bluuebunny/crossref_metadata_2025 huggingface dataset:
Environmental DNA metabarcoding describes biodiversity across marine gradients
Authors: Adams Clare I M , Jeunen Gert-Jan , Cross Hugh , Taylor Helen R , Bagnaro Antoine , Currie Kim , Hepburn Chris , Gemmell Neil J , Urban Lara , Baltar Federico , Stat Michael , Bunce Michael , Knapp Michael
Published: February 2023

In response to climate change, biodiversity patterns in the oceans are predicted to shift rapidly, thus increasing the need for efficient monitoring methods. Environmental DNA (eDNA) metabarcoding recently emerged as a potent and cost-effective candidate to answer this challenge. We targeted three molecular markers to determine multicellular metazoan communities from two timepoints across a long-standing transect in the Southern Hemisphere, the Munida Observational Time Series. We detected four community types across the successive water masses—neritic, sub-tropical, frontal, and sub-Antarctic—crossed by the transect, together with important community differences between the two sampling points. From indicator species analysis, we found diversity patterns were mostly driven by planktonic organisms. Mesopelagic communities differed from surface-water communities in the sub-Antarctic water mass, with at-depth communities dominated by single-cellular organisms. We evaluate the ability of eDNA to detect species-compositional changes across surface and depth gradients and lay the foundations for using this technique in multi-trophic environmental monitoring efforts across long time series. We observed community differences across time and space. More intensive sampling will be critical to fully capture diversity across marine gradients, but this multi-trophic method represents an invaluable opportunity to understand shifts in marine biota.
Mrhst4gene, coding for NAD+-dependent deacetylase is involved in citrinin production ofMonascus ruber
Authors: Hu Yifan , Zheng Yunfan , Liu Baixue , Gong Yunxia , Shao Yanchun
Published: February 2023

Aims

In this study, Mrhst4, encoding a member of NAD+-dependent histone deacetylase (HDAC), was deleted to evaluate its regulation on the production of Monascus azaphilone pigments (MonAzPs) and mycotoxin, as well as the developmental process in Monascusruber.

Methods and results

Agrobacterium tumefaciens-mediated transformation was applied in this study to generate the Mrhst4 null strain. Mrhst4-deleted strain did not display obvious differences in the sexual and asexual reproduction, colonial morphology, and micro-morphology. UV–Vis scan and UPLC detection showed that disruption of Mrhst4 significantly increased the MonAzPs yields, and citrinin content was dramatically enhanced during the tested period. RT-qPCR results showed that the absence of Mrhst4 significantly increased the relative expression of citrinin biosynthetic pathway genes including pksCT, mrl1, mrl2, mrl4, mrl6, and mrl7. The Western blot assay suggested that deletion of Mrhst4 could significantly elevate the acetylation levels of H3K4, H3K9, H3K18, H3K56, and H4K12, but attenuated the lysine acetylation modification of H4Pan, H4K8, and H4K16.

Conclusion

MrHst4 is an important regulator involved in secondary metabolism in Monascus ruber. In particular, MrHst4 plays a pivotal role in regulation of citrinin production.
Unraveling baroclinicity in black hole weather storms
Authors: Wittor Denis , Gaspari Massimo
Published: February 2023

In the intracluster, intragroup, and circumgalactic medium (ICM, IGrM, CGM), turbulence plays a vital role in the self-regulated feedback and feeding cycle of central supermassive black holes (SMBHs). Here, we continue our systematic dissection of the turbulent ‘weather’ in high-resolution hydrodynamical simulations of feedback driven by active galactic nuclei (AGN). In non-barotropic and stratified atmospheres, baroclinicity is expected to generate fresh turbulence via misaligned gradients of density and pressure – such as in cyclonic storms on Earth. In this work, we dissect for the first time baroclinicity and its components in the astrophysical halo weather. Over the macro-scale galaxy cluster, baroclinicity tends to be dynamically subdominant for the enstrophy amplification. However, at and below the meso scale near the SMBH (r < 10 kpc; t < 20 Myr), baroclinicity is important to seed the initial enstrophy during active periods of AGN jet feedback. We find that baroclinicity shows stronger correlation with the density rather than pressure gradients. Despite the density-pressure gradient misalignment being often below 45°, their amplitudes boosted by mechanical AGN feedback are sufficient to enable key enstrophy/turbulence generation. Our study provides a novel step forward in understanding astrophysical atmospheres toward a unified BlackHoleWeather framework, akin to the complexity of Earth’s weather.
Development and Multi-Site External Validation of a Generalizable Risk Prediction Model for Bipolar Disorder
Authors: Walsh Colin G. , Ripperger Michael A. , Hu Yirui , Sheu Yi-han , Wilimitis Drew , Zheutlin Amanda B. , Rocha Daniel , Choi Karmel W. , Castro Victor M. , Kirchner H. Lester , Chabris Christopher F. , Davis Lea K. , Smoller Jordan W.
Published: February 2023

Bipolar disorder is a leading contributor to disability, premature mortality, and suicide. Early identification of risk for bipolar disorder using generalizable predictive models trained on diverse cohorts around the United States could improve targeted assessment of high risk individuals, reduce misdiagnosis, and improve the allocation of limited mental health resources.

This observational case-control study intended to develop and validate generalizable predictive models of bipolar disorder as part of the multisite, multinational PsycheMERGE Consortium across diverse and large biobanks with linked electronic health records (EHRs) from three academic medical centers: in the Northeast (Massachusetts General Brigham), the Mid-Atlantic (Geisinger) and the Mid-South (Vanderbilt University Medical Center).

Predictive models were developed and validated with multiple algorithms at each study site: random forests, gradient boosting machines, penalized regression, including stacked ensemble learning algorithms combining them. Predictors were limited to widely available EHR-based features agnostic to a common data model including demographics, diagnostic codes, and medications. The main study outcome was bipolar disorder diagnosis as defined by the International Cohort Collection for Bipolar Disorder, 2015.

In total, the study included records for 3,529,569 patients including 12,533 cases (0.3%) of bipolar disorder. After internal and external validation, algorithms demonstrated optimal performance in their respective development sites. The stacked ensemble achieved the best combination of overall discrimination (AUC = 0.82 - 0.87) and calibration performance with positive predictive values above 5% in the highest risk quantiles at all three study sites.

In conclusion, generalizable predictive models of risk for bipolar disorder can be feasibly developed across diverse sites to enable precision medicine. Comparison of a range of machine learning methods indicated that an ensemble approach provides the best performance overall but required local retraining. These models will be disseminated via the PsycheMERGE Consortium website.
Ulinastatin Ameliorates Cardiac Ischemia/Reperfusion Injury via Inhibiting the tissue kallikrein-kinin system
Authors: Ran Xiao , Ruan Hang , Li Shu-sheng , Wu Rongxue , Luo Ailin , Zhang Qin
Published: February 2023

Background

Endothelial cells (ECs) are considered more sensitive to cardiac ischemia/reperfusion (I/R) injury compared to cardiomyocytes. However, current research is mainly focused on molecular mechanisms and preventive strategies targeting cardiomyocyte I/R injury, whereas insufficient attention is placed on protecting endothelial function.

Methods and Results

In this study, we established an interlink among ulinastatin (UIT; a serine protease inhibitor), the kallikrein-kinin system (KKS), and EC injury in response to cardiac reperfusion for the first time, using in vitro and in vivo experiments, and bioinformatic analysis. Our data indicated that UTI affected I/R by inhibiting the activation of KKS and simultaneously down-regulating both bradykinin receptor 1 (Bdkrb1) and bradykinin receptor 2 (Bdkrb2) related signaling such as extracellularsignal–regulated kinase (ERK)/inducible nitric oxide synthase (iNOS) and vascular endothelial growth factor (VEGF)/endothelial nitric oxide synthase (eNOS), thereby reducing infarct size, attenuating inflammation and edema, and improving cardiac function and mortality.

Interestingly, UIT significantly suppressed KLK1 activity but did not down-regulate the KKS in normal conditions, suggesting inhibition of KLK1 might be the crucial mechanism for UIT-induced cardioprotection in reperfusion injury. Moreover, knockdown of Bdkrb1 in reperfusion-induced cardiac endothelial cells (MCECs) injury significantly prevented ERK translocation into the nucleus, reducing apoptosis, junction disruption, and expression levels of cytokines, whereas Bdkrb2 deletion could not protect MCECs against I/R injury.

Conclusions

Our findings imply that inhibition of KLK1/Bdkrb1 is a critical target for UIT in the treatment of reperfusion-induced cardiac endothelial inflammation, apoptosis, and leakage and might be a potential therapeutic strategy for cardiac reperfusion injury.
Polygenic risk scores for autoimmune related diseases are significantly different and skewed in cancer exceptional responders
Authors: Chen Siyuan , Tan Amelia LM , Perry Cassandra , Churchill Susanne , Vella Margaret , Mao Jenny , Viswanadham Vinay , Kobren Shilpa , Kohane Isaac S
Published: February 2023

A group of 54 exceptional responders (ERs) to cancer treatment across a variety of cancers and treatments were compared to typical cancer patients using previously defined polygenic risk scores (PRS) for multiple autoimmune-related diseases including type 1 diabetes (T1D), hypothyroidism, psoriasis, rheumatoid arthritis, multiple sclerosis, and inflammatory bowel (IBD) disease. Most of the ERs were not treated with checkpoint inhibitors and included a broad array of tumor types. Significantly elevated PRSs were found between ERs relative to typical cancer patients in T1D, hypothyroidism, and psoriasis. IBD PRS scores were significantly decreased in the ERs.
An adjustable magnetic levator prosthesis for customizable eyelid reanimation in severe blepharoptosis: Design and proof-of-concept
Authors: Kurukuti Nish Mohith , Nadeau Melanie , Paschalis Eleftherios I. , Houston Kevin
Published: February 2023

Purpose

Blepharoptosis is a common oculoplastic condition defined as incomplete opening of the upper eyelid. Although surgical approaches have become the mainstay for correction, they often fail to improve blink function. The purpose of this study was to develop an adjustable magnetic levator prosthesis (aMLP) as a non-surgical treatment option for severe ptosis, that allows blink reanimation.

Methods

Magnetic force required to perform blink reanimation was characterized by evaluation of eye opening and closing using inter-palpebral fissure (IPF) outcomes with various combinations of eyelid array magnet and box magnets. The force that provided the optimal eye opening without limiting eye closing was selected for the development of the aMLP. The aMLP included an eyelid array magnet and an adjustable rotating spectacle magnet that allowed change in the magnetic direction, and hence change in the net magnetic interactive force between the spectacle and lid magnets. The clinical feasibility of the aMLP in improving eye opening without limiting eye closing was evaluated in ptosis patients through a proof-of-concept study using IPF and comfort outcomes.

Results

Optimal eye opening and closing was achieved by a magnet-array combination providing 45gF in the tested ptosis population. Optimal size of spectacle magnet for aMLP was selected based on the simulations of rotating diametrically magnetized cylindrical magnets to achieve force ranges required for blink reanimation. The aMLP was able to modulate eye opening and closing with change in rotation (fitting) of the spectacle magnet in two ptotic patients. The best fitting of aMLP improved IPF opening without limiting eye closing (spontaneous or volitional blinking) with good comfort reported.

Conclusions

Preliminary results suggest that the aMLP can correct ptosis without adversely affecting blink function. Further evaluation in a larger patient population is warranted.

Translational Relevance

A non-surgical, proof-of-concept, adjustable magnetic treatment option for blink reanimation in patients with severe ptosis is presented.
Safety and immunogenicity of SCB-2019, an adjuvanted, recombinant SARS-CoV-2 trimeric S-protein subunit COVID-19 vaccine in healthy 12–17 year-old adolescents
Authors: Lopez Pio , Bravo Lulu , Buntinx Erik , Borja-Tabora Charissa , Velasquez Hector , Rodriguez Edith Johana , Rodriquez Camilo A. , Carlos Josefina , Montellano May Emmeline B. , Alberto Edison R. , Salvani-Bautista Milagros , Huang Yung , Hu Branda , Li Ping , Han Htay Htay , Baccarini Carmen , Smolenov Igor
Published: February 2023

We previously demonstrated efficacy of the COVID-19 vaccine candidate, SCB-2019, in adults in the SPECTRA phase 2/3 efficacy study. We extended the study to include 1278 healthy 12–17-year-old adolescents in Belgium, Colombia and the Philippines who received either two doses of SCB-2019 or placebo 21 days apart, to assess immunogenicity as neutralizing antibodies against prototype SARS-CoV-2 and variants of concern, and safety and reactogenicity as solicited and unsolicited adverse events with a comparator group of young adults (18–25 years). In participants with no evidence of prior SARS-CoV-2 infection SCB-2019 immunogenicity in adolescents was non-inferior to that in young adults; respective geometric mean neutralizing titers (GMT) against prototype SARS-CoV-2 14 days after the second vaccination were 271 IU/mL (95% CI: 211–348) and 144 IU/mL (116–178). Most adolescents (1077, 84.3%) had serologic evidence of prior SAR-CoV-2 exposure at baseline; in these seropositive adolescents neutralizing GMTs increased from 173 IU/mL (135–122) to 982 IU/mL (881–1094) after the second dose. Neutralizing titers against Delta and Omicron BA SARS-CoV-2 variants were also increased, most notably in those with prior exposure.

SCB-2019 vaccine was well tolerated with generally mild or moderate, transient solicited and unsolicited adverse events that were comparable in adolescent vaccine and placebo groups except for injection site pain – reported after 20% of SCB-2019 and 7.3% of placebo injections. SCB-2019 vaccine was highly immunogenic against SARS-CoV-2 prototype and variants in adolescents, especially in those with evidence of prior exposure, with comparable immunogenicity to young adults.

Clinical trial registration

EudraCT 2020-004272-17;ClinicalTrials.govNCT04672395.
To ascertain the awareness among triage staff about clinical conditions treated in the Department of Hand Surgery from their referral pattern : A cross sectional observational study in a tertiary care center
Authors: Sethu Maithreyi , Rajappa Srinivasan
Published: February 2023

Objectives

To ascertain the referral pattern and the awareness about clinical conditions treated in the Department of Hand Surgery among the triage staff.

To determine if is there a difference between the triaging by the doctors and by the junior (less than 5 years in service) and the senior nurses (more than 5 years in service) with reference to clinical conditions which are treated in the Hand surgery Department.

Materials and methods

This was a cross-sectional observational study which was conducted in a tertiary care center in India. The study involved a total of 115 participants with junior nurses, senior nurses and doctors working in the triage service of the hospital.

All participants were shown a semi-structured tool with clinical scenarios which had photographs and clinical information in text, on a computer screen using Microsoft PowerPoint. The clinical scenario was also narrated to them. The referral pattern was noted down and tabulated.

Results

It is interesting to note that,

Only in 1 out of the 20 scenarios, hand surgery was the most frequently referred department.

Most of the Bony injuries of the hand and the forearm were mainly referred to orthopaedics.

Burns and raw areas of the forearm were frequently referred to plastic surgery.

Hand deformities were commonly referred to either plastic surgery or orthopaedics.

Nerve injuries were referred to neurology and orthopaedics typically.

Orthopaedics was the most referred department.

The average reference percentage of the junior nurse was 3.91%, senior nurse was 21.9% and doctors was 23.95%. Junior nurses performed exceedingly poor in referring cases to the department of hand surgery as compared to the other two subgroups.

Conclusion

This study shows us the drawbacks in our present triaging system emphasizing the need for training our staff on new departments referral pattern, the advancements, and updated protocols.
Use of cfDNA and exovesicle-DNA for the molecular diagnosis of chronic Chagas disease
Authors: Lozano Noelia , Samblas Mercedes Gomez , Calabuig Eva , Giménez Martí María José , Gómez Ruiz Maria Dolores , Sahuquillo Arce José Miguel , Molina Moreno José Miguel , Trelis M. , Osuna Antonio
Published: February 2023

Chagas disease is, among others, considered a neglected tropical disease. Given the magnitude of the human movements that have occurred in recent years from Central and South America to other countries, Chagas should now be considered a disease of worldwide distribution, in which the transmission of the parasite is restricted to transplacental transmission or blood or organ donations from infected people.

Parasite detection in chronically ill patients is restricted to serological tests that only determine previous contact and not the presence of the parasite, especially in those patients undergoing treatment evaluation or in newborns.

In this study, we evaluate the use of nucleic acids from both circulating serum exovesicles and cell-free DNA (cfDNA) from 448 serum samples from immunologically diagnosed chronic chagasic patients, which were re-evaluated by nested PCR on the amplicons resulting from amplification with kDNA-specific primers 121F-122R. Of the total number of samples selected, 50 were used to isolate and purify exovesicles from circulating serum and cell-free DNA (cfDNA).

When the nucleic acids thus purified were assayed as a template and amplified with primers 121F-122R and SAT, a percentage positivity of 100% was obtained for all positive samples assayed with the kDNA-specific primers and 96% when SAT primers were used. However, isolation of cfDNA forT. cruziand amplification with SAT primers also showed 100% positivity. Hence, both samples can be used in those cases where it is necessary to demonstrate the active presence of the parasite.
Unraveling the immune signature of herpes zoster: Insights into pathophysiology and the HLA risk profile
Authors: Vandoren Romi , Boeren Marlies , Schippers Jolien , Bartholomeus Esther , Michels Nele , Aerts Olivier , Leysen Julie , Bervoets An , Lambert Julien , Leuridan Elke , Wens Johan , Peeters Karin , Emonds Marie-Paule , Jansens Hilde , Suls Arvid , Van Tendeloo Viggo , Ponsaerts Peter , Delputte Peter , Ogunjimi Benson , Meysman Pieter , Laukens Kris
Published: February 2023

The varicella-zoster virus (VZV) infects over 95% of the population and establishes latency afterwards. Reactivation of VZV causes herpes zoster (HZ), commonly known as shingles, which presents as a painful rash in mostly the elderly and people with a weakened immune system. However, HZ might occur in otherwise healthy individuals too. In this study, we have studied the immune signature of HZ to better understand HZ’s pathophysiology. We provide a general overview of the antiviral state and the activation of innate and adaptive immune responses during HZ. Differential gene expression and gene ontology analyses revealed upregulation of several genes and host immune pathways during herpes zoster, especially related to type I IFN response but also related to adaptive immune responses. Intriguingly, no differences in gene expression were noted during convalescence between HZ patients and controls. Furthermore, we conducted the largest HLA association study on HZ to date using the UK Biobank and identified seven protective and four risk HLA alleles associated with the development of herpes zoster. These findings reveal key genes and pathways involved in the host immune response to symptomatic VZV reactivation and provide new molecular insights into the development of HZ.
APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP
Authors: Walker Logan C. , de la Hoya Miguel , Wiggins George A.R. , Lindy Amanda , Vincent Lisa M. , Parsons Michael T , Canson Daffodil M , Bis-Brewer Dana , Cass Ashley , Tchourbanov Alexander , Zimmermann Heather , Byrne Alicia B , Pesaran Tina , Karam Rachid , Harrison Steven , Spurdle Amanda B
Published: February 2023

The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1 (null variant in a gene where loss-of-function is the mechanism of disease), PS3 (functional assays show damaging effect on splicing), PP3 (computational evidence supports a splicing effect), BS3 (functional assays show no damaging effect on splicing), BP4 (computational evidence suggests no splicing impact), and BP7 (silent change with no predicted impact on splicing). However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation (SVI) Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. Our study utilised empirically derived splicing evidence to: 1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, 2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and 3) exemplify methodology to calibrate bioinformatic splice prediction tools. We propose repurposing of the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely BP7 may be used to capture RNA results demonstrating no impact on splicing for both intronic and synonymous variants, and for missense variants if protein functional impact has been excluded. Furthermore, we propose that the PS3 and BS3 codes are applied only for well-established assays that measure functional impact that is not directly captured by RNA splicing assays. We recommend the application of PS1 based on similarity of predicted RNA splicing effects for a variant under assessment in comparison to a known Pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA assay evidence described aim to help standardise variant pathogenicity classification processes and result in greater consistency when interpreting splicing-based evidence.
Optineurin provides a mitophagy contact site for TBK1 activation
Authors: Yamano Koji , Sawada Momoha , Kikuchi Reika , Nagataki Kafu , Kojima Waka , Sugihara Atsushi , Fujino Tomoshige , Tanaka Keiji , Hayashi Gosuke , Murakami Hiroshi , Matsuda Noriyuki
Published: February 2023

Tank-binding kinase 1 (TBK1) is a Ser/Thr kinase involved in many intracellular processes including innate immunity, cell cycle, and apoptosis. TBK1 is also important for phosphorylating autophagy adaptors critical in selective autophagic removal of damaged mitochondria (mitophagy). However, the mechanism by which TBK1 is activated by PINK1/Parkin-mediated mitophagy remains largely unknown. Here, we show that the autophagy adaptor OPTN provides a unique platform for TBK1 activation. The OPTN-ubiquitin and OPTN-autophagy machinery interaction axes facilitate assembly of the OPTN-TBK1 complex at a contact site between damaged mitochondria and the autophagosome formation site. This assembly point serves as a positive feedback loop for TBK1 activation by accelerating hetero-autophosphorylation of the protein. Furthermore, expression of monobodies engineered in this study against OPTN impaired assembly of OPTN at the contact sites as well as the subsequent activation of TBK1 and mitochondrial degradation. Taken together the findings reveal that a positive reciprocal relationship between OPTN and TBK1 initiates autophagosome biogenesis on damaged mitochondria.
Spatial transcriptomic atlas of shoot organogenesis in tomato callus
Authors: Song Xiehai , Guo Pengru , Wang Meiling , Chen Lichuan , Zhang Jinhui , Xu Mengyuan , Liu Naixu , Liu Min , Fang Liang , Xu Xun , Gu Ying , Xia Keke , Li Bosheng
Published: February 2023

Callus is a reprogrammed transitional cell mass during plant regeneration. Pluripotent callus cells develop into fertile shoots throughde novoshoot organogenesis. This study represents a pioneering effort in exploring the spatial transcriptome of tomato callus during shoot regeneration, using technologies including BGI Stereo-seq, BMKMANU S1000, and 10x Visium. The results indicate that the callus comprises highly heterogeneous cells, classified into various cell types based on spatial gene expression and histological observation, including epidermis, shoot primordium, vascular tissue, inner callus, and outgrowth shoots. The developmental trajectories from shoot primordium to outgrowth shoot are traced, and vascular tissue development is characterized. The single-cell resolution spatial approach reveals the origin of shoot primordia from the sub-epidermis. The spatial full length RNA sequencing shows high incompletely spliced (IS) ratios in the shoot primordium cells. These findings enhance our knowledge of plant organogenesis and highlight the significance of spatial biology in plant research.
A chromosome-level genome assembly of a model conifer plant, the Japanese cedar,Cryptomeria japonicaD. Don
Authors: Fujino Takeshi , Katsushi Yamaguchi , Yokoyama Toshiyuki T , Hamanaka Toshiya , Harazono Yoritaka , Kamada Hiroaki , Kobayashi Wataru , Ujino-Ihara Tokuko , Uchiyama Kentaro , Matsumoto Asako , Izuno Ayako , Tsumura Yoshihiko , Toyoda Atsushi , Shigenobu Shuji , Moriguchi Yoshinari , Ueno Saneyoshi , Kasahara Masahiro
Published: February 2023

Japanese cedar (Cryptomeria japonicaD. Don) is the most important Japanese forest tree, occupying about 44% of artificial forests in Japan, and planted in East Asia, Azores Archipelago, and some islands in the Indian Ocean. Although the huge genome of the species (ca. 11 Gb) with abundant repeat elements might have been an obstacle for genetic analysis, the species is easily propagated by cutting, flowered by plant hormones like gibberellic acid, transformed by agrobacterium, and edited by CRISPR/Cas9. These characteristics ofC. japonicaare preferable to make the species a model conifer for which reference genome sequences are necessary. In this study, we report the first chromosome-level assembly forC. japonica(2n = 22) using a third generation selfed progeny with an estimated homozygosity of 0.96. Young leaf tissue was used to extract high-molecular-weight DNA (>50 kb) for HiFi PacBio long read sequencing and to construct Hi-C/Omni-C library for Illumina short read sequencing. Using the 29× and 26× genome coverage of HiFi and Illumina reads, respectively, de novo assembly resulted in 2,650 contigs (9.1 Gb in total) with N50 contig size of 12.0 Mb. The Hi-C analysis mapped 97% of the nucleotides on the 11 chromosomes. The assembly was verified by comparing with a consensus linkage map of 7,785 markers. The BUSCO analysis confirmed ~91% of conserved genes. Annotations of genes, repeat elements and synteny with other Cupressaceae and Pinaceae species were performed, providing fundamental resources for genomic research of conifers.
Community diversity affects functionality and species sorting during propagation of a natural microbial community
Authors: Leale Alanna , Auxier Ben , Smid Eddy J. , Schoustra Sijmen
Published: February 2023

The influence of community diversity on community function has long been a central question in ecology. Particularly, the dynamics over time of this relationship as a function of levels of diversity remains unclear. Natural populations may vary in levels of species diversity, for instance after they experience disturbances that remove significant amounts of their genetic and species variation, including rare but functionally unique guilds. We investigated the influence of diversity on associated community function by propagating natural microbial communities from a traditionally fermented milk beverage diluted to various levels. Specifically, we assessed the influence of less abundant microbial types such as yeast and rarer bacterial types on community functionality and species sorting trajectories over approximately 100 generations. We observed repeatable changes in bacterial community compositions, metabolic profiles, and acidity related to starting diversity levels. The influence of a single ecological guild, yeast in our study, played a dramatic role on function, but interestingly not on long-term species sorting trajectories of the remaining bacterial community. Our results together evidence ecological selection on the microbial communities in our system and suggest an unexpected niche division between yeast and bacterial communities.
A conformational-dependent interdomain redox relay at the core of Protein Disulfide Isomerase activity
Authors: Melo Eduardo P. , El-Guendouz Soukaina , Correia Cátia , Teodoro Fernando , Lopes Carlos
Published: February 2023

Protein disulfide isomerases (PDIs) are a family of molecular chaperones resident in the endoplasmic reticulum (ER) emerging as important factors in disease. In addition to an holdase function, some members catalyse disulfide bond formation and isomerization, a crucial step for native folding and prevention of aggregation of misfolded proteins. PDIs are characterized by a modular arrangement of thioredoxin-like domains, with the canonical, first identified PDIA1, organized as four thioredoxin-like domains forming a horseshoe with two active sites at the extremities. Using two fluorescent redox sensors, roGFP2 and HyPer, as client substrates either unfolded or native, and thein vitroreconstitution of the full pathways of oxidative protein in the ER, we clarified important aspects underlying the catalytic cycle of PDIA1. The N-terminalaactive site is the main oxidant of thiols and can transfer electrons to the C-terminala’active site relying on the redox-dependent conformational flexibility of PDIA1 that allows the formation of an interdomain disulfide bond. Thea’active site act then as a crossing point to redirect electrons to the ER downstream oxidases or back to client proteins. The two active sites of PDIA1 work cooperatively as an interdomain redox relay that explains PDIA1 oxidative activity to form native disulfides and PDIA1 reductase activity to resolve scrambled disulfides. Moreover, this mechanism reveals a new rational for shutting down oxidative protein folding under ER redox imbalance or when the levels of unfolded proteins and folding intermediates exceed the folding capacity of the system.
Morphological trait evolution inSolanum(Solanaceae): evolutionary lability of key taxonomic characters
Authors: Hilgenhof Rebecca , Gagnon Edeline , Knapp Sandra , Aubriot Xavier , Tepe Eric J. , Bohs Lynn , Giacomin Leandro L. , Gouvêa Yuri F. , Martine Christopher T. , Orejuela Andrés , Orozco Clara Inés , Peralta Iris E. , Särkinen Tiina
Published: February 2023

SolanumL. is one of the world’s largest and economically most important plant genera, including 1,245 currently accepted species and several major and minor crops (e.g., tomato, potato, brinjal eggplant, scarlet eggplant, Gboma eggplant, lulo, and pepino). Here we provide an overview of the evolution of 25 key morphological traits for the major and minor clades of this giant genus based on stochastic mapping using a well-sampled recently published phylogeny ofSolanum. The most evolutionarily labile traits (showing >150 transitions across the genus) relate to plant structure (growth form and sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape and colour), and dispersal (fruit colour). Ten further traits show evolutionary lability with 50-100 transitions across the genus (e.g., specialised underground organs, trichome structure, leaf type, inflorescence position and branching, stamen heteromorphism). Our results reveal a number of highly convergent traits inSolanum, including tubers, rhizomes, simple leaves, yellow corollas, heteromorphic anthers, dioecy, and dry fruits, and some unexpected pathways of trait evolution that could be explored in future studies. We show that informally named clades ofSolanumcan be morphologically defined by trait combinations providing a tool for identification and enabling predictive phylogenetic placement of unsampled species.
Understanding Activity-Stability Tradeoffs in Biocatalysts by Enzyme Proximity Sequencing
Authors: Vanella Rosario , Küng Christoph , Schoepfer Alexandre A. , Doffini Vanni , Ren Jin , Nash Michael A.
Published: February 2023

Understanding the complex relationships between enzyme sequence, folding stability and catalytic activity is crucial for applications in industry and biomedicine. However, current enzyme assay technologies are limited by an inability to simultaneously resolve both stability and activity phenotypes and to couple these to gene sequences at large scale. Here we developed Enzyme Proximity Sequencing (EP-Seq), a deep mutational scanning method that leverages peroxidase-mediated radical labeling with single cell fidelity to dissect the effects of thousands of mutations on stability and catalytic activity of oxidoreductase enzymes in a single experiment. We used EP-Seq to analyze how 6,399 missense mutations influence folding stability and catalytic activity in a D-amino acid oxidase (DAOx) fromR.gracilis. The resulting datasets demonstrate activity-based constraints that limit folding stability during natural evolution, and identify hotspots distant from the active site as candidates for mutations that improve catalytic activity without sacrificing stability. EP-Seq can be extended to other enzyme classes and provides valuable insights into biophysical principles governing enzyme structure and function.
Non-muscle myosin 2 filaments are processive in cells
Authors: Vitriol Eric A. , Quintanilla Melissa A. , Tidei Joseph J. , Troughton Lee D. , Cody Abigail , Cisterna Bruno A. , Jane Makenzie L. , Oakes Patrick W. , Beach Jordan R.
Published: February 2023

Directed transport of cellular components is often dependent on the processive movements of cytoskeletal motors. Myosin 2 motors predominantly engage actin filaments of opposing orientation to drive contractile events, and are therefore not traditionally viewed as processive. However, recentin vitroexperiments with purified non-muscle myosin 2 (NM2) demonstrated myosin 2 filaments could move processively. Here, we establish processivity as a cellular property of NM2. Processive runs in central nervous system-derived CAD cells are most apparent as processive movements on bundled actin in protrusions that terminate at the leading edge. We find that processive velocitiesin vivoare consistent within vitromeasurements. NM2 makes these processive runs in its filamentous form against lamellipodia retrograde flow, though anterograde movement can still occur in the absence of actin dynamics. Comparing the processivity of NM2 isoforms, we find that NM2A moves slightly faster than NM2B. Finally, we demonstrate that this is not a cell-specific property, as we observe processive-like movements of NM2 in the lamella and subnuclear stress fibers of fibroblasts. Collectively, these observations further broaden NM2 functionality and the biological processes in which the already ubiquitous motor can contribute.
U1 AMO (antisense morpholino oligo) disrupts U1 snRNP structure to promote intronic premature cleavage and polyadenylation (PCPA)
Authors: Feng Qiumin , Lin Zejin , Deng Yanhui , Ran Yi , Xiang Andy Peng , Ye Congting , Yao Chengguo
Published: February 2023

Functional depletion of U1 snRNP with a 25 nt U1 AMO (antisense morpholino oligonucleotides) may lead to intronic premature cleavage and polyadenylation (PCPA) of thousands of genes, a phenomenon known as U1 snRNP telescripting; however, the underlying mechanism remains elusive. In this study, we demonstrated that U1 AMO could disrupt U1 snRNP structure both in vitro and in vivo, thereby affecting U1 snRNP/RNAP polymerase II (RNAPII) interaction. We further showed that U1 AMO treatment might promote RNAPII disassociation with pre-mRNA in an RNA pull-down assay. By performing ChIP-seq for phosphorylation of Ser2 (Ser2P) and Ser5 (Ser5P) of the C-terminal domain (CTD) of RNA polymerase II (RNAPII), we showed that transcription elongation was disturbed upon U1 AMO treatment, with a particular high Ser2P signal at intronic cryptic polyadenylation sites (PASs). In addition, we showed that core 3’ processing factors CPSF/CstF are involved in the processing of intronic cryptic PAS. Their recruitment accumulated toward cryptic PASs upon U1 AMO treatment, as indicated by ChIP-seq and iCLIP-seq analysis. Furthermore, we showed that most of these PCPAed transcripts could be exported to cytoplasm and have the potential to be translated. Conclusively, our data provide more insight into U1 snRNP telescripting, and suggest a common theme that modulation of transcription elongation may be an important mode for the regulation of mRNA polyadenylation.
HIV-1 Gag colocalizes with euchromatin histone marks at the nuclear periphery
Authors: Chang Jordan , Parent Leslie J.
Published: February 2023

The retroviral Gag protein of human immunodeficiency virus type 1 (HIV-1) plays a central role in the selection of unspliced viral genomic RNA for packaging into new virions. Previously, we demonstrated that full-length HIV-1 Gag undergoes nuclear trafficking where it associates with unspliced viral RNA (vRNA) at transcription sites. To further explore the kinetics of HIV-1 Gag nuclear localization, we used biochemical and imaging techniques to examine the timing of HIV-1 entry into the nucleus. We also aimed to determine more precisely Gag’s subnuclear distribution to test the hypothesis that Gag would be associated with euchromatin, the transcriptionally active region of the nucleus. We observed that HIV-1 Gag localized to the nucleus shortly after its synthesis in the cytoplasm, suggesting that nuclear trafficking was not strictly concentration-dependent. Furthermore, we found that HIV-1 Gag preferentially localized to the transcriptionally active euchromatin fraction compared to the heterochromatin-rich region in a latently-infected CD4+ T cell line (J-Lat 10.6) treated with latency-reversal agents. Interestingly, HIV-1 Gag was more closely associated with transcriptionally-active histone markers near the nuclear periphery, where the HIV-1 provirus was previously shown to integrate. Although the precise function of Gag’s association with histones in transcriptionally-active chromatin remains uncertain, together with previous reports, this finding is consistent with a potential role for euchromatin-associated Gag molecules to select newly transcribed unspliced vRNA during the initial stage of virion assembly.

Importance

The traditional view of retroviral assembly posits that HIV-1 Gag selection of unspliced vRNA begins in the cytoplasm. However, our previous studies demonstrated that HIV-1 Gag enters the nucleus and binds to unspliced HIV-1 RNA at transcription sites, suggesting that genomic RNA selection may occur in the nucleus. In the present study, we observed nuclear entry of HIV-1 Gag and co-localization with unspliced viral RNA within 8 hours post-expression. In CD4+ T cells (J-Lat 10.6) treated with latency reversal agents, as well as a HeLa cell line stably expressing an inducible Rev-dependent provirus, we found that HIV-1 Gag preferentially localized with histone marks associated with enhancer and promoter regions of transcriptionally active euchromatin near the nuclear periphery, which favors HIV-1 proviral integration sites. These observations support the hypothesis that HIV-1 Gag hijacks euchromatin-associated histones to localize to active transcription sites, promoting capture of newly synthesized genomic RNA for packaging.
Single Cross-Sectional Analysis; Post-Myocardial Infarction Instrumental & Laboratory changes in Prognosis Behavior
Authors: Marzoog Basheer Abdullah , Bloshkina Natalia Igorevna , Gromova Vera Sergeevna , Vanichkina Ekaterina , Gorshinina Elena Ivanovna
Published: February 2023

Background

Cardiovascular events remain one of the frequently reported causes of death globally.

Aims

Assess the early laboratory and instrumental changes in systemic manner in patients with myocardial infarction (MI).

Objectives

Patients with fresh myocardial infarction that has been occurred in less than 30 days before hospitalization in the rehabilitation hospital.

Materials and methods

A single large-scale retrospective cohort sectional study for patients with fresh myocardial infarction for the period 2014-2019, data collected from Mordovia Rehabilitation Hospital. The study involved 154 patients and analysed 76 parameters for each patient. The t test, Pearson’s correlation coefficient, and ROC test have been used. For statistical analysis used Statistica program.

Results

The sample included 154 patients with a history of fresh myocardial infarction. Of 154. 51(33.11%) female and 103 (66.88 %) males. Chronic heart failure (CHF), which is seen in 42 (27.27 %) patients, 101 (65.58 %) did not have CHF and 11 (7.142 %) missing data. Diabetes mellitus (DM) has been observed in 28 (18.18182 %), 118 (76.62 %) without DM, Hypertension has been seen in 118 (76.62 %), 28 (18.18 %) did not have hypertension, chronic kidney disease (CKD) has been seen in 11 (7.14%) patients, 131 (85.064 %) did not have CKD, Chronic obstructive pulmonary disease (COPD) existed in 14 (9.09 %), 132 (85.71 %) did not have COPD. Post myocardial infarction (MI) CHF has been observed in 108 (70.12987%), 42 (27.27 %) did not have CHF. Post MI arrythmia seen in 50 (32.47%) patients, 99 (64.28 %) did not have arrythmia. Early post MI complication such as aneurysm has been seen in 12 (7.79 %), 138 (89.61 %) did not have aneurysm, Dressler syndrome; pericarditis has been seen in 4 (2.59 %) patients, pneumonitis seen in 1 (0.64 %) patient, and pleuritis have not been seen.

Conclusions

Systemic manifestations include kidney function impairment or development of new kidney disease. These changes include an increase in the aorta basement diameter, an increase in the right ventricle size, a decrease in the level of serum red blood cells, the serum potassium level, and serum calcium level, with an increase in the serum myoglobin. The high myoglobin level is associated with the development of chronic heart failure. The higher creatinine level and or LDH is associated with arrythmia development. Hypertension is the predominant concomitant disease in victims of MI. And arrythmia is most commonly reported post-MI complication.

Others

Females are more frequently affected by post-MI urinary tract infection.
Cerebellar Granule Cells Develop Non-neuronal 3D Genome Architecture over the Lifespan
Authors: Tan Longzhi , Shi Jenny , Moghadami Siavash , Wright Cydney P. , Parasar Bibudha , Seo Yunji , Vallejo Kristen , Cobos Inma , Duncan Laramie , Chen Ritchie , Deisseroth Karl
Published: February 2023

The cerebellum contains most of the neurons in the human brain, and exhibits unique modes of development, malformation, and aging. For example, granule cells—the most abundant neuron type—develop unusually late and exhibit unique nuclear morphology. Here, by developing our high-resolution single-cell 3D genome assay Dip-C into population-scale (Pop-C) and virus-enriched (vDip-C) modes, we were able to resolve the first 3D genome structures of single cerebellar cells, create life-spanning 3D genome atlases for both human and mouse, and jointly measure transcriptome and chromatin accessibility during development. We found that while the transcriptome and chromatin accessibility of human granule cells exhibit a characteristic maturation pattern within the first year of postnatal life, 3D genome architecture gradually remodels throughout life into a non-neuronal state with ultra-long-range intra-chromosomal contacts and specific inter-chromosomal contacts. This 3D genome remodeling is conserved in mice, and robust to heterozygous deletion of chromatin remodeling disease-associated genes (Chd8orArid1b). Together these results reveal unexpected and evolutionarily-conserved molecular processes underlying the unique development and aging of the mammalian cerebellum.
Transient cAMP production drives rapid and sustained spiking in brainstem parabrachial neurons to suppress feeding
Authors: Alvarado Jonnathan Singh , Lutas Andrew , Madara Joseph C. , Isaac Jeremiah , Lommer Caroline , Andermann Mark L.
Published: February 2023

Brief stimuli can trigger longer lasting brain states. G protein-coupled receptors (GPCRs) could help sustain such states by coupling slow-timescale molecular signals to neuronal excitability. Brainstem parabrachial nucleus glutamatergic neurons (PBNGlut) regulate sustained brain states such as pain, and express Gs-coupled GPCRs that increase cAMP signaling. We asked whether cAMP directly influences PBNGlutexcitability and behavior. Both brief tail shocks and brief optogenetic stimulation of cAMP production in PBNGlutneurons drove minutes-long suppression of feeding. This suppression matched the duration of prolonged elevations in cAMP, Protein Kinase A (PKA), and calcium activityin vivoandin vitro.Shortening this elevation in cAMP reduced the duration of feeding suppression following tail shocks. cAMP elevations in PBNGlutneurons rapidly lead to sustained increases in action potential firing via PKA-dependent mechanisms. Thus, molecular signaling in PBNGlutneurons helps prolong neural activity and behavioral states evoked by brief, salient bodily stimuli.