Sequence Analysis Approach Research Articles

Wild raccoons demonstrate flexibility and individuality in innovative problem-solving.

Cognitive skills, such as innovative problem-solving, are hypothesized to aid animals in urban environments. However, the significance of innovation in wild populations, and its expression across individuals and socio-ecological conditions, is poorly understood. To identify how and when innovation arises in urban-dwelling species, we used advanced technologies and new testing and analytical methods to evaluate innovative problem-solving abilities of wild raccoons (Procyon lotor). We deployed multi-compartment puzzle boxes with either one or multiple solution types and identified raccoons using radio frequency identification. Raccoons solved these novel extractive foraging tasks, and their success was influenced by age and exploratory diversity. Successful raccoons always discovered multiple different solution types, highlighting flexible problem-solving. Using a unique, comparative sequence analysis approach, we found that variation in raccoon solving techniques was greater between individuals than within individuals, and this self-similarity intensified during times of competition. Finally, the inclusion of an easier solution in the multi-solution trials enabled previously unsuccessful raccoons to bootstrap their learning and successfully open multiple difficult solutions. Our study suggests that innovative problem-solving is probably influenced by many factors and has provided novel field and analytical methods, as well as new insights on the socio-ecological dynamics of urban populations.

Novel Loci (EIF4A2, ADIPOQ, TPRG1) for Triglyceride / High-density Lipoprotein Cholesterol Ratio Longitudinal Change (ΔTHR) among Subjects without Type 2 Diabetes: Evidence from the Long Life Family Study (LLFS) and the Framingham Heart Study (FHS) Offspring Cohort (OS).

Triglyceride (TG) /High density lipoprotein cholesterol (HDL-C) ratio (THR) represents a single surrogate predictor of hyperinsulinemia or insulin resistance that is associated with premature aging processes, risk of diabetes and increased mortality. To identify novel genetic loci for THR change over time (ΔTHR), we conducted genome-wide association study (GWAS) and genome-wide linkage scan (GWLS) among subjects of European ancestry who had complete data from two exams collected about seven years apart from the Long Life Family Study (LLFS, n=1384), a study with familial clustering of exceptional longevity in the US and Denmark. Subjects with diabetes or using medications for dyslipidemia were excluded from this analysis. ΔTHR was derived using growth curve modeling, and adjusted for age, sex, field centers, and principal components (PCs). GWAS was conducted using a linear mixed model accounted for familial relatedness. Our linkage scan was built on haplotype-based IBD estimation with 0.5 cM average spacing. Heritability of ΔTHR was moderate (46%). Our GWAS identified a significant locus at the LPL (p=1.58e-9) for ΔTHR; this gene locus has been reported before influencing baseline THR levels. Our GWLS found evidence for a significant linkage with a logarithm of the odds (LODs) exceeding 3 on 3q28 (LODs=4.1). Using a subset of 25 linkage enriched families (pedigree-specific LODs>0.1), we assessed sequence elements under 3q28 and identified two novel variants (EIF4A2/ADIPOQ-rs114108468, p=5e-6, MAF=1.8%; TPRG1-rs16864075, p=3e-6, MAF=8%; accounted for ~28% and ~29% of the linkage, respectively, and 57% jointly). While the former variant was associated with EIF4A2 (p=7e-5) / ADIPOQ (p=3.49e-2) RNA transcriptional levels, the latter variant was not associated with TPRG1 (p=0.23) RNA transcriptional levels. Replication in FHS OS observed modest effect of these loci on ΔTHR. Of 188 metabolites from 13 compound classes assayed in LLFS, we observed multiple metabolites (e.g., DG.38.5, PE.36.4, TG.58.3) that were significantly associated with the variants (p<3e-4). our linkage-guided sequence analysis approach permitted our discovery of two novel gene variants EIF4A2/ADIPOQ-rs114108468 and TPRG1-rs16864075 on 3q28 for ΔTHR among subjects without diabetes selected for exceptional survival and healthy aging.

A step in time: A sequence analysis and choice modelling approach to examine time allocation in individual activities and the role of neighbourhood crime

The Space-Time Budget (STB) method is used to collect spatial and temporal features of an individual’s activities and is an important technique to explore relationships between the environment and crime. This spatial and temporal approach to the study of everyday activity spaces reveals much about victimisation experiences, the relationship between place, time, and perceptions of safety, and where and when offending may occur. Few studies, however, consider the relationship between living in a criminogenic place (neighbourhood crime) and people’s daily activity patterns. Drawing on disaggregate app-based data for 50 participants tracked over a 7-day period, we use sequence analysis to first delineate time allocation to each activity on a minute-by-minute basis. Next, using result from the sequence analysis we introduce the multiple discrete-continuous extreme value (MDCEV) model to understand how neighbourhood crime and socio-demographic characteristics influence individuals’ time allocation to discrete daily activities. Results reveal that neighbourhood drug and violent incidents exert restrictions on an individual’s propensity to spend time outside the home. Females and older people appear more likely to be constrained by the presence of neighbourhood crime (in particular drug and property incidents) as they allocate less time to outdoor activities. The principal utility of the current study is its methodological advancement and the practical insights for urban planning regarding the design of crime prevention strategies to increase guardianship in public places.

Abstract A036: The genetic landscape of head and neck cancer using brush biopsy

Abstract Oral potentially malignant disorders (OPMDs) are characterized by the presence of dysplasia and DNA copy number aberrations (CNAs) and subsequently progress to oral squamous cell carcinoma (OSCC). OSCC has a 5-year survival rate of only about 50% and varies greatly depending on site and stage. The combination of next-generation sequencing and advanced computational data analysis approaches has revolutionized our understanding of the genomic underpinnings of cancer development and progression. This can reveal individual targetable alterations, mutational load, complex mutation signatures, and tumor-specific antigens, which might inform the utilization of targeted therapies and early diagnosis. Oral brush biopsy represents an attractive non-invasive advantage in the characterization of premalignant and malignant oral lesions. Still, a sufficient number of abnormal cells is mandatory to diagnose. The current study tested the possibility of recreating the genomic landscape of oral cancer using brush biopsy. Materials and methods: As a pilot study to address this question, we analyzed matched tissue and brush biopsy of a patient with synchronous OPMD and OSCC. Brush and tissue biopsy was taken from normal epithelium, OPMD, and OSCC. We scrutinized the evolution and heterogeneity of these three brush/tissue biopsy pairs. The techniques used include whole exome sequencing (WES), mutational signature analysis to evaluate smoking and other aberrant signatures, copy number analysis (using ASCAT), and subclonal architecture reconstruction (using DPclust). Results: To analyze intra-tumoral heterogeneity (ITH), ASCAT and DPclust were used to call copy number aberrations (CNA) and cluster somatic SNVs based on cancer cell fraction (CCF), respectively. We observed a large number of shared SNVs between the OPMD and OSCC lesions suggesting a common evolutionary origin. After adjusting the ploidy and purity based on DPClust results, ASCAT profiles revealed differences in aberrant tumor cell fraction, gains and loss of heterozygosity, and copy number neutral events between the samples. It showed almost similar profiles between the respective lesions' brush and tissue samples, suggesting that brush biopsy can recapitulate the genomic landscape. The OPMD and OSCC lesions showed loss of heterozygosity in chromosome 9 and chromosome 17, which play a potential role in tumorigenesis with loss of function of P53. We inferred the subclonal architecture of each sample, illuminating the clonal relationships between samples and distinct lineages of precursor clones developing independently. Conclusion: Collectively, these results emphasize the possibility of using brush biopsy to reconstruct the genomic characterization of OPMD and OSCC show prognostic potential for diagnosis and intervention strategies, and accelerate progress in precision cancer care. Citation Format: Evit John, Tom Lesluyes, Xiao Zhao, Peter Van Loo. The genetic landscape of head and neck cancer using brush biopsy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A036.

Abstract PO-015: The genetic landscape of head and neck cancer using brush biopsy

Abstract Oral potentially malignant disorders (OPMDs) are characterized by the presence of dysplasia and DNA copy number aberrations (CNAs) and subsequently progress to oral squamous cell carcinoma (OSCC). OSCC has a 5-year survival rate of only about 50% and varies greatly depending on site and stage. The combination of next-generation sequencing and advanced computational data analysis approaches has revolutionized our understanding of the genomic underpinnings of cancer development and progression. This can reveal individual targetable alterations, mutational load, complex mutation signatures, and tumor-specific antigens, which might inform the utilization of targeted therapies and early diagnosis. Oral brush biopsy represents an attractive non-invasive advantage in the characterization of premalignant and malignant oral lesions. Still, a sufficient number of abnormal cells is mandatory to diagnose. The current study tested the possibility of recreating the genomic landscape of oral cancer using brush biopsy. Materials and methods: As a pilot study to address this question, we analyzed matched tissue and brush biopsy of a patient with synchronous OPMD and OSCC. Brush and tissue biopsy was taken from normal epithelium, OPMD, and OSCC. We scrutinized the evolution and heterogeneity of these three brush/tissue biopsy pairs. The techniques used include whole exome sequencing (WES), mutational signature analysis to evaluate smoking and other aberrant signatures, copy number analysis (using ASCAT), and subclonal architecture reconstruction (using DPclust). Results: To analyze intra-tumoral heterogeneity (ITH), ASCAT and DPclust were used to call copy number aberrations (CNA) and cluster somatic SNVs based on cancer cell fraction (CCF), respectively. We observed a large number of shared SNVs between the OPMD and OSCC lesions suggesting a common evolutionary origin. After adjusting the ploidy and purity based on DPClust results, ASCAT profiles revealed differences in aberrant tumor cell fraction, gains and loss of heterozygosity, and copy number neutral events between the samples. It showed almost similar profiles between the respective lesions' brush and tissue samples, suggesting that brush biopsy can recapitulate the genomic landscape. The OPMD and OSCC lesions showed loss of heterozygosity in chromosome 9 and chromosome 17, which play a potential role in tumorigenesis with loss of function of P53. We inferred the subclonal architecture of each sample, illuminating the clonal relationships between samples and distinct lineages of precursor clones developing independently. Conclusion: Collectively, these results emphasize the possibility of using brush biopsy to reconstruct the genomic characterization of OPMD and OSCC and show prognostic potential for diagnosis and intervention strategies and accelerate progress in precision cancer care. Citation Format: Evit John, Tom Lesluyes, Toby Baker, Xiao Zhao, Peter Van Loo. The genetic landscape of head and neck cancer using brush biopsy [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Innovating through Basic, Clinical, and Translational Research; 2023 Jul 7-8; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2023;29(18_Suppl):Abstract nr PO-015.

Sequencing statements: using behaviour sequence analysis with statement analysis to indicate deception

PurposeUnderstanding when an individual is being deceptive is an important part of police and criminal investigations. While investigators have developed multiple methods, the research literature has yet to fully explore some of the newer applied techniques. This study aims to investigate statement analysis, a recent approach in forensic linguistic analysis that has been applied to criminal investigations.Design/methodology/approachReal-world statements of individuals exposed as deceptive or truthful were used in the analyses. A behaviour sequence analysis approach is used to provide a timeline analysis of the individuals’ statements.FindingsResults indicate that sequential patterns are different in deceptive statements compared to truthful statements. For example, deceptive statements were more likely to include vague words and temporal lacunas, to convince investigators into believing that the suspect was not present when the crime occurred. The sample in this research did not use one deceptive indicator, instead, electing to frequently change the order of deceptive indicators. Gaps in deception were also noted, and there was common repetition found in both the deceptive and truthful statements. While gaps are predicted to occur in truthful statements to reflect an absence of deception, gaps occurring in the deceptive statements are likely due to cognitive load.Originality/valueThe current research provides more support for using statement analysis in real-world criminal cases.

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.

Childbearing Trajectories in a West African Setting: A Sequence Analysis Approach

The lagging fertility transition in West Africa has important repercussions for global population growth but remains poorly understood. Inspired by Caldwell and colleagues' fertility transition framework, as well as by subsequent research, we examine diversity in women's holistic childbearing trajectories in Niakhar, Senegal, between the early 1960s and 2018 using a sequence analysis approach. We evaluate the prevalence of different trajectories, their contribution to overall fertility levels, and their association with women's socioeconomic and cultural characteristics. Four trajectories were observed: “high fertility,” “delayed entry,” “truncated,” and “short.” While the high fertility trajectory was most prevalent across cohorts, delayed entry grew in importance. The high fertility trajectory was more common among women born between 1960 and 1969 and was followed less often by divorced women and those from polygynous households. Women with primary education and those from higher status groups were more likely to experience delayed entry. The truncated trajectory was associated with lack of economic wealth, polygynous households, and caste membership. A short trajectory was related to lack of agropastoral wealth, divorce, and possibly secondary sterility. Our study advances knowledge on fertility transitions in Niakhar—and Sahelian West African contexts more generally—by showing the diversity of childbearing trajectories within high fertility regional contexts.

Place and immigrant labour market integration: A sequence analysis approach

Although the process of integrating immigrants into the labor market unfolds over many years, it is often modeled as outcomes (e.g. employment) at specific points in time. We contribute to the literature by providing empirical evidence of the sequence of events leading to active labor market participation of East African and EU15 immigrants to Sweden, whom we follow for up to 28 years. By combining the method of sequence analysis with binomial logit estimation, we can explain why individuals are sorted into different representative labor market sequences. A further contribution is that along the usual initial conditions (individual and geographic), we employ longitudinal micro data to find (1) representative sequences of movements between various types of neighborhoods and (2) an empirical estimate of individual ability, which turns out to be a strong predictor for immigrants entering an active labor market trajectory. Our results show that East Africans tend to reside in neighborhoods with a high degree of socioeconomic and ethnic segregation. Despite this, their labor market activity seems to be less influenced by neighborhood trajectories than EU15 immigrants. The labor market activity of EU15 immigrants and female East African immigrants is positively related to residing in less ethnically segregated and socioeconomically stronger neighborhoods. Our results are relevant to policy development since they point to the importance of the initial location of immigrants and their subsequent residential mobility.

The first detection of two Aeromonas strains in mice of the genus Apodemus

Aeromonas spp. are gram-negative facultatively anaerobic bacilli recovered mainly from aquatic environments. Aeromonas spp. were reported to be associated with infections primarily in aquatic and to a lesser extent in terrestrial animals as well as in humans. Up-to-date little is known about aeromonads associated with wild animals, especially with rodents. This study reported the first isolation and characterization of two Aeromonas spp. from internal organs of apparently healthy wild rodents Apodemus uralensis and Apodemus flavicollis captured in the wild environment in the European part of Russia. Isolates were identified as A. hydrophila M-30 and A. encheleia M-2 using the multilocus sequence analysis (MLSA) approach. The isolation of the A. encheleia from rodents is the first described case. Both strains demonstrated beta-hemolytic activity towards human erythrocytes. Antimicrobial susceptibility testing showed that both Aeromonas strains were resistant and intermediate to carbapenems and piperacillin-tazobactam, which was caused by the expression of the genus-specific CphA carbapenemases. A. hydrophila M-30 also demonstrated trimethoprim resistant phenotype. This is usually caused by the carriage of the dfrA or dfrB genes in aeromonads which are frequently associated with integron class I. The latter however was absent in both isolates. Our results expand our understanding of possible aeromonad reservoirs and demonstrate the likelihood of the formation of natural foci of Aeromonas infection and a new link in the chain of the spread of antimicrobial resistance as well.

Adaptation to the Progress in Cancer Genomic Medicine by a Japanese Community Hospital

Background: Remarkable progress in cancer genomic medicine (CGM) has been made with the advent of next-generation sequencing and advanced computational data analysis approaches. In Japan gene panel testing has been covered by the National Health Insurance System since June 2019. Although Nagoya Memorial Hospital has been designated as a regional medical support hospital, their medical staff are unfamiliar with CGM and generally experience difficulty in explaining the genetic testing to cancer patients.&#x0D; Methods: A multi-disciplinary CGM team was created in July 2019 to adapt to the clinical application of gene panel testing. Hospital functions were then maintained focusing on the following three aspects: a pathology system for handling genetic information, human resource development related to CGM, and a patient support system, including genetic counseling.&#x0D; Results: Third party ISO15189 (International Organization for Standardization) certification was acquired for the Department of Pathology to establish a quality-assured laboratory. Here, we report on 21 cancer patients who consulted and received information from the CGM outpatient department of our hospital. Among them 14 patients were introduced into a group of certified hospitals by the Japanese Ministry of Health, Labour, and Welfare and 10 patients underwent gene panel tests.&#x0D; Conclusions: As a regional medical support hospital dealing with many cancer patients, we will further improve hospital functions to match the progress in CGM.

A new approach for DNA sequence analysis using multiwavelet transform (MWT)

Finding the nucleotide sequence within a DNA (deoxyribonucleic acid) molecule is the process of DNA sequencing. The DNA of every organism is made up of a specific pattern of nucleotides. Scientists can compare the DNA of different organisms by sequence to understand how organisms are connected. Three different forms of DNA sequencing - fragment analysis, Next Generation Sequencing (NGS), and Sanger sequencing - enable many new applications that increase our knowledge of genomes. It significantly impacts how well we understand how the genome works. Finding the hidden structural information of DNA is an important task. This paper introduces Multi-Wavelet Transformation (MWT) for analysis of the sequence of the DNA symbols. The symbolic DNA sequence has four indicator sequences. The MWT assigned symbols to numbers based on DNA structure. It can change each channel’s weighting to optimize energy distribution over MWT output. Analysis of synthetic and actual DNA sequences allowed the researchers to evaluate how well the proposed MWT works. The results show that the MWT has a higher energy dispersion than the regular WT and the bionic wavelet transform (BWT). Future DNA sequence analyses should be able to discover hidden structural features using this MWT approach.

TRNA fragment biomarkers of Neurological Disease: Challenges and Opportunities

Transfer RNAs play a crucial role in protein translation where they bring amino acids to the ribosome to be incorporated into nascent polypeptide chains. During stress conditions tRNAs can be cleaved to generate tRNA-derived fragments. Several ribonucleases have been identified that cleave tRNA, however mutations in the stress-induced ribonuclease Angiogenin have been identified in a range of neurological disorders including Amyotrophic Lateral Sclerosis, Parkinson’s Disease, and Alzheimer’s Disease, suggesting that tRNA cleavage may be dysregulated in neurological disease. tRNA fragments have been detected in biofluids indicating they may be of use as biomarkers for neurological diseases. There is considerable variability in the methods used to quantify tRFs from size selection, adapter ligation, removal of RNA modifications, and sequence analysis approaches which can make it difficult to reconcile multiple studies. Here we review the biology of transfer RNAs and the biogenesis of tRNA-derived fragments, with a focus on the methods used to identify and quantify tRNA fragments and how different methodological approaches can influence tRNA fragment detection. We provide an overview of current literature on the identification of tRNA fragments in neurological disease models and patient samples, with a focus on circulating tRNA fragments as potential biomarkers of neurological diseases.

CD-MAWS: An Alignment-Free Phylogeny Estimation Method Using Cosine Distance on Minimal Absent Word Sets.

Multiple sequence alignment has been the traditional and well established approach of sequence analysis and comparison, though it is time and memory consuming. As the scale of sequencing data is increasing day by day, the importance of faster yet accurate alignment-free methods is on the rise. Several alignment-free sequence analysis methods have been established in the literature in recent years, which extract numerical features from genomic data to analyze sequences and also to estimate phylogenetic relationship among genes and species. Minimal Absent Word (MAW) is an effective concept for representing characteristics of a sequence in an alignment-free manner. In this study, we present CD-MAWS, a distance measure based on cosine of the angle between composition vectors constructed using minimal absent words, for sequence analysis in a computationally inexpensive manner. We have benchmarked CD-MAWS using several AFProject datasets, such as Fish mtDNA, E.coli, Plants, Shigella and Yersinia datasets, and found it to perform quite well. Applied on several other biological datasets such as mammal mtDNA, bacterial genomes and viral genomes, CD-MAWS resolved phylogenetic relationships similar to or better than state-of-the-art alignment-free methods such as Mash, Skmer, Co-phylog and kSNP3.

Complete genome of Vibrio japonicus strain JCM 31412T and assessment of the Nereis clade of the genus Vibrio.

Clade-based taxonomy has become a recognised means of classifying members of the family Vibrionaceae. A multilocus sequence analysis (MLSA) approach based on eight housekeeping genes can be used to infer phylogenetic relationships, which then groups species into monophyletic clades. Recent work on the Vibrionaceae clades added newly described species and updated existing relationships; the Nereis clade currently includes Vibrio nereis and Vibrio hepatarius. A publication characterising Vibrio japonicus as a novel species placed it within the Nereis clade, but this strain was not included in a recently published taxonomic update because a genome sequence was not available for phylogenetic assessment. To resolve this discrepancy and assess the taxonomic position of V. japonicus within the updated clades, we sequenced the complete genome of V. japonicus JCM 31412T and conducted phylogenetic and genomic analyses of this clade. Vibrio japonicus remains within the Nereis clade and phylogenomic, average nucleotide identity (ANI), and average amino acid identity (AAI) analyses confirm this relationship. Additional genomic assessments on all Nereis clade members found gene clusters and inferred functionalities shared among the species. This work represents the first complete genome of a member of the Nereis clade and updates the clade-based taxonomy of the Vibrionaceae family.

ATF6α contributes to rheumatoid arthritis by inducing inflammatory cytokine production and apoptosis resistance.

ObjectiveThe contribution of activating transcription factor 6α (ATF6α) in rheumatoid arthritis (RA) pathogenesis, especially on fibroblast-like synoviocytes (FLSs), has been suggested by its sensitivity to inflammatory stimulus. However, the exact role and therapeutic potential of ATF6α in RA remains to be fully elucidated.MethodsATF6α expression was determined in joint tissues and FLS, and gain-of-function and loss-of-function analyses were applied to evaluate the biological roles of ATF6α in RA FLSs. A murine collagen-induced arthritis (CIA) model, combining both gene deletion of ATF6α and treatment with the ATF6α inhibitor Ceapin-A7, was employed. Joint inflammation, tissue destruction, circulating levels of inflammatory cytokines were assessed in CIA mice. Transcriptome sequencing analysis (RNASeq), molecular biology, and biochemical approaches were performed to identify target genes of ATF6α.ResultsATF6α expression was significantly increased in synovium of RA patients and in synovium of mice subjected to CIA. ATF6α silencing or inhibition repressed RA FLSs viability and cytokine production but induced the apoptosis. CIA-model mice with ATF6α deficiency displayed decreased arthritic progression, leading to profound reductions in clinical and proinflammatory markers in the joints. Pharmacological treatment of mice with Ceapin-A7 reduced arthritis severity in CIA models. RNA-sequencing of wild-type and knockdown of ATF6α in RA FLSs revealed a transcriptional program that promotes inflammation and suppresses apoptosis, and subsequent experiments identified Baculoviral IAP Repeat Containing 3 (BIRC3) as the direct target for ATF6α.ConclusionThis study highlights the pathogenic role of ATF6α-BIRC3 axis in RA and identifies a novel pathway for new therapies against RA.

Population genetic and evolution analysis of Vibrio isolated from Turkish fish farms

The genus Vibrio includes important pathogenic species for human and aquatic organisms such as Vibrio cholera, V. parahaemolyticus, V. vulnificus, V. anguillarum or V. harveyi. At present, Vibrionaceae family consists of >190 described species, classified into nine genera. Vibrio are widespread in shellfish, finfish and marine ecosystems and show resourceful ecologies, which recognized as one of the most diverse bacterial groups for illuminating the genome evolution. In the present study, to clarify the relationship among aquatic species in the genus, a multilocus sequence analysis (MLSA) and typing (MLST) approach was applied to characterize 51 Vibrio isolates from Turkish fish farms, 146 strains deposited in the PubMLST database and 59 type strains from GenBank. For all studied isolates (n = 256), diversity analysis, population structure, determination of recombination, demographic history and gene flow were performed based on the MLST scheme. Vibrio isolates, subjected to the study, showed a high diversity within the Vibrio population and also genetic interactions into the genus. We found 17 new described sequence types by MLST analysis that were isolated from rainbow trout, sea bream and sea bass in Turkish fish farms, which clearly indicate that the genes underwent recombination frequently. While predominant sequence types were found in the presented study, differences of genotypes need to be evaluated in a disease situation or preventing measurements. The findings about genetic recombination possibly helps to understand differences of Vibrio infections in fish. Furthermore, elucidating of genetic variability within species shed light on providing effective measurements in aquaculture by vaccine production and drug applications.

Molecular Characterization of a Novel Relapsing Fever Borrelia Species from the Desert Cottontail (Sylvilagus audubonii) in New Mexico, USA.

The Borrelia genus comprises vector-borne, spirochete bacteria infecting vertebrates worldwide. We characterized a novel relapsing fever Borrelia species from a desert cottontail (Syvilagus audubonii) from New Mexico, US, using an established multilocus sequence analysis approach. Phylogenetic analysis of the flagellin gene (flaB) and four other protein-coding loci (clpX, pepX, recG, rplB) grouped the novel Borrelia species with hard tick relapsing fever borreliae Borrelia lonestari, Borrelia theileri, and Borrelia miyamotoi. The identity of the vectors and other vertebrate hosts, geographic distribution, and zoonotic potential of this novel Borrelia species deserve further investigation.

MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data

The development of third-generation sequencing technology has brought significant changes and influences on genomics. Compared to the second-generation sequencing methods, the third-generation technologies produce around 100 times longer reads to reveal new genomic variations that complete long-term gaps in the human reference genome. However, these reads' excessive length and high error rate severely increase the amount of data and alignment cost. The traditional data analysis platform and serial sequence alignment method can not effectively deal with large-scale long read alignment. There is a critical need for a novel data analysis platform that can deliver fast alignment of large-scale sequences to solve the problem of long read alignment. High-performance computing platforms and efficient, scalable algorithms based on these platforms have significant potential to impact sequence analysis approaches. This paper presented minimapR, a multi-level parallel long-read alignment tool based on minimap2, a popular third-generation read aligner. MinimapR is developed based on the new high-performance distributed framework Ray. Ray fully integrates with the Python environment and can be easily installed with pip. MinimapR can utilize the power of multiple computing nodes, significantly accelerating alignment speeds without sacrificing sensitivity. The minimapR tool was tested on 64 nodes and demonstrated a 50 fold increase in speed with 78 % parallel efficiency. The source code and user manual of minimapR are freely available at https://github.com/Geehome/minimapR.

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis