scholarly journals Diversity and dynamics of the CRISPR-Cas systems associated with Bacteroides fragilis in human population

2021 ◽  
Author(s):  
Tony J. Lam ◽  
Kate Mortensen ◽  
Yuzhen Ye
Keyword(s):  
Human Population ◽  
Population Genomics ◽  
Parallel Evolution ◽  
Mobile Elements ◽  
Type I ◽  
Type Ii ◽  
Holistic View ◽  
Network Modules ◽  
Using Data ◽  
Adaptive Immune Systems

AbstractThe CRISPR-Cas systems are important prokaryotic adaptive immune systems and effectively record the arms-race between bacteria and invading mobile elements in their CRISPR arrays. Using data from culture-based population genomics and metagenomics, we investigated the CRISPR-Cas systems associated with Bacteriodes fragilis, an important gut bacterium, and studied their diversity and dynamics. We analyzed genomes of 601 B. fragilis isolates derived from 12 healthy individuals, among which include time-series isolates from 6 individuals. In addition, we analyzed 222 reference B. fragilis genomes. Three different types of CRISPR-Cas systems (Type I-B, II-C and III-B) were found in analyzed B. fragilis genomes, with Type III-B being the most prevalent whereas the Type II-C being the most dynamic with varying arrays among isolates. Our graph-based summary and visualization of CRISPR arrays provided a holistic view of the organization and the composition of the CRISPR spacers. We observed insertions of different new spacers at the leader ends of the CRISPR arrays of Type II-C CRISPR-Cas systems in different B. fragilis sub-populations in one individual, an example of B. fragilis’ adaptation and parallel evolution within individual microbiomes. A network of B. fragilis and its predicted invaders also revealed microdynamics of B. fragilis CRISPR array, with hairball-like structures representing spacers with multi-target capabilities and network modules revealing the collective targeting of selected mobile elements by many spacers. This work demonstrates the power of using culture-based population genomics to reveal the activities and evolution of the CRISPR-Cas systems of the important gut bacterium B. fragilis in human population.

An economic model comparison of EMSI and IMPLAN

2016 ◽  
Vol 23 (5) ◽  
pp. 1124-1130 ◽  
Author(s):  
Sungsoo Kim ◽  
Chad R. Miller
Keyword(s):  
Model Comparison ◽  
Impact Analysis ◽  
Economic Modeling ◽  
Total Output ◽  
Type I ◽  
Type Ii ◽  
Development Research ◽  
Tourism Research ◽  
Multiplier Effects ◽  
Using Data

Economic Modeling Specialist International (EMSI) model is a common economic development research tool that has begun to be utilized for tourism research. Therefore, it is important to examine the differences between the EMSI model and the commonly used Impact Analysis for Planning (IMPLAN) model. The multiplier effects of the default version of EMSI and IMPLAN were compared using data obtained from a visitor expenditure survey of the Jackson Mississippi Mistletoe Marketplace. The results revealed that IMPLAN estimated larger multiplier effects (both type I and type II) than EMSI for the total output and employment (job supports).

Life tables: construction and interpretation

2021 ◽  
pp. 151-162
Author(s):  
Owen R. Jones
Keyword(s):  
Life Histories ◽  
Worked Examples ◽  
Time Frame ◽  
Life Tables ◽  
Type I ◽  
Type Ii ◽  
Risk Of Death ◽  
Nonhuman Animals ◽  
Using Data ◽  
Diversity Of Life

Life tables, which describe how the risk of death (and sometimes fertility) changes with age, are a fundamental tool for describing and exploring the diversity of life histories. Numerous important life history metrics can be derived from them. This chapter provides a broad coverage of life table construction and use and use with a particular focus on nonhuman animals. The calculation of life tables can be divided into approaches: cohort-based, where the data are obtained from individuals born at (approximately) the same time that are followed until death; and period-based, where the data are obtained from a population of mixed ages followed for a particular time-frame (e.g. a year). Worked examples of both approaches are provided using data from published sources. Emphasis is placed on understanding concepts such as rates vs. probability, life expectancy, and generation time. Links are drawn between the survivorship curve (type I, type II, and type III survivorship) and entropy. The chapter also covers the concept of the Lexis diagram which is used to represent births and deaths for individuals in different cohorts. Finally, the assumptions and limitations of life tables are discussed, with pointers to further reading. Code and data are provided.

scholarly journals CRISPR/cas Loci of Type II Propionibacterium acnes Confer Immunity against Acquisition of Mobile Elements Present in Type I P. acnes

PLoS ONE ◽  
2012 ◽  
Vol 7 (3) ◽  
pp. e34171 ◽  
Author(s):  
Holger Brüggemann ◽  
Hans B. Lomholt ◽  
Hervé Tettelin ◽  
Mogens Kilian
Keyword(s):  
Propionibacterium Acnes ◽  
Mobile Elements ◽  
Type I ◽  
Type Ii

scholarly journals Discovery of widespread type I and type V CRISPR-Cas inhibitors

Science ◽  
2018 ◽  
Vol 362 (6411) ◽  
pp. 240-242 ◽  
Author(s):  
Nicole D. Marino ◽  
Jenny Y. Zhang ◽  
Adair L. Borges ◽  
Alexander A. Sousa ◽  
Lina M. Leon ◽  
...  
Keyword(s):  
Immune Function ◽  
Broad Spectrum ◽  
Mobile Genetic Elements ◽  
Mobile Elements ◽  
Human Cells ◽  
Type I ◽  
Type Ii ◽  
Genetic Elements ◽  
Type V

Bacterial CRISPR-Cas systems protect their host from bacteriophages and other mobile genetic elements. Mobile elements, in turn, encode various anti-CRISPR (Acr) proteins to inhibit the immune function of CRISPR-Cas. To date, Acr proteins have been discovered for type I (subtypes I-D, I-E, and I-F) and type II (II-A and II-C) but not other CRISPR systems. Here, we report the discovery of 12 acr genes, including inhibitors of type V-A and I-C CRISPR systems. AcrVA1 inhibits a broad spectrum of Cas12a (Cpf1) orthologs—including MbCas12a, Mb3Cas12a, AsCas12a, and LbCas12a—when assayed in human cells. The acr genes reported here provide useful biotechnological tools and mark the discovery of acr loci in many bacteria and phages.

scholarly journals QALYs and DALYs are Better with Concurrent ChemoRT than Induction Chemo Followed by ChemoRT in Nasopharyngeal Carcinoma.

2020 ◽  
Author(s):  
Mary R Nittala ◽  
Madhava R. Kanakamedala ◽  
Eswar K. Mundra ◽  
Williams C. Woods ◽  
Maria L. Smith ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Cox Regression ◽  
Disease Onset ◽  
Disease Free Survival ◽  
State Institution ◽  
World Health ◽  
Type I ◽  
Type Ii ◽  
Holistic View ◽  
Type Iii

Abstract Background: As traditional measures such as overall survival (OS) or disease-free survival (DFS) alone does not give a holistic view of the outcomes of a treatment paradigm, we determine to add the evidence of quality-adjusted life year (QALY) and disability-adjusted life year (DALY) to the outcomes of the nasopharyngeal carcinoma patients (NCP) treated with definitive chemoradiation therapy (chemoRT) with or without induction chemotherapy.Methods: This is a retrospective analysis of 85 NCPs treated at an academic state institution. The OS estimated by Kaplan–Meier method and the multivariate Cox regression model determined the co-variables associated with the OS. The relationship between QALYs gained and DALYs saved were calculated from age of the disease onset, duration of the disease, quality of life (QoL) and disability weights.Results: Of the 85 eligible NCPs of this cohort, the disease frequency distribution per the World Health Organization (WHO) classification was 41.2% for Type-I, 42.4% for Type-II, and 16.5% for Type-III. The median follow-up (24 months). The 5-year OS of patients treated with concurrent chemoRT vs. induction chemo followed by concurrent chemoRT was 54.7 vs. 14.8% for WHO Type I, 60.1 vs. 58.3% for WHO Type II, and 83.3 vs. 50.0% for WHO Type III (p= 0.029). The average DALYs saved with concurrent chemoRT was 12.2 years vs. 5 years for induction chemo followed by concurrent chemoRT. The average QALYs gained with concurrent chemoRT was 6.9 years vs. 3.1 years for induction chemo followed by concurrent chemoRT.Conclusion: Patients treated with concurrent chemoRT had an increased QoL when compared to induction chemo followed by concurrent chemoRT. The average DALYs saved were higher in the patients treated with concurrent chemoRT than treated with induction chemo followed by concurrent chemoRT.

Heat-Etching with a Bullivant Type II Simple Freeze-Cleave Device

1970 ◽  
Vol 28 ◽  
pp. 106-107 ◽  
Author(s):  
Ronald S. Weinstein ◽  
N. Scott McNutt
Keyword(s):  
New Zealand ◽  
General Hospital ◽  
Massachusetts General Hospital ◽  
Type I ◽  
Type Ii ◽  
Collaborative Effort ◽  
Temperature And Pressure ◽  
The University

The Type I simple cold block device was described by Bullivant and Ames in 1966 and represented the product of the first successful effort to simplify the equipment required to do sophisticated freeze-cleave techniques. Bullivant, Weinstein and Someda described the Type II device which is a modification of the Type I device and was developed as a collaborative effort at the Massachusetts General Hospital and the University of Auckland, New Zealand. The modifications reduced specimen contamination and provided controlled specimen warming for heat-etching of fracture faces. We have now tested the Mass. General Hospital version of the Type II device (called the “Type II-MGH device”) on a wide variety of biological specimens and have established temperature and pressure curves for routine heat-etching with the device.

Labelling of non-A, non-B hepatitis infected chimpanzee hepatocytes with nuclease-gold conjugates

1984 ◽  
Vol 42 ◽  
pp. 250-251
Author(s):  
G. D. Gagne ◽  
M. F. Miller ◽  
D. A. Peterson
Keyword(s):  
Endoplasmic Reticulum ◽  
Experimental Infection ◽  
Uranyl Acetate ◽  
Type I ◽  
Cellular Injury ◽  
Type Ii ◽  
Tubular Structures ◽  
Type Iii ◽  
Type Iv ◽  
Infected Chimpanzee

Experimental infection of chimpanzees with non-A, non-B hepatitis (NANB) or with delta agent hepatitis results in the appearance of characteristic cytoplasmic alterations in the hepatocytes. These alterations include spongelike inclusions (Type I), attached convoluted membranes (Type II), tubular structures (Type III), and microtubular aggregates (Type IV) (Fig. 1). Type I, II and III structures are, by association, believed to be derived from endoplasmic reticulum and may be morphogenetically related. Type IV structures are generally observed free in the cytoplasm but sometimes in the vicinity of type III structures. It is not known whether these structures are somehow involved in the replication and/or assembly of the putative NANB virus or whether they are simply nonspecific responses to cellular injury. When treated with uranyl acetate, type I, II and III structures stain intensely as if they might contain nucleic acids. If these structures do correspond to intermediates in the replication of a virus, one might expect them to contain DNA or RNA and the present study was undertaken to explore this possibility.

Comparative surface and ultrastructural views of methylotrophic bacteria by TEM, STEM, SE, and freeze-etch electron microscopy.

1987 ◽  
Vol 45 ◽  
pp. 792-793
Author(s):  
T.A. Fassel ◽  
M.J. Schaller ◽  
M.E. Lidstrom ◽  
C.C. Remsen
Keyword(s):  
Cytoplasmic Membrane ◽  
Structural Features ◽  
Methylotrophic Bacteria ◽  
Type I ◽  
Type Ii ◽  
Membrane Complex ◽  
Oxidation Of Methane ◽  
Methane Oxidizing Bacteria ◽  
Wall Structures ◽  
Methylomonas Albus

Methylotrophic bacteria play an Important role in the environment in the oxidation of methane and methanol. Extensive intracytoplasmic membranes (ICM) have been associated with the oxidation processes in methylotrophs and chemolithotrophic bacteria. Classification on the basis of ICM arrangement distinguishes 2 types of methylotrophs. Bundles or vesicular stacks of ICM located away from the cytoplasmic membrane and extending into the cytoplasm are present in Type I methylotrophs. In Type II methylotrophs, the ICM form pairs of peripheral membranes located parallel to the cytoplasmic membrane. Complex cell wall structures of tightly packed cup-shaped subunits have been described in strains of marine and freshwater phototrophic sulfur bacteria and several strains of methane oxidizing bacteria. We examined the ultrastructure of the methylotrophs with particular view of the ICM and surface structural features, between representatives of the Type I Methylomonas albus (BG8), and Type II Methylosinus trichosporium (OB-36).

Heteroscedastic Methods for Performing All Pairwise Comparisons of Regression Lines Associated With J Independent Groups

Methodology ◽  
2015 ◽  
Vol 11 (3) ◽  
pp. 110-115 ◽  
Author(s):  
Rand R. Wilcox ◽  
Jinxia Ma
Keyword(s):  
Least Squares ◽  
Pairwise Comparisons ◽  
Simple Extension ◽  
Type I ◽  
Type I Errors ◽  
Well Elderly ◽  
Using Data

Abstract. The paper compares methods that allow both within group and between group heteroscedasticity when performing all pairwise comparisons of the least squares lines associated with J independent groups. The methods are based on simple extension of results derived by Johansen (1980) and Welch (1938) in conjunction with the HC3 and HC4 estimators. The probability of one or more Type I errors is controlled using the improvement on the Bonferroni method derived by Hochberg (1988) . Results are illustrated using data from the Well Elderly 2 study, which motivated this paper.

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