The TET3 inflammasome senses unique long HSV-1 proteins for virus particle budding from the nucleus.

Inflammasomes play important roles in resisting infections caused by various pathogens. HSV-1 is a highly contagious virus among humans. The process by which HSV-1 particles bud from the nucleus is unique to herpes viruses, but the specific mechanism is still unclear. Here, we screened genes involved in HSV-1 replication. We found that TET3 plays an essential role in HSV-1 infection. TET3 recognizes the UL proteins of HSV-1 and, upon activation, can directly bind to caspase-1 to activate an ASC-independent inflammasome in the nucleus. The subsequent cleavage of GSDMD in the nucleus is crucial for the budding of HSV-1 particles from the nucleus. Inhibiting the perforation ability of GSDMD on the nuclear membrane can significantly reduce the maturation and spread of HSV-1. Our results may provide a new approach for the treatment of HSV-1 in the future.

No substantial neurocognitive impact of COVID-19 across ages and disease severity: a multicenter biomarker study of SARS-CoV-2 positive and negative adult and pediatric patients with acute respiratory tract infections.

BACKGROUND: Compared to intensive care unit patients with SARS-CoV-2 negative acute respiratory tract infections, patients with SARS-CoV-2 are supposed to develop more frequently and more severely neurologic sequelae. Delirium and subsequent neurocognitive deficits (NCD) have implications for patients' morbidity and mortality. However, the extent of brain injury during acute COVID-19 and subsequent NCD still remain largely unexplored. Body-fluid biomarkers may offer valuable insights into the quantification of acute delirium, brain injury and may help to predict subsequent NCD following COVID-19. METHODS: In a multicenter, observational case-control study, conducted across four German University Hospitals, hospitalized adult and pediatric patients with an acute COVID-19 and SARS-CoV-2 negative controls presenting with acute respiratory tract infections were included. Study procedures comprised the assessment of pre-existing neurocognitive function, daily screening for delirium, neurological examination and blood sampling. Fourteen biomarkers indicative of neuroaxonal, glial, neurovascular injury and inflammation were analyzed. Neurocognitive functions were re-evaluated after three months. RESULTS: We enrolled 118 participants (90 adults, 28 children). The incidence of delirium [85 out of 90 patients (94.4%) were assessable for delirium) was comparable between patients with COVID-19 [16 out of 61 patients (26.2%)] and SARS-CoV-2 negative controls [8 out of 24 patients (33.3%); p > 0.05] across adults and children. No differences in outcomes as measured by the modified Rankin Scale, the Short-Blessed Test, the Informant Questionnaire on Cognitive Decline in the Elderly, and the pediatrics cerebral performance category scale were observed after three months. Levels of body-fluid biomarkers were generally elevated in both adult and pediatric cohorts, without significant differences between SARS-CoV-2 negative controls and COVID-19. In COVID-19 patients experiencing delirium, levels of GFAP and MMP-9 were significantly higher compared to those without delirium. CONCLUSIONS: Delirium and subsequent NCD are not more frequent in COVID-19 as compared to SARS-CoV-2 negative patients with acute respiratory tract infections. Consistently, biomarker levels of brain injury indicated no differences between COVID-19 cases and SARS-CoV-2 negative controls. Our data suggest that delirium in COVID-19 does not distinctly trigger substantial and persistent subsequent NCD compared to patients with other acute respiratory tract infections. TRIAL REGISTRATION: ClinicalTrials.gov: NCT04359914; date of registration 24-APR 2020.

Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex lipoprotein(a) KIV-2 VNTR.

BACKGROUND: Repetitive genome regions, such as variable number of tandem repeats (VNTR) or short tandem repeats (STR), are major constituents of the uncharted dark genome and evade conventional sequencing approaches. The protein-coding LPA kringle IV type-2 (KIV-2) VNTR (5.6 kb per unit, 1-40 units per allele) is a medically highly relevant example with a particularly intricate structure, multiple haplotypes, intragenic homologies, and an intra-VNTR STR. It is the primary regulator of plasma lipoprotein(a) [Lp(a)] concentrations, an important cardiovascular risk factor. Lp(a) concentrations vary widely between individuals and ancestries. Multiple variants and functional haplotypes in the LPA gene and especially in the KIV-2 VNTR strongly contribute to this variance. METHODS: We evaluated the performance of amplicon-based nanopore sequencing with unique molecular identifiers (UMI-ONT-Seq) for SNP detection, haplotype mapping, VNTR unit consensus sequence generation, and copy number estimation via coverage-corrected haplotypes quantification in the KIV-2 VNTR. We used 15 human samples and low-level mixtures (0.5 to 5%) of KIV-2 plasmids as a validation set. We then applied UMI-ONT-Seq to extract KIV-2 VNTR haplotypes in 48 multi-ancestry 1000 Genome samples and analyzed at scale a poorly characterized STR within the KIV-2 VNTR. RESULTS: UMI-ONT-Seq detected KIV-2 SNPs down to 1% variant level with high sensitivity, specificity, and precision (0.977 ± 0.018; 1.000 ± 0.0005; 0.993 ± 0.02) and accurately retrieved the full-length haplotype of each VNTR unit. Human variant levels were highly correlated with next-generation sequencing (R2 = 0.983) without bias across the whole variant level range. Six reads per UMI produced sequences of each KIV-2 unit with Q40 quality. The KIV-2 repeat number determined by coverage-corrected unique haplotype counting was in close agreement with droplet digital PCR (ddPCR), with 70% of the samples falling even within the narrow confidence interval of ddPCR. We then analyzed 62,679 intra-KIV-2 STR sequences and explored KIV-2 SNP haplotype patterns across five ancestries. CONCLUSIONS: UMI-ONT-Seq accurately retrieves the SNP haplotype and precisely quantifies the VNTR copy number of each repeat unit of the complex KIV-2 VNTR region across multiple ancestries. This study utilizes the KIV-2 VNTR, presenting a novel and potent tool for comprehensive characterization of medically relevant complex genome regions at scale.

KSHV ORF20 Promotes Coordinated Lytic Reactivation for Increased Infectious Particle Production.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a cancer-causing virus that establishes life-long infection. KSHV is implicated in the etiology of Kaposi's sarcoma, and a number of rare hematopoietic malignancies. The present study focuses on the KSHV open reading frame 20 (ORF20), a member of the conserved herpesvirus UL24 protein family containing five conserved homology domains and a conserved PD-(D/E)XK putative endonuclease motif, whose nuclease function has not been established to date. ORF20 encodes three co-linear protein isoforms, full length, intermediate, and short, though their differential functions are unknown. In an effort to determine the role of ORF20 during KSHV infection, we generated a recombinant ORF20-Null KSHV genome, which fails to express all three ORF20 isoforms. This genome was reconstituted in iSLK cells to establish a latent infection, which resulted in an accelerated transcription of viral mRNAs, an earlier accumulation of viral lytic proteins, an increase in the quantity of viral DNA copies, and a significant decrease in viral yield upon lytic reactivation. This was accompanied by early cell death of cells infected with the ORF20-Null virus. Functional complementation of the ORF20-Null mutant with the short ORF20 isoform rescued KSHV production, whereas its endonuclease mutant form failed to enhance lytic reactivation. Complementation with the short isoform further revealed a decrease in cell death as compared with ORF20-Null virus. Finally, expression of IL6 and CXCL8, previously shown to be affected by the hCMV UL24 homolog, was relatively low upon reactivation of cells infected with the ORF20-Null virus. These findings suggest that ORF20 protein, with its putative endonuclease motif, promotes coordinated lytic reactivation for increased infectious particle production.

ATH434, a promising iron-targeting compound for treating iron regulation disorders.

Cytotoxic accumulation of loosely bound mitochondrial Fe2+ is a hallmark of Friedreich's Ataxia (FA), a rare and fatal neuromuscular disorder with limited therapeutic options. There are no clinically approved medications targeting excess Fe2+ associated with FA or the neurological disorders Parkinson's disease and Multiple System Atrophy. Traditional iron-chelating drugs clinically approved for systemic iron overload that target ferritin-stored Fe3+ for urinary excretion demonstrated limited efficacy in FA and exacerbated ataxia. Poor treatment outcomes reflect inadequate binding to excess toxic Fe2+ or exceptionally high affinities (i.e. ≤10-31) for non-pathologic Fe3+ that disrupts intrinsic iron homeostasis. To understand previous treatment failures and identify beneficial factors for Fe2+-targeted therapeutics, we compared traditional Fe3+ chelators deferiprone (DFP) and deferasirox (DFX) with additional iron-binding compounds including ATH434, DMOG, and IOX3. ATH434 and DFX had moderate Fe2+ binding affinities (Kd's of 1-4  µM), similar to endogenous iron chaperones, while the remaining had weaker divalent metal interactions. These compounds had low/moderate affinities for Fe3+(0.46-9.59 µM) relative to DFX and DFP. While all compounds coordinated iron using molecular oxygen and/or nitrogen ligands, thermodynamic analyses suggest ATH434 completes Fe2+ coordination using H2O. ATH434 significantly stabilized bound Fe2+ from ligand-induced autooxidation, reducing reactive oxygen species (ROS) production, whereas DFP and DFX promoted production. The comparable affinity of ATH434 for Fe2+ and Fe3+ position it to sequester excess Fe2+ and facilitate drug-to-protein iron metal exchange, mimicking natural endogenous iron binding proteins, at a reduced risk of autooxidation-induced ROS generation or perturbation of cellular iron stores.

Comparative genomics reveal unique markers to monitor by routine PCR assay bioinoculant of Sphingobium indicum B90A in hexachlorocyclohexane (HCH) contaminated soils.

Bioinoculants of Sphingobium indicum B90A have been used to decontaminate hexachlorocyclohexane (HCH)-contaminated soils in the past. There is no selective or convenient method available to track the added B90A in HCH-contaminated soils in the presence of several native sphingomonads. Here, we describe a method, BioMarkTrack, for tracking B90A bioinoculant by simple amplification of the B90A specific biomarker genes. Whole-genome sequence data of 120 different genera of sphingomonads (Sphingobium, Novosphingobium, Sphingomonas, Sphingopyxis, and Sphingosinicella) were retrieved from the NCBI database and annotated. Intra- and inter-genus similarity searches, including the genome of B90A as a reference was conducted. 122 unique gene sequences were identified in strain B90A, out of which 45 genes were selected that showed no similarity with the NCBI non-redundant (NR) database or gene sequences in the publicly available database. Primers were designed for amplification of 4 biomarkers. To validate the biomarkers B90A tracking efficacy in bioaugmented soils, a microcosm study was conducted in which sterile garden and HCH-contaminated dumpsite soils were amended with strain B90A. Amplification of the biomarker was observed both in sterile garden soil and HCH-contaminated dumpsite soil but not in control (lacking B90A) samples. Further, the primer set was used to track B90A in a bioremediation field trial soil, demonstrating the convenience and efficiency of the simple PCR-based method, which can be employed for tracking B90A in bioaugmented soils. The approach as presented here can be employed on different bioinoculants to identify unique biomarkers and then tracking these organisms during bioremediation. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-024-01321-7.

Parvovirus B19 Infection Is Associated with the Formation of Neutrophil Extracellular Traps and Thrombosis: A Possible Linkage of the VP1 Unique Region.

Neutrophil extracellular traps (NETs) formation, namely NETosis, is implicated in antiphospholipid syndrome (APS)-related thrombosis in various autoimmune disorders such as systemic lupus erythematosus (SLE) and APS. Human parvovirus B19 (B19V) infection is closely associated with SLE and APS and causes various clinical manifestations such as blood disorders, joint pain, fever, pregnancy complications, and thrombosis. Additionally, B19V may trigger the production of autoantibodies, including those against nuclear and phospholipid components. Thus, exploring the connection between B19V, NETosis, and thrombosis is highly relevant. An in vitro NETosis model using differentiated HL-60 neutrophil-like cells (dHL-60) was employed to investigate the effect of B19V-VP1u IgG on NETs formation. A venous stenosis mouse model was used to test how B19V-VP1u IgG-mediated NETs affect thrombosis in vivo. The NETosis was observed in the dHL-60 cells treated with rabbit anti-B19V-VP1u IgG and was inhibited in the presence of either 8-Br-cAMP or CGS216800 but not GSK484. Significantly elevated reactive oxygen species (ROS), myeloperoxidase (MPO), and citrullinated histone (Cit-H3) levels were detected in the dHL60 treated with phorbol myristate acetate (PMA), human aPLs IgG and rabbit anti-B19V-VP1u IgG, respectively. Accordingly, a significantly larger thrombus was observed in a venous stenosis-induced thrombosis mouse model treated with PMA, human aPLs IgG, rabbit anti-B19V-VP1u IgG, and human anti-B19V-VP1u IgG, respectively, along with significantly increased amounts of Cit-H3-, MPO- and CRAMP-positive infiltrated neutrophils in the thrombin sections. This research highlights that anti-B19V-VP1u antibodies may enhance the formation of NETosis and thrombosis and implies that managing and treating B19V infection could lower the risk of thrombosis.

Piloting the Inclusion of the Key Populations Unique Identifier Code in the South African Routine Health Information Management System: Protocol for a Multiphased Study.

BACKGROUND: The global community has set an ambitious goal to end HIV/AIDS as a public health threat by 2030. Significant progress has been achieved in pursuing these objectives; however, concerns remain regarding the lack of disaggregated routine data for key populations (KPs) for a targeted HIV response. KPs include female sex workers, transgender populations, gay men and other men who have sex with men, people who are incarcerated, and people who use drugs. From an epidemiological perspective, KPs play a fundamental role in shaping the dynamics of HIV transmission due to specific behaviors. In South Africa, routine health information management systems (RHIMS) do not include a unique identifier code (UIC) for KPs. The purpose of this protocol is to develop the framework for improved HIV monitoring and programming through piloting the inclusion of KPs UIC in the South African RHIMS. OBJECTIVE: This paper aims to describe the protocol for a multiphased study to pilot the inclusion of KPs UIC in RHIMS. METHODS: We will conduct a multiphased study to pilot the framework for the inclusion of KPs UIC in the RHIMS. The study has attained the University of Johannesburg Research Ethics Committee approval (REC-2518-2023). This study has four objectives, including a systematic review, according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines (objective 1). Second, policy document review and in-depth stakeholder interviews using semistructured questionnaires (objective 2). Third, exploratory data analysis of deidentified HIV data sets (objective 3), and finally, piloting the framework to assess the feasibility of incorporating KPs UIC in RHIMS using findings from objectives 1, 2, and 3 (objective 4). Qualitative and quantitative data will be analyzed using ATLAS.ti (version 6; ATLAS.ti Scientific Software Development GmbH) and Python (version 3.8; Python Software Foundation) programming language, respectively. RESULTS: The results will encompass a systematic review of literature, qualitative interviews, and document reviews, along with exploratory analysis of deidentified routine program data and findings from the pilot study. The systematic review has been registered in PROSPERO (International Prospective Register of Systematic Reviews; CRD42023440656). Data collection is planned to commence in September 2024 and expected results for all objectives will be published by December 2025. CONCLUSIONS: The study will produce a framework to be recommended for the inclusion of the KP UIC national rollout. The study results will contribute to the knowledge base around the inclusion of KPs UIC in RHIMS data. TRIAL REGISTRATION: PROSPERO CRD42023440656; https://tinyurl.com/msnppany. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/55092.

Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights.

Agrocybe chaxingu is a widely cultivated edible fungus in China, which is rich in nutrients and medicinal compounds. However, the lack of a high-quality genome hinders further research. In this study, we assembled the telomere-to-telomere genomes of two sexually compatible monokaryons (CchA and CchB) derived from a primarily cultivated strain AS-5. The genomes of CchA and CchB were 50.60 Mb and 51.66 Mb with contig N50 values of 3.95 Mb and 3.97 Mb, respectively. Each contained 13 complete chromosomes with telomeres at both ends. The high mapping rate, uniform genome coverage, high LAI score, all BUSCOs with 98.5%, and all base accuracy exceeding 99.999% indicated the high level of integrity and quality of these two assembled genomes. Comparison of the two genomes revealed that approximately 30% of the nucleotide sequences between homologous chromosomes were non-syntenic, including 19 translocations, 36 inversions, and 15 duplications. An additional gene CchA_000467 was identified at the Mat A locus of CchA, which was observed exclusively in the Cyclocybe cylindracea species complex. A total of 613 (4.26%) and 483 (3.4%) unique genes were identified in CchA and CchB, respectively, with over 80% of these being hypothetical proteins. Transcriptomic analysis revealed that the expression levels of unique genes in CchB were significantly higher than those in CchA, and both CchA and CchB had unique genes specifically expressed at stages of mycelium and fruiting body. It was indicated that the growth and development of the A. chaxingu strain AS-5 required the coordinated action of two different nuclei, with CchB potentially playing a more significant role. These findings contributed to a more profound comprehension of the growth and developmental processes of basidiomycetes.

Implementing telemedicine with 5G technologies in a nursing home for reducing emergency admissions- study protocol of a mixed-methods study.

BACKGROUND: By transmitting various types of data, telemedical care enables the provision of care where physicians and patients are physically separated. In nursing homes, telemedicine has the potential to reduce hospital admissions in nonemergency situations. In this study, telemedicine devices were implemented with the new 5G mobile communications standard in selected wards of a large nursing home in Northwest Germany. The main aim of this study is to investigate which individual and organizational factors are associated with the use of telemedicine devices and how users perceive the feasibility and implementation of such devices. Moreover, it is investigated whether the telemedical devices help to reduce the number of emergency admissions. METHODS: Telemedicine devices are implemented over an 18-month period using a private 5G network, and all users receive training. This study uses qualitative and quantitative methods: To assess the individual and organizational factors associated with the use of telemedicine devices, survey data from employees before and after the implementation of these devices are compared. To assess the perception of the implementation process as well as the feasibility and usability of the telemedical devices, the nursing staff, physicians, medical assistants and residents are interviewed individually. Moreover, every telemedicine consultation is evaluated with a short survey. To assess whether the number of emergency admissions decreased, data from one year before implementation and one year after implementation are compared. The data are provided by the integrated dispatch centre and emergency medical services (EMS) protocols. The interview data are analysed via structured qualitative content analysis according to Kuckartz. Survey data are analysed using multivariable regression analysis. DISCUSSION: Learnings from the implementation process will be used to inform future projects implementing telemedicine in care organizations, making the final telemedicine implementation and care concept available to more nursing homes and hospitals. Moreover, the study results can be used to provide use cases for appropriate and targeted application of telemedicine in nursing homes and to define the role of 5G technologies in these use cases. If the intervention is proven successful, the results will be used to promote 5G network rollout. TRIAL REGISTRATION: German Clinical Trials Register - trial registration number: DRKS00030598.

Considerations for the use of biological therapies in elderly patients with rheumatoid arthritis.

INTRODUCTION: Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease that primarily affects middle-aged individuals but is increasingly prevalent among the elderly due to longer life expectancies. Treating elderly onset RA (EORA) is challenging for clinicians because of unique disease characteristics, comorbidities, polypharmacy, age-related physiological changes, and limited studies on the safety and efficacy of biological therapies in this population. This review aims to evaluate the use of various biological therapies in elderly RA patients. AREAS COVERED: This narrative review examines various aspects of RA in the elderly using published literature, randomized control trials, meta-analyses, and recommendations from the National Institute for Health and Care Excellence (NICE) and The European Alliance of Associations for Rheumatology (EULAR). EXPERT OPINION: In EORA patients, the initiation of biological therapy is often delayed. Methotrexate remains the first-line treatment for both EORA and young onset RA (YORA). The combination of methotrexate and biological treatment shows comparable safety and efficacy in both EORA and YORA, except for rituximab, which is less effective in patients over 75. For elderly RA patients, biological (b-) disease-modifying antirheumatic drugs (DMARDs) are preferred as the first advanced therapy over targeted synthetic (ts-) DMARDs due to their superior safety profile.

Secure data communication in WSHN using EXP-MD5 and DHSK-ECC.

BACKGROUND: In the Healthcare (HC) sector, the usage of Wireless Sensor Healthcare Networks (WSHN) is attaining specific importance. The sensor device is implanted into the patient's body, and the sensed health information of patients is transformed via data aggregating devices like mobile devices, cameras, and so on, to the doctors. Thus, the early signs of diseases are identified, and remote monitoring of the patient's health is carried out by the physician on time. This aids in improving the health condition of the people and reduces the severity of disorders. But, the security gap in HC remains unresolved, despite various advantages. OBJECTIVE: This work proposes secured data communication in WSHN using Exponential Message Digest5 (EXP-MD5) and Diffie Hellman Secret Key-based Elliptic Curve Cryptography (DHSK-ECC) techniques. METHODS: Primarily, the patient registers their details in the Hospital Cloud Server (HCS). With hospital ID and patient ID, public and private keys are generated during registration. Afterward, by utilizing the Navie Shuffling (NS) technique, nCr combinations are created and shuffled. After shuffling, any of the randomly selected combinations are encoded utilizing the American Standard Code for Information Interchange (ASCII) code. For patient authentication, the ASCII code is further converted into a Quick Response(QR) code. Upon successful registration, the patient logs in to HCS. The patient can book for doctor's appointment if the login details are verified with those of the registered details. On consulting the doctor at the pre-informed time, the digital signature is created utilizing the Universal Unique Salt-based Digital Signature Algorithm (UUS-DSA) for authenticating the patient details. Further, for providing accessibility to all the authorized patients, the registered patients on HCS are considered as nodes. Then, an authorized path is created using the EXP-MD5 technique to protect each individual patient's details. The patient's IoT data is sensed, followed by authorized path creation. The data is encrypted via the DHSK-ECC algorithm for secure data transmission. Lastly, all the information is stored in HCS, so that the patient's health condition is regularly monitored by the doctor and the needy advice is suggested to the patients in the future. Also, hash matching is carried out when the doctor needs to access data. RESULTS: The proposed technique's efficacy is validated by the performance analysis in comparison with other conventional techniques. CONCLUSION: In this proposed research, the authentication is performed in multiple scenarios to enhance data security and user privacy. The patient details are authenticated during registration and verification to access the online consultation only by the authorized person. Further, the patient health information is encrypted in the proposed work after consultation so that the intrusion of medical records by malicious users and data tampering is prevented. Also, the sensed data gathered from patients are transferred to the HCS by creating the authorized path, which further enhances the security of patient data. Thus, the data communication of the WSHN is well-secured in this work through multi-level authentication and improved cryptography techniques.

Emergency department utilization among adults with epilepsy: A multi-state cross-sectional analysis, 2010-2019.

OBJECTIVE: We described patterns and trends in ED use among adults with epilepsy in the United States. METHODS: Utilizing inpatient and ED discharge data from seven states, we conducted a cross-sectional analysis to identify adult ED visits diagnosed with epilepsy or seizures from 2010 to 2019. Using ED visit counts and estimates of state-level epilepsy prevalence, we calculated ED visit rates overall and by payer, condition, and year. RESULTS: Our data captured 304,935 ED visits with epilepsy as a primary or secondary diagnosis in 2019. Across the seven states, visit rates ranged between 366 and 726 per 1000 and were higher than rates for adults without epilepsy in all states but one. ED visit rates were highest among Medicare and Medicaid beneficiaries (vs commercial or self-pay). Adults with epilepsy were more likely to be admitted as inpatients. Visits for nervous system disorders were 6.3-8.2 times higher among people with epilepsy, and visits for mental health conditions were 1.2-2.6 times higher. Increases in ED visit rates from 2010 to 2019 among people with epilepsy exceeded increases among adults without by 6.0-27.3 percentage points. CONCLUSION: Adults with epilepsy visit the ED frequently and visit rates have been increasing over time. These results underscore the importance of identifying factors contributing to ED use and designing tailored interventions to improve ambulatory care quality.

Metagenome comparison (MC): A new framework for detecting unique/enriched OMUs (operational metagenomic units) derived from whole-genome sequencing reads.

BACKGROUND: Current methods for comparing metagenomes, derived from whole-genome sequencing reads, include top-down metrics or parametric models such as metagenome-diversity, and bottom-up, non-parametric, model-free machine learning approaches like Naïve Bayes for k-mer-profiling. However, both types are limited in their ability to effectively and comprehensively identify and catalogue unique or enriched metagenomic genes, a critical task in comparative metagenomics. This challenge is significant and complex due to its NP-hard nature, which means computational time grows exponentially, or even faster, with the problem size, rendering it impractical for even the fastest supercomputers without heuristic approximation algorithms. METHOD: In this study, we introduce a new framework, MC (Metagenome-Comparison), designed to exhaustively detect and catalogue unique or enriched metagenomic genes (MGs) and their derivatives, including metagenome functional gene clusters (MFGC), or more generally, the operational metagenomic unit (OMU) that can be considered the counterpart of the OTU (operational taxonomic unit) from amplicon sequencing reads. The MC is essentially a heuristic search algorithm guided by pairs of new metrics (termed MG-specificity or OMU-specificity, MG-specificity diversity or OMU-specificity diversity). It is further constrained by statistical significance (P-value) implemented as a pair of statistical tests. RESULTS: We evaluated the MC using large metagenomic datasets related to obesity, diabetes, and IBD, and found that the proportions of unique and enriched metagenomic genes ranged from 0.001% to 0.08 % and 0.08%-0.82 % respectively, and less than 10 % for the MFGC. CONCLUSION: The MC provides a robust method for comparing metagenomes at various scales, from baseline MGs to various function/pathway clusters of metagenomes, collectively termed OMUs.

Covalent Bond Torsion-Enabled Unique Crystal-Phase Transformation of an Organic Semiconductor for Multicolor Light-Emitting Transistors.

High-mobility and color-tunable highly emissive organic semiconductors (OSCs) are highly promising for various optoelectronic device applications and novel structure-property relationship investigations. However, such OSCs have never been reported because of the great trade-off between mobility, emission color, and emission efficiency. Here, we report a novel strategy of molecular conformation-induced unique crystalline polymorphism to realize the high mobility and color-tunable high emission in a novel OSC, 2,7-di(anthracen-2-yl) naphthalene (2,7-DAN). Interestingly, 2,7-DAN has unique crystalline polymorphism, which has an almost identical packing motif but slightly different molecular conformation enabled by the small bond rotation angle variation between anthracene and naphthalene units. More remarkably, the subtle covalent bond rotation angle change leads to a big change in color emission (from blue to green) but does not significantly modify the mobility and emission efficiency. The carrier mobility of 2,7-DAN crystals can reach up to a reliable 17 cm2 V-1 s-1, which is rare for the reported high-mobility OSCs. Based on the unique phenomenon, high-performance light-emitting transistors with blue to green emission are simultaneously demonstrated in an OSC crystal. These results open a new way for designing emerging multifunctional organic semiconductors toward next-generation advanced molecular (atomic)-scale optoelectronics devices.

Primary cell cultures from the single-chromosome ant Myrmecia croslandi.

The number of chromosomes varies tremendously across species. It is not clear whether having more or fewer chromosomes could be advantageous. The probability of non-disjunction should theoretically decrease with smaller karyotypes, but too long chromosomes should enforce spatial constraint for their segregation during the mitotic anaphase. Here, we propose a new experimental cell system to acquire novel insights into the mechanisms underlying chromosome segregation. We collected the endemic Australian ant Myrmecia croslandi, the only known species with the simplest possible karyotype of a single chromosome in the haploid males (and one pair of chromosomes in the diploid females), since males are typically haploid in hymenopteran insects. Five colonies, each with a queen and a few hundreds of workers, were collected in the Canberra district (Australia), underwent karyotype analysis to confirm the presence of a single pair of chromosomes in worker pupae, and were subsequently maintained in the laboratory in Paris (France). Starting from dissociated male embryos, we successfully conducted primary cell cultures comprised of single-chromosome cells. This could be developed into a unique model that will be of great interest for future genomic and cell biology studies related to mitosis.

Unique molecular identifier-based amplicon sequencing of microhaplotypes for background noise mitigation.

Microhaplotypes (MHs), comprising two or more single-nucleotide polymorphisms in a short fragment, are promising forensic markers owing to their remarkable polymorphic nature. Several studies have demonstrated the utility of MHs through massively parallel sequencing (MPS). Nevertheless, the background noise level associated with MHs in MPS, which imposes a practical detection limit for the system, remains uninvestigated. Currently, unique molecular identifier (UMI) systems are known to effectively mitigate background noise by tracking original DNA molecules and facilitating PCR and MPS error corrections. Hence, this study aimed to design a UMI-based amplicon sequencing system, designated MH-UMIseq, which can amplify 46 MHs simultaneously and generate MPS libraries in four steps: barcoding PCR, nuclease reaction, boosting PCR, and indexing PCR. The performance of the MH-UMIseq system was evaluated using the Illumina NextSeq 550 and MiniSeq systems with 31 sets for 5 ng, 1 ng, and 200 pg of input DNA. The fgbio toolkit was used in conjunction with STRait Razor 3.0 and Visual Microhap to analyze the UMI data on MHs. The corresponding average not suppressed noise proportion of MH-UMIseq were 0.1 %, 0.3 %, and 0.7 % for 5 ng, 1 ng, and 200 pg of DNA, respectively, which substantially suppressed the background noise for more than 1 ng of DNA. Interestingly, the proportion of not suppressed noise in MH-UMIseq notably decreased as the amount of input DNA increased. The number of UMI families was proportional to the copy number of the template DNA and closely correlated with the system resolution. Therefore, the resolution of MH-UMIseq system is expected to be higher than that of conventional MPS for the deconvolution of mixtures containing more than 1 ng of DNA.

Hexa-atom Pt Catalyst Fabricated by a Ligand Engineering Strategy for Efficient Hydrogen Oxidation Reaction.

Atomically precise supported nanocluster catalysts (APSNCs), which feature exact atomic composition, well-defined structures, and unique catalytic properties, offer an exceptional platform for understanding the structure-performance relationship at the atomic level. However, fabricating APSNCs with precisely controlled and uniform metal atom numbers, as well as maintaining a stable structure, remains a significant challenge due to uncontrollable dispersion and easy aggregation during synthetic and catalytic processes. Herein, we developed an effective ligand engineering strategy to construct a Pt6 nanocluster catalyst stabilized on oxidized carbon nanotubes (Pt6/OCNT). The structural analysis revealed that Pt6 nanoclusters in Pt6/OCNT were fully exposed and exhibited a planar structure. Furthermore, the obtained Pt6/OCNT exhibited outstanding acidic HOR performances with a high mass activity of 18.37 A ⋅ mgpt -1 along with excellent stability during a 24 h constant operation and good CO tolerance, surpassing those of the commercial Pt/C. Density functional theory (DFT) calculations demonstrated that the unique geometric and electronic structures of Pt6 nanoclusters on OCNT altered the hydrogen adsorption energies on catalytic sites and thus lowered the HOR theoretical overpotential. This work presents a new prospect for designing and synthesizing advanced APSNCs for efficient energy electrocatalysis.

Growth hormone receptor antagonist pegvisomant and its role in the medical therapy of growth hormone excess.

Pegvisomant is a growth-hormone (GH) receptor antagonist that prevents the formation of the active heterotrimer of the dimerised GH receptor and the GH molecule necessary for downstream signal transduction. Over the past 20 years, it has become a key therapeutic option for physicians treating syndromes of GH/IGF-1 excess. Sufficient longitudinal follow-up data suggest that it can be deemed both safe and effective. It is the drug with the greatest potential for achieving an amelioration of the biochemical effects of GH excess with a corresponding normalisation of IGF-1 levels; however, insufficient dose titration has lessened real-world therapeutic outcomes. Theoretical concerns about stimulating tumour growth have been resolved as this has not been observed, while derangement of liver enzymes and local skin-related adverse reactions may occur in a minority of the patients. It may be a particularly impactful medication for the treatment of children, young people, and those with inherited disorders of GH excess, where other treatment modalities often fail. Combination therapy of pegvisomant with first- and second-generation somatostatin receptor ligands or with dopamine agonists remains an ongoing area of interest and research. High cost remains a barrier to the use of pegvisomant in many settings.

Two newly established and mutually related subfamilies GH13_48 and GH13_49 of the α-amylase family GH13.

Currently, the main α-amylase family GH13 has been divided into 47 subfamilies in CAZy, with new subfamilies regularly emerging. The present in silico study was performed to highlight the groups, represented by the maltogenic amylase from Thermotoga neapolitana and the α-amylase from Haloarcula japonica, which are worth of creating their own new GH13 subfamilies. This enlarges functional annotation and thus allows more precise prediction of the function of putative proteins. Interestingly, those two share certain sequence features, e.g. the highly conserved cysteine in the second conserved sequence region (CSR-II) directly preceding the catalytic nucleophile, or the well-preserved GQ character of the end of CSR-VII. On the other hand, the two groups bear also specific and highly conserved positions that distinguish them not only from each other but also from representatives of remaining GH13 subfamilies established so far. For the T. neapolitana maltogenic amylase group, it is the stretch of residues at the end of CSR-V highly conserved as L-[DN]. The H. japonica α-amylase group can be characterized by a highly conserved [WY]-[GA] sequence at the end of CSR-II. Other specific sequence features include an almost fully conserved aspartic acid located directly preceding the general acid/base in CSR-III or well-preserved glutamic acid in CSR-IV. The assumption that these two groups represent two mutually related, but simultaneously independent GH13 subfamilies has been supported by phylogenetic analysis as well as by comparison of tertiary structures. The main α-amylase family GH13 has thus been expanded by two novel subfamilies GH13_48 and GH13_49. KEY POINTS: • In silico analysis of two groups of family GH13 members with characterized representatives • Identification of certain common, but also some specific sequence features in seven CSRs • Creation of two novel subfamilies-GH13_48 and GH13_49 within the CAZy database.