Mycobacterium tuberculosis strain lineage in mixed tribal population across India and Andaman Nicobar Island

In India, the tribal population constitutes almost 8.6% of the nation's total population. Despite their large presence, there are only a few reports available on Mycobacterium tuberculosis (M. tb) strain prevalence in Indian tribal communities considering the mobile nature of this population and also the influence of the mainstream populations they coexist within many areas for their livelihood. This study attempts to provide critical information pertaining to the TB strain diversity, its public health implications, and distribution among the tribal population in eleven Indian states and Andaman & Nicobar (A&N) Island. The study employed a population-based molecular approach. Clinical isolates were received from 66 villages (10 states and Island) and these villages were selected by implying situation analysis. A total of 78 M. tb clinical isolates were received from 10 different states and A&N Island. Among these, 16 different strains were observed by spoligotyping technique. The major M. tb strains spoligotype belong to the Beijing, CAS1_DELHI, and EAI5 family of M. tb strains followed by EAI1_SOM, EAI6_BGD1, LAM3, LAM6, LAM9, T1, T2, U strains. Drug-susceptibility testing (DST) results showed almost 15.4% of clinical isolates found to be resistant to isoniazid (INH) or rifampicin (RMP) + INH. Predominant multidrug-resistant (MDR-TB) isolates seem to be Beijing strain. Beijing, CAS1_DELHI, EAI3_IND, and EAI5 were the principal strains infecting mixed tribal populations across India. Despite the small sample size, this study has demonstrated higher diversity among the TB strains with significant MDR-TB findings. Prevalence of Beijing MDR-TB strains in Central, Southern, Eastern India and A&N Island indicates the transmission of the TB strains.

Edoxaban for treatment of venous thromboembolism in patient groups with different types of cancer: Results from the Hokusai VTE Cancer study

BACKGROUND

The safety and efficacy of edoxaban and dalteparin is unclear for several cancer groups.

METHODS

We evaluated the occurrence of the primary outcome in large cancer groups. The primary outcome was the composite of recurrent VTE or major bleeding over 12 months.

RESULTS

In patients with gastrointestinal cancer, the primary outcome occurred in 19.4% patients given edoxaban and in 15.0% given dalteparin (risk difference [RD], 4.4%; 95%-CI, -4.1% to 12.8%). The corresponding rates for edoxaban and dalteparin were 10.4% and 10.7% for lung cancer (RD, -0.3%; 95%-CI, -10.0% to 9.5%), 13.6% and 12.5% for urogenital cancer (RD, 1.1; 95%-CI, -10.1-12.4), 3.1% and 11.7% for breast cancer (RD, -8.6; 95%-CI, -19.3-2.2), 8.9% and 10.9% for hematological malignancies (RD, -2.0; 95%-CI, -13.1-9.1), and 10.4% and 17.4% for gynecological cancer (RD, -7.0; 95%-CI, -19.8-5.7). In the subgroup of gastrointestinal cancer, edoxaban was associated with a 3.5% lower absolute risk of recurrent VTE and a 7.9% higher risk of major bleeding.

CONCLUSION

Edoxaban has a similar risk-benefit ratio to dalteparin in most cancer groups. In those with gastrointestinal cancer, the lower risk of recurrent VTE and the advantages of oral therapy need to be balanced against the increased risk of major bleeding.

Treatment algorithm in cancer-associated thrombosis: Canadian expert consensus

Management of anticoagulant therapy for the treatment of venous thromboembolism (vte) in cancer patients is complex because of an increased risk of recurrent vte and major bleeding complications in those patients relative to the general population. Subgroups of patients with cancer also show variation in their risk for recurrent vte and adverse bleeding events. Accordingly, a committee of 10 Canadian clinical experts developed the consensus risk- stratification treatment algorithm presented here to provide guidance on tailoring anticoagulant treatment choices for the acute and extended treatment of symptomatic and incidental vte, to prevent recurrent vte, and to minimize the bleeding risk in patients with cancer. During a 1-day live meeting, a systematic review of the literature was performed, and a draft treatment algorithm was developed. The treatment algorithm was refined through the use of a Web-based platform and a series of online teleconferences. Clinicians using this treatment algorithm should consider the bleeding risk, the type of cancer, and the potential for drug-drug interactions in addition to informed patient preference in determining the most appropriate treatment for patients with cancer-associated thrombosis. Anticoagulant therapy should be regularly reassessed as the patient's cancer status and management change over time.

Characteristics predicting outcomes of allogeneic stem-cell transplantation in relapsed acute myelogenous leukemia

BACKGROUND

Allogeneic hematopoietic stem-cell transplantation (ahsct) is associated with significant morbidity and mortality, but it can cure carefully selected patients with acute myeloid leukemia (aml) in second remission (cr2). In a cohort of patients with aml who underwent ahsct in cr2, we determined the pre-transplant factors that predicted for overall survival (os), relapse, and non-relapse mortality. We also sought to validate the prognostic risk groups derived by Michelis and colleagues in this independent population.

METHODS

In a retrospective chart review, we obtained data for 55 consecutive patients who underwent ahsct for aml in cr2. Hazard ratios were used to describe the independent effects of pre-transplant variables on outcome, and Kaplan-Meier curves were used to assess outcomes in the three prognostic groups identified by Michelis and colleagues.

RESULTS

At 1, 3, and 5 years post-transplant, os was 60%, 45.5%, and 37.5% respectively. Statistically significant differences in os, relapse mortality, and non-relapse mortality were not identified between the prognostic risk groups identified by Michelis and colleagues. Women were less likely than men to relapse, and a modified European Society for Blood and Marrow Transplantation (mebmt) score of 3 or less was associated with a lower non-relapse mortality.

CONCLUSIONS

The 37.5% 5-year os in this cohort suggests that, compared with other options, ahsct offers patients with aml in cr2 a better chance of cure. Our study supports the use of the mebmt score to predict non-relapse mortality in this population.

Disorders of the lymphatic system of the abdomen

The lymphatic system of the abdomen comprises of the cisterna chyli, its major and minor lymphatic tributaries, and lymph nodes. Disorders of the lymphatic system of the abdomen are rarely encountered and consist of primary and secondary types. Abdominal lymphangiomas constitute the majority and have characteristic imaging features. Complicated lymphangiomas may pose a diagnostic dilemma. Generalised systemic lymphangiomatosis is a rare condition and affects major organs with a poor prognosis. Retroperitoneal lymphangiectasia in the appropriate setting might predict underlying infection, such as filariasis. Other acquired conditions include iatrogenic or treatment-induced chylocoele. Chylous ascites can be secondary to multiple causes and can be confirmed by biochemical testing and lymphangiogram in appropriate settings.

Sonographic detection of tracheal or esophageal intubation: A cadaver study

Background:

The correct position of the endotracheal tube is confirmed by various modalities, most of which are not entirely reliable. Ultrasound is now increasingly available to anesthesiologists in the operating theater and is an attractive alternative. To investigate the usefulness of sonography in identifying the correct tracheal tube position in human cadavers.

Materials and Methods:

Endotracheal tubes placed randomly into trachea or esophagus was identified with a linear ultrasound probe placed transversely just above the suprasternal notch by a single anesthesiologist.

Results:

Of the 100 intubations performed at random, 99 were correctly identified to give a sensitivity of 100% and a specificity of 97.9%.

Conclusion:

Sonography is a useful technique to identify correct position of the tracheal tube.

Rivaroxaban for treatment of suspected or confirmed heparin-induced thrombocytopenia study

Essentials Heparin-induced thrombocytopenia (HIT) is a thrombogenic condition that is difficult to treat. We evaluated rivaroxaban as a treatment option in patients with suspected or confirmed HIT. One patient had recurrent thrombosis and 9/10 patients with thrombocytopenia had platelet recovery. Rivaroxaban may be an effective and safe treatment option for HIT.

SUMMARY

Background Rivaroxaban is a direct oral anti-Xa inhibitor that has the potential to greatly simplify treatment of heparin-induced thrombocytopenia (HIT). Objectives To evaluate the efficacy and safety of rivaroxaban in this patient population, we conducted a multicenter, single-arm, prospective cohort study of patients with suspected or confirmed HIT. Patients/Methods Twenty-two consecutive adults with suspected or confirmed HIT received rivaroxaban 15 mg bid until a local HIT assay result was available. Participants with a positive local assay result continued rivaroxaban 15 mg bid until platelet recovery (or until day 21 if they had acute thrombosis at study entry), then stepped down to rivaroxaban 20 mg daily until day 30. Results and Conclusions The primary outcome measure, incidence of new symptomatic, objectively-confirmed venous and arterial thromboembolism at 30 days, occurred in one HIT-positive participant (4.5%; 95% confidence interval [CI], 0-23.5%) and one HIT-positive participant required limb amputation despite platelet recovery. Platelet recovery was achieved in nine out of 10 HIT-positive patients with thrombocytopenia. Rivaroxaban appears to be effective for treating patients with confirmed HIT, although the small number of patients enrolled limits precision.

Canadian consensus recommendations on the management of venous thromboembolism in patients with cancer. Part 2: treatment

Patients with cancer are at increased risk of venous thromboembolism (vte). Anticoagulation therapy is used to treat vte; however, patients with cancer have unique clinical circumstances that can often make decisions surrounding the administration of therapeutic anticoagulation complicated. No national Canadian guidelines on the management of established cancer-associated thrombosis have been published. We therefore aimed to develop a consensus-based, evidence-informed guideline on the topic. PubMed was searched for clinical trials and meta-analyses published between 2002 and 2013. Reference lists of key articles were hand-searched for additional publications. Content experts from across Canada were assembled to review the evidence and make recommendations. Low molecular weight heparin is the treatment of choice for cancer patients with established vte. Direct oral anticoagulants are not recommended for the treatment of vte at this time. Specific clinical scenarios, including the presence of an indwelling venous catheter, renal insufficiency, and thrombocytopenia, warrant modifications in the therapeutic administration of anticoagulation therapy. Patients with recurrent vte should receive extended (>3 months) anticoagulant therapy. Incidental vte should generally be treated in the same manner as symptomatic vte. There is no evidence to support the monitoring of anti-factor Xa levels in clinically stable cancer patients receiving prophylactic anticoagulation; however, levels of anti-factor Xa could be checked at baseline and periodically thereafter in patients with renal insufficiency. Follow-up and education about the signs and symptoms of vte are important components of ongoing patient care.

Canadian consensus recommendations on the management of venous thromboembolism in patients with cancer. Part 1: prophylaxis

Patients with cancer are at increased risk of venous thromboembolism (vte). Anticoagulation therapy has been shown to prevent vte; however, unique clinical circumstances in patients with cancer can often complicate the decisions surrounding the administration of prophylactic anticoagulation. No national Canadian guidelines on the prevention of cancer-associated thrombosis have been published. We therefore aimed to develop a consensus-based, evidence-informed guideline on the topic. PubMed was searched for clinical trials and meta-analyses published between 2002 and 2013. Reference lists of key articles were hand-searched for additional publications. Content experts from across Canada were assembled to review the evidence and make recommendations. Low molecular weight heparin can be used prophylactically in cancer patients at high risk of developing vte. Direct oral anticoagulants are not recommended for vte prophylaxis at this time. Specific clinical scenarios, including renal insufficiency, thrombocytopenia, liver disease, and obesity can warrant modifications in the administration of prophylactic anticoagulant therapy. There is no evidence to support the monitoring of anti-factor Xa levels in clinically stable cancer patients receiving prophylactic anticoagulation; however, factor Xa levels could be checked at baseline and periodically in patients with renal insufficiency. The use of anticoagulation therapy to prolong survival in cancer patients without the presence of risk factors for vte is not recommended.

Clinical challenges in patients with cancer-associated thrombosis: Canadian expert consensus recommendations

Venous thromboembolism is a common complication in cancer patients, and thromboembolism is the second most common cause of death after cancer progression. A number of clinical practice guidelines provide recommendations for the management of cancer-associated thrombosis. However, the guidelines lack recommendations covering commonly encountered clinical challenges (for example, thrombocytopenia, recurrent venous thromboembolism, etc.) for which little or no evidence exists. Accordingly, recommendations were developed to provide expert guidance to medical oncologists and other health care professionals caring for patients with cancer-associated thrombosis. The current expert consensus was developed by a team of 21 clinical experts. For each identified clinical challenge, the literature in medline, embase, and Evidence Based Medicine Reviews was systematically reviewed. The quality of the evidence was assessed, summarized, and graded. Consensus statements were generated, and the experts voted anonymously using a modified Delphi process on their level of agreement with the various statements. Statements were progressively revised through separate voting iterations and were then finalized. Clinicians using these recommendations and suggestions should tailor patient management according to the risks and benefits of the treatment options, patient values and preferences, and local cost and resource allocations.

Preparation and evaluation of transdermal drug delivery system of etoricoxib using modified chitosan

In the present investigation chitosan has been chemically modified by treating with two different aldehydes like acetaldehyde and propionaldehyde to form Schiff’s bases. Schiff’s bases of chitosan with acetaldehyde and propionaldehyde were named as polymer A and polymer B, respectively. Fourier Transform Infra Red (FTIR) spectral data have confirmed the reaction carried out on chitosan. Drug free polymeric films of chitosan, chemically modified chitosan and chitosan/hydroxypropylmethylcellulose blend were prepared and evaluated for various physicochemical characters. Further, the films were incorporated with anti-inflammatory drug, etoricoxib using glycerol as plasticizer. The drug loaded films were cross-linked with sodium citrate and studied for permeation characteristics across dialysis membrane and rat skin. All the films were evaluated for bursting strength, swelling index, moisture uptake, thickness uniformity, drug content uniformity, tensile strength, percent elongation at break, percent flatness, water vapour transmission rate and in vitro drug permeation study.

Chlamydomonas reinhardtii, a model system for functional validation of abiotic stress responsive genes

Stress tolerance is a multigenic character and there are many stress responsive genes, which are stress specific. Although many of these have been cloned, their functional significance remains fragmentary. Hence it is important to identify the relevant stress genes involved in altering the metabolism for adaptation. Overexpression is one of the several approaches and Chlamydomonas is a suitable system to study the functional relevance of stress genes. Stress responses can only be assessed on prior exposure to sublethal induction stress. In this study the acclimation response of Chlamydomonas was assessed for different abiotic stresses using physiological screens like chlorophyll stability, membrane damage, cell viability, accumulation of free radicals, survival and recovery growth. We demonstrate that Chlamydomonas responds to diverse stresses and is a potential system to study the relevance of stress genes. The relevance of choline oxidase A (codA), a key enzyme in glycinebetaine biosynthesis, was examined by developing transformants expressing codA gene from Arthrobacter globiformis. Southern positive transformants showed enhanced accumulation of glycinebetaine. The transformants also showed enhanced growth under salinity, high light coupled with methylviologen-induced oxidative stress, high temperature and cold stress. However the transgenics were not tolerant to PEG-mediated simulated osmotic stress, LiCl, menadione and UV stress. Increased cell survival and decreased chlorophyll degradation in transformants under acclimated conditions further confirmed the relevance of codA in imparting stress tolerance. Our results indicated that the relevance of stress responsive genes can be efficiently validated for diverse abiotic stresses using Chlamydomonas system.

Production of exopolysaccharides by Agrobacterium sp. CFR-24 using coconut water - a byproduct of food industry

AIMS

The work is intended to explore the suitability of underutilized coconut water (a byproduct of food industry) for the production of exopolysaccharides (EPS) by Agrobacterium sp. CFR 24.

METHODS AND RESULTS

Besides checking the suitability of coconut water for the production of water-soluble (WS) and water-insoluble (WIS) EPS, certain fermentation parameters, such as initial pH, incubation period and kinetics of EPS production were investigated. The coconut water medium was found to support the production of both types of EPS. The optimal initial pH and temperature was found to be 6.0 and 30 degrees C, respectively. In shake flask (150 rev min(-1)) studies, high-cell density inoculum resulted in the production of 11.50 g l(-1) of WIS-EPS and 4.01 g l(-1) WS-EPS after 72 and 96 h of fermentation, respectively.

CONCLUSIONS

Coconut water was found suitable for the production of microbial EPS by Agrobacterium sp. CFR 24 strain. Under optimum conditions, it produced a good amount of WIS-EPS, which is comparable with that of the sucrose medium (11 g l(-1)).

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report on the use of coconut water as a fermentation medium for the production of any microbial EPS. Besides producing value-added products, use of this food industry byproduct, which is often being drained out, can significantly reduce the problem of environmental pollution.

MURCS association

The MURCS association i.e. MUllerian duct aplasia, Renal aplasia, Cervicothoracic Somite dysplasia is a rare developmental disorder. The authors report a case of MURCS association with supernumerary ribs in a 7-month-old infant who presented with failure to thrive.

Cytogenetic, fluorescent in situ hybridization & reverse transcriptase-polymerase chain reaction analysis in acute promyelocytic leukaemia patients

BACKGROUND & OBJECTIVES

The presence of t(15;17) or PML-RAR alpha fusion transcript is the diagnostic hallmark of patients with acute promyelocytic leukaemia (APL). Cytogenetic (CG), fluorescent in situ hybridization (FISH) and reverse transcriptase-polymerase chain reaction (RT-PCR) are mainly the techniques used for detecting this abnormality. The objective of this study was to compare and assess the role of CG, FISH and RT-PCR in the diagnosis of APL.

METHODS

CG, FISH and RT-PCR analysis were performed in 29 patients with APL (28 M3, 1 M3v; 27 studied at diagnosis and 2 at relapse).

RESULTS

Karotypes obtained in 25 patients revealed t(15;17) in 21 normal karyotype in 3 and trisomy 8 in 1 patient. In 26 patients FISH was positive for PML-RAR alpha fusion in both interphase (IP) and metaphase, two were negative and one patient had no cells for FISH analysis. IP FISH confirmed the fusion of PML-RAR alpha in all patients with t(15;17) detected by CG. RT-PCR was positive in the 22 patients analyzed (7 patients did not have RT-PCR). PCR was positive in the 3 patients with cytogenetically normal karyotypes and in one patient when karyotyping was a failure. CG detected 21 (72.4%) patients with t(15;17) of which additional chromosomal abnormalities were detected in 20 per cent of patients with successful karyotype.

INTERPRETATION & CONCLUSION

FISH and RT-PCR were useful in detecting PML-RAR alpha fusion in cytogenetically normal patients and those in when karyotyping was a failure and can be used in routine analysis for rapid confirmation of t(15;17) in patients with acute myeloid leukaemia.

Vectorial efficacy of Phlebotomus argentipes in Kala-azar endemic foci of Bihar (India) under natural and artificial conditions

Ability of Phlebotomus argentipes to acquire Leishmania donovani the causative agent of Indian Kala-azar was evaluated in the laboratory. Flies were fed artificially on infected blood suspensions, using a chick-skin-membrane feeding apparatus, and naturally on Leishmania donovani infected mice. In addition flies collected from different endemic areas were dissected and examined for natural infection. Flies fed on infected mice showed significantly higher feeding rate (14.4%, p < 0.01) compared to that of other experiments (9%, 8.75%) but the percentage of infection was very low (2.43%). No Chi-square comparison was made between infection rate and feeding rate because of low value in infection rate (less than 5). Flies dissected for natural infection showed only 0.1% infection. Not much difference was observed in the intensity of Leishmania donovani infection in the mid gut of sandflies examined from any of these experiments. These observations have confirmed that Phlebotomus argentipes has ability to acquire infection and it provides the final piece of evidence that Phlebotomus argentipes is the vector of Leishmania donovani in Bihar State.

Intranuclear localization of human papillomavirus 16 E7 during transformation and preferential binding of E7 to the Rb family member p130

To study intracellular pathways by which the human papillomavirus 16 oncogene E7 participates in carcinogenesis, we expressed an inducible chimera of E7 by fusion to the hormone-binding domain of the estrogen receptor. The chimeric protein (E7ER) transformed rodent fibroblast cell lines and induced DNA synthesis on addition of estradiol. In coimmunoprecipitation experiments, E7ER preferentially bound p130 when compared to p107 and pRb. After estradiol addition, E7ER localization changed to a more intense intranuclear staining. Induction of E7 function was not correlated with binding to p130 or pRb but rather with intranuclear localization and modest induction of binding to p107.

ProClass Protein Family Database

ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PROSITE patterns and PIR superfamilies. By combining global similarities and functional motifs into a single classification scheme, ProClass helps to reveal domain and family relationships and classify multi-domain proteins. The database currently consists of more than 120 000 sequence entries, approximately 60% of which is classified into about 3500 families. To maximize family information retrieval, the database provides links to various protein family/domain and structural class databases and contains multiple motif alignments of all PROSITE patterns as well as global alignments of PIR superfamilies. The motif sequences are retrieved from both PIR-International and SWISS-PROT databases, including a large number of new members detected by our GeneFIND family identification system. ProClass can be used to support full-scale genomic annotation, because of its high classification rate. The ProClass database is available for on-line search and record retrieval from our WWW server at http://diana.uthct.edu/proclass.html

Proclass protein family database: new version with motif alignments

ProClass is a protein family database which organizes non-redundant sequence entries into families defined collectively by the ProSite patterns and PIR superfamilies. The database consists of about 100,000 entries, more than half of which are classified in about 3,000 families. The new version includes links to various protein family/domain and structural class databases and contains gapped motif alignments for all ProSite patterns. The motif sequences are retrieved from both SwissProt and PIR-international databases, including numerous new members detected by our GeneFIND family identification system. The motif collection represents a 50% increase from those catalogued in ProSite. The ProClass database can be used to maximize family information retrieval, help organize protein sequence databases, and support full-scale genomic annotation. The database and its query program are freely available for on-line record retrieval and direct file transfer from our WWW server at http:/(/)diana.uthct.edu/proclass.html+ ++.

GeneFIND web server for protein family identification and information retrieval

An integrated database and search system has been developed for protein family identification and information retrieval, as an approach to undertake the highly complex, genomic-scale problem of molecular sequence database search and organization.

AVAILABILITY

http://diana.uthct.edu

CONTACT

wu@uthct.edu

Evidence for linkage of regions on chromosomes 6 and 11 to plasma glucose concentrations in Mexican Americans

The genetic factors involved in type II diabetes are still unknown. To address this problem, we are creating a 10 to 15 cM genetic map on 444 individuals from 32 Mexican American families ascertained on a type II diabetic proband. Using highly polymorphic microsatellite markers and a multipoint variance components method, we found evidence for linkage of plasma glucose concentration 2 hr after oral glucose administration to two regions on chromosome 11: beta-hemoglobin (HBB) and markers D11S899/D11S1324 near the sulfonylurea receptor (SUR) gene. Iod scores at these two loci were 2.77 and 3.37, respectively. The SUR gene region accounted for 44.7% of the phenotypic variance. Evidence for linkage to fasting glucose concentration was also observed for two loci on chromosome 6, one of which is identical to a proposed susceptibility locus for type I diabetes (D6S290). When diabetics were excluded from the analyses, all Iod scores became zero, suggesting that the observed linkages were with the trait diabetes rather than with normal variation in glucose levels. Results were similar whether all diabetics were included in the analyses or only those who were not under treatment with oral antidiabetic agents or insulin.

Leptospirosis in Madras--a clinical and serological study

Leptospirosis was confirmed by Microscopic Agglutination Test (MAT) and/or ELISA in 57 patients admitted to the Government General Hospital, Madras, India, during November and December of 1990 and 1991 with symptomatology suggestive of the disease. Fifty (88%) of the 57 cases were males; the mean age of all the cases was 39.6 years (range 17-72). The main clinical features were: fever 100% jaundice 84%, Myalgia 82%, acute renal failure 72% and conjunctival suffusion 58%. Non-azotemic jaundice occurred in 19% of cases. Renal failure was non-oliguric in 24% of cases. 3.5% of patients died. 23 patients underwent peritoneal and/or hemodialysis. ELISA IgM titres ranged from 1:80 to 1:10240 (geometric mean tire 911). MAT titres > or = 1:1600 and > or = 1:800 occurred in 39 of 54 and 51 of 54 cases respectively. Autumnalis was the serogroup most commonly recorded serologically, and Leptospira interrogans serovar autumnalis was isolated from one patient. This study shows that leptospirosis is a significant health problem in Madras, though normally grossly underestimated due to the absence of routine laboratory diagnostic facilities for the disease. Gross under-reporting is also likely in other high rainfall third world areas.

Back-propagation and counter-propagation neural networks for phylogenetic classification of ribosomal RNA sequences

A neural network system has been developed for rapid and accurate classification of ribosomal RNA sequences according to phylogenetic relationship. The molecular sequences are encoded into neural input vectors using an n-gram hashing method. A SVD (singular value decomposition) method is used to compress and reduce the size of long and sparse n-gram input vectors. The neural networks used are three-layered, feed-forward networks that employ supervised learning paradigms, including the back-propagation algorithm and a modified counter-propagation algorithm. A pedagogical pattern selection strategy is used to reduce the training time. After trained with ribosomal RNA sequences of the RDP (Ribosomal Database Project) database, the system can classify query sequences into more than one hundred phylogenetic classes with a 100% accuracy at a rate of less than 0.3 CPU second per sequence on a workstation. When compared to other sequence similarity search methods, including Similarity Rank, Blast and Fasta, the neural network method has a higher classification accuracy at a speed of about an order of magnitude faster. The software tool will be made available to the biology community, and the system may be extended into a gene identification system for classifying indiscriminately sequenced DNA fragments.

Two wnt genes in Caenorhabditis elegans

wnt genes encode secretory glycoproteins that have been implicated in growth control and development in mice, frogs and insects. In this report we examine properties of two wnt genes recently identified in the nematode Caenorhabditis elegans. The first gene, Ce-wnt-1, was previously identified by a polymerase chain reaction-based screen of genomic DNA, and the second, Ce-wnt-2, was fortuitously encountered in a survey of clones in a cDNA library by the Caenorhabditis Genome Project. Full-length or nearly full-length cDNAs representing both mRNAs encode proteins that are similar in length, sequence and functional domains to other Wnt proteins. Primary products of 372 and 362 amino acids begin with a hydrophobic signal peptide, include two potential N-linked glycosylation sites and contain the 22 cysteine residues conserved throughout the wnt family. In contrast to mammalian and insect wnt genes with four or five exons and conserved intron-exon boundaries, Ce-wnt-1 has nine coding exons; only one of the eight identified introns interrupts the coding sequence at a position homologous to an intron position in other wnt genes. The major transcript derived from Ce-wnt-1 is 1.4 kb in length, and the 22 nucleotides at its 5' end are added by a trans-splicing mechanism. Ce-wnt-2 is also expressed via a single major transcript, 1.5 kb in length. Both RNAs are detectable in all larval forms and adults, but they are most abundant at the embryonic stage. Ce-wnt-1 is localized to the left arm of chromosome II and Ce-wnt-2 maps to a cluster of genes on chromosome IV.

T cell receptor alpha/beta expressing double-negative (CD4-/CD8-) and CD4+ T helper cells in humans augment the production of pathogenic anti-DNA autoantibodies associated with lupus nephritis

It is generally accepted that human Th cells express the surface glycoproteins CD4 and alpha/beta-chain heterodimer of the TCR whereas cytotoxic/suppressor cells are usually CD8+ and alpha/beta TCR+. Another minor set of T cells found in the periphery are CD4-/CD8- (double negative) and express the gamma/delta TCR; these cells can manifest MHC-restricted or nonrestricted cytotoxicity but no helper function. Herein we describe the existence of an unusual Th population in the peripheral blood of humans that are CD4-/CD8- and alpha/beta TCR+. These double-negative Th were markedly expanded in patients with the autoimmune disease SLE and along with CD4+ Th, they induced production of the pathogenic variety of anti-DNA autoantibodies that are IgG in class and cationic in charge. The cationic anti-DNA antibodies induced by the Th were markedly restricted in spectrotype indicating that an oligoclonal population of B cells were committed to produce the pathogenic autoantibodies in active lupus. IL-2-dependent T cell lines were also derived from the patients with active lupus nephritis but the majority of those T cell lines lacked pathogenic autoantibody-inducing capability. Only 4 out of 42 T cell lines from a lupus patient could induce the production of cationic IgG class anti-DNA autoantibodies. The phenotypes of the pathogenic autoantibody-inducing Th lines were similar to the Th subsets: CD4+, alpha/beta TCR+ or CD4-/CD8-, alpha/beta TCR+. These studies suggest that production of pathogenic autoantibodies in human lupus is mediated by mechanisms that are distinct from the generalized, nonspecific polyclonal B cell hyperactivity that leads to excessive production of natural autoantibodies.