bluuebunny/crossref_metadata_2025 huggingface dataset:
Repeated vaccination with homologous influenza hemagglutinin broadens human antibody responses to unmatched flu viruses
Authors: Deng Yixiang , Tang Melbourne , Ross Ted M. , Schmidt Aaron G. , Chakraborty Arup K. , Lingwood Daniel
Published: March 2024

The on-going diversification of influenza virus necessicates annual vaccine updating. The vaccine antigen, the viral spike protein hemagglutinin (HA), tends to elicit strain-specific neutralizing activity, predicting that sequential immunization with the same HA strain will boost antibodies with narrow coverage. However, repeated vaccination with homologous SARS-CoV-2 vaccine eventually elicits neutralizing activity against highly unmatched variants, questioning this immunological premise. We evaluated a longitudinal influenza vaccine cohort, where each year the subjects received the same, novel H1N1 2009 pandemic vaccine strain. Repeated vaccination gradually enhanced receptor-blocking antibodies (HAI) to highly unmatched H1N1 strains within individuals with no initial memory recall against these historical viruses. Anin silicomodel of affinity maturation in germinal centers integrated with a model of differentiation and expansion of memory cells provides insight into the mechanisms underlying these results and shows how repeated exposure to the same immunogen can broaden the antibody response against diversified targets.
Genetic risk score for coronary artery calcification predicts coronary artery disease beyond traditional risk factors
Authors: Mishra Pashupati P. , Mishra Binisha H. , Lyytikäinen Leo-Pekka , Goebeler Sirkka , Martiskainen Mika , Hakamaa Emma , Kleber Marcus E. , Delgado Graciela E. , März Winfried , Kähönen Mika , Karhunen Pekka J. , Lehtimäki Terho
Published: March 2024

Aim

The modest added predictive value of the existing genetic risk scores (GRSs) for coronary artery disease (CAD) could be partly due to missing genetic components, hidden in the genetic architecture of intermediate phenotypes such as coronary artery calcification (CAC). In this study, we investigated the predictive ability of CAC GRS for CAD.

Materials and methods

We investigated the association of CAC GRSs with CAD and coronary calcification among the participants in the Ludwigshafen Risk and Cardiovascular Health study (LURIC) (n=2742), the Tampere Vascular Study (TVS) (n=133), and the Tampere Sudden Death Study (TSDS) (n=660) using summary data from the largest multi-ancestry GWAS meta-analysis of CAC to date. Added predictive value of the CAC GRS over the traditional CVD risk factors was tested with standard train–test machine learning approach using the LURIC data, which had the largest sample size.

Results

CAC GRS was significantly associated with CAD in LURIC (OR=1.41, 95% CI [1.28–1.55]), TVS (OR=1.79, 95% CI [1.05–3.21]) as well as in TSDS (OR=4.20, 95% CI [1.74–10.52]). CAC GRS showed strong association with calcification areas in left (OR=1.78, 95% CI [1.16-2.74]) and right (OR=1.71, 95% CI [1.98-2.67]) coronary arteries. In addition, there was statistically significant added predictive value of the CAC GRS for CAD over the used traditional CVD risk factors (AUC 0.734 vs 0.717, p-value = 0.02).

Conclusions

This study showed that CAC GRS is a new risk marker for CAD in three European cohorts, with added predictive value over the traditional CVD risk factors.
A novel GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE 13 is involved in the Phosphate starvation-induced lipid remodeling in rice
Authors: Dang Duong Thi Thuy , Nguyen Thi Linh , Tran Anh-Tuan , Tran Tam Thi Thanh , Tran Tuan-Anh , Vo Kieu Thi Xuan , Jeon Jong-Seong , Vu Tien Van , Kim Jae-Yean , Nguyen Phuong Nhue , Chu Hoang Ha , Do Phat Tien , To Huong Thi Mai
Published: March 2024

Phosphorus (P) is one of the most vital macronutrient determinants in plant development and productivity. However, the bioavailability of inorganic phosphate (Pi), the only form that plants can assimilate, is limited in the soil, thus significantly affecting plant development. Plants have adopted various specialized strategies to modify their morphological, physiological, and biochemical properties for better adaptation to Pi deficiency conditions. GLYCEROPHOSPHODIESTER PHOSPHODIESTERASES (GDPDs), generally known as phospholipid remodeling proteins, have been suggested to play essential roles in maintaining phosphate homeostasis. The previous genome-wide association studies (GWAS) in a Vietnamese rice collection led to the discovery of a robust QTL namedqRST9.14associating with the phosphate adaption in rice, in whichOsGDPD13is located within this locus. Interestingly, we discovered an absence ofOsGDPD13from theIndicareference genome. A subcellular localization study showed that the GDPD13 protein localizes to the plasma membrane, cytoplasmic speckles, and plasmodesmata. Theosgdpd13knockout mutant was generated in theJaponicacv Kitaake background to characterize its function. Phenotypic analysis indicated that mutation ofOsGDPD13significantly lowered crown root number and reduced the plant height under Pi deficient condition. Moreover,osgdpd13lines reduce the capability to degrade total phospholipids compared to the wild type under Pi starvation conditions. This finding suggests the involvement of theOsGDPD13gene in rice growth and the Phosphate starvation-induced lipid remodeling under P deficiency. This work will provide valuable information for developing crop plants with higher Phosphate use efficiency.
Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment including Long Indels
Authors: Iglhaut Clara , Pečerska Jūlija , Gil Manuel , Anisimova Maria
Published: March 2024

Despite having important biological implications, insertion and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search.

Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modelling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages.

Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well-suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.
ZFAND6 is a subunit of a TRAF2-cIAP E3 ubiquitin ligase complex essential for mitophagy
Authors: Shaikh Kashif , Bowman Melissa , McCormick Sarah M. , Gao Linlin , Zhang Jiawen , Tawil John , Kapoor Arun , Arav-Boger Ravit , Choi Young Bong , Pekosz Andrew , Klein Sabra L. , Lanza Matthew , Fanburg-Smith Julie C. , García-Sastre Adolfo , Norbury Christopher C. , Chroneos Zissis C. , Harhaj Edward W.
Published: March 2024

The A20 ubiquitin-editing enzyme is a critical negative regulator of NF-κB signaling and inflammation. While the mechanisms by which A20 restricts inflammation have been extensively studied, the physiological functions of other A20-like proteins are largely unknown. Here, we report a previously unknown function of the A20 family member ZFAND6 as a novel regulator of mitophagy. Deletion of ZFAND6 in bone marrow-derived macrophages (BMDMs) promotes the upregulation of reactive oxygen species (ROS) and the accumulation of damaged mitochondria due to impaired mitophagy. Consequently, mitochondrial DNA (mtDNA) is released into the cytoplasm, triggering the spontaneous expression of interferon-stimulated genes (ISGs) in a cGAS-STING dependent manner, which leads to enhanced viral resistancein vitro. However, mice lacking ZFAND6 exhibit increased morbidity and mortality upon challenge with a sublethal dose of influenza A virus (IAV) due to impaired myeloid cell activation and diminished type I IFN signaling. Mechanistically, ZFAND6 bridges a TRAF2-cIAP1 interaction, which is required for the initiation of ubiquitin-dependent mitophagy. Our results suggest that ZFAND6 is a subunit of a TRAF2-cIAP E3 ligase complex that promotes the clearance of damaged mitochondria by mitophagy to maintain mitochondrial homeostasis.
Building a Collaborative DNA Barcode Library for the Diptera of Churchill, Canada: A Resource for Northern Research
Authors: Majoros S.E. , Wang J. , Levesque-Beaudin V. , Borkent C.J. , Brodo F. , Brooks S.E. , Boucher S. , Cumming J.M. , Currie D.C. , Ekrem T. , Elliott T.A. , Hebert P.D.N. , Savage J. , Schaefer P. , Sinclair B.J. , Skevington J.H. , Solecki A.M. , Stur E. , Wheeler T.A. , Woodcock T.S. , Young A. D. , Young C. , Adamowicz S.J.
Published: March 2024

Churchill, Manitoba, Canada is a diverse Subarctic region that has been the focus of DNA barcoding efforts and research for decades. Despite this effort, there are still taxa in this region that are underrepresented in public databases, particularly hyperdiverse insect groups. We present a collaborative large-scale DNA barcode reference library for Diptera based on molecular data and expert taxonomic identification. The reference library contains 16786 specimens sampled around Churchill from 2005 to 2011. Specimens were identified by morphological means, sequenced for the animal barcode marker, and sorted into 2235 Molecular Operational Taxonomic Units (using Barcode Index Numbers: BINs) representing 68 families and 1211 named species. Eighty-four species shared a BIN with another species, 98 species were split across several BINs, and 1028 species were assigned to a unique BIN. The intraspecific and nearest neighbour distances varied across families, but most species can be easily distinguished from their nearest neighbours. By combining molecular data with taxonomic expertise, the barcode library provides species-level information for 12612 specimens, supplying future researchers with detailed taxonomic information and the opportunity to perform barcode-based specimen identifications for large-scale studies through sequence matching. Comparison of the Diptera composition of Churchill to other geographic regions reflected likely postglacial colonization northwards as well as a Beringian component. This study provides a publicly available, detailed reference library for use in future research, as well as new insights into the current diversity of Diptera present among the diverse habitats in this Subarctic region.
A geographic history of human genetic ancestry
Authors: Grundler Michael C. , Terhorst Jonathan , Bradburd Gideon S.
Published: March 2024

Describing the distribution of genetic variation across individuals is a fundamental goal of population genetics. In humans, traditional approaches for describing population genetic variation often rely on discrete genetic ancestry labels, which, despite their utility, can obscure the complex, multifaceted nature of human genetic history. These labels risk oversimplifying ancestry by ignoring its temporal depth and geographic continuity, and may therefore conflate notions of race, ethnicity, geography, and genetic ancestry. Here, we present a method that capitalizes on the rich genealogical information encoded in genomic tree sequences to infer the geographic locations of the shared ancestors of a sample of sequenced individuals. We use this method to infer the geographic history of genetic ancestry of a set of human genomes sampled from Europe, Asia, and Africa, accurately recovering major population movements on those continents. Our findings demonstrate the importance of defining the spatial-temporal context of genetic ancestry to describing human genetic variation and caution against the oversimplified interpretations of genetic data prevalent in contemporary discussions of race and ancestry.
Formation and Retrieval of Cell Assemblies in a Biologically Realistic Spiking Neural Network Model of Area CA3 in the Mouse Hippocampus
Authors: Kopsick Jeffrey D. , Kilgore Joseph A. , Adam Gina C. , Ascoli Giorgio A.
Published: March 2024

The hippocampal formation is critical for episodic memory, with area Cornu Ammonis 3 (CA3) a necessary substrate for auto-associative pattern completion. Recent theoretical and experimental evidence suggests that the formation and retrieval of cell assemblies enable these functions. Yet, how cell assemblies are formed and retrieved in a full-scale spiking neural network (SNN) of CA3 that incorporates the observed diversity of neurons and connections within this circuit is not well understood. Here, we demonstrate that a data-driven SNN model quantitatively reflecting the neuron type-specific population sizes, intrinsic electrophysiology, connectivity statistics, synaptic signaling, and long-term plasticity of the mouse CA3 is capable of robust auto-association and pattern completion via cell assemblies. Our results show that a broad range of assembly sizes could successfully and systematically retrieve patterns from heavily incomplete or corrupted cues after a limited number of presentations. Furthermore, performance was robust with respect to partial overlap of assemblies through shared cells, substantially enhancing memory capacity. These novel findings provide computational evidence that the specific biological properties of the CA3 circuit produce an effective neural substrate for associative learning in the mammalian brain.
Evidence that the monoamine oxidase B (MAO-B) plays a central role in the inotropic dysfunction induced by genetic deletion of the Mas-related-G protein-coupled receptor D (MrgD) in mice
Authors: Rodrigues-Ribeiro Lucas , Rezende-Ribeiro Julia , Scalzo Sérgio , Dias Maria Luiza , Sanches Bruno de Lima , Eliezeck Marcos , de Jesus Itamar Couto , Medeiros Evaristo Joseph Albert , Sampaio Kinulpe Honorato , Peruchetti Diogo B. , Cruz Jader Santos , Nogueira Fábio César Sousa , Campagnole-Santos Maria José , Guatimosim Silvia , Santos Robson Augusto Souza , Verano-Braga Thiago
Published: March 2024

The renin-angiotensin system (RAS) plays a critical role in the regulation of the cardiovascular system. The Mas-related G protein receptor member D (MrgD) is the receptor of alamandine, and both are components of the RAS noncanonical arm. Alamandine/MrgD induces vasodilation, anti-inflammatory, anti-fibrotic and anti-oxidative effects. In contrast,Mrgdgene deletion leads to a remarkable dilated cardiomyopathy (DCM) in mice. Here, we aimed to investigate the molecular mechanisms of DCM triggered by the deletion of MrgD in the left ventricle and isolated ventricular cardiomyocytes from 8-12 weeks old mice using phosphoproteomics. Our findings revealed an increased oxidative stress not caused by angiotensin II/AT1 hyperactivation but instead due to the up-regulation of the monoamine oxidase B (MAO-B), leading to a higher catabolism of dopamine and epinephrine in the MrgD-KO cardiac tissues. The oxidative environment induced by MAO-B hyperactivation seems to be the cause of the observed alteration in ionic dynamics - altered Ca2+transient and Na+/K+-ATPase activity - leading to altered resting membrane potential (RMP) and decreased contraction of MrgD-KO cardiomyocytes. In addition, cardiac Troponin-I phosphorylation, and Titin dephosphorylation seem to contribute to the contractile dysfunction observed in MrgD-KO. The treatment of cardiomyocytes from MrgD-KO mice with the MAO-B inhibitor Pargyline reverted the observed impaired contraction, corroborating the hypothesis that MAO-B hyperactivation is, at least partially, the cause of the failing heart observed in MrgD-KO mouse. The findings reported here provide important insights into the pathogenesis of heart failure and suggest a potential therapeutic target (MrgD activation) for managing failing hearts.
Inferring Ancestry with the Hierarchical Soft Clustering Approach tangleGen
Authors: Burger Klara Elisabeth , Klepper Solveig , von Luxburg Ulrike , Baumdicker Franz
Published: March 2024

Understanding the genetic ancestry of populations is central to numerous scientific and societal fields. It contributes to a better understanding of human evolutionary history, advances personalized medicine, aids in forensic identification, and allows individuals to connect to their genealogical roots. Existing methods, such as ADMIXTURE, have significantly improved our ability to infer ancestries. However, these methods typically work with a fixed number of independent ancestral populations. As a result, they provide insight into genetic admixture, but do not include a hierarchical interpretation. In particular, the intricate ancestral population structures remain difficult to unravel. Alternative methods with a consistent inheritance structure, such as hierarchical clustering, may offer benefits in terms of interpreting the inferred ancestries. Here, we present tangleGen, a soft clustering tool that transfers the hierarchical machine learning framework Tangles, which leverages graph theoretical concepts, to the field of population genetics. The hierarchical perspective of tangleGen on the composition and structure of populations improves the interpretability of the inferred ancestral relationships. Moreover, tangleGen adds a new layer of explainability, as it allows identifying the SNPs that are responsible for the clustering structure. We demonstrate the capabilities and benefits of tangleGen for the inference of ancestral relationships, using both simulated data and data from the 1000 Genomes Project.
A Comprehensive Model of Blood Flow Restriction in the Post-surgical Rat
Authors: Fosam Andin , Ramos Nakandakari Susana Castelo Branco , Ohashi Yuichi , Bai Hualong , O’Connell Julie , Raines Andrew , Miranda Isabella Chavez , Dardik Alan , Allen Christina , Perry Rachel J.
Published: March 2024

Blood flow restriction (BFR) with low-load exercise (BFR-exercise) is an increasingly popular tool used to increase muscle strength and attenuate muscle atrophy, especially after injury or surgery. However, the mechanisms underlying BFR-mediated muscle growth are not well understood. Likely contributing to the mechanistic knowledge gap, rodent models of BFR-exercise have not been well described. In this methods paper, we demonstrate a comprehensive, clinically relevant protocol to establish BFR-exercise in awake rats. This protocol includes generating a muscle loss state via bilateral ACL-R, determining targeted blood flow occlusion pressures, and performing weighted hind-limb knee extension exercises with BFR. These methods can be used for further application in mechanistic and physiologic studies of BFR-exercise.
Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives
Authors: Sahoo Ajaya Kumar , Chivukula Nikhil , Madgaonkar Shreyes Rajan , Ramesh Kundhanathan , Marigoudar Shambanagouda Rudragouda , Sharma Krishna Venkatarama , Samal Areejit
Published: March 2024

Plastics are widespread pollutants found in atmospheric, terrestrial and aquatic ecosystems due to their extensive usage and environmental persistence. Plastic additives, that are utilized to achieve specific functionality in plastics, leach into the environment upon plastic degradation and pose considerable risk to ecological and human health. Limited knowledge concerning the presence of plastic additives throughout the plastic life cycle has hindered their effective regulation, thereby posing risks to product safety. In this study, we leveraged the adverse outcome pathway (AOP) framework to understand the mechanisms underlying plastic additives-induced toxicities. We first identified an exhaustive list of 6470 plastic additives from chemicals documented to be found in plastics. Next, we leveraged heterogenous toxicogenomics and biological endpoints data from five exposome-relevant resources, and identified associations between 1287 plastic additives and 322 complete and high quality AOPs within AOP-Wiki. Based on these plastic additive-AOP associations, we constructed a stressor-centric AOP network, wherein the stressors are categorized into 10 priority use sectors and AOPs are linked to 27 disease categories. We visualized the plastic additives-AOP network for each of the 1287 plastic additives and made them available in a dedicated website:https://cb.imsc.res.in/saopadditives/. Finally, we showed the utility of the constructed plastic additives-AOP network by identifying 28 highly relevant AOPs associated with benzo[a]pyrene, and thereafter, explored the associated toxicity pathways leading to respiratory and gastrointestinal system diseases in humans and developmental disorders in aquatic species. Overall, the constructed plastic additives-AOP network will enable regulatory risk assessment of plastic additives, thereby contributing towards a toxic-free circular economy for plastics.
Identifying the gene responsible for NPQ reversal inPhaeodactylum tricornutum
Authors: Ware Maxwell A. , Paton Andrew J. , Bai Yu , Kassaw Tessema , Lohr Martin , Peers Graham
Published: March 2024

Algae such as diatoms and haptophytes have distinct photosynthetic pigments from plants, including a novel set of carotenoids. This includes a primary xanthophyll cycle comprised of diadinoxanthin and its de-epoxidation product diatoxanthin that enables the switch between light harvesting and non-photochemical quenching (NPQ)-mediated dissipation of light energy. The enzyme responsible for the reversal of this cycle was previously unknown. Here, we identified zeaxanthin epoxidase 3 (ZEP3) fromPhaeodactylum tricornutumas the candidate diatoxanthin epoxidase. Knocking out the ZEP3 gene caused a loss of rapidly reversible NPQ following saturating light exposure. This correlated with the maintenance of high concentrations of diatoxanthin during recovery in low light. Xanthophyll cycling and NPQ relaxation were restored via complementation of the wild type ZEP3 gene. Thezep3knockout strains showed reduced photosynthetic rates at higher light fluxes and reduced specific growth rate in variable light regimes, likely due to the mutant strains becoming locked in a light energy dissipation state. We were able to toggle the level of NPQ capacity in a time and dose dependent manner by placing the ZEP3 gene under the control of an inducible promoter. Identification of this gene provides deeper understanding of the diversification of photosynthetic control in algae compared to plants and suggests a potential target to improve the productivity of industrial-scale cultures.
Prevalent co-release of glutamate and GABA throughout the mouse brain
Authors: Ceballos Cesar C. , Ma Lei , Qin Maozhen , Zhong Haining
Published: March 2024

Several neuronal populations in the brain transmit both the excitatory and inhibitory neurotransmitters, glutamate, and GABA, to downstream neurons. However, it remains largely unknown whether these opposing neurotransmitters are co-released onto the same postsynaptic neuron simultaneously or are independently transmitted at different time and locations (called co-transmission). Here, using whole-cell patch-clamp recording on acute mouse brain slices, we observed biphasic miniature postsynaptic currents, i.e., minis with time-locked excitatory and inhibitory currents, in striatal spiny projection neurons (SPNs). This observation cannot be explained by accidental coincidence of monophasic miniature excitatory and inhibitory postsynaptic currents (mEPSCs and mIPSCs, respectively), arguing for the co-release of glutamate and GABA. Interestingly, these biphasic minis could either be an mEPSC leading an mIPSC or vice versa. Although dopaminergic axons release both glutamate and GABA in the striatum, deletion of dopamine neurons did not eliminate biphasic minis, indicating that the co-release originates from another neuronal type. Importantly, we found that both types of biphasic minis were detected in other neuronal subtypes in the striatum as well as in nine out of ten additionally tested brain regions. Our results suggest that co-release of glutamate and GABA is a prevalent mode of neurotransmission in the brain.
Development and Application of Decontamination Methods for the Re-Use of Laboratory Grade Plastic Pipette Tips
Authors: Lee Sang Hyuk , Kastor William , Fu Xiao , Soni Vikas , Keidar Michael , Donohue Marc , Wood Steve , Karunasena Enusha
Published: March 2024

During the SARS-CoV-2 pandemic, a need for methods to decontaminate and reuse personal protective equipment (PPE) and medical plastics became a priority. In this investigation we aimed to develop a contamination evaluation protocol for laboratory pipette tips, after decontamination. Decontamination methods tested in this study included cleaning with a common laboratory detergent (2.5% Alconox® solution followed with steam decontamination), exposure of ozone vapor at 250 and 14400 PPM * minute, and exposure to cold atmospheric plasma (CAP). All tips (control and experimental groups) were introduced to the methods described, while tips exposed to DNA extracts ofAeromonas hydrophila(ATCC-23211) were assessed for experimental groups. Decontamination was determined by turnover ratio and log reduction in detectable genomic material on the contaminated products using real-time quantitative PCR (qPCR) assay.

Our results showed, cleaning tips with lab detergents along with steam decontamination removed genetic material, resulting in the highest log reduction, compared with ozone or CAP treatments. Detergent/washing methods showed the highest turnover ratio (95.9 %) and log reduction (5.943). However, the excessive residue (post-cleaning) on the plastic, within inner filters, and tip boxes suggested that washing with lab detergents was not favorable for reuse. Ozone vapor at 14400 PPM * minutes showed the second highest turnover ratio (98.4 %) and log reduction (4.511). CAP exposure with tips inverted (the tip end exposed closer to the plasma flame) for 1 minute showed a turnover ratio of (68.3 %) and log reduction (4.002). Relatively, lower turnover ratio and log reduction of CAP could be attributed to development/optimization of treatment conditions, including increases in exposure time and relative to tip positioning.
A modular and flexible open source cell incubator system for mobile and stationary use
Authors: Duru Jens , Maurer Benedikt , Ruff Tobias , Hengsteler Julian , Girardin Sophie , Vörös János , Ihle Stephan J.
Published: March 2024

Culturing living cellsin vitrorequires the maintenance of physiological conditions for extended periods of time. Here, we introduce a versatile and affordable incubation system, addressing the limitations of traditional incubation systems. Conventionally, stationary cell incubators maintain constant temperature and gas levels forin vitrocell culturing. Combining such incubators with additional lab equipment proves challenging. The presented platform offers modularity and adaptability, enabling customization to diverse experimental needs. The system includes a main unit with a user-friendly interface as well as an interchangeable incubation chamber. We present two incubation chambers targeting two completely different use cases. The first chamber, named “inkugo” facilitates the transportation of cells for up to two hours without external power and for more than a day without an external CO2source. The second chamber termed “inkubox” was designed to enable continuous electrophysiological recordings. Recordings from up to four neural cultures growing on high-density microelectrode arrays can be performed in parallel. The system’s unique feature lies in its separability of control and incubation components, allowing one control unit to manage various custom chambers. The design’s simplicity and the use of widely accessible components make the here proposed incubation system replicable for any laboratory. This platform fosters collaboration and experimentation in both decentralized and traditional laboratory settings, making it an invaluable addition to any cell culturing pipeline.

Specifications table
Single nucleus RNA-sequencing reveals transcriptional synchrony across different relationships
Authors: Brusman Liza E. , Sadino Julie M. , Fultz Allison C. , Kelberman Michael A. , Dowell Robin D. , Allen Mary A. , Donaldson Zoe R.
Published: March 2024

As relationships mature, partners share common goals, improve their ability to work together, and experience coordinated emotions. However, the neural underpinnings responsible for this unique, pair-specific experience remain largely unexplored. Here, we used single nucleus RNA-sequencing to examine the transcriptional landscape of the nucleus accumbens (NAc) in socially monogamous prairie voles in peer or mating-based relationships. We show that, regardless of pairing type, prairie voles exhibit transcriptional synchrony with a partner. Further, we identify genes expressed in oligodendrocyte progenitor cells that are synchronized between partners, correlated with dyadic behavior, and sensitive to partner separation. Together, our data indicate that the pair-specific social environment profoundly shapes transcription in the NAc. This provides a potential biological mechanism by which shared social experience reinforces and strengthens relationships.
Widespread transcription initiation within coding sequences marks tissue identity and accessible chromatin
Authors: Wang Xutong , Duan Jingbo , Clark Chancelor B. , Feng Wanjie , Ma Jianxin
Published: March 2024

Alternative transcription initiation (ATI) appears to be a ubiquitous regulatory mechanism of gene expression in eukaryotes, but the extent to which it affects the products of gene expression, and how it evolves and is regulated remain unknown. We first identified transcription start sites (TSSs) in eight soybean tissues using recently developed STRIPE-seq and then analyzed ATI in the context of tissue identity and chromatin architecture. We defined 193,579 TSS clusters/regions (TSRs) in 37,911 annotated genes, with 56.5% located in putative regulatory regions upstream of start codons and 43.5% from start codons to 3’ untranslated regions, which, together, are responsible for changes in open reading frames of 24,131 genes. Overall, duplicated genes possess more TSRs, exhibited lower degrees of tissue-specificity, and have undergone stronger purifying selection than singletons. Strikingly, 6,845 genes possess ATI within coding sequences (CDSs). These CDS-TSRs are highly tissue-specific, shorter than those located in canonical regulatory regions, and do not have TATA-boxes typical for the core promoters. Furthermore, the CDS-TSRs are embedded in nucleosome-free regions and flanked by nucleosomes with enhanced levels of active histone marks associated with transcriptionally active chromatin, suggesting that non-canonical ATI is epigenetically regulated and largely responsible for tissue-specific functions and tissue identity. Our study highlights the genomic and epigenomic factors shaping the distribution patterns and tissue-specificity of ATI in regulatory and coding sequences, as well as the significance of ATI in the alternation of proteins encoded by tissue-specifically expressed genes in the context of genome duplication and fractionation.
Clinical application of Complete Long Read genome sequencing identifies a 16kb intragenic duplication in EHMT1 in a patient with suspected Kleefstra syndrome
Authors: Gorzynski John E , Marwaha Shruti , Reuter Chloe M , Jensen Tanner , Ferrasse Alexis , Raja Archana , Fernandez Liliana , Kravets Elijah , Carter Jennefer , Bonner Devon , Sutton Shirley ,   Undiagnosed Diseases Network (UDN), Ruzhnikov Maura , Hudgins Louanna , Fisher Paul G , Bernstein Jonathan , Wheeler Matthew T , Ashley Euan A
Published: March 2024

Long read sequencing offers benefits for the detection of structural variation in Mendelian disease. Here, we applied a new technology that generates contiguous long reads via tagmentation and sequencing by synthesis to a small cohort of patients with undiagnosed disease from the Undiagnosed Diseases Network. We first compare sequencing from the HG002 benchmark sample from Genome In A Bottle using nanopore sequencing (R10.4.1, duplex reads, Oxford Nanopore), single molecule real time sequencing (Revio SMRT cell, Pacific Biosciences) and complete long read sequencing (S4 flowcell, Novaseq, Illumina). Coverage was 33-35x across platforms. Read length N50 was 6.5kb (ICLR), 16.9kb (SMRT), and 33.8kb (ONT). We noted small differences in single nucleotide variant F1 scores across long read technologies with single nucleotide variant F1 scores (0.985-0.999) exceeding indel scores (0.78-0.99) and structural variant scores (0.74-0.96). We applied CLR sequencing to seven undiagnosed patients. In one patient, we detected and prioritized a novel 16kb intragenic duplication encompassing exons 5 and 6 in EHMT1. Resolution of the breakpoints and examination of flanking sequences revealed that the duplication was present in tandem and was predicted to result in a frameshift of the amino acid sequence and an early termination codon. It resulted in a diagnosis of Kleefstra syndrome. The variant was confirmed with targeted EHMT1 clinical testing and detected via nanopore and SMRT sequencing. In summary, we report the early clinical application of complete long read sequencing to a small cohort of undiagnosed patients.
Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses
Authors: Buddle Sarah , Forrest Leysa , Akinsuyi Naomi , Bernal Luz Marina Martin , Brooks Tony , Venturini Cristina , Miller Charles , Brown Julianne R , Storey Nathaniel , Atkinson Laura , Best Timothy , Roy Sunando , Goldsworthy Sian , Castellano Sergi , Simmonds Peter , Harvala Heli , Golubchik Tanya , Williams Rachel , Breuer Judith , Morfopoulou Sofia , Montaguth Oscar Enrique Torres
Published: March 2024

Background

Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, barriers to broader take-up include the need for high sequencing depths, long turnaround times, and limited sensitivity. Newer metagenomics protocols based on Oxford Nanopore Technologies (ONT) sequencing allow acquisition and analysis of data in real time, potentially reducing the need for high-volume sequencing and enabling point-of-care testing. Furthermore, targeted approaches that selectively amplify known pathogens could improve sensitivity.

Methods

We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Biosciences Comprehensive Viral Research Panel (VRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers.

Results

Capture with the Twist VRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6,000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the VRP and ONT.

Conclusions

Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist VRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.
Study protocol: A national cross-sectional study on psychology and behavior investigation of Chinese residents in 2023, PBICR
Authors: Liu Diyue , Fan Siyuan , Huang Xincheng , Gu Wenjing , Yin Yifan , Zhang Ziyi , Ma Baotong , Xia Ruitong , Lu Yuanwei , Liu Jingwen , Xin Hanjia , Cao Yumeng , Yang Saier , Li Runqing , Li Han , Zhao Ji , Zhang Jin , Gao Zheng , Zeng Yaxin , Ding Yixiao , Ren Zhuolun , Guan Yan , Zhang Na , Li Jia , Ma Yan , Wei Pei , Dong Jingjing , Zhou Yajing , Dong Yong , Qian Yan , chen Chen , Zhao Yujie , Li Yimiao , Zheng Yujia , Chen Rongyi , Li Xiaomeng , Han Yuke , Xia Yaoyao , Xu Huixin , Wu Zhaolin , Wu Mingyou , Wu Xinrui , Hou Junyi , Cai Yuelai , Dai Xiaofan , Li Wenbo , Nie Ting , Zhang Chongzhe , Wang Xiaoya , Li Dan , Yan Siyao , Liu Chenxi , Zhang Xinyue , Shi Lei , Li Haomiao , Jiang Feng , Zhou Xiaoming , Sun Xinying , Wu Yibo
Published: March 2024

Background

This study protocol specifies the primary research line and theoretical framework of the 2023 Survey of the Psychology and Behavior on Chinese Population. It aims to establish a database focused on psychology and behavior among Chinese residents through a multicenter, large-sample cross-sectional survey to provide strong data support for research and development in related fields. It will track the public’s physical and psychological health more comprehensively and systematically.

Methods

The study was conducted from 20 June 2023 to 31 August 2023, using stratified and quota sampling methods, and a total of 150 cities, 202 districts and counties, 390 townships/streets, and 800 communities/villages were surveyed (excluding Taiwan, which were selected from 23 provinces, five autonomous regions, and four municipalities directly under the central government in China). The questionnaires were distributed face-to-face by trained surveyors. The questionnaires included basic information about the individual, personal health status, basic information about the family, the social environment in which the individual lives, psychological condition scales, behavioral level scales, other scales, and attitudes towards topical social issues. Supervisors conducted quality control during the distribution process and returned questionnaires, logically checked and cleaned for data analysis.

Discussion

Data collection has been finished, and scientific outputs based on this data will support the development of health promotion strategies in China and globally. In the aftermath of the pandemic, it will guide policymakers and healthcare organizations to improve their existing policies and services to maximize the physical and mental health of the Chinese population.
Synthetic mycolates derivatives as molecular tools to decipher protein mycoloylation, a unique post-translational modification in bacteria
Authors: Lesur Emilie , Zhang Yijie , Dautin Nathalie , Dietrich Christiane , de la Sierra-Gallay Ines Li , Augusto Luis , Rollando Paulin , Lazar Noureddine , Urban Dominique , Doisneau Gilles , Constantinesco-Becker Florence , Van Tilbeurgh Herman , Guianvarc’h Dominique , Bourdreux Yann , Bayan Nicolas
Published: March 2024

Protein mycoloylation is a newly characterized post-translational modification (PTM) specifically found inCorynebacteriales, an order of bacteria that includes numerous human pathogens. Their envelope is composed of a unique outer membrane, the so-called mycomembrane made of very-long chain fatty acids, named mycolic acids. Recently, some mycomembrane proteins including PorA have been unambiguously shown to be covalently modified with mycolic acids in the model organismCorynebacterium glutamicumby a mechanism that relies on the mycoloyltransferase MytC. This PTM represents the first example of proteinO-acylation in prokaryotes and the first example of protein modification by mycolic acid. Through the design and synthesis of trehalose monomycolate (TMM) analogs, we prove thati) MytC is the mycoloyltransferase directly involved in this PTM,ii) TMM, but not TDM, is a suitable mycolate donor for PorA mycoloylation,iii) MytC is able to discriminate between an acyl and a mycoloyl chainin vitrounlike other trehalose mycoloyltransferases. We also solved the structure of MytC acyl-enzyme obtained with a soluble short TMM analogs which constitutes the first mycoloyltransferase structure with a covalently linked to an authentic mycolic acid moiety. These data highlight the great conformational flexibility of the active site of MytC during the reaction cycle and pave the way for a better understanding of the catalytic mechanism of all members of the mycoloyltransferase family including the essential Antigen85 enzymes inMycobacteria.
Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation
Authors: Amamo Yuki , Sachdeva Rohan , Gittins Daniel , Anantharaman Karthik , Lei Shufei , Valentin Alvarado Luis E , Diamond Spencer , Beppu Hikari , Iwatsuki Teruki , Mochizuki Akihito , Miyakawa Kazuya , Ishii Eiichi , Murakami Hiroaki , Jaffe Alexander L. , Castelle Cindy , Lavy Adi , Suzuki Yohey , Banfield Jill F.
Published: March 2024

Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan. We reconstructed draft genomes for >90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.
A new cellular platform for studying autophagy
Authors: Goldin-Azulay Korina , Fraiberg Milana , Trofimyuk Olena , Levin Yishai , Reuven Nina , Kopitman Ekaterina , Elazar Zvulun
Published: March 2024

Atg8 proteins play a crucial role in autophagy. There is a single Atg8 isoform in yeast, while mammals have up to seven homologs categorized into LC3s and GABARAPs. The GABARAP subfamily consists of GABARAP, GABARAPL1, and GABARAPL2/GATE16, implicated in various stages along the pathway. However, the intricacies among GABARAP proteins are complex and require a more precise delineation.

Here, we introduce a new cellular platform to study autophagy using CRISPR/Cas9-mediated tagging of endogenous genes of the GABARAP subfamily with different fluorescent proteins. This platform allows robust examination of autophagy by flow cytometry of cell populations and monitoring of GABARAP homologs at single-cell resolution using fluorescence microscopy. Strikingly, the simultaneous labeling of the different endogenous GABARAPs allows the identification and isolation of autophagosomes differentially marked by these proteins. Using this system, we found that the different GABARAPs are associated with different autophagosomes. We argue that this new cellular platform will be crucial in studying the unique roles of individual GABARAP proteins in autophagy and other putative cellular processes.
Plant Cleavage Factor I complex is essential for precise cleavage and polyadenylation site determination
Authors: Szewc Lukasz , Zhang Xiaojuan , Bajczyk Mateusz , Bielewicz Dawid , Zimna Marta , Yura Kei , Kato Mariko , Nomoto Mika , Garcia-León Marta , Rubio Vicente , Tada Yasuomi , Furumoto Tsuyoshi , Aoyama Takashi , Szweykowska-Kulinska Zofia , Staiger Dorothee , Jarmolowski Artur , Tsuge Tomohiko
Published: March 2024

Cleavage factor I (CFI) is a four-subunit protein complex of the pre-mRNA 3’ end processing machinery in eukaryotes. In Arabidopsis, AtCFI25a, AtCFI25b, AtCFI59, and AtCFI68 have been identified as potential components of AtCFI,in silico. Here, we show that the AtCFI25a, AtCFI59, and AtCFI68 proteins each pulled down all components of the CFI, confirming that these subunits form the plant CFI complex. Furthermore, either AtCFI59 or AtCFI68 was essential for nuclear localization of the smallest subunit, AtCFI25a. Mutants with single loss-of-function forAtCFI59orAtCFI68showed no obvious morphological defects compared to wild-type plants, while the double mutant displayed pleiotropic morphological defects, identical to those previously reported forAtCFI25aloss-of-function plants. Moreover, these morphological defects correlated with alterations in the usage of 3’ UTR cleavage and polyadenylation sites.atcfi25a,atcfi25a atcfi25bandatcfi59 atcfi68double mutants showed widespread changes in the choice of cleavage and polyadenylation sites. In most cases, more proximal cleavage and polyadenylation sites were used, leading to shorter 3’ UTRs. In particular, genes involved in light intensity, light harvesting, photosynthesis and cold responses showed significant dependence on AtCFI function. Furthermore, transcripts coding for AtCFI subunits showed altered 3’ end processing in these mutants, suggesting self-regulation function of AtCFI in plants.