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Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms

Kaur M, Blair J, Devkota B, Fortunato S, Clark D, Lawrence A, et al.

Am J Med Genet A, 2023 Aug;191(8):2113-2131.
PMID: 37377026 DOI: 10.1002/ajmg.a.63247

Cornelia de Lange Syndrome (CdLS) is a rare, dominantly inherited multisystem developmental disorder characterized by highly variable manifestations of growth and developmental delays, upper limb involvement, hypertrichosis, cardiac, gastrointestinal, craniofacial, and other systemic features. Pathogenic variants in genes encoding cohesin complex structural subunits and regulatory proteins (NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the major pathogenic contributors to CdLS. Heterozygous or hemizygous variants in the genes encoding these five proteins have been found to be contributory to CdLS, with variants in NIPBL accounting for the majority (>60%) of cases, and the only gene identified to date that results in the severe or classic form of CdLS when mutated. Pathogenic variants in cohesin genes other than NIPBL tend to result in a less severe phenotype. Causative variants in additional genes, such as ANKRD11, EP300, AFF4, TAF1, and BRD4, can cause a CdLS-like phenotype. The common role that these genes, and others, play as critical regulators of developmental transcriptional control has led to the conditions they cause being referred to as disorders of transcriptional regulation (or "DTRs"). Here, we report the results of a comprehensive molecular analysis in a cohort of 716 probands with typical and atypical CdLS in order to delineate the genetic contribution of causative variants in cohesin complex genes as well as novel candidate genes, genotype-phenotype correlations, and the utility of genome sequencing in understanding the mutational landscape in this population.

Matched MeSH terms: Phenotype
Fulltext Turner syndrome in diverse populations

Kruszka P, Addissie YA, Tekendo-Ngongang C, Jones KL, Savage SK, Gupta N, et al.

Am J Med Genet A, 2020 Feb;182(2):303-313.
PMID: 31854143 DOI: 10.1002/ajmg.a.61461

Turner syndrome (TS) is a common multiple congenital anomaly syndrome resulting from complete or partial absence of the second X chromosome. In this study, we explore the phenotype of TS in diverse populations using clinical examination and facial analysis technology. Clinical data from 78 individuals and images from 108 individuals with TS from 19 different countries were analyzed. Individuals were grouped into categories of African descent (African), Asian, Latin American, Caucasian (European descent), and Middle Eastern. The most common phenotype features across all population groups were short stature (86%), cubitus valgus (76%), and low posterior hairline 70%. Two facial analysis technology experiments were conducted: TS versus general population and TS versus Noonan syndrome. Across all ethnicities, facial analysis was accurate in diagnosing TS from frontal facial images as measured by the area under the curve (AUC). An AUC of 0.903 (p < .001) was found for TS versus general population controls and 0.925 (p < .001) for TS versus individuals with Noonan syndrome. In summary, we present consistent clinical findings from global populations with TS and additionally demonstrate that facial analysis technology can accurately distinguish TS from the general population and Noonan syndrome.

Matched MeSH terms: Phenotype
Genetic markers of an aboriginal Taiwanese population

Chen KH, Cann H, Chen TC, Van West B, Cavalli-Sforza L

Am. J. Phys. Anthropol., 1985 Mar;66(3):327-37.
PMID: 3857010

A group of Taiwan aborigines, the Toroko, was typed for 21 classical genetic loci. This is part of an ongoing program aimed at a comprehensive study of Taiwan aborigines. In this first paper a short summary of historical, archeological, and anthropological data in the literature is made, and results of the present survey are compared with older results from other aborigine tribes. An analysis of other neighboring populations from southeast Asia has also been carried out in order to give a preliminary answer to the question of origin of Taiwanese aborigines. Fifteen populations were studied for 13 loci by tree analysis, principal components, and isolation by distance. Tree analysis and principal component analysis gave results in fairly good agreement and indicate three major population clusters: a northeast cluster (Ainu, Korea, Japan, and Ryukyu); a southeast cluster (south China, Thailand, Vietnam, Philippines, Taiwan, and Toroko); and a third cluster including Malaya and Borneo. The positions of Polynesia, Micronesia, and Melanesia are somewhat peripheral. Analysis of the tree shows some potential cases of convergence, perhaps owing to admixture, and of divergence. The analysis of isolation by distance shows that geographic propinquity is a reasonably good predictor of general similarity in this area.

Matched MeSH terms: Phenotype
Differential Correlations Informed Metabolite Set Enrichment Analysis to Decipher Metabolic Heterogeneity of Disease

Lin G, Dong L, Cheng KK, Xu X, Wang Y, Deng L, et al.

Anal Chem, 2023 Aug 22;95(33):12505-12513.
PMID: 37557184 DOI: 10.1021/acs.analchem.3c02246

Metabolic pathways are regarded as functional and basic components of the biological system. In metabolomics, metabolite set enrichment analysis (MSEA) is often used to identify the altered metabolic pathways (metabolite sets) associated with phenotypes of interest (POI), e.g., disease. However, in most studies, MSEA suffers from the limitation of low metabolite coverage. Random walk (RW)-based algorithms can be used to propagate the perturbation of detected metabolites to the undetected metabolites through a metabolite network model prior to MSEA. Nevertheless, most of the existing RW-based algorithms run on a general metabolite network constructed based on public databases, such as KEGG, without taking into consideration the potential influence of POI on the metabolite network, which may reduce the phenotypic specificities of the MSEA results. To solve this problem, a novel pathway analysis strategy, namely, differential correlation-informed MSEA (dci-MSEA), is proposed in this paper. Statistically, differential correlations between metabolites are used to evaluate the influence of POI on the metabolite network, so that a phenotype-specific metabolite network is constructed for RW-based propagation. The experimental results show that dci-MSEA outperforms the conventional RW-based MSEA in identifying the altered metabolic pathways associated with colorectal cancer. In addition, by incorporating the individual-specific metabolite network, the dci-MSEA strategy is easily extended to disease heterogeneity analysis. Here, dci-MSEA was used to decipher the heterogeneity of colorectal cancer. The present results highlight the clustering of colorectal cancer samples with their cluster-specific selection of differential pathways and demonstrate the feasibility of dci-MSEA in heterogeneity analysis. Taken together, the proposed dci-MSEA may provide insights into disease mechanisms and determination of disease heterogeneity.

Matched MeSH terms: Phenotype
Fulltext Ancestral Variations in the Shape and Size of the Zygoma

Oettlé AC, Demeter FP, L'abbé EN

Anat Rec (Hoboken), 2017 01;300(1):196-208.
PMID: 28000408 DOI: 10.1002/ar.23469

The variable development of the zygoma, dictating its shape and size variations among ancestral groups, has important clinical implications and valuable anthropological and evolutionary inferences. The purpose of the study was to review the literature regarding the variations in the zygoma with ancestry. Ancestral variation in the zygoma reflects genetic variations because of genetic drift as well as natural selection and epigenetic changes to adapt to diet and climate variations with possible intensification by isolation. Prominence of the zygoma, zygomaxillary tuberosity, and malar tubercle have been associated with Eastern Asian populations in whom these features intensified. Prominence of the zygoma is also associated with groups from Eastern Europe and the rest of Asia. Diffusion of these traits occurred across the Behring Sea to the Arctic areas and to North and South America. The greatest zygomatic projections are exhibited in Arctic groups as an adaptation to extreme cold conditions, while Native South American groups also present with other features of facial robusticity. Groups from Australia, Malaysia, and Oceania show prominence of the zygoma to a certain extent, possibly because of archaic occupations by undifferentiated Southeast Asian populations. More recent interactions with Chinese groups might explain the prominent cheekbones noted in certain South African groups. Many deductions regarding evolutionary processes and diversifications of early groups have been made. Cognisance of these ancestral variations also have implications for forensic anthropological assessments as well as plastic and reconstructive surgery. More studies are needed to improve accuracy of forensic anthropological identification techniques. Anat Rec, 300:196-208, 2017. © 2016 Wiley Periodicals, Inc.

Matched MeSH terms: Phenotype
Association of azoospermia factor region deletions in infertile male subjects among Malaysians

Hussein AA, Vasudevan R, Patimah I, Prashant N, Nora FA

Andrologia, 2015 Mar;47(2):168-77.
PMID: 24528375 DOI: 10.1111/and.12240

Azoospermia factor region (AZF) deletions (AZFa, AZFb, AZFc and AZFd) in the Y chromosome were analysed in male infertility subjects in various populations with conflicting results. This study comprised of 54 infertile males and 63 fertile controls, and the frequency of AZFa, AZFb, AZFc and AZFd deletions were determined using conventional polymerase chain reaction (PCR) as well as real-time PCR-high resolution melting analysis-based methods. The results of this study showed that, three of 54 cases (5.55%) had AZF (a, b and c) deletions (two had AZFc and one had AZFa deletions). Four cases were found to have AZFd deletions (7.4%) with two of them being associated with AZFc deletions (P = 0.028). The frequency of AZF (a, b and c) deletions in Malaysian infertile male subjects was found to be comparable with other populations. AZFd deletions were found to be significant (P < 0.05) in male infertility and it may be associated with other types of AZF deletions.

Matched MeSH terms: Phenotype
The red cell 'X'-protein system in goats: evidence for a third allele in a Malaysian breed

Hasima N, Dhaliwal SS, Mukherjee TK

Anim. Genet., 1988;19(1):37-41.
PMID: 3377277

Genetic polymorphism of the 'X'-protein in red cells from Malaysian Katjang goats was demonstrated by starch gel electrophoresis at pH 7.3. Two new phenotypes were observed, suggesting that one new allele is involved. A new nomenclature for the 'X'-protein system in goats is proposed.

Matched MeSH terms: Phenotype
Fulltext Genome analysis of streptococcus gordonii sk12

Khairuldin AM, Ibrahim IK, Wakiyuddin SB, Z, Wenning, AO, Lesley, SJ, Nicholas, et al.

Ann Dent, 2014;21(2):17-26.
MyJurnal

The gram-positive, mesophilic and non-motile coccus Streptococcus gordonii is an important causative agent of infective endocarditis (IE). This pioneer species of dental plaque also causes bacteraemia in immune-supressed patients. In this study, we analysed the genome of a representative strain, Streptococcus gordonii SK12 that was originally isolated from the oral cavity. To gain a better understanding of the biology, virulence and phylogeny, of this potentially pathogenic organism, high-throughput Illumina HiSeq technology and different bioinformatics approaches were performed. Genome assembly of SK12 was performed using CLC Genomic Workbench 5.1.5 while RAST annotation revealed the key genomic features. The assembled draft genome of Streptococcus gordonii SK12 consists of 27 contigs, with a genome size of 2,145,851 bp and a G+C content of 40.63%. Phylogenetic inferences have confirmed that SK12 is closely related to the widely studied strain Streptococcus gordonii Challis. Interestingly, we predicted 118 potential virulence genes in SK12 genome which may contribute to bacterial pathogenicity in infective endocarditis. We also discovered an intact prophage which might be recently integrated into the SK12 genome. Examination of genes present in genomic islands revealed that this oral strain
might has potential to acquire new phenotypes/traits including strong defence system, bacitracin
resistance and collateral detergent sensitivity. This detailed analysis of S. gordonii SK12 further improves our understanding of the genetic make-up of S. gordonii as a whole and may help to elucidate how this species is able to transition between living as an oral commensal and potentially causing the lifethreatening condition infective endocarditis.

Matched MeSH terms: Phenotype
Distribution of group-specific component (Gc) subtypes in several Mongoloid populations of East Asia

Saha N

Ann Hum Biol, 1989 1 1;16(1):53-60.
PMID: 2919862

The distribution of group-specific component (Gc) subtypes was determined by isoelectric focussing in thin layer polyacrylamide gels of pH range 4 to 6.5, in a group of 2412 individuals from 10 Mongoloid populations of East Asia. The sample comprised 959 Chinese from different localities (Singapore, 249; Malaysia, 347; Taiwan, 246; Hong Kong, 57; Fuzhou mainland, 60), 338 Koreans, 277 Filipinos, 484 Thais, 330 Malays and 24 Indonesians. The Filipinos and Malays had lower frequencies of Gc2 (0.15 and 0.18) compared to other Mongoloid populations (0.23 to 0.32) and the Chinese (0.24 to 0.32). The frequencies of Gc1F varied from 0.39 to 0.49 in the Chinese and 0.35 to 0.52 in other Mongoloid populations. Low frequency of rarer variants was observed in most of the populations. The average frequency of Gc2 was higher in the Japanese (0.26 +/- 0.01) than in the Chinese (0.24 +/- 0.02), and in Mongoloids of East Asia (0.23 +/- 0.01) and South-East Asia (0.17 +/- 0.01). The average frequencies of Gc1F and Gc1S were similar in the Chinese and Japanese, whereas the Mongoloids of South-East Asia had a much higher frequency of Gc1F and a lower frequency of Gc1S than the Chinese, Japanese and East Asian Mongoloid populations.

Matched MeSH terms: Phenotype
Beta-thalassaemia mutations in west Malaysia: a new thalassaemia clinical score system

George E

Ann Acad Med Singap, 1994 Jan;23(1):89-93.
PMID: 7514384

The clinical severity of the mutations causing beta-thalassaemia in West Malaysia is presented. Thalassaemia clinical scores (Thal CS), a scoring system, has been formulated to predict clinical severity. It is the type of beta-thalassaemia mutation present that decides on the clinical phenotype. The most severe beta-thalassaemia mutation is assigned a score of 4. A score of 8 indicates a severe thalassaemia phenotype. Alpha-thalassaemia, increased synthesis of Hb F, and glucose-6-phosphate deficiency may ameliorate the clinical condition at phenotype level, and the co-inheritance of hereditary ovalocytosis aggravates it.

Matched MeSH terms: Phenotype
Hybrid acute leukaemia--a report of 3 cases

Ng SC, Wong TK, Lin HP

Ann Acad Med Singap, 1989 Nov;18(6):721-3.
PMID: 2624424

The simultaneous expression of both lymphoid and myeloid phenotypic features in acute leukaemia is rare. We report 3 cases of biphenotypic hybrid acute leukaemia seen in our institution. All 3 patients achieved remission with treatment for acute lymphoblastic leukaemia but two subsequently relapsed while on treatment. The hybrid acute leukaemias are important areas for further research both for delineation of basic biology and choice of optimal treatment.

Matched MeSH terms: Phenotype
Distribution of haptoglobins in different dialect groups of Chinese, Malays and Indians in Singapore

Saha N, Ong YW

Ann Acad Med Singap, 1984 Jul;13(3):498-501.
PMID: 6517517

A total of 870 subjects comprising 524 Chinese (from different dialect groups), 231 Malays and 115 Tamil Indians were investigated for the distribution of haptoglobin types and ABO blood groups. Haptoglobins were typed by PAG electrophoresis using discontinuous buffer system. The frequencies of Hp,1 Hp2 and Hp0 were found to be 0.330, 0.670 and 0.029 in Chinese; 0.298, 0.702 and 0.004 in Malays; and 0.167, 0.833 and 0.009 in Indians. The Hainanese had the highest frequency of Hp1 (0.375) followed by Cantonese (0.348), Teochew (0.333) and Hakkas (0.288). The distribution of all the phenotypes of haptoglobin was at equilibrium in all the population groups studied. No association of ABO blood groups was detected with the haptoglobin types. However, there was an excess of AB blood group in persons carrying Hp2 compared with those with Hp1.

Matched MeSH terms: Phenotype
Distribution of hair on the dorsum of the phalanges of the hand in a Chinese population from Malaysia

Dharap AS, Lim BC, Ong LB

Anthropol Anz, 1996 Dec;54(4):311-6.
PMID: 9008788

Hair distribution on the dorsum of phalanges of the hand was studied on 302 Chinese subjects (134 males and 168 females) randomly selected from the residents of Kota Bharu, Malaysia. Proximal phalangeal hair was seen on the dorsum of both hands in 99.3% of male subjects but in only 85.1% of female subjects. Chinese females showed a significantly lower (p < 0.05) incidence of proximal phalangeal hair on the hands than Chinese males. Comparison with other racial groups showed that Chinese females had significantly less (p < 0.05) hair on the proximal phalanges of the hands than Malay and African (Nigerian) females. The least common digital combination of proximal phalangeal hair in female subjects was the presence of proximal phalangeal hair only on the fourth digit (ring finger) and was noted in 0.6% of subjects. This has not been reported before. The frequency of middle phalangeal hair (MPH) distribution in Chinese falls between that in Malays and in Japanese which is probably explained by the fact that all these three racial groups originate from Asia. A study of digital combination of MPH in Chinese showed that the most common and the least common combinations in the Chinese differ considerably from those in other races. A total of 16 patterns of hair distribution was noted on the dorsum of the phalanges of the hands in Chinese subjects. Our study showed that though Chinese females had less digital hair on the hands than Chinese males, they showed a much larger variety of patterns of digital hair distribution than males.

Matched MeSH terms: Phenotype
Incidence, density and direction of hair on the dorsum of phalanges of the hands in Malays

Dharap AS, Varma SL, Chary TV

Anthropol Anz, 1995 Sep;53(3):269-76.
PMID: 7486886

In this study 200 Malay subjects (100 males and 100 females) were randomly selected from patients attending outpatient clinics of Hospital USM, Kelantan, Malaysia, to find out the incidence, density and direction of hair on the dorsum of phalanges of the hand. These features have not been studied so far in females nor has such a study been conducted in Malays. The probability of density of hair distribution among the digits of both hands showed significant correlation on proximal phalanges (p < 0.05) in both sexes. Significant correlation was not observed, however, in the middle phalangeal hair (MPH) of the hands. The direction of proximal phalangeal hair, from little finger to the thumb, showed significant changes from ulnar to radial in both sexes (p < 0.05). Identification of isolated digits, which is of medicolegal importance, would be more accurate if the direction and the density of hair on the digits are both considered together. MPH was present in 48% of males and in 33% of females studied. Comparisons with presence of MPH in other populations show that Malays are ethnically similar to other Asiatic populations.

Study site: utpatient clinics of Hospital USM, Kelantan, Malaysi

Matched MeSH terms: Phenotype
Five anthroposcopic traits of the ear in a Malaysian population

Dharap AS, Than M

Anthropol Anz, 1995 Dec;53(4):359-63.
PMID: 8579342

Five anthroposcopic traits concerning the ear, namely ear lobe attachment, position of ears, shape of the helix, presence of Darwin's tubercle and hairy ears have been studied in a Malay population from Malaysia. The results of the present study are compared with similar reports in other ethnic groups.

Matched MeSH terms: Phenotype
Fulltext Genotypic and phenotypic profiles of Escherichia coli isolates belonging to clinical sequence type 131 (ST131), clinical non-ST131, and fecal non-ST131 lineages from India

Hussain A, Ranjan A, Nandanwar N, Babbar A, Jadhav S, Ahmed N

Antimicrob Agents Chemother, 2014 Dec;58(12):7240-9.
PMID: 25246402 DOI: 10.1128/AAC.03320-14

In view of the epidemiological success of CTX-M-15-producing lineages of Escherichia coli and particularly of sequence type 131 (ST131), it is of significant interest to explore its prevalence in countries such as India and to determine if antibiotic resistance, virulence, metabolic potential, and/or the genetic architecture of the ST131 isolates differ from those of non-ST131 isolates. A collection of 126 E. coli isolates comprising 43 ST131 E. coli, 40 non-ST131 E. coli, and 43 fecal E. coli isolates collected from a tertiary care hospital in India was analyzed. These isolates were subjected to enterobacterial repetitive intergenic consensus (ERIC)-based fingerprinting, O typing, phylogenetic grouping, antibiotic sensitivity testing, and virulence and antimicrobial resistance gene (VAG) detection. Representative isolates from this collection were also analyzed by multilocus sequence typing (MLST), conjugation, metabolic profiling, biofilm production assay, and zebra fish lethality assay. All of the 43 ST131 E. coli isolates were exclusively associated with phylogenetic group B2 (100%), while most of the clinical non-ST131 and stool non-ST131 E. coli isolates were affiliated with the B2 (38%) and A (58%) phylogenetic groups, respectively. Significantly greater proportions of ST131 isolates (58%) than non-ST131 isolates (clinical and stool E. coli isolates, 5% each) were technically identified to be extraintestinal pathogenic E. coli (ExPEC). The clinical ST131, clinical non-ST131, and stool non-ST131 E. coli isolates exhibited high rates of multidrug resistance (95%, 91%, and 91%, respectively), extended-spectrum-β-lactamase (ESBL) production (86%, 83%, and 91%, respectively), and metallo-β-lactamase (MBL) production (28%, 33%, and 0%, respectively). CTX-M-15 was strongly linked with ESBL production in ST131 isolates (93%), whereas CTX-M-15 plus TEM were present in clinical and stool non-ST131 E. coli isolates. Using MLST, we confirmed the presence of two NDM-1-positive ST131 E. coli isolates. The aggregate bioscores (metabolite utilization) for ST131, clinical non-ST131, and stool non-ST131 E. coli isolates were 53%, 52%, and 49%, respectively. The ST131 isolates were moderate biofilm producers and were more highly virulent in zebra fish than non-ST131 isolates. According to ERIC-based fingerprinting, the ST131 strains were more genetically similar, and this was subsequently followed by the genetic similarity of clinical non-ST131 and stool non-ST131 E. coli strains. In conclusion, our data provide novel insights into aspects of the fitness advantage of E. coli lineage ST131 and suggest that a number of factors are likely involved in the worldwide dissemination of and infections due to ST131 E. coli isolates.

Matched MeSH terms: Phenotype
Fulltext Genetic mechanisms and correlated risk factors of antimicrobial-resistant ESKAPEE pathogens isolated in a tertiary hospital in Malaysia

Ngoi ST, Chong CW, Ponnampalavanar SSS, Tang SN, Idris N, Abdul Jabar K, et al.

Antimicrob Resist Infect Control, 2021 04 23;10(1):70.
PMID: 33892804 DOI: 10.1186/s13756-021-00936-5

BACKGROUND: Knowledge on the epidemiology, genotypic and phenotypic features of antimicrobial-resistant (AMR) ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli) and their association with hospital-acquired infections (HAIs) are limited in Malaysia. Therefore, we evaluated the AMR features and resistance mechanisms of the ESKAPEE pathogens collected in a tertiary hospital located in the capital of Malaysia.
METHODS: A total of 378 AMR-ESKAPEE strains were obtained based on convenience sampling over a nine-month study period (2019-2020). All strains were subjected to disk diffusion and broth microdilution assays to determine the antimicrobial susceptibility profiles. Polymerase chain reaction (PCR) and DNA sequence analyses were performed to determine the AMR genes profiles of the non-susceptible strains. Chi-square test and logistic regression analyses were used to correlate the AMR profiles and clinical data to determine the risk factors associated with HAIs.
RESULTS: High rates of multidrug resistance (MDR) were observed in A. baumannii, K. pneumoniae, E. coli, and S. aureus (69-89%). All organisms except E. coli were frequently associated with HAIs (61-94%). Non-susceptibility to the last-resort drugs vancomycin (in Enterococcus spp. and S. aureus), carbapenems (in A. baumannii, P. aeruginosa, and Enterobacteriaceae), and colistin (in Enterobacteriaceae) were observed. Both A. baumannii and K. pneumoniae harbored a wide array of extended-spectrum β-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaOXA). Metallo-β-lactamase genes (blaVEB, blaVIM, blaNDM) were detected in carbapenem-resistant strains, at a higher frequency compared to other local reports. We detected two novel mutations in the quinolone-resistant determining region of the gyrA in fluoroquinolone-resistant E. coli (Leu-102-Ala; Gly-105-Val). Microbial resistance to ampicillin, methicillin, and cephalosporins was identified as important risk factors associated with HAIs in the hospital.
CONCLUSION: Overall, our findings may provide valuable insight into the microbial resistance pattern and the risk factors of ESKAPEE-associated HAIs in a tertiary hospital located in central Peninsular Malaysia. The data obtained in this study may contribute to informing better hospital infection control in this region.

Matched MeSH terms: Phenotype
Amycolatopsis vastitatis sp. nov., an isolate from a high altitude subsurface soil on Cerro Chajnantor, northern Chile

Idris H, Nouioui I, Pathom-Aree W, Castro JF, Bull AT, Andrews BA, et al.

Antonie Van Leeuwenhoek, 2018 Sep;111(9):1523-1533.
PMID: 29428970 DOI: 10.1007/s10482-018-1039-3

The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5T, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H4) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina, its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5T (= NCIMB 14970T = NRRL B-65279T).

Matched MeSH terms: Phenotype
Phenotypic and genotypic characteristics and epidemiological significance of ctx+ strains of Vibrio cholerae isolated from seafood in Malaysia

Chen CH, Shimada T, Elhadi N, Radu S, Nishibuchi M

Appl Environ Microbiol, 2004 Apr;70(4):1964-72.
PMID: 15066786

Of 97 strains of Vibrio cholerae isolated from various seafoods in Malaysia in 1998 and 1999, 20 strains carried the ctx gene and produced cholera toxin. Fourteen, one, and five of these toxigenic strains belonged to the O139, O1 Ogawa, and rough serotypes, respectively. The rough strains had the rfb gene of the O1 serotype. The toxigenic strains varied in their biochemical characteristics, the amount of cholera toxin produced, their antibiograms, and the presence or absence of the pTLC plasmid sequence. DNA fingerprinting analysis by arbitrarily primed PCR, ribotyping, and a pulsed-field gel electrophoresis method classified the toxigenic strains into 3, 7, and 10 types, respectively. The relatedness of these toxigenic strains to clinical strains isolated in other countries and from international travelers was examined by using a dendrogram constructed from the pulsed-field gel electrophoresis profiles. The results of the examination of the antibiogram and the possession of the toxin-linked cryptic plasmid were consistent with the dendrogram-based relatedness: the O139 strains isolated from Malaysian seafoods could be separated into two groups that appear to have been introduced from the Bengal area independently. The rough strains of Malaysian seafood origin formed one group and belonged to a cluster unique to the Thailand-Malaysia-Laos region, and this group may have persisted in this area for a long period. The single O1 Ogawa strain detected in Malaysian seafood appears to have an origin and route of introduction different from those of the O139 and the rough strains.

Matched MeSH terms: Phenotype
Fulltext Mitochondrial Respiration Is Reduced in Atherosclerosis, Promoting Necrotic Core Formation and Reducing Relative Fibrous Cap Thickness

Yu EPK, Reinhold J, Yu H, Starks L, Uryga AK, Foote K, et al.

Arterioscler Thromb Vasc Biol, 2017 12;37(12):2322-2332.
PMID: 28970293 DOI: 10.1161/ATVBAHA.117.310042

OBJECTIVE: Mitochondrial DNA (mtDNA) damage is present in murine and human atherosclerotic plaques. However, whether endogenous levels of mtDNA damage are sufficient to cause mitochondrial dysfunction and whether decreasing mtDNA damage and improving mitochondrial respiration affects plaque burden or composition are unclear. We examined mitochondrial respiration in human atherosclerotic plaques and whether augmenting mitochondrial respiration affects atherogenesis.
APPROACH AND RESULTS: Human atherosclerotic plaques showed marked mitochondrial dysfunction, manifested as reduced mtDNA copy number and oxygen consumption rate in fibrous cap and core regions. Vascular smooth muscle cells derived from plaques showed impaired mitochondrial respiration, reduced complex I expression, and increased mitophagy, which was induced by oxidized low-density lipoprotein. Apolipoprotein E-deficient (ApoE-/-) mice showed decreased mtDNA integrity and mitochondrial respiration, associated with increased mitochondrial reactive oxygen species. To determine whether alleviating mtDNA damage and increasing mitochondrial respiration affects atherogenesis, we studied ApoE-/- mice overexpressing the mitochondrial helicase Twinkle (Tw+/ApoE-/-). Tw+/ApoE-/- mice showed increased mtDNA integrity, copy number, respiratory complex abundance, and respiration. Tw+/ApoE-/- mice had decreased necrotic core and increased fibrous cap areas, and Tw+/ApoE-/- bone marrow transplantation also reduced core areas. Twinkle increased vascular smooth muscle cell mtDNA integrity and respiration. Twinkle also promoted vascular smooth muscle cell proliferation and protected both vascular smooth muscle cells and macrophages from oxidative stress-induced apoptosis.
CONCLUSIONS: Endogenous mtDNA damage in mouse and human atherosclerosis is associated with significantly reduced mitochondrial respiration. Reducing mtDNA damage and increasing mitochondrial respiration decrease necrotic core and increase fibrous cap areas independently of changes in reactive oxygen species and may be a promising therapeutic strategy in atherosclerosis.

Matched MeSH terms: Phenotype

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