Cluster Analysis Of Sequences Research Articles

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.

Trajectories of Service Contact before Suicide in People with Substance Use Disorders—A National Register Study

Objective This study aimed to identify trajectories of service use during the last year before suicide death and the characteristics associated with the trajectories in patients with substance use disorders. Methods This study used a national registry data linkage, which included all patients with substance use disorders who died by suicide in Norway between 2010 and 2018. In- and outpatient contacts with mental health or substance use services during the last year before suicide death was analyzed by week using Sequence State Analysis and cluster analysis to identify trajectories. Logistic regression was used to measure the association between the characteristics and the trajectories. Results We identified four trajectories of service contact. A brief contact trajectory (n = 366) with a low proportion of weeks in contact (M weeks = 8.3), associated with less psychosis or bipolar disorder (aOR = 0.13 (0.08–0.22)) and higher age. A regular contact trajectory (n = 160), with a higher proportion of contact (M weeks = 47.9), associated with psychosis or bipolar disorder (aOR = 3.66 (2.10–6.47)) and depressive or anxiety disorder (aOR = 3.11 (1.93–5.13)). An intermittent contact trajectory (n = 195) with most contacts with outpatient substance use disorder services (M weeks = 9.7). A continuous contact trajectory (n = 109) with a high proportion of inpatient contact (M weeks = 44.5), strongly associated with psychosis or bipolar disorder (aOR = 6.08 (3.26–11.80)). Conclusion Longitudinal descriptions of service use reveal different trajectories that are important to consider when developing policies or interventions to reduce the risk of suicide death in patients with substance use disorders.

Venomics survey of six myrmicine ants provides insights into the molecular and structural diversity of their peptide toxins

Among ants, Myrmicinae represents the most speciose subfamily. The venom composition previously described for these social insects is extremely variable, with alkaloids predominant in some genera while, conversely, proteomics studies have revealed that some myrmicine ant venoms are peptide-rich. Using integrated transcriptomic and proteomic approaches, we characterized the venom peptidomes of six ants belonging to the different tribes of Myrmicinae. We identified a total of 79 myrmicitoxins precursors which can be classified into 38 peptide families according to their mature sequences. Myrmicine ant venom peptidomes showed heterogeneous compositions, with linear and disulfide-bonded monomers as well as dimeric toxins. Several peptide families were exclusive to a single venom whereas some were retrieved in multiple species. A hierarchical clustering analysis of precursor signal sequences led us to divide the myrmicitoxins precursors into eight families, including some that have already been described in other aculeate hymenoptera such as secapin-like peptides and voltage-gated sodium channel (NaV) toxins. Evolutionary and structural analyses of two representatives of these families highlighted variation and conserved patterns that might be crucial to explain myrmicine venom peptide functional adaptations to biological targets.

Herbs and Spices Modulate Gut Bacterial Composition in Adults at Risk for CVD: Results of a Prespecified Exploratory Analysis from a Randomized, Crossover, Controlled-Feeding Study

Herbs and spices are rich in polyphenolic compounds that may influence gut bacterial composition. The effect of culinary doses of herbs and spices consumed as part of a well-defined dietary pattern on gut bacterial composition has not been previously studied. The aim of this prespecified exploratory analysis was to examine gut bacterial composition following an average American diet (carbohydrate: 50% kcal; protein: 17%; total fat: 33%; saturated fat: 11%) containing herbs and spices at 0.5, 3.3, and 6.6 g.d-1.2100 kcal-1 [low-, moderate-, and high-spice diets, respectively (LSD, MSD, and HSD)] in adults at risk for CVD. Fifty-four adults (57% female; mean ± SD age: 45 ± 11 y; BMI: 29.8 ± 2.9 kg/m2; waist circumference: 102.8 ± 7.1 cm) were included in this 3-period, randomized, crossover, controlled-feeding study. Each diet was provided for 4 wk with a minimum 2-wk washout period. At baseline and the end of each diet period, participants provided a fecal sample for 16S rRNA gene (V4 region) sequencing. QIIME2 was used for data filtration, sequence clustering, taxonomy assignment, and statistical analysis. α-diversity assessed by the observed features metric ( P = 0.046) was significantly greater following the MSD as compared with the LSD; no other between-diet differences in α-diversity were detected. Differences in β-diversity were not observed between the diets ( P = 0.45). Compared with baseline, β-diversity differed following all diets ( P < .02). Enrichment of the Ruminococcaceae family was observed following the HSD as compared with the MSD (relative abundance = 22.14%, linear discriminant analysis = 4.22, P = 0.03) and the LSD (relative abundance = 24.90%, linear discriminant analysis = 4.47, P = 0.004). The addition of herbs and spices to an average American diet induced shifts in gut bacterial composition after 4 wk in adults at risk for CVD. The metabolic implications of these changes merit further investigation. This trial was registered at clinicaltrials.gov as NCT03064932.

How do low-income single-mothers get by when unemployment strikes: Patterns of multiple program participation after transition from employment to unemployment.

Little is known about longitudinal patterns of welfare program participation among single mothers after they transition from employment to unemployment. To better understand how utilization patterns of these welfare programs may change during the 12 months after a job loss, we used the 2008 Survey of Income and Program Participation to examine the patterns of participation in Medicaid, the Supplemental Nutrition Assistance Program, Temporary Assistance for Needy Families, and unemployment insurance among 342 single mothers who transitioned from employment to unemployment during the Great Recession. Using sequence analysis and cluster analysis, this paper identified four distinct patterns of program participation: (a) constantly receiving in-kind benefits; (b) primarily but not solely receiving food stamps; (c) inconsistent unemployment insurance or Medicaid-based benefits; and (d) limited or no benefits. Almost two-fifths of our sample of single mothers received inconsistent, limited, or no benefits. Results of the multinomial regression revealed that race, work disability, poverty, homeownership, and region of residence were significant factors that influenced whether study subjects participated in or had access to social safety net programs. Our findings illustrate the heterogeneity in patterns of multiple program participation among single mothers transitioning from employment to unemployment. Better understanding these varied patterns may inform decisions that increase the accessibility of US social safety net programs for single mothers during periods of personal economic hardship.

Work and fertility in Taiwan: how do women's and men's career sequences associate with fertility outcomes?

There has been much debate over the micro-level relationship between employment situations and fertility in Europe and Northern America. However, related research in East Asia is scant, although countries in this region have some of the lowest fertility rates in the world. Moreover, most studies analyse the employment-fertility relationship from a static perspective and only for women, which underemphasises life course dynamics and gender heterogeneity of employment careers and their fertility implications. Drawing on retrospective data from the 2017 Taiwan Social Change Survey (TSCS), this study explores women's and men's career trajectories between ages 18 and 40 in Taiwan using sequence cluster analyses. It also examines how career variations associate with different timing and quantum of birth. Empirical results show that economically inactive women experience faster motherhood transitions and have more children by age 40 than women with stable full-time careers. For men, having an unstable career associates with slower fatherhood transitions and a lower number of children. For both genders, self-employed people are the earliest in parenthood transitions and have the highest number of children by midlife. Our findings demonstrate sharp gender contrasts in employment careers and their diversified fertility implications in low-fertility Taiwan.

P.138 A small RNA signature from extracellular vesicles in patient plasma correlates with recurrence or progression of high-grade gliomas

Background: While managing patients with high-grade gliomas (HGG), predicting recurrence, or differentiating between pseudoprogression (radiation necrosis) and true tumour progression would be invaluable in improving overall prognosis. Characterizing small RNA (sRNA) expression profiles from plasma-derived extracellular vesicles (EVs) over the course of a patient’s treatments, may allow for patient-specific treatment modifications and improve outcomes. Methods: EVs were isolated using Vn96 capture from plasma obtained longitudinally from HGG patients perioperatively and with routine, follow-up surveillance imaging. sRNA was enriched from the EVs, upon which sequencing and unsupervised hierarchal clustering of sRNA signatures were completed. Expression profiles were grouped longitudinally with the clinical status of patients. Results: Cluster analysis of sequences from nine HGG patients, has revealed a sRNA signature that is able to distinguish between tumours showing evidence of progression and those remaining stable over time. Those samples obtained from patients where a clinical diagnosis of tumour progression or pseudoprogression were uncertain, were found to cluster into progression vs. stable signatures. Clinical follow up of these patients will reveal the predictive value of these identified clusters. Conclusions: These preliminary findings demonstrate the potential utility of small RNA profiling of EVs obtained from patients with high-grade gliomas as non-invasive biomarkers for recurrent/progressive disease or stability/pseudoprogression.

3-D spatial cluster analysis of seismic sequences through density-based algorithms

SUMMARY With seismic catalogues becoming progressively larger, extracting information becomes challenging and calls upon using sophisticated statistical analysis. Data are typically clustered by machine learning algorithms to find patterns or identify regions of interest that require further exploration. Here, we investigate two density-based clustering algorithms, DBSCAN and OPTICS, for their capability to analyse the spatial distribution of seismicity and their effectiveness in discovering highly active seismic volumes of arbitrary shapes in large data sets. In particular, we study the influence of varying input parameters on the cluster solutions. By exploring the parameter space, we identify a crossover region with optimal solutions in between two phases with opposite behaviours (i.e. only clustered and only unclustered data points). Using a synthetic case with various geometric structures, we find that solutions in the crossover region consistently have the largest clusters and best represent the individual structures. For identifying strong anisotropic structures, we illustrate the usefulness of data rescaling. Applying the clustering algorithms to seismic catalogues of recent earthquake sequences (2016 Central Italy and 2016 Kumamoto) confirms that cluster solutions in the crossover region are the best candidates to identify 3-D features of tectonic structures that were activated in a seismic sequence. Finally, we propose a list of recipes that generalizes our analyses to obtain such solutions for other seismic sequences.

Beyond HIV outbreaks: protocol, rationale and implementation of a prospective study quantifying the benefit of incorporating viral sequence clustering analysis into routine public health interventions

IntroductionHIV continues to have great impact on millions of lives. Novel methods are needed to disrupt HIV transmission networks. In the USA, public health departments routinely conduct contact tracing and...

SARS-CoV-2 gained a novel spike protein S1–N-Terminal Domain (S1-NTD)

The clue behind the SARS-CoV-2 origin is still a matter of debate. Here, we report that SARS-CoV-2 has gained a novel spike protein S1–N-terminal domain (S1-NTD). In our CLuster ANalysis of Sequences (CLANS) analysis, SARS-CoV/SARS-CoV-2 S1-NTDs displayed a close relationship with OC43 and HKU1. However, in the complete and S1-NTD-free spike protein, SARS-CoV/SARS-CoV-2 revealed closeness with MERS-CoV. Further, we have divided the S1-NTD of SARS-CoV-2 related viruses into three distinct types (Type-I to III S1-NTD) and the S1-NTD of viruses associated with SARS-CoVs into another three classes (Type-A to C S1-NTD) using CLANS and phylogenetic analyses. In particular, the results of our study indicate that SARS-CoV-2, RaTG13, and BANAL-20-52 viruses carry Type-I-S1-NTD and other SARS-CoV-2-related-bat viruses have Type-II and III. In addition, it was revealed that the Pangolin-GX and Pangolin-Guangdong lineages inherited Type-I-like and Type–II–like S1-NTD, respectively. Then our CLANS study shows the potential for evolution of Type-I and Type-III S1-NTD from SARS-CoV-related viruses Type-A and Type-B S1-NTDs, respectively. Furthermore, our analysis clarifies the possibility that Type-II S1-NTDs may have evolved from Type-A-S1-NTD of SARS-CoV-related viruses through Type-I S1-NTDs. We also observed that BANAL-20-103, BANAL-20-236, and Pangolin-Guangdong-lineage viruses containing Type–II–like S1-NTD are very close to SARS-CoV-2 in spike genetic areas other than S1-NTD. Possibly, it suggests that the common ancestor spike gene of SARS-CoV-2/RaTG13/BANAL-20-52-like virus may have evolved by recombining the Pangolin-Guangdong/BANAL-20-103/BANAL-20-236-like spike gene to Pangolin-GX-like Type-I-like-S1-NTD in the unsampled bat or undiscovered intermediate host or possibly pangolin. These may then have evolved into SARS-CoV-2, RaTG13, and BANAL-20-52 virus spike genes by host jump mediated evolution. The potential function of the novel Type-I-S1-NTD and other types of S1-NTDs needs to be studied further to understand better its importance in the ongoing COVID-19 outbreak and for future pandemic preparedness.

Single molecule localization-based analysis of clathrin-coated pit and caveolar dynamics.

Clathrin-coated pits and caveolae are nanoscale invaginations of the plasma membrane of cells, forming through the assembly of membrane coat and accessory proteins in a tightly regulated process. We have analyzed the development of these membrane coat structures with high spatial and temporal resolution and sensitivity using super-resolution single-molecule localization microscopy (SMLM) on live cells. To this end, we developed a sophisticated clustering and data analysis workflow that automatically extracts the relevant information from SMLM image sequences taken on live cells. We quantified lifetime distributions of clathrin-coated and caveolar structures, and analyzed their growth dynamics. Moreover, we observed hotspots in the plasma membrane where coat structures appear repeatedly. The stunningly similar temporal development of clathrin-coated and caveolar structures suggests that key accessory proteins, some of which are shared between the two types of membrane coat structures, orchestrate the temporal evolution of these complex architectures.

Characterization of complete mitochondrial genome and ribosomal operon for Carassotrema koreanum Park, 1938 (Digenea: Haploporidae) by means of next-generation sequencing data.

We obtained new data on the complete mitochondrial DNA (mtDNA) and the ribosomal operon of the trematode Carassotrema koreanum (Digenea: Haploporata: Haploporidae), an intestinal parasite of Carassius auratus, using next-generation sequencing. The mtDNA of C. koreanum contained 13,965 bp, including 12 protein-coding genes, two ribosomal genes, 22 transport RNA (tRNA) genes and a non-coding region. The ribosomal operon of C. koreanum was 10,644 bp in length, including ETS1 (1449 bp), 18S ribosomal RNA (rRNA) gene (1988 bp), ITS1 ribosomal DNA (rDNA) (558 bp), 5.8S rRNA gene (157 bp), ITS2 rDNA (274 bp), 28S rRNA gene (4152 bp) and ETS2 (2066 bp). Phylogenetic analysis based on mtDNA protein-coding regions showed that C. koreanum was closely related to Parasaccocoelium mugili, a species from the same suborder Haploporata. Bayesian phylogenetic tree topology was the most reliable and confirmed the validity of the Haploporata. The results of sequence cluster analysis based on codon usage bias demonstrated some agreement with the results of the phylogenetic analysis. In particular, Schistosoma spp. were differentiated from the other members of Digenea and the members of Pronocephalata were localized within the same cluster. Carassotrema koreanum and P. mugili fell within different clusters. The grouping of C. koreanum and P. mugili within the same cluster was obtained on the basis of frequencies of 13 specified codons, of which three codon pairs were degenerate. A similarity was found between two haploporid species and two Dicrocoelium spp. in the presence of TTG start codon of the mitochondrial nad5 gene. Our results confirmed the taxonomical status of the Haploporata identified in the previous studies and revealed some characteristic features of the codon usage in its representatives.

Heterogeneity in Family Life Course Patterns and Intra-Cohort Wealth Disparities in Late Working Age

Considering soaring wealth inequalities in older age, this research addresses the relationship between family life courses and widening wealth differences between individuals as they age. We holistically examine how childbearing and marital histories are associated with personal wealth at ages 50–59 for Western Germans born between 1943 and 1967. We propose that deviations from culturally and institutionally-supported family patterns, or the stratified access to them, associate with differential wealth accumulation over time and can explain wealth inequalities at older ages. Using longitudinal data from the German Socio-Economic Panel Study (SOEP, v34, waves 2002–2017), we first identified typical family trajectory patterns between ages 16 and 50 with multichannel sequence analysis and cluster analysis. We then modelled personal wealth ranks at ages 50–59 as a function of family patterns. Results showed that deviations from the standard family pattern (i.e. stable marriage with, on average, two children) were mostly associated with lower wealth ranks at older age, controlling for childhood characteristics that partly predict selection into family patterns and baseline wealth. We found higher wealth penalties for greater deviation and lower penalties for moderate deviation from the standard family pattern. Addressing entire family trajectories, our research extended and nuanced our knowledge of the role of earlier family behaviour for later economic wellbeing. By using personal-level rather than household-level wealth data, we were able to identify substantial gender differences in the study associations. Our research also recognised the importance of combining marital and childbearing histories to assess wealth inequalities.

The course of bipolar disorder in pregnant versus non-pregnant women

Background and rationaleAlthough it has been suggested that pregnancy may influence the course of bipolar disorder (BD), studies show contradictory results. Until now, no studies included a finegrained validated method to report mood symptoms on a daily basis, such as the lifechart method (LCM). The aim of the present study is to investigate the course of BD during pregnancy by comparing LCM scores of pregnant and non-pregnant women.MethodsStudy design: Comparison of LCM scores of two prospective observational BD cohort studies, a cohort of pregnant women (n = 34) and a cohort of non-pregnant women of childbearing age (n = 52). Main study parameters are: (1) proportions of symptomatic and non-symptomatic days; (2) symptom severity, frequency, and duration of episodes; (3) state sequences, longitudinal variation of symptom severity scores.ResultsNo differences in clinical course variables (symptomatic days, average severity scores, frequency, and duration of episodes in BD were found between pregnant and non-pregnant women. With a combination of State Sequence Analysis (SSA) and cluster analysis on the sequences of daily mood scores three comparable clusters were found in both samples: euthymic, moderately ill and severely ill. The distribution differences between pregnant and non-pregnant women were significant, with a majority of the pregnant women (68%) belonging to the moderately ill cluster and a majority of the non-pregnant women (46%) to the euthymic cluster. In pregnant women the average daily variation in mood symptoms as assessed with Shannon’s entropy was less than in non-pregnant women (respectively 0.43 versus 0.56).ConclusionsAlthough the use of daily mood scores revealed no difference in overall course of BD in pregnant versus non-pregnant women, more pregnant than non-pregnant women belonged to the moderately ill cluster, and during pregnancy the variation in mood state was less than in non-pregnant women. Further research is necessary to clarify these findings.

Biodiversity and biocatalyst activity of culturable hydrocarbonoclastic fungi isolated from Marac\u2013Moruga mud volcano in South Trinidad

Mud volcanoes (MVs) are visible signs of oil and gas reserves present deep beneath land and sea. The Marac MV in Trinidad is the only MV associated with natural hydrocarbon seeps. Petrogenic polyaromatic hydrocarbons (PAHs) in its sediments must undergo biogeochemical cycles of detoxification as they can enter the water table and aquifers threatening ecosystems and biota. Recurrent hydrocarbon seep activity of MVs consolidates the growth of hydrocarbonoclastic fungal communities. Fungi possess advantageous metabolic and ecophysiological features for remediation but are underexplored compared to bacteria. Additionally, indigenous fungi are more efficient at PAH detoxification than commercial/foreign counterparts and remediation strategies remain site-specific. Few studies have focused on hydrocarbonoclastic fungal incidence and potential in MVs, an aspect that has not been explored in Trinidad. This study determined the unique biodiversity of culturable fungi from the Marac MV capable of metabolizing PAHs in vitro and investigated their extracellular peroxidase activity to utilize different substrates ergo their extracellular oxidoreductase activity (> 50% of the strains decolourized of methylene blue dye). Dothideomycetes and Eurotiomycetes (89% combined incidence) were predominantly isolated. ITS rDNA sequence cluster analysis confirmed strain identities. 18 indigenous hydrocarbonoclastic strains not previously reported in the literature and some of which were biosurfactant-producing, were identified. Intra-strain variability was apparent for PAH utilization, oil-tolerance and hydroxylase substrate specificity. Comparatively high levels of extracellular protein were detected for strains that demonstrated low substrate specificity. Halotolerant strains were also recovered which indicated marine-mixed substrata of the MV as a result of deep sea conduits. This work highlighted novel MV fungal strains as potential bioremediators and biocatalysts with a broad industrial applications.

Exploring the relationship between working history, retirement transition and women's life satisfaction

AbstractHow does the transition to retirement affect female subjective wellbeing? The major theoretical perspectives that have been applied as frameworks to study the heterogeneous adjustment to retirement include role theory and continuity theory. They have often been integrated with a lifecourse approach, which allows us to study retirement as a transition set inside a lifelong process. In this paper, I assess how working life courses are related to changes in subjective wellbeing before and after retirement, using data from the Survey of Health, Ageing and Retirement in Europe (SHARE) and concentrating on women. Firstly, I conduct sequence analysis and cluster analysis to identify groups of typical working lifecourses from ages 20 to 50. Secondly, regression models estimate how retirement transition is associated with changes in life satisfaction, according to the different working trajectories. The results show that some of the trajectories, constituted of discontinuity or part-time periods, exhibit a continuous increase in life satisfaction, passing from employment (or unemployment) to retirement. For other trajectories, such as the full-time one, retirement seems not to have implications for subjective wellbeing.

Herbs and Spices Modulate Gut Microbiota Composition: A Randomized, Crossover, Controlled-Feeding Study

Abstract Objectives The effect of culinary doses of herbs and spices, consumed as part of a well-defined dietary pattern, on gut microbiota composition has not been previously studied. The aim of this study was to examine gut microbial composition following an average American diet (carbohydrate: 50% kcal; protein: 17%; total fat: 33%; saturated fat: 11%; sodium: 3000 mg/d) containing herbs and spices at 0.5 (Low Spice Diet; LSD), 3.3 (Moderate Spice Diet; MSD) and 6.6 (High Spice Diet; HSD) g/day/2100 kcal in adults at-risk for cardiovascular disease (CVD). Methods Fifty-four adults (57% female; 45 ± 11 years, BMI 29.8 ± 2.9 kg/m2; waist circumference 102.8 ± 7.1 cm) were included in this three-period, randomized, crossover, controlled-feeding study. Each diet was provided for 4-weeks with a minimum 2-week wash-out period. At baseline and the end of each diet period subjects provided a fecal sample for 16S rRNA gene sequencing. QIIME2 was used for data filtration, sequence clustering, taxonomy assignment and statistical analysis. Linear discriminant analysis Effect Size (LEfSe) analyses were used to determine enriched biomarker taxa following each diet. Results No between-diet differences in alpha diversity were observed based on Faith's Phylogenetic Diversity, Observed Operational Taxonomic Units (OTUs), and Pielou's Evenness (Kruskal-Walllis, P &amp;gt; 0.05). Principal coordinate analysis showed beta-diversity following the HSD significantly differed from baseline (PERMANOVA, P = 0.030). LEfSe pairwise analyses identified multiple taxa that were differentially abundant following the spice-containing diets vs. baseline. Compared to baseline, 34 taxa were enriched with the HSD, 22 taxa were enriched with the MSD and 20 taxa were enriched with the LSD. Members of the taxa enriched with the HSD are known short-chain fatty acid producers (Faecalibacterium and Butyricimonas). Conclusions The addition of herbs and spices at 0.5, 3.3, and 6.6 g/day/2100 kcal to an average American diet altered gut microbiota composition, and resulted in enrichment of short-chain fatty acid producers, after 4-weeks in adults at elevated risk for CVD. Funding Sources McCormick Science Institute; NCATS NIH (1UL1TR002014–01); Grant from the Howard Hughes Medical Institute through the Precollege and Undergraduate Science Education Program to Juniata College supported the computational research.

Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov.

Xanthomonas translucens is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink’s-boric acid–cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including X. translucens from necrotic wheat leaf tissues. Maximum likelihood cluster analysis of 16S rRNA sequences grouped the strains into 10 distinct genera. Pseudomonas (32.7%) and Pantoea (28.6%) were the dominant genera while Xanthomonas, Clavibacter and Curtobacterium had 8.2%, each. Erwinia and Sphingomonas had two strains, each. BLAST and phylogenetic analyses of multilocus sequence analysis (MLSA) of specific housekeeping genes taxonomically assigned all the strains to validly described bacterial species, except three strains (10L4B, 12L4D and 32L3A) of Pseudomonas and two (23L3C and 15L3B) of Sphingomonas. Strains 10L4B and12L4D had Pseudomonas caspiana as their closest known type strain while strain 32L3A was closest to Pseudomonas asturiensis. Sphingomonas sp. strains 23L3C and 15L3B were closest to S. faeni based on MLSA analysis. Our data on MLSA, whole genome-based cluster analysis, DNA-DNA hybridization and average nucleotide identity, matrix-assisted laser desorption/ionization-time-of-flight, chemotaxonomy and phenotype affirmed that these 5 strains constitute three novel lineages and are taxonomically described in this study. We propose the names, Sphingomonas albertensis sp. nov. (type strain 23L3CT = DOAB 1063T = CECT 30248T = LMG 32139T), Pseudomonas triticumensis sp. nov. (type strain 32L3AT = DOAB 1067T = CECT 30249T = LMG 32140T) and Pseudomonas foliumensis sp. nov. (type strain 10L4BT = DOAB 1069T = CECT 30250T = LMG 32142T). Comparative genomics of these novel species, relative to their closest type strains, revealed unique repertoires of core secretion systems and secondary metabolites/antibiotics. Also, the detection of CRISPR-Cas systems in the genomes of these novel species suggests an acquired mechanism for resistance against foreign mobile genetic elements. The results presented here revealed a cohabitation, within the BLS lesions, of diverse bacterial species, including novel lineages.

First next-generation sequencing data for Haploporidae (Digenea: Haploporata): characterization of complete mitochondrial genome and ribosomal operon for Parasaccocoelium mugili Zhukov, 1971.

The first data on a whole mitochondrial genome of Haploporidae, Parasaccocoelium mugili (Digenea: Haploporata: Haploporidae) was generated using the next-generation sequencing (NGS) approach. We sequenced the complete mitochondrial DNA (mtDNA) and ribosomal operon of Parasaccocoelium mugili, intestine parasite of mullet fish. The mtDNA of P. mugili contained 14,021 bp, including 12 protein-coding genes, two ribosomal genes, 22 tRNA genes, and non-coding region. The ribosomal operon of P. mugili was 8308 bp in length, including 18S rRNA gene (1981 bp), ITS1 rDNA (955 bp), 5.8S rRNA gene (157 bp), ITS2 rDNA (268 bp), 28S rRNA gene (4180 bp), and ETS (767 bp). We used the mtDNA protein-coding regions to make phylogenetic reconstructions of Haploporidae. Additionally, we performed the sequence cluster analysis based on codon usage bias of most of currently available mitochondrial genome data for trematodes. The observed gene arrangement in mtDNA sequence of P. mugili is identical to those of Plagiorchis maculosus (Rudolphi, 1802). Results of maximum likelihood (ML) phylogenetic analysis showed that P. mugili was closely related to Paragonimus species from the suborder Xiphidiata. The results of sequence cluster analysis based on codon usage bias showed that P. mugili has the highest similarity with Plagiorchis maculosus (Xiphidiata). Our results do not contradict to proposing a new suborder for Haploporoidea-Haploporata. On the basis of obtained results, the relationship between mitochondrial protein-coding gene rearrangements and synonymous nucleotide substitutions in mitochondrial genomes has been suggested.

Identification of Cannabis Sativa L. Based on rbcL Sequence.

Objective To assess the feasibility of the rbcL sequence of chloroplast DNA as a genetic marker to identify Cannabis sativa L. Methods The rbcL sequences in 62 Cannabis sativa L. samples, 10 Humulus lupulus samples and 10 Humulus scandens DNA samples were detected, and 96 rbcL sequences of the Cannabaceae family were downloaded from Genbank. Sequence alignment was performed by MEGA X software, the intraspecific and interspecific Kimura-2-Parameter （K2P） genetic distances were calculated, and the system clustering tree was constructed. Results The rbcL sequence length acquired by sequencing of Cannabis sativa L. and Humulus scandens were 617 bp and 649 bp, respectively, and two haplotypes of Cannabis sativa L. were observed in the samples. The BLAST similarity search results showed that the highest similarity between the sequences acquired by sequencing and Cannabis sativa L. rbcL sequences available from Genbank was 100%. The genetic distance analysis showed that the maximum intraspecific genetic distance （0.004 9） of Cannabis sativa L. was less than the minimum interspecific genetic distance （0.012 9）. The results of median-joining network and system clustering tree analysis showed that Cannabis sativa L. and other members of the Cannabaceae family were located in different branches. Conclusion The rbcL sequence could be used as a DNA barcode for identifying Cannabis sativa L., and combined with comparative analysis of the rbcL sequence and system cluster analysis could be a reliable and effective detection method for Cannabis sativa L. identification in forensic investigation.