Phylogeny of Mycobacterium avium strains inferred from glycopeptidolipid biosynthesis pathway genes

The Mycobacterium avium complex (MAC) encompasses two species, M. avium and Mycobacterium intracellulare, which are opportunistic pathogens of humans and animals. The standard method of MAC strain differentiation is serotyping based on a variation in the antigenic glycopeptidolipid (GPL) composition. To elucidate the relationships among M. avium serotypes a phylogenetic analysis of 13 reference and clinical M. avium strains from 8 serotypes was performed using as markers two genomic regions (890 bp of the gtfB gene and 2150 bp spanning the rtfA–mtfC genes) which are associated with the strains' serological properties. Strains belonging to three other known M. avium serotypes were not included in the phylogeny inference due to apparent lack of the marker sequences in their genomes, as revealed by PCR and Southern blot analysis. These studies suggest that serotypes prevalent in AIDS patients have multiple origins. In trees inferred from both markers, serotype 1 strains, known to have the simplest and shortest GPLs among all other serotypes, were polyphyletic. Likewise, comparisons of the inferred phylogenies with the molecular typing results imply that the existing tools used in epidemiological studies may be poor estimators of M. avium strain relatedness. Additionally, trees inferred from each marker had significantly incongruent topologies due to a well supported alternative placement of strain 2151, suggesting a complex evolutionary history of this genomic region.

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Novel Rhamnosyltransferase Involved in Biosynthesis of Serovar 4-Specific Glycopeptidolipid from Mycobacterium avium Complex

Journal of Bacteriology ◽

10.1128/jb.00554-10 ◽

2010 ◽

Vol 192 (21) ◽

pp. 5700-5708 ◽

Cited By ~ 6

Author(s):

Yuji Miyamoto ◽

Tetsu Mukai ◽

Takashi Naka ◽

Nagatoshi Fujiwara ◽

Yumi Maeda ◽

...

Keyword(s):

Mycobacterium Avium ◽

Protein Gene ◽

Functional Characterization ◽

Epidemiological Studies ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

Opportunistic Pathogens ◽

Fucose Residue

ABSTRACT Glycopeptidolipids (GPLs) are one of the major glycolipid components present on the surface of Mycobacterium avium complex (MAC) that belong to opportunistic pathogens distributed in the natural environment. The serovars of MAC, up to around 30 types, are defined by the variable oligosaccharide portions of the GPLs. Epidemiological studies show that serovar 4 is the most prevalent type, and the prognosis of pulmonary disease caused by serovar 4 is significantly worse than that caused by other serovars. However, little is known about the biosynthesis of serovar 4-specific GPL, particularly the formation of the oligosaccharide portion that determines the properties of serovar 4. To investigate the biosynthesis of serovar 4-specific GPL, we focused on one segment that included functionally unknown genes in the GPL biosynthetic gene cluster of a serovar 4 strain. In this segment, a putative hemolytic protein gene, hlpA, and its downstream gene were found to be responsible for the formation of the 4-O-methyl-rhamnose residue, which is unique to serovar 4-specific GPL. Moreover, functional characterization of the hlpA gene revealed that it encodes a rhamnosyltransferase that transfers a rhamnose residue via 1→4 linkage to a fucose residue of serovar 2-specific GPL, which is a key pathway leading to the synthesis of oligosaccharide of serovar 4-specific GPL. These findings may provide clues to understanding the biological role of serovar 4-specific GPL in MAC pathogenicity and may also provide new insights into glycosyltransferase, which generates structural and functional diversity of GPLs.

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High-resolution Introgressive Region Map Reveals Spatiotemporal Genome Evolution in Asian Rice Domestication

10.1101/829168 ◽

2019 ◽

Author(s):

Hajime Ohyanagi ◽

Kosuke Goto ◽

Sónia Negrão ◽

Rod A. Wing ◽

Mark A. Tester ◽

...

Keyword(s):

Molecular Mechanisms ◽

Rice Genome ◽

Definitive Answer ◽

Asian Rice ◽

Multiple Origins ◽

Genome Wide ◽

Time Calibration ◽

History Of ◽

Genomic Regions ◽

Rice Domestication

AbstractDomestication is anthropogenic evolution that fulfills mankind’s critical food demand. As such, elucidating the molecular mechanisms behind this process promotes the development of future new food resources including crops. With the aim of understanding the long-term domestication process of Asian rice and by employing the Oryza sativa subspecies (indica and japonica) as an Asian rice domestication model, we scrutinized past genomic introgressions between them as traces of domestication. Here we show the genome-wide introgressive region (IR) map of Asian rice, by utilizing 4,587 accession genotypes with a stable outgroup species, particularly at the finest resolution through a machine learning-aided method. The IR map revealed that 14.2% of the rice genome consists of IRs, including both wide IRs (recent) and narrow IRs (ancient). This introgressive landscape with their time calibration indicates that introgression events happened in multiple genomic regions over multiple periods. From the correspondence between our wide IRs and the so-called selective sweep regions, we provide a definitive answer to a long-standing controversy over the evolutionary origin of Asian rice domestication, single or multiple origins: It heavily depends upon which regions you pay attention to, implying that wider genomic regions represent immediate short history of Asian rice domestication as a likely support to the single origin, while its ancient history is interspersed in narrower traces throughout the genome as a possible support to the multiple origin.

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The Mycobacterium avium Complex gtfTB Gene Encodes a Glucosyltransferase Required for the Biosynthesis of Serovar 8-Specific Glycopeptidolipid

Journal of Bacteriology ◽

10.1128/jb.00911-08 ◽

2008 ◽

Vol 190 (24) ◽

pp. 7918-7924 ◽

Cited By ~ 5

Author(s):

Yuji Miyamoto ◽

Tetsu Mukai ◽

Yumi Maeda ◽

Masanori Kai ◽

Takashi Naka ◽

...

Keyword(s):

Mycobacterium Avium ◽

Mycobacterium Smegmatis ◽

Cell Envelope ◽

Gene Clusters ◽

Genomic Region ◽

Open Reading Frames ◽

Opportunistic Pathogens ◽

Glucose Residue ◽

Functional Analyses ◽

Reading Frames

ABSTRACT Mycobacterium avium complex (MAC) is one of the most common opportunistic pathogens widely distributed in the natural environment. The 28 serovars of MAC are defined by variable oligosaccharide portions of glycopeptidolipids (GPLs) that are abundant on the surface of the cell envelope. These GPLs are also known to contribute to the virulence of MAC. Serovar 8 is one of the dominant serovars isolated from AIDS patients, but the biosynthesis of serovar 8-specific GPL remains unknown. To clarify this, we compared gene clusters involved in the biosynthesis of several serovar-specific GPLs and identified the genomic region predicted to be responsible for GPL biosynthesis in a serovar 8 strain. Sequencing of this region revealed the presence of four open reading frames, three unnamed genes and gtfTB, the function of which has not been elucidated. The simultaneous expression of gtfTB and two downstream genes in a recombinant Mycobacterium smegmatis strain genetically modified to produce serovar 1-specific GPL resulted in the appearance of 4,6-O-(1-carboxyethylidene)-3-O-methyl-glucose, which is unique to serovar 8-specific GPL, suggesting that these three genes participate in its biosynthesis. Furthermore, functional analyses of gtfTB indicated that it encodes a glucosyltransferase that transfers a glucose residue via 1→3 linkage to a rhamnose residue of serovar 1-specific GPL, which is critical to the formation of the oligosaccharide portion of serovar 8-specific GPL. Our findings might provide a clue to understanding the biosynthetic regulation that modulates the biological functions of GPLs in MAC.

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Concurrent circulation of dengue serotype 1, 2 and 3 among acute febrile patients in Cameroon

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0009860 ◽

2021 ◽

Vol 15 (10) ◽

pp. e0009860

Author(s):

Huguette Simo Tchetgna ◽

Francine Sado Yousseu ◽

Basile Kamgang ◽

Armel Tedjou ◽

Philip J. McCall ◽

...

Keyword(s):

Clinical Signs ◽

Epidemiological Studies ◽

Simultaneous Occurrence ◽

Envelope Gene ◽

Rt Pcr ◽

Genotype Iii ◽

Serotype 1 ◽

Genomic Regions ◽

Genotype V ◽

Genotype Ii

Acute febrile patients presenting at hospitals in Douala, Cameroon between July and December 2020, were screened for dengue infections using RT-PCR on fragments of the 5’ and 3’ UTR genomic regions. In total, 12.8% (41/320) of cases examined were positive for dengue. Dengue virus 3 (DENV-3) was the most common serotype found (68.3%), followed by DENV-2 (19.5%) and DENV-1 (4.9%). Co-infections of DENV-3 and DENV-2 were found in 3 cases. Jaundice and headache were the most frequent clinical signs associated with infection and 56% (23/41) of the cases were co-infections with malaria. Phylogenetic analysis of the envelope gene identified DENV-1 as belonging to genotype V, DENV-2 to genotype II and DENV-3 to genotype III. The simultaneous occurrence of three serotypes in Douala reveals dengue as a serious public health threat for Cameroon and highlights the need for further epidemiological studies in the major cities of this region.

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Concurrent circulation of dengue serotype 1, 2 and 3 among acute febrile patients in Cameroon

10.1101/2021.05.10.21256254 ◽

2021 ◽

Author(s):

Huguette Dorine SIMO TCHETGNA ◽

Francine SADO YOUSSEU ◽

Basile Kamgang ◽

Armel TEDJOU ◽

Philip McCall ◽

...

Keyword(s):

Clinical Signs ◽

Epidemiological Studies ◽

Simultaneous Occurrence ◽

Envelope Gene ◽

Rt Pcr ◽

Genotype Iii ◽

Serotype 1 ◽

Genomic Regions ◽

Genotype V ◽

Genotype Ii

Acute febrile patients presenting at hospitals in Douala, Cameroon between July and December 2020, were screened for dengue infections using RT-PCR on fragments of the 5 and 3 UTR genomic regions. In total, 12.8% (41/320) of cases examined were positive for dengue. Dengue virus 3 (DENV-3) was the most common serotype found (68.3%), followed by DENV-2 (19.5%) and DENV-1 (4.9%). Co-infections of DENV-3 and DENV-2 were found in 3 cases. Jaundice and headache were the most frequent clinical signs associated with infection and 176 cases (55%) were co-infections with malaria. Phylogenetic analysis of the envelope gene identified DENV-1 as belonging to genotype V, DENV-2 to genotype II and DENV-3 to genotype III. The simultaneous occurrence of three serotypes in Douala reveals dengue as a serious public health threat for Cameroon and highlights the need for further epidemiological studies in the major cities of this region.

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Suicidal Behavior in German Adolescents

Zeitschrift für Kinder- und Jugendpsychiatrie und Psychotherapie ◽

10.1024/1422-4917/a000331 ◽

2015 ◽

Vol 43 (1) ◽

pp. 39-45 ◽

Cited By ~ 4

Author(s):

Joana Straub ◽

Ferdinand Keller ◽

Nina Sproeber ◽

Michael G. Koelch ◽

Paul L. Plener

Keyword(s):

Suicidal Behavior ◽

Suicide Attempts ◽

Depression Scale ◽

Epidemiological Studies ◽

Present Sample ◽

Manic Symptoms ◽

Symptoms Of Depression ◽

Adolescent Sample ◽

History Of ◽

Sum Scores

Objective: Research in adults has identified an association between bipolar disorder and suicidal behavior. This relationship, however, has been insufficiently investigated in adolescents to date. Methods: 1,117 adolescents from 13 German schools (mean age = 14.83, SD = .63; 52.7% females) completed an extended German version of the Center for Epidemiological Studies Depression Scale (CES-D), which assesses depressive and manic symptoms during the last week, as well as the Self-Harm Behavior Questionnaire (SHBQ) for the assessment of lifetime suicidal behavior. Results: In the present sample 39.4% of the girls and 23.1% of the boys reported lifetime suicidal thoughts and 7.1% of the girls as well as 3.9% of the boys a lifetime history of suicide attempts. 18.7% of the adolescent sample revealed elevated symptoms of depression and 9% elevated levels of mania symptoms. Elevated sum scores of depression and mania were associated with a higher number of suicidal ideations and suicide attempts. A block-wise regression analysis revealed that sum scores of depression and mania predicted suicidal ideations best. Concerning suicide attempts, the best predictors were age as well as depression and mania sum scores. Conclusions: Suicidal behavior was reported more often when adolescents demonstrate symptoms of mania as well as symptoms of depression than when they demonstrate only depressive symptoms. The presence of bipolar symptoms in adolescents should alert clinicians to the heightened possibility of suicidal behavior.

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High susceptibility to varicella among urban and rural pregnant women in South India: a brief report

Epidemiology and Infection ◽

10.1017/s0950268821000492 ◽

2021 ◽

Vol 149 ◽

Author(s):

Leeberk Raja Inbaraj ◽

Sindhulina Chandrasingh ◽

Nalini Arun Kumar ◽

Jothi Suchitra ◽

Abi Manesh

Keyword(s):

Pregnant Women ◽

South India ◽

Significant Proportion ◽

Prevalence Ratio ◽

Epidemiological Studies ◽

Lethal Outcome ◽

Factors Associated ◽

Rural And Urban ◽

History Of ◽

Secondary Hospital

Abstract Varicella infection during pregnancy has serious and/or difficult implications and in some cases lethal outcome. Though epidemiological studies in developing countries reveal that a significant proportion of patients may remain susceptible during pregnancy, such an estimate of susceptible women is not known in India. We designed this study to study the prevalence and factors associated with susceptibility to varicella among rural and urban pregnant women in South India. We prospectively recruited 430 pregnant women and analysed their serum varicella IgG antibodies as surrogates for protection. We estimated seroprevalence, the validity of self-reported history of chickenpox and factors associated with varicella susceptibility. We found 23 (95% CI 19.1–27.3) of women were susceptible. Nearly a quarter (22.2%) of the susceptible women had a history of exposure to chickenpox anytime in the past or during the current pregnancy. Self-reported history of varicella had a positive predictive value of 82.4%. Negative history of chickenpox (adjusted prevalence ratio (PR) 1.85, 95% CI 1.15–3.0) and receiving antenatal care from a rural secondary hospital (adjusted PR 4.08, 95% CI 2.1–7.65) were significantly associated with susceptibility. We conclude that high varicella susceptibility rates during pregnancy were noted and self-reported history of varicella may not be a reliable surrogate for protection.

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3D reconstruction of genomic regions from sparse interaction data

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab017 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Julen Mendieta-Esteban ◽

Marco Di Stefano ◽

David Castillo ◽

Irene Farabella ◽

Marc A Marti-Renom

Keyword(s):

3D Models ◽

Genomic Region ◽

Gene Promoters ◽

Chromosome Conformation ◽

The Matrix ◽

Chromatin Structural ◽

A Cell ◽

Similar Accuracy ◽

Genomic Regions ◽

Interaction Matrices

Abstract Chromosome conformation capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within the nucleus in a cell or a population of cells. Some of these 3C technologies retrieve interactions involving non-contiguous sets of loci, resulting in sparse interaction matrices. One of such 3C technologies is Promoter Capture Hi-C (pcHi-C) that is tailored to probe only interactions involving gene promoters. As such, pcHi-C provides sparse interaction matrices that are suitable to characterize short- and long-range enhancer–promoter interactions. Here, we introduce a new method to reconstruct the chromatin structural (3D) organization from sparse 3C-based datasets such as pcHi-C. Our method allows for data normalization, detection of significant interactions and reconstruction of the full 3D organization of the genomic region despite of the data sparseness. Specifically, it builds, with as low as the 2–3% of the data from the matrix, reliable 3D models of similar accuracy of those based on dense interaction matrices. Furthermore, the method is sensitive enough to detect cell-type-specific 3D organizational features such as the formation of different networks of active gene communities.

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Estimated Burden of Fungal Infections in Oman

Journal of Fungi ◽

10.3390/jof7010005 ◽

2020 ◽

Vol 7 (1) ◽

pp. 5

Author(s):

Abdullah M. S. Al-Hatmi ◽

Mohammed A. Al-Shuhoumi ◽

David W. Denning

Keyword(s):

Fungal Infection ◽

Fungal Infections ◽

Epidemiological Studies ◽

Vaginal Candidiasis ◽

Skin Infections ◽

Opportunistic Pathogens ◽

Fungal Rhinosinusitis ◽

Populations At Risk ◽

Different Populations ◽

Underlying Pathology

For many years, fungi have emerged as significant and frequent opportunistic pathogens and nosocomial infections in many different populations at risk. Fungal infections include disease that varies from superficial to disseminated infections which are often fatal. No fungal disease is reportable in Oman. Many cases are admitted with underlying pathology, and fungal infection is often not documented. The burden of fungal infections in Oman is still unknown. Using disease frequencies from heterogeneous and robust data sources, we provide an estimation of the incidence and prevalence of Oman’s fungal diseases. An estimated 79,520 people in Oman are affected by a serious fungal infection each year, 1.7% of the population, not including fungal skin infections, chronic fungal rhinosinusitis or otitis externa. These figures are dominated by vaginal candidiasis, followed by allergic respiratory disease (fungal asthma). An estimated 244 patients develop invasive aspergillosis and at least 230 candidemia annually (5.4 and 5.0 per 100,000). Only culture and microscopy are currently available for diagnosis, so case detection is suboptimal. Uncertainty surrounds these figures that trigger the need for urgent local epidemiological studies with more sensitive diagnostics.

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Systematic evidence from gene duplication and regulation

Australian Systematic Botany ◽

10.1071/sb9900145 ◽

1990 ◽

Vol 3 (1) ◽

pp. 145

Author(s):

DJ Colgan

Keyword(s):

Gene Duplication ◽

Evolutionary History ◽

Tandem Duplication ◽

Fragment Length Polymorphism ◽

Duplicate Genes ◽

Polymorphism Analysis ◽

Multiple Origins ◽

The Family ◽

History Of ◽

Phylogenetic Hypotheses

This paper is a review of the use of information regarding the presence of duplicate genes and their regulation in systematics. The review concentrates on data derived from protein electrophoresis and restriction fragment length polymorphism analysis. The appearance of a duplication in a subset of a group of species implies that the members of the subset belong to the same clade. Suppression of the duplication may render this clade apparently paraphyletic, but may itself be informative of relations within the lineage through patterns of loss of expression in all, or some tissues, or through restrictions of the formation of functional heteropolymers in polymeric enzymes. Examples are given of studies which have used such information to establish phylogenetic hypotheses at the family level, to identify an auto- or allo-polyploid origin of polyploid species and to determine whether there have been single or multiple origins of such species. The likelihood of homoplasy in the patterns of appearance and regulation of duplicates depends on the molecular basis of the duplication. In particular, the contrast between the expected consequences of tandem duplication and the expression of pseudogenes emphasises the value of determining the mechanism of the original duplication. Many instances of sporadic gene duplication are now known, and polyploidisation is a common event in the evolutionary history of both plants and animals. So the opportunities to discover duplicationrelated characters will arise in many systematic studies. A program is presented to increase the chances that such useful information will be recognisable during the studies.

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