scholarly journals Structures of three actinobacteriophage capsids: Roles of symmetry and accessory proteins

2020 ◽  
Author(s):  
Jennifer Podgorski ◽  
Joshua Calabrese ◽  
Lauren Alexandrescu ◽  
Deborah Jacobs-Sera ◽  
Welkin Pope ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Major Capsid Protein ◽  
Undergraduate Research ◽  
Multiple Drug Resistance ◽  
Structural Diversity ◽  
Bioinformatic Analysis ◽  
Multiple Drug ◽  
Accessory Proteins ◽  
Human Pathogens ◽  
Research Experience

AbstractMycobacterium tuberculosis and abscessus are major human pathogens that are part of the Actinobacteria phylum. Increasing multiple drug resistance in these bacteria has led to a renewed interest in using viruses that infect these bacteria for therapy. In order to understand these viruses, a course-based undergraduate research experience (CURE) program run by SEA-PHAGES at the University of Pittsburgh and HHMI has isolated, sequenced, and annotated over 3000 actinobacteriophages (viruses that infect Actinobacteria). Little work has been done to investigate the structural diversity of these phage, all of which are thought to use a common protein fold, the HK97-fold, in their major capsid protein. Here we describe the structure of three actinobacteriophage capsids isolated by students that infect Mycobacterium smegmatis. The capsid structures were resolved to approximately 6 angstroms, which allowed confirmation that each phage uses the HK97-fold to form their capsid. One phage, Rosebush, has a novel variation of the HK97-fold. Four novel accessory proteins, that form the capsid head along with the major capsid protein, were identified that show limited or no homology to known proteins. The genes that encode the proteins were identified using SDS-PAGE and mass spectrometry. Bioinformatic analysis of the accessory proteins suggest they are used in many actinobacteriophage capsids.

scholarly journals Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 294 ◽  
Author(s):  
Jennifer Podgorski ◽  
Joshua Calabrese ◽  
Lauren Alexandrescu ◽  
Deborah Jacobs-Sera ◽  
Welkin Pope ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Capsid Protein ◽  
Mycobacterium Smegmatis ◽  
Major Capsid Protein ◽  
Bioinformatic Analysis ◽  
Capsid Proteins ◽  
Accessory Proteins ◽  
Sds Page ◽  
Novel Variation

Here, we describe the structure of three actinobacteriophage capsids that infect Mycobacterium smegmatis. The capsid structures were resolved to approximately six angstroms, which allowed confirmation that each bacteriophage uses the HK97-fold to form their capsid. One bacteriophage, Rosebush, may have a novel variation of the HK97-fold. Four novel accessory proteins that form the capsid head along with the major capsid protein were identified. Two of the accessory proteins were minor capsid proteins and showed some homology, based on bioinformatic analysis, to the TW1 bacteriophage. The remaining two accessory proteins are decoration proteins that are located on the outside of the capsid and do not resemble any previously described bacteriophage decoration protein. SDS-PAGE and mass spectrometry was used to identify the accessory proteins and bioinformatic analysis of the accessory proteins suggest they are used in many actinobacteriophage capsids.

scholarly journals Fermentation revival in the classroom: investigating ancient human practices as CUREs for modern diseases

2020 ◽  
Vol 367 (21) ◽  
Author(s):  
Jennifer K Lyles ◽  
Monika Oli
Keyword(s):  
Undergraduate Research ◽  
Bioinformatic Analysis ◽  
Research Experience ◽  
Group Presentation ◽  
Student Knowledge ◽  
Laboratory Equipment ◽  
Lecture Material ◽  
Hands On ◽  
Human Practices ◽  
Survey Responses

ABSTRACT A course-based undergraduate research experience (CURE) was designed to integrate key microbiological principles and techniques into an authentic research experience in a classroom setting and was implemented in an undergraduate microbiology laboratory course. Students conducted a 6-week study in order to determine the identity and quantity of unique probiotic species from various types of kefir. This course module followed an inquiry-based pedagogical approach in which students use the scientific process to investigate an unknown question with no predetermined outcome. During each lab, relevant microbiological topics and laboratory concepts were presented. Students then performed various laboratory techniques, reinforcing the lecture material with hands-on experience. In addition, students participated in reflection through group presentation of their results, bioinformatic analysis and literature review. Based on data collected from pre- and post-study survey responses, both student knowledge and attitudes towards the topics covered improved due to participation in this CURE. Importantly, this CURE can be implemented at many levels of education, requiring only minimal resources and common laboratory equipment.

scholarly journals A functional genomics screen identifying blood cell development genes in Drosophila by undergraduates participating in a course-based research experience

2021 ◽  
Vol 11 (1) ◽  
pp. 1-23
Author(s):  
Cory J Evans ◽  
John M Olson ◽  
Bama Charan Mondal ◽  
Pratyush Kandimalla ◽  
Ariano Abbasi ◽  
...  
Keyword(s):  
Blood Cell ◽  
Functional Genomics ◽  
Undergraduate Students ◽  
Undergraduate Research ◽  
Cell Types ◽  
Bioinformatic Analysis ◽  
Research Experience ◽  
Loss Of Function ◽  
Fluorescent Reporter ◽  
Stem Retention

Abstract Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes important for hematopoiesis in Drosophila. This screen disrupted the function of approximately 3500 genes and identified 137 candidate genes for which loss of function leads to observable changes in the hematopoietic development. Targeting RNAi to maturing, progenitor, and regulatory cell types identified key subsets that either limit or promote blood cell maturation. Bioinformatic analysis reveals gene enrichment in several previously uncharacterized areas, including RNA processing and export and vesicular trafficking. Lastly, the participation of students in this course-based undergraduate research experience (CURE) correlated with increased learning gains across several areas, as well as increased STEM retention, indicating that authentic, student-driven research in the form of a CURE represents an impactful and enriching pedagogical approach.

scholarly journals Identification of hidden N4-like viruses and their interactions with hosts in global metagenomes

2021 ◽  
Author(s):  
Kaiyang Zheng ◽  
Yantao Liang ◽  
David Paez-Espino ◽  
Sijun Huang ◽  
Xiao Zou ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Rna Polymerase ◽  
Capsid Protein ◽  
Major Capsid Protein ◽  
Host Cells ◽  
Marker Genes ◽  
Specific Marker ◽  
Human Pathogens ◽  
Phylogenic Tree

Abstract Background: N4-like viruses, with specific genomic features and propagation signatures, comprise a unique viral clade within the Podoviridae family. N4-like viruses are commonly characterized by the N4-like major capsid protein (MCP) and a giant virion-encapsulated RNA polymerase (N4-like RNAP) with a size of approximately 3,500-aa, which is the largest viral protein so far described. To date, our understanding of N4-like viruses is largely derived from 80 viral isolates that infect bacteria. Thus, it is necessary to expand the diversity of N4-like viruses in culturing-independent methods.Methods: A Hidden-Markov-Module based method was designed based on two characterized N4-specific marker genes, major capsid protein and N4-like virion-encapsulated RNA polymerase. Viral sub-clades were classified based on the monophyly presented in phylogenic tree and the results of pangenome analysis. Further analysis assessed different distribution patterns, genomic properties, hosts’ metabolism reprogramming potentialities, significance of viral tRNA and horizontal gene transfer landscape.Results: We identified 1,000 N4-like virus sequences from genomes and metagenomes representing diverse habitats from around the world. N4-like viruses have been classified into 27 sub-clades and detected in almost all habitats from pole to pole, including some novel habitats, such as oral mucosa and Antarctica. Virulent factors might be crucial for some human-associated N4-like viruses to reprogram the metabolism of host cells and mediate their pathogenic ability through horizontal gene transfer. From the pangenome analysis, the protein diversity was expended over 7-fold and 17 conserved house-keeping genes were identified. Transcriptional compensation of tRNA indicates that producing progeny virion might be the main significance of viral tRNAs. From the horizontal gene transfer network, some N4-like viral sub-clades were observed that potentially infect some important human pathogens, such as Campylobacteria and Veillonella , which have not been considered as potential hosts of N4-like virus or even any virus.Conclusion: This study expands the knowledge of N4-like viruses via global metagenomic datasets, reveals the novel ecological and genomic signatures of these viruses and will provide the backbone for further N4-like virus studies.

scholarly journals Characterization of virulent Escherichia coli strains isolated from patients with urological infection

2022 ◽  
Vol 98 (6) ◽  
pp. 671-684
Author(s):  
P. V. Slukin ◽  
E. I. Astashkin ◽  
E. M. Aslanyan ◽  
M. G. Ershova ◽  
E. D. Poletaeva ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Galleria Mellonella ◽  
Multiple Drug Resistance ◽  
Dilution Method ◽  
Multiple Drug ◽  
Human Pathogens ◽  
Class 1 ◽  
Serial Dilution Method ◽  
Tract Infections ◽  
Sequence Types

Objective. Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) affect 150 million people annually.Purpose: Characteristics of non-hospital strains of UPEC isolated from patients with UTI in Yaroslavl in 2016– 2017.Materials and methods. Susceptibility of UPEC strains (n = 20) to antibacterials was measured by the serial dilution method; the antibiotic resistance and virulence genes, phylogroups, O-serogroups and sequence types were identified by PCR and whole genome sequencing. The virulence of the strains was studied using the model of Galleria mellonella larvae.Results. UPEC strains were classified as resistant (n = 11) and multi-drug resistant (n = 9) pathogens. Betalactamase genes blaTEM (n = 10), blaCTX-M (n = 6), class 1 integrons (n = 8), and gene cassettes dfrA17-aadA5 (n = 2), dfrA1 (n = 1) and aacA4-cmlA1 (n = 1) were identified. UPEC-virulence genetic determinants coding adhesins fimH, papG, sfaS, focG, afa/draBC, csgA, siderophores iroN, fyuA, iutA, counteracting factors of host immunity ompT, traT, toxins hlyA, cnf1, usp, capsule transporter kpsMTII, colicin cvaC, and pathogenicity islands I536, II536, III536, IV536, IIJ96 и IICFT073 were detected. Highly virulent and slightly virulent for G. mellonella larvae UPEC strains were obtained with LD50 104–105 and 106–107 CFU, respectively. The phylogroups A, B1, B2, E and F, serogroups О2, О4, О6, O9, O11, О15, О18, О25, О75 and O89, known sequence types ST14, ST58, ST69, ST73, ST93, ST127, ST131, ST-141, ST165, ST297, ST457, ST537, ST744, ST1434 and novel ST9239 and ST10102 were revealed.Conclusions. The identified genetic diversity of non-hospital UPEC strains is consistent with the observed global trend in the spread of human pathogens, which are characterized with both high virulence and multiple drug resistance. This makes possible to assess prospectively the current epidemiological situation, give a forecast for its development in the future, as well as determine the optimal therapeutic options.

Surgical Site Infections - A Hospital Havoc: Retrospective Study of Surgical Site Infections in Tertiary Health Care Centre in North East India

2018 ◽  
Vol 3 (01) ◽  
Author(s):  
V Singh ◽  
A B Khyriem, W V Lyngdoh ◽  
C J Lyngdoh
Keyword(s):  
Surgical Site Infection ◽  
Multiple Drug Resistance ◽  
Surgical Site Infections ◽  
Multidrug Resistant ◽  
Multiple Drug ◽  
Site Infection ◽  
Retrospective Case ◽  
Acinetobacter Baumanii ◽  
Health Care Centre ◽  
North East

Objectives - Surgical site infections (SSI) has turn out to be a major problem even in hospital with most modern facilities and standard protocols of pre -operative preparation and antibiotic prophylaxis. Objective of this study is to know the prevalence of surgical site infection among the postoperative patients and to identify the relationship between SSI and etiological pathogens along with their antimicrobial susceptibility at North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Shillong. Methods - A retrospective case study conducted at NEIGRIHMS, among patients admitted to the surgical departments during the period between January 1st and December 31st 2016. Swabs from the surgical sites were collected under sterile conditions and standard bacteriological tests were performed for identification and appropriate statistical methods were employed to look for association between SSI and etiological pathogens. Results - Out of the 1284 samples included in the study, 192 samples showed evidence of SSI yielding an infection rate of 14.9%. The most commonly isolated bacteria were: Escherichia coli, Acinetobacter baumanii and Staphylococcus aureus, of the gram negative isolates 6.2% were multidrug resistant of which 19% were carbapenem resistant. Conclusion - SSI with multiple drug resistance strains and polymicrobial etiology reflects therapeutic failure. The outcome of the SSI surveillance in our hospital revealed that in order to decrease the incidence of SSI we would have to: a) incorporate a proper antibiotic stewardship  b) conduct periodic surveillance to keep a check on SSI d) educate medical staffs regarding the prevention of surgical site infection.

INFLUENCE OF GENOTYPIC VARIABILITY OF M. TUBERCULOSIS ON THE COURSE OF TUBERCULOSIS WITH MULTIPLE DRUG RESISTANCE

2020 ◽  
pp. 68-71
Author(s):  
V. S. Krutko ◽  
L. H. Nikolaieva ◽  
T. V. Maistat ◽  
O. A. Oparin ◽  
Anton Viktorovych Rohozhyn
Keyword(s):  
Clinical Laboratory ◽  
Multiple Drug Resistance ◽  
Multidrug Resistant ◽  
Multiple Drug ◽  
Genotypic Variability ◽  
Intensive Phase ◽  
Resistant Tuberculosis ◽  
Multidrug Resistant Tuberculosis ◽  
Promising Area ◽  
Infection Source

Tuberculosis is infectious and socially dependent disease, being now one of the most pressing issues in practical health care. As well the usual types of tuberculosis infection, chemoresistant tuberculosis is spreading rapidly in the world. The WHO estimates that about 500,000 people on the planet are infected with M. tuberculosis, which is resistant to standard anti−tuberculosis drugs. The probability of successful treatment decreases with emergence of new genotypes of M. tuberculosis with total resistance. In the modern epidemiology of tuberculosis, it is important to identify genotypes on certain signs, allowing to address issues such as their origin, identification of the infection source, possible routes and factors of transmission, as well as to reveal cases and spread of resistance to anti−tuberculosis drugs. To evaluate the therapy efficiency of multidrug−resistant tuberculosis patients with revealed genotypic variability during treatment, 10 patients with chemoresistant pulmonary tuberculosis having M. tuberculosis genotypic variability were treated. In these patients, the clinical, laboratory and radiological dynamics of disease in intensive phase of treatment were studied. Analysis of treatment results for patients with chemoresistant tuberculosis with genotypic variability of M. tuberculosis was evaluated by the intoxication syndrome dynamics of, the timing of closure of the decay cavities and cessation of bacterial excretion. The study found that the genotypic variability of M. tuberculosis is characterized by the change of less virulent genotypes of M. tuberculosis to more virulent. Signs of intoxication have been shown to change from less virulent M. tuberculosis genotypes to M. tuberculosis Beijing genotypes. Genotypic variability of mycobacteria in hospital suggests that hospitalization in tuberculosis facilities is a risk of exogenous tuberculosis superinfection. Studying the influence of genotypic variability of M. tuberculosis on the course of multidrug−resistant tuberculosis requires more extensive research, being a very relevant and promising area in phthisiology. Key words: Mycobacterium tuberculosis, genotypic variability, VNTR−genotyping, treatment.

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