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PubMed1989

[Cutaneous tuberculosis with multifocal visceral involvement].

The case of a young Senegalese man who developed a form of cutaneous tuberculosis associated with a disseminated disease, successfully treated with appropriate antitubercular chemotherapy is reported. We found Mycobacterium Microti in the cutaneous ulcers, the only organism isolated after many cultural and microscopical examinations of different exudates and tissues. This mycobacterium was considered up to now to be pathogenic to rodents, but not man. Its possible pathogenicity to man (under certain situations) is also suggested, and it is expected that this possibility will be supported by other reports in the near future. In addition, stress is laid on the problems of diagnosis and classification of the cutaneous tuberculosis, so uncommon in the Western Hemisphere, and its possible association with leprosy.

Antitubercular Agents↗

PubMed2006

Retinal nerve fiber layer analysis in the diagnosis of glaucoma.

PURPOSE OF REVIEW: The detection of optic disc and retinal nerve fiber layer damage and change is the cornerstone of glaucoma management. Assessment of the retinal nerve fiber layer for localized and diffuse damage has been traditionally based on clinical examination, with documentation of change primarily qualitative. With the latest improvements in optical imaging instruments, objective and quantitative measurements of the retinal nerve fiber layer are now possible. This review summarizes the results from recent cross-sectional studies evaluating the discriminating ability of automated retinal nerve fiber layer measurements to detect glaucoma, and from longitudinal studies assessing the ability to predict and monitor glaucomatous changes. RECENT FINDINGS: Numerous cross-sectional studies have documented good diagnostic accuracy of a scanning laser polarimeter (GDx VCC), the optical coherence tomograph (Stratus), and the Heidelberg Retina Tomograph retinal nerve fiber layer measurements for differentiating between healthy and glaucoma eyes. There are only limited data available on the ability of these retinal nerve fiber layer measurements to document change over time. SUMMARY: It is essential that the clinician understand the specific strengths and weaknesses of each technique so that only good quality retinal nerve fiber layer information will be used in conjunction with careful clinical examination and visual function testing for glaucoma management decisions. Longitudinal studies are needed to evaluate the ability of these instruments to document retinal nerve fiber layer change over time.

Diagnostic Imaging↗

PubMed1993

Sensitive detection and strain classification of Trypanosoma cruzi by amplification of a ribosomal RNA sequence.

A sequence of about 100 bp of the 24S alpha ribosomal RNA was investigated for sensitive detection of Trypanosoma cruzi. It was shown that the target sequence is specific for this parasite and no cross-reactivity was observed with different species of pathogenic Leishmania, two strains of Trypanosoma rangeli or human RNA. Amplification of the sequence was obtained by reverse transcription coupled to polymerase chain reaction. Following this procedure the equivalent to 0.1% of the nucleic acid content of a single parasite cell could be detected either by ethidium staining or blot hybridization. The distribution of the target sequence in sixteen strains of T. cruzi was investigated. Positive amplification was obtained for all samples employing the same oligonucleotides as primers. However, amplified fragments of 125 bp were obtained in eight strains, while fragments of 110 bp were detected in the remaining eight isolates. No amplification of both classes of fragments has been detected in any of the strains examined. Dimorphism in the target region was confirmed by hybridization to specific internal probes and sequencing, allowing the division of T. cruzi strains in two groups. It is proposed that sensitive parasite detection could be achieved by rRNA amplification followed by hybridization to two probes derived from the target sequences of both groups of T. cruzi strains. Furthermore, the sequence dimorphism found in this sequence opens the perspective of strain typing simultaneous with parasite detection.

Animals↗

PubMed2004

Identification of a highly divergent HIV type 2 and proposal for a change in HIV type 2 classification.

We report the complete genome sequence of a highly divergent strain of human immunodeficiency virus type 2 (HIV-2), 96FR12034, identified in France from a patient of West African origin. This lineage, H, represents only the third definitive instance of a monkey-to-human transfer of SIVsm that has given rise to pathogenic HIV-2. As the different "subtypes" of HIV-2 are analogous to the different groups of HIV-1 we propose that HIV-2 subtypes henceforth by renamed groups in agreement with the HIV Nomenclature Committee. The single-strain lineages C to G and the 96FR12034 lineage identified here should be considered only as putative groups until related strains are identified that confirm circulation of these viruses in the human population.

Adult↗

PubMed2025

Whole genome sequencing and phylogenetic classification accelerate the implementation of respiratory syncytial virus genomic surveillance in Canada: a pilot study.

UNLABELLED: Whole genome sequencing (WGS) has emerged as a powerful tool to facilitate the study of existing and emerging infectious diseases. WGS-based genomic surveillance provides information on the genetic diversity and tracks the evolution of important viral pathogens, including respiratory syncytial virus (RSV). Multiplex tiling polymerase chain reaction (PCR) assays have been used to facilitate sequencing of a variety of pathogens in support of genomics-based surveillance initiatives. We developed, optimized, and implemented multiplex tiling PCR assays for RSVA and RSVB capable of generating near-complete genomes in the majority of contemporaneous specimens tested. A pilot data set comprising 52 RSVA and 37 RSVB genomes derived from Canadian clinical specimens during the 2022-2023 respiratory virus season was used to perform phylogenetic analyses using both near-complete genome and glycoprotein (G) sequences. Overall, the RSV phylogenetic tree built with whole genomes showed identical lineage clusters as compared to the G gene but was more discriminatory. Moreover, the availability of complete genomes enables the identification of a broader range of mutations. For instance, mutations identified in the fusion protein among Canadian isolates tested here, including S377N, K272M, S276N, S211N, S206I, and S209Q, could affect the efficacy of current vaccines or antiviral-based therapeutics. In conclusion, our work reinforces other recent studies demonstrating the utility of multiplex tiling PCR assays to facilitate high-throughput WGS of RSV, which is capable of supporting enhanced genomic surveillance initiatives, as well as the more comprehensive genomic analyses required to inform public health strategies for the development and usage of vaccines and antiviral drugs. IMPORTANCE: We present assays to efficiently sequence genomes of RSVA and RSVB. This enables researchers and public health agencies to acquire high-quality genomic data using rapid and cost-effective approaches. Genomic data-based comparative analysis can be used to conduct surveillance and monitor circulating isolates for efficacy of vaccines and antiviral therapeutics.

Humans↗

PubMed2005

Complete small subunit rRNA gene sequence of the scuticociliate Miamiensis avidus pathogenic to olive flounder Paralichthys olivaceus.

Eight isolates of Miamiensis avidus (scuticociliates) were collected from olive flounder Paralichthys olivaceus with symptoms of severe ulcers and haemorrhages at several culture farms in 1999 and 2003. Cloned strains were produced and the complete small subunit ribosomal RNA gene (SSU rRNA) of each strain was sequenced for classification and phylogenic study. The SSU rRNA is 1759 bp in length and the sequence was deposited in the GenBank under accession number AY550080. All 8 strains exhibited the same sequence, but this sequence did not match any previously deposited scuticociliate SSU rRNA sequence. Phylogenetic analysis placed Miamiensis avidus in a sister lineage to Cohnilembus verminus, Pseudocohnilembus hargisi and P. marinus.

Animals↗

PubMed1977

[Classification of bronchial asthma].

The bronchial asthma disease is divided into 5 groups: 1. bronchial asthma caused by allergy, 2. bronchial asthma caused by infection, 3. bronchial asthma caused by physicochemical irritants, 4. bronchial asthma caused by exercise, 5. combination between the groups 1--4. Etiological factors, immunologic phenomena so far as known and pathogenic mechanisms are listed for each group and discussed.

Aspirin↗

PubMed2006

Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution.

Glutathione S-transferases (GSTs) comprise a diverse superfamily of enzymes found in organisms from all kingdoms of life. GSTs are involved in diverse processes, notably small-molecule biosynthesis or detoxification, and are frequently also used in protein engineering studies or as biotechnology tools. Here, we report the high-resolution X-ray structure of Atu5508 from the pathogenic soil bacterium Agrobacterium tumefaciens (atGST1). Through use of comparative sequence and structural analysis of the GST superfamily, we identified local sequence and structural signatures, which allowed us to distinguish between different GST classes. This approach enables GST classification based on structure, without requiring additional biochemical or immunological data. Consequently, analysis of the atGST1 crystal structure suggests a new GST class, distinct from previously characterized GSTs, which would make it an attractive target for further biochemical studies.

Agrobacterium tumefaciens↗

PubMed1999

Rapid subtyping of dengue viruses by restriction site-specific (RSS)-PCR.

Dengue is a major public health problem worldwide. It is caused by four dengue virus serotypes, each further divided into distinct genetic subtypes. Strain typing is important for understanding the epidemiology and viral factors associated with disease transmission. However, most of the existing subtyping methods are expensive and technically unwieldy for timely, practical applications in developing countries. Here we describe a simple, rapid, PCR-based subtyping method, restriction site-specific (RSS)-PCR, which we used to analyze dengue virus serotypes 2 and 3. For each serotype, four primers targeted to sequences spanning polymorphic endonuclease restriction sites in the envelope gene were used to reverse transcribe and amplify viral RNA. These RT-PCR products generated distinct electrophoretic band patterns for different strains. Analysis of 73 dengue-2 strains and 54 dengue-3 strains representing a broad geographic distribution over several decades revealed that the RSS-PCR fingerprints reproducibly fell into 7 and 3 groups, respectively. These groups correlated well with previous phylogenetic classifications. This one-step assay should be widely accessible and allow more detailed epidemiologic investigations in dengue-endemic countries. This novel PCR approach to subtyping organisms based on restriction site polymorphisms should be applicable to other pathogens.

Dengue Virus↗

PubMed2004

Leprosy (Hansen's Disease).

Leprosy (Hansen's disease) causes the most common treatable form of neuropathy in the world. Several endemic countries account for the majority of the world's cases and most of the cases seen in the US are amongst immigrants. However, endemic cases of leprosy occur in the US. The pathogen is Mycobacterium leprae, a slow-growing, obligate intracellular pathogen that consistently infects skin and peripheral nerves. The clinical appearance of the skin and neurologic deficits develop months to years after infection and are determined by the host's response to the infection. An individual's disease classification can change over time based on the immune status of the individual. Immune-mediated "reactional states" may also occur that require additional recognition and treatment. Varied in its manifestations, a successful treatment approach relies on proper recognition and classification of disease.

Journal Article↗

PubMed2004

Aspergillus flavus expressed sequence tags for identification of genes with putative roles in aflatoxin contamination of crops.

Aflatoxins, produced primarily by Aspergillus flavus and A. parasiticus, are among the most toxic and carcinogenic naturally occurring compounds. In an attempt to identify genes potentially involved in aflatoxin contamination of crops, and to better understand the biology of A. flavus, a large scale sequencing of A. flavus expressed sequence tags (EST) was conducted. The 5' ends of 26,110 cDNA clones from a normalized cDNA expression library were sequenced. After annotation, a total of 7218 unique ESTs in A. flavus were assembled into 3749 tentative concensus sequences and 3469 singleton sequences. The functional classifications of the genes or Gene Ontology (GO) terms were assigned to these ESTs. Genes potentially involved in the aflatoxin contamination process were identified in the ESTs sequenced. These include the aflatoxin biosynthetic pathway, signal transduction, global regulation, pathogenicity of the fungus, and stress response.

Aflatoxins↗

PubMed2005

Naip5/Birc1e and susceptibility to Legionella pneumophila.

Genetic analysis in mice is a powerful approach for the identification of genes and proteins that have a key role at the interface of the host-pathogen interaction. The Lgn1 locus has been found to control the intracellular replication of Legionella pneumophila in murine macrophages. Using functional complementation in transgenic mice, the Naip5/Birc1e gene has been identified as responsible for the Lgn1 effect. The classification of Naip5/Birc1e as a member of the NLR protein family suggests that Naip5/Birc1e acts as an intracellular sensor of L. pneumophila. The nature of the signal transduced by Naip5/Birc1e in response to Legionella products is of great interest but is currently unknown. Here, several possible scenarios are presented.

Animals↗

PubMed2003

The dual role of IL-10.

Classification of cytokines as pro-versus anti-inflammatory might not apply to the pleiotropic effects of interleukin-10 (IL-10). Several reports suggest that IL-10 enhances the function of natural killer cells, which leads, through pathogen destruction, to increased antigen availability. In addition, by inhibiting the maturation of antigen-presenting cells (APCs), IL-10 preserves their ability for antigen uptake while simultaneously hampering their migration to draining lymph nodes. This review suggests that this "antigen-loading" phase might constitute an important component of the innate immune reaction to a pathogen. Additional proinflammatory stimuli might subsequently lead to maturation of "loaded" APCs that could migrate to draining lymph nodes or recruit and activate adaptive immune effectors locally.

Animals↗

PubMed1997

Potato cysteine proteinase inhibitor gene family: molecular cloning, characterisation and immunocytochemical localisation studies.

Potato cysteine proteinase inhibitors (PCPIs) represent a distinct group of proteins as they show no homology to any other known cysteine proteinase inhibitor superfamilies, but they all belong to the Kunitz-type soybean trypsin inhibitor family. cDNA clones for five PCPIs have been isolated and sequenced. Amino acid substitutions occurring in the limited regions forming loops on the surface of these proteins suggest a further classification of PCPIs into three subgroups. Accumulation of PCPI was observed in vacuoles of stems after treatment with jasmonic acid (JA) using immunocytochemical localisation, implying that these inhibitors are part of a potato defence mechanism against insects and pathogens. Genomic DNA analysis show that PCPIs form a multigene family and suggest that their genes do not possess any introns.

Amino Acid Sequence↗

PubMed2025

Creating an atlas of variant effects to resolve variants of uncertain significance and guide cardiovascular medicine.

Cardiovascular diseases are leading global causes of death and disability, often presenting as interrelated phenotypes of atherosclerotic vascular disease, heart failure and arrhythmias. Cardiovascular diseases arise from interactions between environmental factors and predisposing genotypes and include common Mendelian lipid disorders, cardiomyopathies and arrhythmia syndromes. The identification of a pathogenic variant through genetic testing can inform disease diagnosis, risk prediction, treatment and family screening. However, a major roadblock in genomic medicine is that for many variants, especially missense variants, we lack sufficient evidence to enable a definitive classification, and therefore these variants are deemed as 'variants of uncertain significance'. In this Review, we describe how multiplexed assays of variant effects can enable the functional assessment of nearly all coding variants in a target sequence, potentially offering a proactive approach to identifying the functional significance of gene variants that are observed later in a patient. We discuss validation, including the role of in silico variant effect predictors, and how multiplexed experimental methods are informing cardiovascular disease biology and ultimately resolving the problem of variants of uncertain significance at scale.

Humans↗

PubMed2001

A novel actin-related protein gene of Colletotrichum gloeosporioides f. sp. malvae shows altered expression corresponding with spore production.

A novel actin-related protein (arp) was found in the plant pathogenic fungus, Colletotrichum gloeosporioides f. sp. malvae (Cgm), which causes anthracnose disease of round-leaved mallow (Malva pusilla). Sequence comparisons showed that this gene, arpA, belongs to the highly divergent 'other arps' category in the current arp classification system. ArpA is most similar to the arp11 gene of Mus musculus but has a unique structure with deletions at the C-terminus similar to that of the arp10 gene of Saccharomyces cerevisiae. A portion of another putative arp gene, arpB, was found immediately downstream of arpA. Expression of arpA was compared to the constitutively expressed Cgm actin gene, actA. In culture, the relative expression of arpA increased when growth conditions favored sporulation. During infection, arpA expression was greatest at the late necrotrophic phase, when sporulation occurred. Arps have been shown to be important in nuclear migration in fungal hyphae, and the expression pattern of arpA indicates that it may have a particular role during sporulation.

Actins↗

PubMed2026

Emerging genes implicated in human congenital heart disease: a 2023-2025 scoping review.

BACKGROUND: Congenital heart disease (CHD) is the most common major congenital anomaly and a leading cause of infant morbidity and mortality. The rapid expansion of genomic technologies has accelerated the discovery of rare genetic variants implicated in CHD pathogenesis. However, most individuals with CHD still lack an identifiable molecular etiology. The purpose of this scoping review is to systematically characterize genes reported in the recent literature as candidate CHD-associated genes and contextualize these findings within the stages of cardiac morphogenesis. METHODS: PubMed was searched using predefined terms related to CHD and genetic variants, supplemented by a prospectively maintained internal database. We included human studies published between January 2023 and December 2025 that identified pathogenic, likely pathogenic, or uncertain monogenic variants in at least one patient with CHD. Animal-only studies, chromosomal abnormalities, copy number variants, multigenic associations, transcriptomic/proteomic analyses, reviews, and maternal-only genetic studies were excluded. Gene-disease validity classifications were assigned using the Clinical Genome Resource (ClinGen) CHD Gene Curation Expert Panel framework. RESULTS: Of 2,834 screened articles, 391 studies met inclusion criteria, identifying 912 unique genes reported as candidate CHD-associated genes. Frequently reported genes included PTPN11, NOTCH1, GATA4, JAG1, MYH6, GATA6, and LZTR1. Identified genes spanned all major stages of cardiogenesis, including developmental priming, cardiac progenitor specification, left-right axis formation, neural crest migration, outflow tract development, septation, and postnatal structural remodeling. Studies increasingly implicated ciliary dysfunction, transcriptional regulation, ribosomal biology, and multigenic inheritance in CHD pathogenesis. Emerging methodologies included stem cell-derived cardiac models, machine learning-based gene prioritization, and epigenetic analyses. CONCLUSIONS: Recent literature substantially expands the catalog of candidate genes that may be associated with CHD and highlights the biologic complexity underlying cardiac morphogenesis. Integration of genomic, developmental, and functional approaches will be essential to improve mechanistic understanding, refine genetic counseling, and support future precision medicine strategies for CHD.

Cardiac development↗

PubMed1999

Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region.

The internal transcribed spacer (ITS) region, covering the ITS1, ITS2 and 5.8S ribosomal DNA was used to evaluate phylogenetic relationships within the fungal family Arthrodermataceae. Sequences of variable length, ranging between 522 and 684 base pairs were aligned. An unrooted consensus tree based on parsimony analysis showed Trichophyton to be polyphyletic, and Microsporum to be paraphyletic. Non-monophyly of these two genera is in conflict with traditional classification. But this relation is not strongly supported by bootstrap analysis. Phylogenetic analysis showed that the two known members of the genus Epidermophyton grouped widely apart from each other. Within Trichophyton, our results suggest a separation of human pathogenic species and primarily geophilic species. Bootstrap support for these two groups is fairly high and both groups are recognized by current taxonomy. Three lineages were revealed within the T. mentagrophytes species complex. Microsporum canis, M. audouinii and M. equinum were found to be closely related. The topology of the tree was robust to various methods of analysis (parsimony and distance) and a different weighting scheme. Weighting of transversions over transitions did not improve the status of poorly supported branches of the tree.

Animals↗