Cluster Analysis Of Sequences Research Articles

Ethnic-specific characteristics associated with longitudinal response patterns from prebirth to 12 years: evidence from Growing Up in New Zealand

BackgroundLongitudinal studies can generate valuable scientific knowledge, but can be compromised by systematic attrition. Previous research shows that sociodemographic characteristics (eg, ethnicity, age, educational level, socioeconomic circumstances) are associated with...

Gender-differences in retirement from entrepreneurship: the influence of pension policies across Europe

PurposeThe interest in older entrepreneurs increases due to population aging. Previous research showed clear gender-differences among older entrepreneurs. This study investigates whether such gender-differences also exist in the retirement transition from entrepreneurship. It explores the influence of pension regulations for entrepreneurs on these gender-differences.Design/methodology/approachLongitudinal micro-level data from the Survey of Health, Aging and Retirement in Europe is analyzed in multichannel sequence analyses and cluster analyses. Developments from age 50 to 69 are compared in the dimensions of entrepreneurship, employment and old-age pensions.FindingsEntrepreneurs retire in three different transition patterns: (1) entrepreneurs becoming pensioners at 60, (2) entrepreneurs becoming pensioners at 65 and (3) individuals combining entrepreneurship with employment until they become pensioners at 65. Female entrepreneurs follow the same transition patterns as their male counterparts but retire earlier. Pension regulations for entrepreneurs modify the extent of the gender-differences within a country. Mandatory pension schemes with identical state pension ages for men and women reduce gender-differences, whereas mandatory schemes with gender-differences in the state pension age increase them. Schemes without mandatory coverage range in between the other two.Originality/valueThis article expands our knowledge on gender-differences among older entrepreneurs. These gender-differences also extent to how entrepreneurs transition into retirement. Pension regulations for entrepreneurs influence the extent of the gender-differences. Therefore, pension regulations for entrepreneurs constitute tools for promoting or hindering gender equality.

Discovery of a new class of cell-penetrating peptides by novel phage display platform

The primary hurdles for small interference RNA (siRNA) in clinical use are targeted and cytosolic delivery. To overcome both challenges, we have established a novel platform based on phage display, called NNJA. In this approach, a lysosomal cathepsin substrate is engineered within the flexible loops of PIII, that is displaying a unique random sequence at its N-terminus. NNJA library selection targeting cell-expressed targets should yield specific peptides localized in the cytoplasm. That is because phage internalization and subsequent localization to lysosome, upon peptide binding to the cell expressed target, will result in cleavage of PIII, rendering phage non-infective. Such phage will be eliminated from the selected pool and only peptide-phage that escapes lysosomes will advance to the next round. Proof of concept studies with the NNJA library demonstrated cytosolic localization of selected peptide-phage and peptide-siRNA, confirmed through confocal microscopy. More importantly, conjugation of siHPRT to monomeric or multimeric NNJA peptides resulted in significant reduction in HPRT mRNA in various cell types without significant cytotoxicity. Sequence similarity and clustering analysis from NGS dataset provide insights into sequence composition facilitating cell penetration. NNJA platform offers a highly efficient peptide discovery engine for targeted delivery of oligonucleotides to cytosol.

Characterization of Acinetobacter baumannii at a tertiary hospital in Guangzhou: a genomic and clinical study

Acinetobacter baumannii (AB) infections have become a global public health concern due to the continued increase in the incidence of infection and the rate of resistance to carbapenems. This study aimed to investigate the genomic features of AB strains recovered from a tertiary hospital and assess the clinical implications of the findings. A total of 217 AB strains were collected between 2016 and 2018 at a tertiary hospital in Guangzhou, with 183 (84.33%) being carbapenem-resistant AB (CRAB), with the main mechanism being the carriage of the blaOXA-23 gene. The overall mortality rate of patients caused by such strains was 15.21% (n = 33). Artificial lung ventilation and the use of meropenem were mortality risk factors in AB-infected patients, while KL2 AB infection was negatively associated. Core genome multilocus sequence typing and clustering analysis were performed on the integrated AB genome collection from the NCBI database and this study to illustrate the population structure among China. The results revealed diverse core genome profiles (n = 17) among AB strains from China, and strains from this single hospital exhibited most of the core genome profiles (n = 13), suggesting genetic variability within the hospital and transmission across the country. These findings show that the high transmission potential of the CRAB strains and meropenem usage that confers a selective advantage of CRAB clinically are two major factors that pose significant challenges to the effective clinical management of AB infections. Understanding the genetic features and transmission patterns of clinical AB strains is crucial for the effective control of infections caused by this pathogen.

Clustering care pathways of people with alcohol dependence using a data linkage of routine data in Bremen, Germany

BackgroundAlthough many individuals with alcohol dependence (AD) are recognized in the German healthcare system, only a few utilize addiction-specific treatment services. Those who enter treatment are not well characterized regarding their prospective pathways through the highly fragmented German healthcare system. This paper aims to (1) identify typical care pathways of patients with AD and their adherence to treatment guidelines and (2) explore the characteristics of these patients using routine data from different healthcare sectors.MethodsWe linked routinely collected register data of individuals with a documented alcohol-related diagnosis in the federal state of Bremen, Germany, in 2016/2017 and their addiction-specific health care: two statutory health insurance funds (outpatient pharmacotherapy for relapse prevention and inpatient episodes due to AD with and without qualified withdrawal treatment (QWT)), the German Pension Insurance (rehabilitation treatment) and a group of communal hospitals (outpatient addiction care). Individual care pathways of five different daily states of utilized addiction-specific treatment following an index inpatient admission due to AD were analyzed using state sequence analysis and cluster analysis. The follow-up time was 307 days (10 months). Individuals of the clustered pathways were compared concerning current treatment recommendations (1: QWT followed by postacute treatment; 2: time between QWT and rehabilitation). Patients’ characteristics not considered during the cluster analysis (sex, age, nationality, comorbidity, and outpatient addiction care) were then compared using a multinomial logistic regression.ResultsThe analysis of 518 individual sequences resulted in the identification of four pathway clusters differing in their utilization of acute and postacute treatment. Most did not utilize subsequent addiction-specific treatment after their index inpatient episode (n = 276) or had several inpatient episodes or QWT without postacute treatment (n = 205). Two small clusters contained pathways either starting rehabilitation (n = 26) or pharmacotherapy after the index episode (n = 11). Overall, only 9.3% utilized postacute treatment as recommended.ConclusionsA concern besides the generally low utilization of addiction-specific treatment is the implementation of postacute treatments for individuals after QWT.

What if it is not just an additional income? Poverty risks of non‐standard employment histories in Germany

AbstractWhile the poverty risks associated with transitions to and from different forms of non‐standard employment (NSE) have been studied extensively, poverty research on NSE histories remains fuzzy. Therefore, this study focuses on persons with NSE histories whose earnings contribute significantly to the household income, asking to what extent they are exposed to income poverty risks during their main career phase and examining the role of employment, family and sociodemographic characteristics. Employment histories were observed over 10 years using German Socio‐Economic Panel data from 2001 to 2020. A sequence cluster analysis identified four NSE clusters with increased poverty risks, namely, those with increasing and permanent low‐part‐time work, those who were mainly temporary agency‐employed or had long episodes of fixed‐term employment. Multivariate regressions considering employment‐specific, care‐related and sociodemographic characteristics revealed a network of cumulative disadvantages related to gender, occupational position, care obligations and structural disadvantages for those clusters.

T-cell immunity against Severe Acute Respiratory Syndrome Coronavirus 2 proteins in patients with type 1 diabetes.

Individuals with type 1 diabetes (T1D) do not appear to have an elevated risk of severe Coronavirus Disease 19 (COVID-19). Pre-existing immune reactivity to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in unexposed individuals may serve as a protective factor. Hence, our study was designed to evaluate the existence of T cells with reactivity against SARS-CoV-2 antigens in unexposed patients with T1D. Peripheral blood mononuclear cells (PBMCs) were collected from SARS-CoV-2 unexposed patients with T1D and healthy control subjects. SARS-CoV-2 specific T cells were identified in PBMCs by ex-vivo interferon (IFN)γ-ELISpot and flow cytometric assays. The epitope specificity of T cells in T1D was inferred through T Cell Receptor sequencing and GLIPH2 clustering analysis. T1D patients unexposed to SARS-CoV-2 exhibited higher rates of virus-specific T cells than controls. The T cells primarily responded to peptides from the ORF7/8, ORF3a, and nucleocapsid proteins. Nucleocapsid peptides predominantly indicated a CD4+ response, whereas ORF3a and ORF7/8 peptides elicited both CD4+ and CD8+ responses. The GLIPH2 clustering analysis of TCRβ sequences suggested that TCRβ clusters, associated with the autoantigens proinsulin and Zinc transporter 8 (ZnT-8), might share specificity towards ORF7b and ORF3a viral epitopes. Notably, PBMCs from three T1D patients exhibited T cell reactivity against both ORF7b/ORF3a viral epitopes and proinsulin/ZnT-8 autoantigens. The increased frequency of SAR-CoV-2- reactive T cells in T1D patients might protect against severe COVID-19 and overt infections. These results emphasise the long-standing association between viral infections and T1D.

Evolution of the profiles of new psychotropic drug users before and during the COVID-19 crisis: an original longitudinal approach through multichannel sequence analysis using the French health-care database.

The COVID-19 pandemic has had a substantial impact on mental health. An increase in the use of anxiolytic, hypnotic, and antidepressant drugs has been highlighted in France, but with no information at the individual level (trajectories) or concerning patient characteristics. The objective of this study was to describe the profile of new psychotropic drug users since the beginning of the pandemic. We formed two historical cohorts using the Pays-de-la-Loire regional component of the National Health Data System (SNDS): a "COVID-19 crisis cohort" (2020-2021) and a "control cohort" (2018-2019). We analyzed reimbursements for psychotropic medications (anxiolytics, antidepressants, hypnotics, mood stabilizers, and antipsychotics) using a multichannel sequence analysis and performed clustering analysis of sequences. The proportion of new consumers of psychotropic drugs was higher in the COVID-19 crisis cohort (18.0%) than that in the control cohort (16.0%). In the COVID-19 cohort, three clusters of psychotropic drug users were identified, whereas four clusters were identified in the control cohort. A time lag in treatment initiation was observed in the COVID-19 crisis cohort (September) compared with the control cohort (July). This study is one of the first to analyze the profile of psychotropic treatment users during the COVID-19 crisis. Our analysis sheds light on changes in patterns of psychotropic drug use during the COVID-19 pandemic, possibly associated with changes in prescribing conditions and mental health conditions during the crisis. This study also provides an example of the application of an innovative longitudinal analysis methodology in the field of pharmacoepidemiology.

Farmed Chinese Perch (Siniperca chuatsi) Coinfected with Parasites and Oomycete Pathogens

Farming Chinese perch in aquaculture systems with artificial diets is a new method and developing trend. This method of raising Chinese perch has led to outbreaks of new diseases. In 2022, a disease outbreak occurred among farmed Chinese perch fed an artificial diet in Jiangxi Province, China, during which 50% of the fish died. The clinical signs exhibited by the diseased Chinese perch included decreased physical vitality, anorexia, emaciation, and dorsal fin ulceration with white cysts and flocs. Coinfection with ciliate parasites and an oomycete was found. No pathogenic bacteria were isolated from the microbial test, and the viral detection results were negative. After morphological and 18S or 28S rDNA sequence clustering analysis, the parasites were identified as Epistylis wuhanensis and Zoothamnium sp., while the oomycete was identified as Achlya klebsiana. This article discusses the interaction between parasitic and oomycete coinfections in Chinese perch from the perspective of the characteristics of Chinese perch raised with an artificial diet. The relationships between parasites, oomycete, and fish were also briefly discussed. This is the first report of the coinfection of Chinese perch with Epistylis wuhanensis, Zoothamnium sp. and Achlya klebsiana.

DBHC: Discrete Bayesian HMM Clustering

Sequence data mining has become an increasingly popular research topic as the availability of data has grown rapidly over the past decades. Sequence clustering is a type of method within this field that is in high demand in the industry, but the sequence clustering problem is non-trivial and, as opposed to static cluster analysis, interpreting clusters of sequences is often difficult. Using Hidden Markov Models (HMMs), we propose the Discrete Bayesian HMM Clustering (DBHC) algorithm, an approach to clustering discrete sequences by extending a proven method for continuous sequences. The proposed algorithm is completely self-contained as it incorporates both the search for the number of clusters and the search for the number of hidden states in each cluster model in the parameter inference. We provide a working example and a simulation study to explain and showcase the capabilities of the DBHC algorithm. A case study illustrates how the hidden states in a mixture of HMMs can aid the interpretation task of a sequence cluster analysis. We conclude that the algorithm works well as it provides well-interpretable clusters for the considered application.

High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA.

We investigated transmission dynamics of a large human immunodeficiency virus (HIV) outbreak among persons who inject drugs (PWID) in KY and OH during 2017-20 by using detailed phylogenetic, network, recombination, and cluster dating analyses. Using polymerase (pol) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including Subtype B (44.6 per cent); numerous circulating recombinant forms (CRFs) including CRF02_AG (2.5 per cent) and CRF02_AG-like (21.8 per cent); and many unique recombinant forms composed of CRFs with major subtypes and sub-subtypes [CRF02_AG/B (24.3 per cent), B/CRF02_AG/B (0.5 per cent), and A6/D/B (6.4 per cent)]. Cluster analysis of sequences using a 1.5 per cent genetic distance identified thirteen clusters, including a seventy-five-member cluster composed of CRF02_AG-like and CRF02_AG/B, an eighteen-member CRF02_AG/B cluster, Subtype B clusters of sizes ranging from two to twenty-three, and a nine-member A6/D and A6/D/B cluster. Recombination and phylogenetic analyses identified CRF02_AG/B variants with ten unique breakpoints likely originating from Subtype B and CRF02_AG-like viruses in the largest clusters. The addition of contact tracing results from OH to the genetic networks identified linkage between persons with Subtype B, CRF02_AG, and CRF02_AG/B sequences in the clusters supporting de novo recombinant generation. Superinfection prevalence was 13.3 per cent (8/60) in persons with multiple specimens and included infection with B and CRF02_AG; B and CRF02_AG/B; or B and A6/D/B. In addition to the presence of multiple, distinct molecular clusters associated with this outbreak, cluster dating inferred transmission associated with the largest molecular cluster occurred as early as 2006, with high transmission rates during 2017-8 in certain other molecular clusters. This outbreak among PWID in KY and OH was likely driven by rapid transmission of multiple HIV-1 variants including de novo viral recombinants from circulating viruses within the community. Our findings documenting the high HIV-1 transmission rate and clustering through partner services and molecular clusters emphasize the importance of leveraging multiple different data sources and analyses, including those from disease intervention specialist investigations, to better understand outbreak dynamics and interrupt HIV spread.

PacBio Full-Length Transcriptome of a Tetraploid Sinocyclocheilus multipunctatus Provides Insights into the Evolution of Cavefish.

Sinocyclocheilus multipunctatus is a second-class nationally protected wild animal in China. As one of the cavefish, S. multipunctatus has strong adaptability to harsh subterranean environments. In this study, we used PacBio SMRT sequencing technology to generate a first representative full-length transcriptome for S. multipunctatus. Sequence clustering analysis obtained 232,126 full-length transcripts. Among all transcripts, 40,487 were annotated in public databases, while 70,300 microsatellites, 2384 transcription factors, and 16,321 long non-coding RNAs were identified. The phylogenetic tree showed that S. multipunctatus shows a closer relationship to Carassius auratus and Cyprinus carpio, phylogenetically diverging from the common ancestor ~14.74 million years ago (Mya). We also found that between 15.6 and 17.5 Mya, S. multipunctatus also experienced an additional whole-genome duplication (WGD) event, which may have promoted the species evolution of S. multipunctatus. Meanwhile, the overall rates of evolutionary of polyploid S. multipunctatus were significantly higher than those of the other cyprinids, and 220 positively selected genes (PSGs) were identified in two sub-genomes of S. multipunctatus. These PSGs are likely to fulfill critical roles in the process of adapting to diverse cave environments. This study has the potential to facilitate future investigations into the genomic characteristics of S. multipunctatus and provide valuable insights into revealing the evolutionary history of polyploid S. multipunctatus.

Do Working and Parenting Trajectories Influence Retirement Timing? Evidence From Spain, Using a Sequence Analysis Approach and Focusing on Women

Abstract This paper investigates the association between accumulated experiences in the working and parenting spheres and retirement timing among Spanish women, utilizing data from the Survey of Health, Ageing and Retirement in Europe (SHARE). The study examines whether labor market attachment or cumulative disadvantage characterizes women’s retirement and how these factors relate with the number of children. Firstly, multichannel sequence analysis and cluster analysis were employed to identify distinct work–family life courses from ages 20 to 50. Seven clusters were identified: “Full-time work with 2+ children,” “Out of the labour force and 2+ children,” “Mid-life discontinuity and 2+ children,” “Full-time work and 1 child,” “Full-time work and childless,” “Part-time work and 2+ children,” and “Part-time work or out of the labor force and 1 child.” Secondly, the study examines the association between these identified groups and retirement timing. The results indicate that Spanish women who have experienced more unstable careers characterized by extended periods of inactivity or part-time work, particularly in combination with having 2 or more children, are more likely to retire at a later age compared with women with continuous careers, with or without children. These findings underscore the ongoing challenges of balancing unpaid care work and wage work in Spain, while also revealing notable variations among women.

Deciphering the Origin of DNA Viruses (Replication-Associated Parvo-NS1) That Infect Vertebrates from Invertebrate-Infecting Viruses.

DNA replication is a standard and essential function among DNA viruses; however, this functional domain's common ancestor, origin, and evolutionary path in invertebrate- and vertebrate-infecting viruses are not yet fully understood. Here, we present evidence, using a combination of phylogenetic relationships, coevolution, and CLANS (cluster analysis of sequences) analysis, that the parvo-NS1 domain (nonstructural protein NS1, DNA helicase domain) of these DNA viruses that infect vertebrates potentially originated from the invertebrate (Platyhelminthes) parvo-NS1 domain of parvovirus-related sequences (PRSs). Our results suggest that papillomaviruses and the parvovirus subfamilies Densovirinae and Hamaparvovirinae DNA helicase evolved directly from the Platyhelminthes NS1 domain (PRSs). Similarly, the parvovirus subfamily Parvovirinae NS1 domain displayed evolutionary heritage from the PRSs through Hamaparvovirinae. Further, our analysis also clarified that herpesviruses and adenoviruses independently obtained the parvo-NS1 domain from Dependoparvovirus (Parvovirinae). Furthermore, virus-host coevolution analysis revealed that the parvovirus NS1 domain has coevolved with hosts, from flatworms to humans, and it appears that the papillomavirus may have obtained the DNA helicase during the early stages of parvovirus evolution and later led to the development of the DNA helicase of adomavirus and polyomavirus. Finally, herpesviruses and adenoviruses likely inherited the parvo-NS1 domain from Dependoparvovirus in the later stages of evolution. To the best of our knowledge, this is the first evolutionary evidence to suggest that the DNA helicase of viruses that infect vertebrates originated from the invertebrate PRSs. IMPORTANCE DNA replication of DNA viruses is an essential function. This allows DNA replication of viruses to form virus particles. The DNA helicase domain is responsible for this primary function. This domain is present in parvoviruses, papillomaviruses, polyomaviruses, herpesviruses, and adenoviruses. But little is known about the common ancestor, origin, and evolutionary path of DNA helicase in invertebrate- and vertebrate-infecting viruses. Here, we report the possibility of the origin of DNA viruses (DNA helicase) infecting vertebrates from Platyhelminthes (invertebrate) PRSs. Our study established that the parvovirus subfamily Parvovirinae NS1 domain displayed evolutionary heritage from the Platyhelminthes PRSs through Hamaparvovirinae. Furthermore, our study suggests that the papillomavirus DNA helicase may have evolved in the early stages of parvovirus evolution and then led to the development of the adomavirus and polyomavirus. Our study suggests that the herpesviruses and adenoviruses likely inherited the parvo-NS1 domain through gene capture from Dependoparvovirus in the later stages of parvovirus evolution in their hosts.

Diversity Profiling and the Distribution of Pathotypes and Mating Types in Indian Isolates of Ascochyta rabiei Causing Ascochyta Blight of Chickpea

The prevalence and distribution of pathotypes and mating types of Ascochyta rabiei (Pass.) Labr. were evaluated during the winter (October to March) seasons of 2017-18 and 2018-19. Forty-five A. rabiei isolates were obtained from six different states. From the survey results, the state of Punjab recorded the highest disease rating (Rating 9) compared with other chickpea-growing areas. The β-tubulin gene was amplified (330 bp) from all the isolates, and sequence analysis was performed. The phylogenetic tree produced by cluster analysis of β-tubulin gene sequences differentiated the 44 A. rabiei isolates . Using multiplex PCR, mating types were identified. From the mating type (MAT) study of all the A. rabiei isolates, amplification was observed at the 490-bp size, which corresponds to mating type 2 (MAT1-2). The four pathotypes (I, II, III, IV) and six physiological races were delineated based on the differential reaction of the disease. The most widely distributed pathotype was pathotype III (52.27%) among the surveyed regions of North Indian states, except Uttarakhand (where only pathotype II was recorded), followed by the least aggressive pathotype I (22.7%), highly aggressive pathotype IV (15.9%), and aggressive pathotype II (9.1%). Among the six physiological races identified, the most common races were race 5 (25%), followed by race 1 (22.73%), race 6 (18.18%), race 4 (18.18%), race 3 (9.09%), and race 2 (6.82%). Because of the prevalence of a single mating type among the surveyed locations in India, we opine that there may be less diversity in A. rabiei compared with isolates reported from other countries. However, to substantiate this conclusion, evaluation of more isolates of A. rabiei is required. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Prevalence and Biological Characteristics of Listeria Species Isolated from Livestock and Poultry Meat in Gansu Province, China.

Listeria monocytogenes is a widespread foodborne pathogen contaminating foods during their production or processing stages. Fresh meat is susceptible to such contamination if it is not properly preserved. Our study was conducted to reveal the level of contamination and prevalence of Listeria spp. present in livestock and poultry meat from Gansu province. A total of 1,387 samples were collected from five cities in Gansu Province according to standard sampling procedures, of which 174 samples (12.5%) were positive for Listeria species. Among them, 14 isolates of L. monocytogenes (1.0%), 150 isolates of Listeria innocua (10.8%), and ten isolates of Listeria welshimeri (0.7%) were identified by conventional bacteriological and molecular identification methods. All isolates were subjected to serological assays, antimicrobial susceptibility tests, growth curve assays, determination of biofilm-forming capacity, and cluster analysis of the 16S rRNA gene sequences. Four predominant serotypes of L. monocytogenes were identified, including 1/2a (35.7%, 5/14), 1/2b (14.3%, 2/14), 1/2c (42.9%, 6/14), and 4b (7.1%, 1/14). All L. monocytogenes isolates were resistant to tetracycline and cefoxitin. Most L. innocua isolates (63.6%, 14/22) and L. welshimeri (40%, 4/10) were resistant to tetracycline. The high biofilm-forming ability was observed among 1/2c and 1/2a serotype isolates. The cluster analysis of the 16S rRNA gene sequences revealed a close genetic relationship between the three Listeria species. This study fills the gap in the knowledge of livestock and poultry meat that carry Listeria in slaughterhouses and markets in Gansu Province.

Grape cytochrome P450 CYP90D1 regulates brassinosteroid biosynthesis and increases vegetative growth

Vine vigor or vegetative growth is an important factor related to berry quality and vinicultural training management, but brassinosteroid (BR)-induced molecular mechanisms underlying vine growth remain unclear. In this study, the hypothesis that the Vitis vinifera CYP90D1 gene VvCYP90D1, one of the genes for BR biosynthesis, plays a critical role in shoot elongation was tested. RNA sequencing analysis of shoots collected from the vigorous cultivar Koshu (KO) and the reference cultivar Pinot Noir (PN) 7 days after bud break showed higher expression levels of various genes in the BR biosynthesis pathway in KO than in PN. The VvCYP90D1 expression level in KO was highest in meristems, followed by internodes and leaves. Cluster analysis of amino acid sequences including those in other plant species showed that the isolated gene belonged to the CYP90D1 group. The vegetative growth and the endogenous BR (brassinolide; BL) content were significantly higher in VvCYP90D1-overexpressing Arabidopsis than in wild type. VvCYP90D1-overexpressing Arabidopsis treated with brassinazole (Brz), a BR biosynthesis inhibitor, showed recovery of vegetative growth. These results indicate that VvCYP90D1 in grapevine has a vegetative growth promoting effect via BR biosynthesis. Our findings on the mechanism of BR-induced grape shoot growth will contribute to the development of new shoot control techniques for grapevine.

Temporal learning analytics to explore traces of self-regulated learning behaviors and their associations with learning performance, cognitive load, and student engagement in an asynchronous online course.

Self-regulated learning (SRL) plays a critical role in asynchronous online courses. In recent years, attention has been focused on identifying student subgroups with different patterns of online SRL behaviors and comparing their learning performance. However, there is limited research leveraging traces of SRL behaviors to detect student subgroups and examine the subgroup differences in cognitive load and student engagement. The current study tracked the engagement of 101 graduate students with SRL-enabling tools integrated into an asynchronous online course. According to the recorded SRL behaviors, this study identified two distinct student subgroups, using sequence analysis and cluster analysis: high SRL (H-SRL) and low SRL (L-SRL) groups. The H-SRL group showed lower extraneous cognitive load and higher learning performance, germane cognitive load, and cognitive engagement than the L-SRL group did. Additionally, this study articulated and compared temporal patterns of online SRL behaviors between the student subgroups combining lag sequential analysis and epistemic network analysis. The results revealed that both groups followed three phases of self-regulation but performed off-task behaviors. Additionally, the H-SRL group preferred activating mastery learning goals to improve ethical knowledge, whereas the L-SRL group preferred choosing performance-avoidance learning goals to pass the unit tests. The H-SRL group invested more in time management and notetaking, whereas the L-SRL group engaged more in surface learning approaches. This study offers researchers both theoretical and methodological insights. Additionally, our research findings help inform practitioners about how to design and deploy personalized SRL interventions in asynchronous online courses.

Identification of cell culture contamination by an unusual species of Mycoplasma related to the M. mycoides cluster.

Mycoplasma contamination is a significant problem in cell culture replication and maintenance. From more than 200 known species, a limited number of Mycoplasma species have been detected in cell cultures, representing new species or variants that can escape detection systems. A qPCR commercial kit was used for Mycoplasma detection in cell cultures. Furthermore, an amplified Mycoplasma species was sequenced and summited for sequence assembly, clustering, and evolutionary analysis study. Our work has identified a new and unusual variant or species of Mycoplasma that possesses a high degree of homology with species related with M. mycoides cluster. This variant is usually associated with cattle but has been detected contaminating a cell culture. Mycoplasma testing (even for unusual species) in cell cultures is essential to ensure the validity and reproducibility of research that uses cell cultures and to ensure the quality of cell line deposits in biobanks. For this reason, it is necessary to perform continuous checks for the absence of Mycoplasma in cell cultures and engage in the continuous adaptation of relevant detection systems.

Biosynthesis and function of microbial methylmenaquinones.

The membranous quinone/quinol pool is essential for the majority of life forms and its composition has been widely used as a biomarker in microbial taxonomy. The most abundant quinone is menaquinone (MK), which serves as an essential redox mediator in various electron transport chains of aerobic and anaerobic respiration. Several methylated derivatives of MK, designated methylmenaquinones (MMKs), have been reported to be present in members of various microbial phyla possessing either the classical MK biosynthesis pathway (Men) or the futalosine pathway (Mqn). Due to their low redox midpoint potentials, MMKs have been proposed to be specifically involved in appropriate electron transport chains of anaerobic respiration. The class C radical SAM methyltransferases MqnK, MenK and MenK2 have recently been shown to catalyse specific MK methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesise 8-MMK, 7-MMK and 7,8-dimethylmenaquinone (DMMK). MqnK, MenK and MenK2 from organisms such as Wolinella succinogenes, Adlercreutzia equolifaciens, Collinsella tanakaei, Ferrimonas marina and Syntrophus aciditrophicus have been functionally produced in Escherichia coli, enabling extensive quinone/quinol pool engineering of the native MK and 2-demethylmenaquinone (DMK). Cluster and phylogenetic analyses of available MK and MMK methyltransferase sequences revealed signature motifs that allowed the discrimination of MenK/MqnK/MenK2 family enzymes from other radical SAM enzymes and the identification of C-7-specific menaquinone methyltransferases of the MenK2 subfamily. It is envisaged that this knowledge will help to predict the methylation status of the menaquinone/menaquinol pool of any microbial species (or even a microbial community) from its (meta)genome.