scholarly journals Genomic Analysis and Initial Characterization of the Chitinolytic System of Microbulbifer degradans Strain 2-40

2003 ◽  
Vol 185 (11) ◽  
pp. 3352-3360 ◽  
Author(s):  
Michael B. Howard ◽  
Nathan A. Ekborg ◽  
Larry E. Taylor ◽  
Ronald M. Weiner ◽  
Steven W. Hutcheson
Keyword(s):  
Glycosyl Hydrolase ◽  
Genomic Analysis ◽  
Degree Of Polymerization ◽  
Specific Pattern ◽  
Future Research ◽  
Draft Sequence ◽  
Sugar Transporters ◽  
A Genome ◽  
Chitin Binding Protein ◽  
K 12

ABSTRACT The marine bacterium Microbulbifer degradans strain 2-40 produces at least 10 enzyme systems for degrading insoluble complex polysaccharides (ICP). The draft sequence of the 2-40 genome allowed a genome-wide analysis of the chitinolytic system of strain 2-40. The chitinolytic system includes three secreted chitin depolymerases (ChiA, ChiB, and ChiC), a secreted chitin-binding protein (CbpA), periplasmic chitooligosaccharide-modifying enzymes, putative sugar transporters, and a cluster of genes encoding cytoplasmic proteins involved in N-acetyl-d-glucosamine (GlcNAc) metabolism. Each chitin depolymerase was detected in culture supernatants of chitin-grown strain 2-40 and was active against chitin and glycol chitin. The chitin depolymerases also had a specific pattern of activity toward the chitin analogs 4-methylumbelliferyl-β-d-N,N′-diacetylchitobioside (MUF-diNAG) and 4-methylumbelliferyl-β-d-N,N′,N"-triacetylchitotrioside (MUF-triNAG). The depolymerases were modular in nature and contained glycosyl hydrolase family 18 domains, chitin-binding domains, and polycystic kidney disease domains. ChiA and ChiB each possessed polyserine linkers of up to 32 consecutive serine residues. In addition, ChiB and CbpA contained glutamic acid-rich domains. At 1,271 amino acids, ChiB is the largest bacterial chitinase reported to date. A chitodextrinase (CdxA) with activity against chitooligosaccharides (degree of polymerization of 5 to 7) was identified. The activities of two apparent periplasmic (HexA and HexB) N-acetyl-β-d-glucosaminidases and one cytoplasmic (HexC) N-acetyl-β-d-glucosaminidase were demonstrated. Genes involved in GlcNAc metabolism, similar to those of the Escherichia coli K-12 NAG utilization operon, were identified. NagA from strain 2-40, a GlcNAc deacetylase, was shown to complement a nagA mutation in E. coli K-12. Except for the GlcNAc utilization cluster, genes for all other components of the chitinolytic system were dispersed throughout the genome. Further examination of this system may provide additional insight into the mechanisms by which marine bacteria degrade chitin and provide a basis for future research on the ICP-degrading systems of strain 2-40.

scholarly journals Optimization and Ev a Luation of Viral Metagenomic Amplification and Sequencing Methods Toward a Genome -le Vel Resolution of the Human Fecal DNA Virome

2021 ◽  
Author(s):  
Guangyang Wang ◽  
Shenghui Li ◽  
Qiulong Yan ◽  
Ruochun Guo ◽  
Yue Zhang ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Pcr Amplification ◽  
Genomic Analysis ◽  
Optimal Number ◽  
Future Research ◽  
Metagenomic Sequencing ◽  
Optimal Method ◽  
Viral Genomes ◽  
A Genome ◽  
Long Read

Abstract Background: Viruses in the human gut have been linked to health and disease. Deciphering of the gut virome is dependent on metagenomic sequencing of the virus-like particles purified from the fecal specimens. A major limitation of conventional viral metagenomic sequencing is the low recoverability of viral genomes from the metagenomic dataset. Results: Herein, we developed an optimal method for viral amplification and metagenomic sequencing to maximize the recovery of viral genomes. Using 5 fecal specimens with multiple repetitions, we revealed the optimal number of PCR cycles of high-fidelity enzyme-based amplification and the reliability of multiple displacement amplification in virome DNA preparation, verified the reproducibility of the optimally whole viral metagenomic experimental process, and tested the capability of long-read sequencing for improving viral metagenomic assembly. Based on our optimized results, we generated 151 high-quality viruses using the data combined from short-read (15 cycles for PCR amplification) and long-read sequencing. Genomic analysis of these viruses found that most (60.3%) of them were previously unknown and showed a remarkable diversity of viral functions, especially the existence of 206 viral auxiliary metabolic genes. Finally, we compared the viral metagenomic and bulk metagenomic sequencing approaches and revealed significant differences in the efficiency and coverage of viral identification between them. Conclusions: Our study demonstrates the potential of optimized experiment and sequencing strategies in uncovering viral genomes from fecal specimens, which will facilitate future research about genome-level characterization of complex viral communities.

scholarly journals Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer

2021 ◽  
Vol 9 (2) ◽  
pp. 348
Author(s):  
Florian Tagini ◽  
Trestan Pillonel ◽  
Claire Bertelli ◽  
Katia Jaton ◽  
Gilbert Greub
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic ◽  
Mycobacterium Kansasii ◽  
Type Vii Secretion ◽  
A Genome ◽  
Genes Encoding ◽  
Associated Proteins ◽  
Immunosuppressed Patients ◽  
Type Vii Secretion System ◽  
Clinical Records

The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity.

scholarly journals Negotiating (dis-)engagement in K-12 blended learning

2021 ◽  
Author(s):  
Nina Bergdahl ◽  
Melissa Bond
Keyword(s):  
Active Learning ◽  
Blended Learning ◽  
Digital Technologies ◽  
Vital Role ◽  
Future Research ◽  
Socially Disadvantaged ◽  
Leadership Engagement ◽  
Upper Secondary ◽  
K 12 ◽  
Engagement And Disengagement

AbstractIt is well-recognised that engagement is critical for learning and school success. Engagement (and disengagement) are, however, also influenced by context. Thus, as digital technologies add complexity to the educational context, they influence classroom leadership, lesson designs and related practices, and thereby engagement. Despite being critical, engagement and disengagement are not well explored concerning these influences, with a lack of research undertaken within socially disadvantaged schools. In this qualitative study, 14 classroom observations were conducted, during five months, in twelve classes in an upper secondary school in Sweden, along with dialogues with teachers (n=12) and students (n=32). The data were analysed using thematic analysis and descriptive statistics. Identified themes include digital context, teacher leadership, engagement and disengagement. A network of relations between the (dis-)engagement compound and themes is presented. The results identified processes in which engagement shifted into disengagement and vice versa; in particular, that the intention of active learning does not automatically translate to active learning for all students, although teachers employed a higher work pace than did their students. Teacher self-efficacy and awareness of how to manage digital technologies in and outside the classroom was found to play a vital role in facilitating engagement. Understanding the (dis-)engagement compound in blended learning environments is key to inform active and visible learning for future research and supportive organisational structures.

Influences on Academic Talent Development of Black Girls in K-12: A Systematic Review

2021 ◽  
pp. 1932202X2110138
Author(s):  
Brenda K. Davis
Keyword(s):  
Systematic Review ◽  
Racial Identity ◽  
Thematic Analysis ◽  
Systematic Approach ◽  
Talent Development ◽  
Academic Development ◽  
Black Girls ◽  
Personal Attributes ◽  
Future Research ◽  
K 12

Black girls experience numerous challenges to their academic development. This study examines the literature from the last 30 years related to the influences on the academic talent development of school-aged Black girls. Environmental and intrapersonal influences to Black girls academic talent development are explored. Using a systematic approach, 43 articles are reviewed and summarized. Thematic analysis conducted on the results and findings sections from each article reveal four major themes related to personal attributes, racial identity, relationships, and institutions. The themes expand the understanding of the complexity of talent development of Black girls and identify several intrapersonal and environmental influences that can promote or hinder academic achievement. Implications for future research are discussed.

Gifted Classroom Environments and the Creative Process: A Systematic Review

2021 ◽  
pp. 016235322110014
Author(s):  
Lindsay Ellis Lee ◽  
Melanie S. Meyer ◽  
Kacey Crutchfield
Keyword(s):  
Systematic Review ◽  
Creative Process ◽  
Classroom Culture ◽  
Systematic Evaluation ◽  
Future Research ◽  
Critical Examination ◽  
Process Skills ◽  
Classroom Environments ◽  
Creative Processes ◽  
K 12

As the expectations for including creativity in K–12 education continually grow, creative process skills equip students with thinking strategies to generate and evaluate ideas. This systematic review explored existing research on elementary and secondary gifted classroom environments that promote creative process skills. A database search yielded peer-reviewed literature, empirical and practitioner-focused, for systematic evaluation. A critical examination of literature published from 2011 to 2019 identified characteristics of educational environments that foster creative processes and highlighted key themes, including integrating creative process skills, adaptive environments, reflective classroom culture, and challenges to implementation. Implications for classroom application and suggestions for future research are discussed.

Educator Knowledge and Implementation of Assistive Technology to Support Challenging Behaviors: An Exploratory Inquiry

2021 ◽  
Vol 36 (3) ◽  
pp. 162-174
Author(s):  
Christopher R. Emerling ◽  
Sarah Wilkinson ◽  
Daniel M. Maggin
Keyword(s):  
Assistive Technology ◽  
Lived Experience ◽  
Students With Disabilities ◽  
Challenging Behaviors ◽  
Future Research ◽  
Structured Interviews ◽  
Dynamic Learning ◽  
Behavioral Challenges ◽  
Emerging Trends ◽  
K 12

Emerging trends and advancements in technology allow educators to develop dynamic learning environments to support their students’ academic and behavioral needs. The study documented the lived experience of special educators using assistive technology (AT) to support behavioral challenges in students with disabilities and the environmental factors that support educator’s use of AT. Fifteen educators who worked in K–12 schools participated in semi-structured interviews and completed a researcher-developed Assistive Technology Treatment Integrity Checklist (ATTIC). This exploratory study indicated that participants had limited experiences using AT to target challenging behaviors. However, participants used technology to support evidence-based interventions or customized instructional technologies to manage students’ needs. Our findings also indicated that school structures impacted AT-related attitudes and eventual use. The findings from this study add to the literature on technology supports for students with challenging behaviors. Implications for practice and future research are also discussed.

scholarly journals A Systematic Review of Evidence-Based Video Modeling for Students with Emotional and Behavioral Disorders

2018 ◽  
Vol 8 (4) ◽  
pp. 170 ◽  
Author(s):  
Soonhwa Seok ◽  
Boaventura DaCosta ◽  
Mikayla McHenry-Powell ◽  
Linda Heitzman-Powell ◽  
Katrina Ostmeyer
Keyword(s):  
Systematic Review ◽  
Quality Indicators ◽  
Behavioral Disorders ◽  
Video Modeling ◽  
Evidence Based Practice ◽  
Emotional And Behavioral Disorders ◽  
Future Research ◽  
Evidence Based ◽  
K 12 ◽  
Students With Ebd

This systematic review examined eight studies showing that video modeling (VM) can have a positive and significant effect for students with emotional and behavioral disorders (EBD). Building upon meta-analyses that sought evidence of video-based interventions decreasing problem behaviors of students with EBD in K-12 education, the review examined the standards of the Council for Exceptional Children (CEC) for evidence-based practice as well as additional quality indicators, neglected quality indicators, strategies combined with VM, the impact of the independent variables on the dependent variables, and common recommendations offered for future research. Findings revealed that the eight studies met the CEC standards for evidence-based practices as well as other quality indicators. For instance, all studies reported content and setting, participants, intervention agents, description of practice, as well as interobserver agreement and experimental control. According to the findings, fidelity index and effect size were the two most neglected quality indicators. Furthermore, instructions, reinforcement system, and feedback or discussion were the most common strategies used. Finally, generalizability—across settings, populations, treatment agents, target behaviors in the real world, and subject matter—was the most common recommendation for future research. While further investigation is warranted, these findings suggest that VM is an effective evidence-based practice for students with EBD when the CEC standards are met.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals White Matter Integrity and Nicotine Dependence: Evaluating Vertical and Horizontal Pleiotropy

2021 ◽  
Vol 15 ◽  
Author(s):  
Zhenyao Ye ◽  
Chen Mo ◽  
Song Liu ◽  
Kathryn S. Hatch ◽  
Si Gao ◽  
...  
Keyword(s):  
White Matter ◽  
Nicotine Dependence ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Smoking Status ◽  
Brain Regions ◽  
Future Research ◽  
Cerebral White Matter ◽  
A Genome ◽  
Causal Pathway

Tobacco smoking is an addictive behavior that supports nicotine dependence and is an independent risk factor for cancer and other illnesses. Its neurogenetic mechanisms are not fully understood but may act through alterations in the cerebral white matter (WM). We hypothesized that the vertical pleiotropic pathways, where genetic variants influence a trait that in turn influences another trait, link genetic factors, integrity of cerebral WM, and nicotine addiction. We tested this hypothesis using individual genetic factors, WM integrity measured by fractional anisotropy (FA), and nicotine dependence-related smoking phenotypes, including smoking status (SS) and cigarettes per day (CPDs), in a large epidemiological sample collected by the UK Biobank. We performed a genome-wide association study (GWAS) to identify previously reported loci associated with smoking behavior. Smoking was found to be associated with reduced WM integrity in multiple brain regions. We then evaluated two competing vertical pathways: Genes → WM integrity → Smoking versus Genes → Smoking → WM integrity and a horizontal pleiotropy pathway where genetic factors independently affect both smoking and WM integrity. The causal pathway analysis identified 272 pleiotropic single-nucleotide polymorphisms (SNPs) whose effects on SS were mediated by FA, as well as 22 pleiotropic SNPs whose effects on FA were mediated by CPD. These SNPs were mainly located in important susceptibility genes for smoking-induced diseases NCAM1 and IREB2. Our findings revealed the role of cerebral WM in the maintenance of the complex addiction and provided potential genetic targets for future research in examining how changes in WM integrity contribute to the nicotine effects on the brain.

scholarly journals Exploring the Relationships Between High School Course Enrollment, Achievement, and First-Semester College GPA

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jeffrey M Warren ◽  
Camille L Goins
Keyword(s):  
High School ◽  
Advanced Placement ◽  
Future Research ◽  
Course Enrollment ◽  
Honors Courses ◽  
Grade Point ◽  
First Semester ◽  
College Gpa ◽  
K 12 ◽  
The Impact

This study explored the impact of Advanced Placement and honors course enrollment and high school grade point average (GPA) on first-semester college GPA. Data were collected from 131 college freshmen enrolled at a minority-serving institution who graduated from a public school during the previous academic year. A four-step hierarchical multiple regression analysis indicated that family structure, college status, enrollment in one or more Advanced Placement courses, and enrollment in five or more honors courses accounted for a significant amount of variance explained in first-semester college GPA, both individually and in combination. High school GPA intervened in these variables relationships with first-semester college GPA accounting for a significant amount of variance. Based on these findings, opportunities for future research and implications for K–12 schools and colleges are provided.

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