scholarly journals Distribution and Identification of Mycobacterium tuberculosis Lineage in Kashgar Prefecture

2021 ◽  
Author(s):  
Ai-Min Xu ◽  
Chuan-Jiang He ◽  
Xiang Chen ◽  
Li Li ◽  
AniKiz Abuduaini ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Phylogenetic Tree ◽  
Geographical Location ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Clinical Strains ◽  
Lineage 2 ◽  
Composition Structure ◽  
And Control ◽  
Kashgar Prefecture

Abstract Objectives In order to understand the composition of Mycobacterium tuberculosis(M.tb) lineage and find specific tags to distinguish lineage of the M.tb in Kashgar prefecture, so as to provide a basis for the prevention of tuberculosis in this area. Methods Whole genome sequencing (WGS) of M.tb clinical strains (161 cases) was conducted. The phylogenetic tree was constructed by Maximum Likelihood (ML) on the basis of single nucleotide polymorphisms (SNPs) and verified via principal component analysis (PCA). The composition structure of M.tb in different regions was analyzed by combining geographic information. Results The M.tb clinical strains were composed of lineage 2 (73/161, 45.34%), lineage 3 (52/161, 32.30%) and lineage 4 (36/161, 22.36%) in Kashgar prefecture. And the 3 lineages were subdivided into 11 sublineages, among which lineage 2 includes lineage 2.2.2/Asia Ancestral 1(9/73, 12.33%),lineage 2.2.1-Asia Ancestral 2(9/73, 12.33%)༌lineage 2.2.1-Asia Ancestral 3(18/73, 24.66%) and lineage 2.2.1-Modern Beijing(39/73, 53.42%).Lineage 3 includes lineage 3.2(14/52, 26.92%)and lineage 3.3(38/52, 73.08%)༌lineage 4 includes lineage 4.1(3/36, 8.33%)༌lineage 4.2(2/36, 5.66%)༌lineage 4.4.2(1/36, 2.78%)༌lineage 4.5(28/36, 77.78%) and lineage 4.8(2/36, 5.66%)༌all of which were consistent with the PCA results. Among the identified 21438 SNPs ,there are 136 markers proposed to discriminate known circulating strains. Reconstruction of a phylogenetic tree using the 136 SNPs for all 161 samples resulted in a tree with the same number of delineated clades. Based on geographical location analysis, the composition of Lineage 2 in Kashgar prefecture (45.34%) is lower than other regions level in China(54.35%-90.27%), and the composition of Lineage 3 (32.30%)is much higher than other regions level in China (0.92%-2.01%), but it is lower than the bordering Pakistan (70.40%). Conclusion In summary, M.tb clinical strains from Kashgar prefecture were identifed 3 lineages and 11 sublineages, with 136 Branch-Specific SNP. Kashgar borders countries with a high incidence of tuberculosis such as Pakistan and India, resulting in a large difference between the M.tb lineage and sublineage distribution in this region and other provinces in China. This research provides a theoretical basis for the prevention and control of tuberculosis in Xinjiang.

scholarly journals The Genetic and Environmental Adaptation of the Associated Liana Species Derris trifoliata Lour. (Leguminosae) in Mangroves

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1375
Author(s):  
Yun Zhang ◽  
Kun Xin ◽  
Baowen Liao ◽  
Xihang Ai ◽  
Nong Sheng
Keyword(s):  
Clonal Growth ◽  
Environmental Changes ◽  
Principal Component ◽  
Clonal Diversity ◽  
Control Measures ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Sexual Propagation ◽  
Specific Locus ◽  
And Control

Derris trifoliata Lour. is an indigenous and associated liana species of mangroves in China; however, its rapid dispersal is threatening mangrove survival. To explore and evaluate their persistence in past disturbances and their potential resistance to future climate and environmental changes, 120 D. trifoliata samples were collected from three sites in Guangdong Province, China, and they were used to develop single nucleotide polymorphic markers using specific-locus amplified fragment sequencing technology. A total of 351.59 Mb reads and 97,998 polymorphic specific-locus amplified fragment sequencing tags were identified, including 360,672 single nucleotide polymorphisms. The principal component analysis, phylogenetic tree, and genetic structure all clustered the samples according to their geographic positions. The three populations showed medium genetic diversity levels and high clonal diversity, indicating that sexual propagation played vital roles in the populations’ succession, although clonal growth was intense within the populations. An association analysis revealed that 9 out of 16 markers were correlated with nitrogen, which indicated the positive roles of nitrogen in population formation and maintenance. This study provides an ecological and molecular basis for understanding the outbreaks of D. trifoliata in mangroves. To control the further expansion of D. trifoliata in mangroves, preventive and control measures should be taken against clonal growth and sexual propagation, respectively; obstructing the clonal growth, especially that of the stolon, should be mainly considered at the junctions of D. trifoliata and mangroves.

scholarly journals DNA Polymorphisms in the pepA and PPE18 Genes among Clinical Strains of Mycobacterium tuberculosis: Implications for Vaccine Efficacy

2007 ◽  
Vol 75 (12) ◽  
pp. 5798-5805 ◽  
Author(s):  
Andrea M. Hebert ◽  
Sarah Talarico ◽  
Dong Yang ◽  
Riza Durmaz ◽  
Carl F. Marrs ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Amino Acid ◽  
Genomic Diversity ◽  
Dna Polymorphisms ◽  
Effective Vaccine ◽  
Nucleotide Polymorphisms ◽  
T Cell Epitopes ◽  
Phase I Clinical Trials ◽  
Clinical Strains ◽  
Different Strains

ABSTRACT Tuberculosis continues to be a leading cause of death worldwide. Development of an effective vaccine against Mycobacterium tuberculosis is necessary to reduce the global burden of this disease. Mtb72F, consisting of the protein products of the pepA and PPE18 genes, is the first subunit tuberculosis vaccine to undergo phase I clinical trials. To obtain insight into the ability of Mtb72F to induce an immune response capable of recognizing different strains of M. tuberculosis, we investigated the genomic diversity of the pepA and PPE18 genes among 225 clinical strains of M. tuberculosis from two different geographical locations, Arkansas and Turkey, representing a broad range of genotypes of M. tuberculosis. A combination of single nucleotide polymorphisms (SNPs) and insertion/deletions resulting in amino acid changes in the PPE18 protein occurred in 47 (20.9%) of the 225 study strains, whereas SNPs resulted in amino acid changes in the PepA protein in 14 (6.2%) of the 225 study strains. Of the 122 Arkansas study strains and the 103 Turkey study strains, 32 (26.2%) and 15 (14.6%), respectively, had at least one genetic change leading to an alteration of the amino acid sequence of the PPE18 protein, and many of the changes occurred in regions previously reported to be potential T-cell epitopes. Thus, immunity induced by Mtb72F may not recognize a proportion of M. tuberculosis clinical strains.

scholarly journals Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Gary Napier ◽  
Susana Campino ◽  
Yared Merid ◽  
Markos Abebe ◽  
Yimtubezinash Woldeamanuel ◽  
...  
Keyword(s):  
Public Health ◽  
Mycobacterium Tuberculosis ◽  
Phylogenetic Tree ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Whole Genome Sequencing Data ◽  
Global Public Health ◽  
Sequencing Data ◽  
Public Health Burden ◽  
And Control

Abstract Background Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Fast and accurate tracking of MTBC strains is therefore crucial for infection control, and our previous work developed a 62-single nucleotide polymorphism (SNP) barcode to inform on the phylogenetic identity of 7 human lineages and 64 sub-lineages. Methods To update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~ 1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. bovis, M. tuberculosis var. caprae and M. tuberculosis var. orygis). The data was partitioned into training (N = 17,903, 50.7%) and test (N = 17,395, 49.3%) sets and were analysed using an integrated phylogenetic tree and population differentiation (FST) statistical approach. Results By constructing a phylogenetic tree on the training MTBC isolates, we characterised 90 lineages or sub-lineages or species, of which 30 are new, and identified 421 robust barcoding mutations, of which a minimal set of 90 was selected that included 20 markers from the 62-SNP barcode. The barcoding SNPs (90 and 421) discriminated perfectly the 86 MTBC isolate (sub-)lineages in the test set and could accurately reconstruct the clades across the combined 35k samples. Conclusions The validated 90 SNPs can be used for the rapid diagnosis and tracking of MTBC strains to assist public health surveillance and control. To facilitate this, the SNP markers have now been incorporated into the TB-Profiler informatics platform (https://github.com/jodyphelan/TBProfiler).

scholarly journals Phylogenetic analysis by SNP and development of SSR marker in Passiflora

2020 ◽  
Author(s):  
Yanyan Wu ◽  
Qinglan Tian ◽  
Weihua Huang ◽  
Jieyun Liu ◽  
Xiuzhong Xia ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Reference Genome ◽  
Evolutionary Relationship ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Marker Transferability ◽  
High Quality Snps ◽  
Simple Sequence

AbstractInformation of the Passiflora genome is still very limited. Understand the evolutionary relationship between different species of Passiflora, and develop a large number of SSR markers to provide a basis for the genetic improvement of Passiflora. Applying restriction site associated DNA sequencing (RAD-Seq) technology, we studied the phylogeny, simple sequence repeat (SSR) and marker transferability of 10 accessions of 6 species of Passiflora. Taking the partial assembly sequence of accessions P4 as the reference genome, we constructed the phylogenetic tree using the detected 46,451 high-quality single nucleotide polymorphisms (SNPs), showing that P6, P7, P8 and P9 were a single one while P5 and P10 were clustered together, and P1, P2, P3 and P4 were closer in genetic relationship. Using P8 as the reference genome, a total of 12,452 high-quality SNPs were used to construct phylogenetic tree. P3, P4, P7, P8, P9 and P10 were all single branch while P1 and P2 were clustered together, and P5 and P6 were clustered into one branch. A principal component analysis (PCA) revealed a similar population structure, which four cultivated passion fruits forming a tight cluster. A total of 2,614 SSRs were identified in the genome of 10 Passiflora accessions. The core motifs were AT, GA, AAG etc., 2-6 bases, 4-16 repeats, and 2,515 pairs of SSR primer were successfully developed. Tthe SSR transferability in cultivated passion fruits is the best. These results will contribute to the study of genomics and molecular genetics in passion fruit.

Turkey’s foreign policy in perspective: Some regional and national interests

2020 ◽  
Vol 2020 (10-3) ◽  
pp. 82-92
Author(s):  
Gekkaya Funda
Keyword(s):  
Foreign Policy ◽  
Political Ideology ◽  
Geographical Location ◽  
National Interests ◽  
Security Culture ◽  
Center Stage ◽  
External Relations ◽  
The World ◽  
Transit Route ◽  
And Control

The formation of external policy of any country aims at serving the state’s interests. For this matter, many countries seek their way through this by taking into account the potential prospects available to them. The fundamental subtleties and factors that influence a state’s choices of external policy include geographical location, history, security, culture, trade, political ideology, military might, et cetera. Countries often make external contacts based on some regulations and response to unfolding events. Thus, external policy to an extent pertains to the guiding principles outlined to be pursued through state values, decisions and actions taken by the states themselves and their attempt to develop, manage and control the external relations of national societies. In this regard, the Caucasian region has been an important factor in Turkey’s foreign policy. Since these states emerged in the early 1990s, energy has taken a center stage within the region, while Turkey remains a transit route to the world...

UPLC-Q-TOF/MS based Untargeted Metabolite and Lipid Analysis on Premature Ovarian Insufficiency Plasma Samples.

2020 ◽  
Vol 16 ◽  
Author(s):  
Yasemin Taşcı ◽  
Rahime Bedir Fındık ◽  
Meryem Kuru Pekcan ◽  
Ozan Kaplan ◽  
Mustafa Çelebier
Keyword(s):  
Lipid Analysis ◽  
Principal Component ◽  
Premature Ovarian Insufficiency ◽  
Plasma Samples ◽  
Ovarian Insufficiency ◽  
Analytical Methodology ◽  
Drug Molecules ◽  
New Treatment ◽  
And Control ◽  
Phenyl Alanine

Background: Metabolomics is one of the main areas to understand cellular process at molecular level by analyzing metabolites. In recent years metabolomics has been emerged as key tool to understand molecular basis of disease, find diagnostic and prognostic biomarkers, and develop new treatment opportunities and drug molecules. Objective: In this study, an untargeted metabolite and lipid analysis were performed to identify potential biomarkers on premature ovarian insufficiency plasma samples. 43 POI subject plasma samples were compared with 32 healthy subject plasma samples. Methods: Plasma samples were pooled and extracted using chloroform:methanol:water (3:3:1 v/v/v) mixture. Agilent 6530 LC/MS Q-TOF instrument equipped with ESI source was used for analysis. A C18 column (Agilent Zorbax 1.8 μM, 50 x 2.1 mm) was used for separation of metabolites and lipids. XCMS, an “R software” based freeware program, was used for peak picking, grouping and comparing the findings. Isotopologue Parameter Optimization (IPO) software was used in order to optimize XCMS parameters. The analytical methodology and data mining process were validated according to the literature. Results: 83 metabolite peaks and 213 lipid peaks were found to be in semi-quantitatively and statistically different (fold change >1.5, p <0.05) between the POI plasma samples and control subjects. Conclusion: According to the results, two groups were successfully separated through principal component analysis. Among the peaks, phenyl alanine, decanoyl-L-carnitine, 1-palmitoyllysophosphatidylcholine and PC(O-16:0/2:0) were identified through auto MS/MS and matched with human metabolome database and proposed as plasma biomarker for POI and monitoring the patients in treatment period.

scholarly journals Spatio-temporal evolution and influencing mechanism of the COVID-19 epidemic in Shandong province, China

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jinlong Shi ◽  
Xing Gao ◽  
Shuyan Xue ◽  
Fengqing Li ◽  
Qifan Nie ◽  
...  
Keyword(s):  
Prevention And Control ◽  
Temporal Evolution ◽  
Geographical Location ◽  
Shandong Province ◽  
Control Measures ◽  
Middle Aged ◽  
Health Crisis ◽  
Aged People ◽  
Spatio Temporal ◽  
And Control

AbstractThe novel coronavirus pneumonia (COVID-19) outbreak that emerged in late 2019 has posed a severe threat to human health and social and economic development, and thus has become a major public health crisis affecting the world. The spread of COVID-19 in population and regions is a typical geographical process, which is worth discussing from the geographical perspective. This paper focuses on Shandong province, which has a high incidence, though the first Chinese confirmed case was reported from Hubei province. Based on the data of reported confirmed cases and the detailed information of cases collected manually, we used text analysis, mathematical statistics and spatial analysis to reveal the demographic characteristics of confirmed cases and the spatio-temporal evolution process of the epidemic, and to explore the comprehensive mechanism of epidemic evolution and prevention and control. The results show that: (1) the incidence rate of COVID-19 in Shandong is 0.76/100,000. The majority of confirmed cases are old and middle-aged people who are infected by the intra-province diffusion, followed by young and middle-aged people who are infected outside the province. (2) Up to February 5, the number of daily confirmed cases shows a trend of “rapid increase before slowing down”, among which, the changes of age and gender are closely related to population migration, epidemic characteristics and intervention measures. (3) Affected by the regional economy and population, the spatial distribution of the confirmed cases is obviously unbalanced, with the cluster pattern of “high–low” and “low–high”. (4) The evolution of the migration pattern, affected by the geographical location of Wuhan and Chinese traditional culture, is dominated by “cross-provincial” and “intra-provincial” direct flow, and generally shows the trend of “southwest → northeast”. Finally, combined with the targeted countermeasures of “source-flow-sink”, the comprehensive mechanism of COVID-19 epidemic evolution and prevention and control in Shandong is revealed. External and internal prevention and control measures are also figured out.

scholarly journals Sensory Profile of Chihuahua Cheese Manufactured from Raw Milk

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Sarai Villalobos-Chaparro ◽  
Erika Salas-Muñóz ◽  
Néstor Gutiérrez-Méndez ◽  
Guadalupe Virginia Nevárez-Moorillón
Keyword(s):  
Principal Component Analysis ◽  
Geographical Location ◽  
Principal Component ◽  
Raw Milk ◽  
Component Analysis ◽  
Sensory Profile ◽  
Different Seasons ◽  
Quantitative Descriptive ◽  
Traditional Manufacturing ◽  
Chihuahua Cheese

Chihuahua cheese is a local artisanal cheese traditionally produced from raw milk. When this cheese is produced with pasteurized milk, cheesemakers complain that there are differences in taste and aroma as compared with traditional manufacturing. This work aimed to obtain a descriptive sensory analysis of Chihuahua cheese manufactured with raw milk under traditional conditions. Samples were collected in five cheese dairies at two different seasons (summer and autumn), and a Quantitative Descriptive Sensorial Analysis was done by a panel of trained judges. For aroma descriptors, cooked descriptor showed differences between dairies, and whey was different among dairies and sampling seasons (P<0.01); diacetyl, fruity (P<0.01), as well as free fatty acids, nutty and sulphur (P<0.05) descriptors varied between seasons. For flavour descriptors, bitter perception was different between dairies and seasons (P<0.01). Salty and creamy cheese was also different among dairies (P<0.01). A Principal Component Analysis for differences among dairies and sampling season demonstrated that the first three components accounted for 90% of the variance; variables were more affected by the sampling seasons than by the geographical location or if the dairy was operated by Mennonites. Chihuahua cheese sensorial profile can be described as a semi-matured cheese with a bitter flavour, slightly salted, and with a cream flavour, with aroma notes associated with whey and sour milk. Principal Component Analysis demonstrated season influence on flavour and aroma characteristics.

scholarly journals Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 832
Author(s):  
Nina Moravčíková ◽  
Radovan Kasarda ◽  
Radoslav Židek ◽  
Luboš Vostrý ◽  
Hana Vostrá-Vydrová ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Structure ◽  
Principal Component ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
German Shepherd ◽  
German Shepherd Dog ◽  
Genome Wide ◽  
Scale Population ◽  
History Effect

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

scholarly journals An Introduction to Development of Centralized and Distributed Stochastic Approximation Algorithm with Expanding Truncations

Algorithms ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 174
Author(s):  
Wenxiao Zhao
Keyword(s):  
Approximation Algorithm ◽  
Stochastic Approximation ◽  
Probabilistic Method ◽  
Principal Component ◽  
Stochastic Approximation Algorithm ◽  
The Past ◽  
Systems And Control ◽  
Ode Method ◽  
Centralized Algorithm ◽  
And Control

The stochastic approximation algorithm (SAA), starting from the pioneer work by Robbins and Monro in 1950s, has been successfully applied in systems and control, statistics, machine learning, and so forth. In this paper, we will review the development of SAA in China, to be specific, the stochastic approximation algorithm with expanding truncations (SAAWET) developed by Han-Fu Chen and his colleagues during the past 35 years. We first review the historical development for the centralized algorithm including the probabilistic method (PM) and the ordinary differential equation (ODE) method for SAA and the trajectory-subsequence method for SAAWET. Then, we will give an application example of SAAWET to the recursive principal component analysis. We will also introduce the recent progress on SAAWET in a networked and distributed setting, named the distributed SAAWET (DSAAWET).

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