoring of visceral inputs. However, cardiorespiratory correlation is affected by both heartbeats counting and controlled breathing tasks. Based on these results, we concluded that variations in heart and breathing rates are confounding factors in the assessment of interoceptive abilities and relative fluctuations in breathing and heart rates should be considered to be a mode of covariate measurement of interoceptive processes.
Long non-coding RNA L13Rik promotes high glucose-induced mesangial cell injury by regulating miR-2861/CDKN1B axis
Authors: Sun Linlin , Ding Miao , Chen Fuhua , Zhu Dingyu , Xie Xinmiao
Published: June 2022

Diabetic nephropathy (DN) is a frequent and severe microvascular complication of diabetes. Glomerular mesangial cell (MC) injury occurs at the initial phase of DN and acts as a critical role in the pathogenesis of DN. Given the importance of long non-coding RNA (lncRNA) in regulating MC hyperplasia and extracellular matrix (ECM) accumulation, it is essential to identify functional lncRNAs during MC injury. Here a novel lncRNA, C920021L13Rik (L13Rik for short), was identified to up-regulated in DN progression. The expression of L13Rik in DN patients and diabetic rats was assessed using quantitative real-time PCR (qRT-PCR), and the function of L13Rik on regulating HG-induced MC injury was assessed using cell counting kit-8 (CCK-8) and western blot assay to analyze MC viability and ECM accumulation. We found that L13Rik level was significantly increased while miR-2861 level was significantly decreased in peripheral blood of DN patients, renal tissues of diabetic rats, and HG-treated MCs. Functionally, both L13Rik depletion and miR-2861 overexpression effectively reduced HG-induced MC survival, ECM accumulation, and cell hypertrophy. Mechanistically, L13Rik functioned as a competing endogenous RNA (ceRNA) to sponge miR-2861, resulting in the de-repression of its target cyclin-dependent kinase inhibitor 1B (CDKN1B), a gene known to accelerate MC injury. Collectively, the current results demonstrate that up-regulated L13Rik is correlated with DN, and may be a hopeful therapeutic target for DN.
Association of Striatal Connectivity Gradients to Functional Domains Across Psychiatric Disorders
Authors: Mulders Peter C.R. , van Eijndhoven Philip F.P. , van Oort Jasper , Oldehinkel Marianne , Duyser Fleur A. , Kist Josina D. , Collard Rose M. , Vrijsen Janna N. , Haak Koen V. , Beckmann Christian F. , Tendolkar Indira , Marquand Andre F.
Published: June 2022

Objective

To uncover transdiagnostic domains of functioning across stress- and neurodevelopmental disorders, and to map these on to the topographic functional organization of cortico-striatal circuitry.

Methods

In a clinical sample (n=186) of subjects with high rates of comorbidity of major depressive disorder, anxiety disorder, attention-deficit/hyperactivity disorder and/or autism spectrum disorder, we use exploratory factor analysis on a wide range of clinical questionnaires to identify consistent functional domains of symptomatology across disorders, then replicate these functional domains in an independent dataset (n=188). Then, we use canonical correlation analysis link these functional domains to the topographic organization of the striatum as represented by connectopic maps.

Results

We reveal four functional domains that transcend current diagnostic categories relating to negative valence, cognition, social functioning and inhibition/arousal. These functional domains are replicated in an independent sample and are associated with the fine-grained topographical organization of functional connectivity in the striatum (out of sample r=0.20, p=0.026), a central hub in motor, cognitive, affective and reward-related brain circuits.

Conclusions and relevance

Functional domains across stress- and neurodevelopmental disorders are associated with the functional organization of the striatum. We propose that investigating psychiatric symptoms across disorders is a promising path to linking them to underlying biology, and can help bridge the gap between neuroscience and clinical psychiatry.
Population Transcriptome and Phenotype Reveal that theRht-D1bContribute a Larger Seedling Roots to Modern Wheat Cultivars
Authors: Wang Xiaoming , Zhao Peng , Guo Xiaolong , Liu Zihui , Ma Xiuyun , Zhao Yuqian , Lai Xiangjun , Huang Liuying , Wang Wanying , Han Dejun , Kang Zhensheng , Xu Shengbao
Published: June 2022

The crop root system is pivotal for water and nutrient uptake. Although the breeding selection significantly increased the yield of modern wheat cultivars, then how this selection reshapes the root system remains largely unknown. Here we performed a large-scale transcriptomic and phenotypical investigations on the seedling root of 406 wheat accessions, which demonstrated modern cultivars (MC) had significantly changed in the root transcriptome and root development. The MC had a significantly larger seedling root system than that in landraces (LA), and this was mainly due to theRht-D1ballele introduction. Physiological and cytological investigations showed that theRht-D1bsuppressed gibberellin (GA) signaling, thus inhibiting the cell length in above-ground tissue but increasing the cell length in roots. This distinct regulation of GA signaling between above- and under-ground tissues contributed to MC having a significantly larger root-shoot ratio. Moreover,Rht-D1balso has a GA-independent role to enlarge root cell width that enhanced the root diameter, ultimately contribute to a larger root surface and volume to MC seedlings. These findings provide new insights to understand the successful application of GA-suppressing alleles in modern wheat breeding and its futural application to form a robust wheat root system.

Short Summary

Rht-D1bis the major allele that contribute a larger root system and higher root-shoot ratio to modern wheat cultivars.
Route of self-amplifying mRNA vaccination modulates the establishment of pulmonary resident memory CD8 and CD4 T cells
Authors: Künzli Marco , O’Flanagan Stephen D. , LaRue Madeleine , Talukder Poulami , Dileepan Thamotharampillai , Soerens Andrew G. , Quarnstrom Clare F. , Wijeyesinghe Sathi , Ye Yanqi , McPartlan Justine , Mitchell Jason S. , Mandl Christian W. , Vile Richard , Jenkins Marc K. , Ahmed Rafi , Vezys Vaiva , Chahal Jasdave , Masopust David
Published: June 2022

Respiratory tract resident memory T cells (Trm), typically generated by local vaccination or infection, can accelerate control of pulmonary infections that evade neutralizing antibody. It is unknown whether mRNA vaccination establishes respiratory Trm. We generated a self-amplifying mRNA vaccine encoding the influenza A virus nucleoprotein that is encapsulated in modified dendron-based nanoparticles. Here we report how routes of immunization in mice, including contralateral versus ipsilateral intramuscular boosts, or intravenous and intranasal routes, influence influenza-specific cell-mediated and humoral immunity. Parabiotic surgeries revealed that intramuscular immunization was sufficient to establish CD8 Trm in lung and draining lymph node. Contralateral, compared to ipsilateral, intramuscular boosting broadened the distribution of LN Trm and T follicular helper cells, but slightly diminished resulting levels of serum antibody. Intranasal mRNA delivery established modest circulating CD8 and CD4 T cell memory, but augmented distribution to the respiratory mucosa. Of note, combining intramuscular immunizations with an intranasal mRNA boost achieved high levels of both circulating T cell memory and lung Trm. Thus, routes of mRNA vaccination influence humoral and cell-mediated immunity, and intramuscular prime-boosting establishes lung Trm that can be further enhanced by an additional intranasal immunization.