Central and Peripheral Nervous System Involvement in a Patient with Scrub Infection.

Scrub infection is an important differential of undifferentiated febrile illness in the subtropical and tropical countries. Neurological complications of scrub infection have a varied spectrum of presentation involving both the central nervous system, among which meningitis and meningoencephalitis are the most common presentations. The peripheral nervous system manifestations include Guillain-Barre syndrome (GBS) is not commonly reported. The coexistence of both central and peripheral involvement is rare, and we would like to report a case of a patient who was diagnosed with scrub infection and presented with meningoencephalitis and later developed GBS in the course of the disease on treatment for scrub infection.

Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates.

BACKGROUND: Var genes encode a family of virulence factors known as PfEMP1 (Plasmodium falciparum erythrocyte membrane protein 1) which are responsible for both antigenic variation and cytoadherence of infected erythrocytes. Although these molecules play a central role in malaria pathogenesis, the mechanisms generating variant antigen diversification are poorly understood. To investigate var gene evolution, we compared the variant antigen repertoires from three geographically diverse parasite isolates: the 3D7 genome reference isolate; the recently sequenced HB3 isolate; and the IT4/25/5 (IT4) parasite isolate which retains the capacity to cytoadhere in vitro and in vivo. RESULTS: These comparisons revealed that only two var genes (var1csa and var2csa) are conserved in all three isolates and one var gene (Type 3 var) has homologs in IT4 and 3D7. While the remaining 50 plus genes in each isolate are highly divergent most can be classified into the three previously defined major groups (A, B, and C) on the basis of 5' flanking sequence and chromosome location. Repertoire-wide sequence comparisons suggest that the conserved homologs are evolving separately from other var genes and that genes in group A have diverged from other groups. CONCLUSION: These findings support the existence of a var gene recombination hierarchy that restricts recombination possibilities and has a central role in the functional and immunological adaptation of var genes.

Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene.

Leishmania parasites (order Kinetoplastida, family Trypanosomatidae) cause a spectrum of human diseases ranging from asymptomatic to lethal. The approximately 33.6 Mb genome is distributed among 36 chromosome pairs that range in size from approximately 0.3 to 2.8 Mb. The complete nucleotide sequence of Leishmania major Friedlin chromosome 1 revealed 79 protein-coding genes organized into two divergent polycistronic gene clusters with the mRNAs transcribed towards the telomeres. We report here the complete nucleotide sequence of chromosome 3 (384 518 bp) and an analysis revealing 95 putative protein-coding ORFs. The ORFs are primarily organized into two large convergent polycistronic gene clusters (i.e. transcribed from the telomeres). In addition, a single gene at the left end is transcribed divergently towards the telomere, and a tRNA gene separates the two convergent gene clusters. Numerous genes have been identified, including those for metabolic enzymes, kinases, transporters, ribosomal proteins, spliceosome components, helicases, an RNA-binding protein and a DNA primase subunit.

Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project.

BACKGROUND: Seattle Biomedical Research Institute (SBRI) as part of the Leishmania Genome Network (LGN) is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is annotated using a combination of trained and untrained non-consensus gene-prediction algorithms with ARTEMIS, an annotation platform with rich and user-friendly interfaces. RESULTS: Here we describe a methodology used to import results from three different protein-coding gene-prediction algorithms (GLIMMER, TESTCODE and GENESCAN) into the ARTEMIS sequence viewer and annotation tool. Comparison of these methods, along with the CODONUSAGE algorithm built into ARTEMIS, shows the importance of combining methods to more accurately annotate the L. major genomic sequence. CONCLUSION: An improvised and powerful tool for gene prediction has been developed by importing data from widely-used algorithms into an existing annotation platform. This approach is especially fruitful in the Leishmania genome project where there is large proportion of novel genes requiring manual annotation.

Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER.

We compare the annotation of three complete genomes using the ab initio methods of gene identification GeneScan and GLIMMER. The annotation given in GenBank, the standard against which these are compared, has been made using GeneMark. We find a number of novel genes which are predicted by both methods used here, as well as a number of genes that are predicted by GeneMark, but are not identified by either of the nonconsensus methods that we have used. The three organisms studied here are all prokaryotic species with fairly compact genomes. The Fourier measure forms the basis for an efficient non-consensus method for gene prediction, and the algorithm GeneScan exploits this measure. We have bench-marked this program as well as GLIMMER using 3 complete prokaryotic genomes. An effort has also been made to study the limitations of these techniques for complete genome analysis. GeneScan and GLIMMER are of comparable accuracy insofar as gene-identification is concerned, with sensitivities and specificities typically greater than 0.9. The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a significant number of cases, similar results are provided by the two techniques. This suggests that there could be some as-yet unidentified additional genes in these three genomes, and also that some of the putative identifications made hitherto might require re-evaluation. All these cases are discussed in detail.

Congenital adrenal hyperplasia: long-term evaluation of feminizing genitoplasty and psychosocial aspects.

Analyzing the long-term outcome in females with congenital adrenal hyperplasia (CAH) is crucial to evaluate effectiveness of treatment strategies. The aim of the study was to evaluate the long-term results in patients with CAH after feminizing surgery from the pediatric intersex clinic. Of 163 patients of CAH being followed (1980-2005), 50 responded for review. The patients had undergone feminizing genitoplasty and hormonal therapy. Evaluation included filling a detailed questionnaire along with physical examination and a structured interview in privacy. Assessment was performed for cosmetic results (50), psychosocial adjustment (42) above 5-year age, and functional outcome in 19 cases above 14-year age. Mean age at clitoroplasty was 3.6 years (1-16 years) and at time of the study was 14.6 years (4-23 years), with a mean post-op follow up of 6 years after the final surgery (6 months-17 years). The cosmetic outcome of clitoroplasty was excellent in 37, satisfactory in 10, and poor in 3. Gender identity was female, male, and mixed in 45, 4, and 1, respectively. The attitude to self and life was positive in 36 and negative in 6. The functional outcome of vaginoplasty was satisfactory, unsatisfactory, and undetermined in 11, 4, and 4, respectively. Endocrine control was satisfactory in 36/50. A novel assessment system has been adopted for analyzing the results of clitoroplasty and vaginoplasty. Endocrine control and surgical treatment are complimentary to each other to achieve satisfactory results in majority of CAH patients.

Comparative genomics of trypanosomatid parasitic protozoa.

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease.

Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.

The genome of the kinetoplastid parasite, Leishmania major.

Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.

Diagnosis of symptomatic kala-azar by polymerase chain reaction using patient's blood.

BACKGROUND: Detection of Leishmania parasite in patients by classical methods at the early stage of infection is limited. Several studies have shown that polymerase chain reaction (PCR) is more effective for the diagnosis of visceral Leishmaniasis (VL) in clinical samples. The purpose of this study was to develop a simple, specific and sensitive PCR-based assay for detecting VL caused by any species of the genus Leishmania. MATERIAL/METHODS: We examined blood samples from twenty suspected kala-azar patients by polymerase chain reaction (PCR) using Leishmania specific primers. The results of the PCR-based procedure were compared with those of the Leishman-Donovan (LD) body test, immunodiffusion assay (IDA), and direct agglutination test (DAT). RESULTS: Out of the twenty samples, only five were found to be positive using all four tests. However, twelve samples were positive using the PCR assay, and among these only ten samples were found to be positive by LD body test of bone marrow smears. The results clearly indicated that, unlike the LD body test routinely used for diagnosis of kala-azar, the PCR assay is 100% sensitive. CONCLUSIONS: This method is very useful for primary screening of blood samples of patients suffering from kala-azar-like symptoms, especially in endemic areas.