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M D'Souza

Publications and source records attributed to M D'Souza.

At least 19 recordsLinked to original sources
PubMed2003

Experimental determination and system level analysis of essential genes in Escherichia coli MG1655.

Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential E. coli genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.

Aerobiosis↗
PubMed2002

Dyschromatosis universalis hereditaria.

Dyschromatosis universalis hereditaria is a clinically heterogenous disorder. We report two unrelated Indian patients with dyschromatosis universalis hereditaria, who had generalized and progressive reticulate hyper- and hypo-pigmentation of the skin. The oral mucosa and tongue also showed mottled pigmentation. Intriguingly, the palms and soles were also affected with a diffuse hyper-pigmentation interspersed with spotty de-pigmented macules. Dystrophic nail changes with pterygium formation were seen in one case. Histopathology revealed a variable degree of pigmentary incontinence. Although the precise aetiology of this disorder is not yet known, the clinicopathological findings implicate an inherent abnormality of melanosomes or melanin processing.

Adolescent↗
PubMed2001

Hermansky-Pudlak syndrome type 3 in Ashkenazi Jews and other non-Puerto Rican patients with hypopigmentation and platelet storage-pool deficiency.

Hermansky-Pudlak syndrome (HPS), consisting of oculocutaneous albinism and a bleeding diathesis due to the absence of platelet dense granules, displays extensive locus heterogeneity. HPS1 mutations cause HPS-1 disease, and ADTB3A mutations cause HPS-2 disease, which is known to involve abnormal intracellular vesicle formation. A third HPS-causing gene, HPS3, was recently identified on the basis of homozygosity mapping of a genetic isolate of HPS in central Puerto Rico. We now describe the clinical and molecular characteristics of eight patients with HPS-3 who are of non-Puerto Rican heritage. Five are Ashkenazi Jews; three of these are homozygous for a 1303+1G-->A splice-site mutation that causes skipping of exon 5, deleting an RsaI restriction site and decreasing the amounts of mRNA found on northern blotting. The other two are heterozygous for the 1303+1G-->A mutation and for either an 1831+2T-->G or a 2621-2A-->G splicing mutation. Of 235 anonymous Ashkenazi Jewish DNA samples, one was heterozygous for the 1303+1G-->A mutation. One seven-year-old boy of German/Swiss extraction was compound heterozygous for a 2729+1G-->C mutation, causing skipping of exon 14, and resulting in a C1329T missense (R396W), with decreased mRNA production. A 15-year-old Irish/English boy was heterozygous for an 89-bp insertion between exons 16 and 17 resulting from abnormal splicing; his fibroblast HPS3 mRNA is normal in amount but is increased in size. A 12-year-old girl of Puerto Rican and Italian background has the 3,904-bp founder deletion from central Puerto Rico on one allele. All eight patients have mild symptoms of HPS; two Jewish patients had received the diagnosis of ocular, rather than oculocutaneous, albinism. These findings expand the molecular diagnosis of HPS, provide a screening method for a mutation common among Jews, and suggest that other patients with mild hypopigmentation and decreased vision should be examined for HPS.

Adaptor Protein Complex 3↗
PubMed2001

Biochemical and biological characterization of a human Rac2 GTPase mutant associated with phagocytic immunodeficiency.

The Rho GTPase, Rac2, is expressed only in hematopoietic cell lineages, suggesting a specific cellular function in these cells. Genetic targeting studies in mice showed that Rac2 is an essential regulator of neutrophil chemotaxis, L-selectin capture and rolling, and superoxide production. Recently, a dominant negative mutation of Rac2, D57N, has been reported to be associated with a human phagocytic immunodeficiency. To understand further the cellular phenotypes associated with this D57N Rac2 mutant we examined its biochemical characteristics and functional effects when expressed in primary murine bone marrow cells. When compared with wild type (WT) Rac2, D57N Rac2 displayed approximately 10% GTP binding ability resulting from a markedly enhanced rate of GTP dissociation and did not respond to the guanine nucleotide exchange factors. These results suggest that D57N Rac2 may act in a dominant negative fashion in cells by sequestering endogenous guanine nucleotide exchange factors. When expressed in hematopoietic cells, D57N Rac2 reduced endogenous activities of not only Rac2, but also Rac1 and decreased cell expansion in vitro in the presence of growth factors due to increased cell apoptosis. Unexpectedly, D57N expression had no effect on proliferation. In contrast, expansion of cells transduced with WT Rac2 and a dominant active mutant, Q61L, was associated with significantly increased proliferation. Transplantation of transduced bone marrow cells into lethally irradiated recipients showed that the percentage of D57N-containing peripheral blood cells decreased markedly from 40% at 1 month to <5% by 3 months postinjection. Neutrophils derived in vitro from the transduced progenitor cells containing D57N demonstrated markedly impaired migration and O(2)(-) responses to formyl-methionyl-leucyl-phenylalanine, reflecting the same cellular phenotype in these differentiated cells as those described previously in patient cells. These data suggest that the phenotypic abnormalities associated with D57N Rac2 may involve not only neutrophil cellular functions, but also abnormal cell survival in other hematopoietic cells and that overexpression of Rac leads to increased proliferation of normal cells in vitro, whereas deficiency of Rac leads to increased apoptosis.

Amino Acid Substitution↗
PubMed2001

BMP signaling stimulates chondrocyte maturation and the expression of Indian hedgehog.

Mutant BMP receptors were transfected into cultured embryonic upper sternal chrondrocytes using retroviral vectors to determine if BMP signaling is required for chondrocyte maturation and the expression of a key regulatory molecule, Indian hedgehog (Ihh). Chondrocytes infected with replication competent avian retroviruses (RCAS) viruses carrying constitutive active (CA) BMPR-IA and BMPR-IB had enhanced expression of type X collagen and Ihh mRNA. Addition of PTHrP, a known inhibitor of chondrocyte maturation, abolished the expression of type X collagen, BMP-6, and Ihh mRNAs in control cells. In contrast, PTHrP treated cultures infected with of CA BMPR-IA or CA BMPR-IB had low levels of BMP-6 and type X collagen, but high levels of Ihh expression. Although dominant negative (DN) BMPR-IA had no effect, DN BMPR-IB inhibited the expression of type X collagen and BMP-6, and decreased alkaline phosphatase activity, even in the presence of exogenously added BMP-2 and BMP-6. DN BMPR-IB also completely blocked Ihh expression. Overall, the effect of DN BMPR-IB mimicked the effects of PTHrP. To determine if there is an autocrine role for the BMPs in chondrocyte maturation, the cultures were treated with noggin and follistatin, molecules that bind BMP-2/-4 and BMP-6/-7, respectively. While noggin and follistatin inhibited the effects of recombinant BMP-2 and BMP-6, respectively, they had only minimal effects on the spontaneous maturation of chondrocytes in culture, suggesting that more than one subgroup of BMPs regulates chondrocyte maturation. The results demonstrate that: (i) BMP signaling stimulates chondrocyte maturation; (ii) BMP signaling increases Ihh expression independent of maturational effects; and (iii) BMP signaling can partially overcome the inhibitory effects of PTHrP on maturation.

Animals↗
PubMed2001

Fine needle aspiration cytology (FNAC) of nerves in leprosy.

Leprosy is primarily a disease of the peripheral nerves and a technique that is simpler than nerve biopsy is required to evaluate nerve involvement, especially in pure neuritic (PN) leprosy. This study was designed to evaluate the role of FNAC of the nerve in the diagnosis and classification of leprosy. A prospective study was carried out on 25 patients with clinically active leprosy and at least one thickened peripheral sensory nerve. Nerve aspirates were evaluated by May-Grunwald-Giemsa and Fite's staining. Lepromin test, slit skin smears (SSS), skin biopsies (except PN cases) and nerve biopsies were performed and compared with FNAC. FNAC of nerve from 23 cases (92%) yielded diagnostic aspirates. Acid fast bacilli were observed in six cases by FNAC. FNAC and nerve pathology were equally comparable with the other parameters evaluated. Based on the results, cytological criteria were developed for interpreting nerve aspirates and the cases were classified as paucibacillary (18), BB (2), BL (2), LL (1) and non-diagnostic (2). All PN cases showed diagnostic paucibacillary type cytology. FNAC of the nerve yields diagnostic aspirates in leprosy comparable with nerve pathology and the proposed cytological criteria may be useful in classification of nerve aspirates.

Adult↗
PubMed2000

Direct reversal of DNA damage by mutant methyltransferase protein protects mice against dose-intensified chemotherapy and leads to in vivo selection of hematopoietic stem cells.

Direct reversal of O6 adducts caused by chemotherapy agents is accomplished in mammalian cells by the protein O6-methylguanine DNA methyltransferase (MGMT). Some tumors overexpress MGMT and are resistant to alkylator therapy. One future approach to treatment of these tumors may rely on concurrent pharmacological depletion of tumor MGMT with O6-benzylguanine (6-BG) and protection of sensitive tissues, such as hematopoietic stem and progenitor cells, using genetic modification with 6-BG-resistant MGMT mutants. We have used retroviral-mediated gene transfer to transduce murine hematopoietic bone marrow cells with MGMT point mutants showing resistance to 6-BG depletion in vitro. These mutants include proline to alanine and proline to lysine substitutions at the 140 position (P140A and P140K, respectively), which show 40- and 1000-fold resistance to 6-BG compared with wild-type (WT) MGMT. Lethally irradiated mice were reconstituted with murine stem cells transduced with murine stem cell virus retrovirus expressing each mutant, WT MGMT, or mock-infected cells and then treated with a combination of 30 mg/kg 6-BG and 10 mg/kg 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) or with 40 mg/kg BCNU alone. Compared with mice treated with BCNU alone, significant myeloid toxicity and death occurred in mice reconstituted with mock-infected or WT MGMT (<0.1 probability of survival) or the P140A mutant (0.13 probability of survival) MGMT cDNAs. In contrast, after an initial period of mild cytopenia, mice reconstituted with the P140K mutant (0.83 probability of survival) recovered nearly normal blood counts, even during continued treatment. Comparison of peripheral blood neutrophils after completion of 5 weekly treatments in these animals showed a direct correlation between the treatment and in vivo selection for progeny of transduced cells (pretreatment, approximately 8-12% transduced cells; no treatment, approximately 6% transduced cells; BCNU only, 51% transduced cells; 6-BG/BCNU, 93% transduced cells). To determine whether this selection occurred at the stem cell level, bone marrow from each treatment group was infused into secondary recipients. Whereas animals that received bone marrow from untreated animals reconstituted with 2% transduced cells, animals receiving marrow from 6-BG/BCNU-treated animals reconstituted with 94% transduced cells, demonstrating nearly complete selection for stem cells in the primary animals. Mice reconstituted with marrow from animals treated with BCNU only demonstrated 23% transduced cells, consistent with partial selection of stem cells in the primary mice. The levels of transduced cells also correlated with survival during a second round of intensive combination chemotherapy (probability of survival: 6-BG/BCNU, 1.0; BCNU alone, >0.70; no treatment, <0.1). These data demonstrate that mutant MGMT expressed in the bone marrow can protect mice from time- and dose-intensive chemotherapy and that the combination of 6-BG and BCNU leads to uniform selection of transduced stem cells in vivo in mice.

3T3 Cells↗
PubMed2000

PTHrP expression in chondrocytes, regulation by TGF-beta, and interactions between epiphyseal and growth plate chondrocytes.

Although PTHrP has been identified as a key regulator of chondrocyte differentiation in the growth plate, the factors directly regulating PTHrP expression have not been identified. Furthermore, while cells from the epiphysis are considered the physiologic source of PTHrP, the relative expression of PTHrP in epiphyseal and growth plate chondrocytes has not been defined. PTHrP expression was examined in chondrocytes isolated from 3- to 5-week-old chick long bones. The expression of PTHrP mRNA was 10-fold higher in epiphyseal chondrocytes compared to cells from the growth plate. Growth plate chondrocytes were isolated into populations with distinct maturational characteristics by countercurrent centrifugal elutriation and analyzed for PTHrP expression. The expression was highest in the least mature cells and progressively declined with the onset of maturation. The regulation of PTHrP expression was further examined in epiphyseal chondrocytes. Both TGF-beta1 and cis-retinoic acid stimulation markedly increased PTHrP mRNA levels, while BMP-2 and PTHrP stimulation decreased the expression of this transcript. The effects of TGF-beta1 (8.9-fold stimulation) and TGF-beta3 (9.2-fold) were slightly greater than the effects of TGF-beta2 (4.9-fold). The effect of TGF-beta was dose-dependent and increases could be detected after 68 h of treatment. To analyze the paracrine effect of epiphyseal and growth plate chondrocytes on each other, these cells were placed in coculture and the mRNA from each of the populations was harvested separately after 24 h. Following coculture the PTHrP mRNA levels increased in the epiphyseal cells while the expression of type X collagen and Indian hedgehog transcripts decreased in growth plate chondrocytes. The results demonstrate potentially important paracrine interactions between these cell populations, possibly mediated by TGF-beta and PTHrP.

Animals↗
PubMed2000

WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.

The WIT (What Is There) (http://wit.mcs.anl.gov/WIT2/) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions based on chromosomal sequences and metabolic modules from the EMP/MPW family of databases. This system contains data derived from about 40 completed or nearly completed genomes. Sequence homologies, various ORF-clustering algorithms, relative gene positions on the chromosome and placement of gene products in metabolic pathways (metabolic reconstruction) can be used for the assignment of gene functions and for development of overviews of genomes within WIT. The integration of a large number of phylogenetically diverse genomes in WIT facilitates the understanding of the physiology of different organisms.

Databases, Factual↗
PubMed2000

SENTRA, a database of signal transduction proteins.

SENTRA, available via URL http://wit.mcs.anl.gov/WIT2/Sentra/, is a database of proteins associated with microbial signal transduction. The database currently includes the classical two-component signal transduction pathway proteins and methyl-accepting chemotaxis proteins, but will be expanded to also include other classes of signal transduction systems that are modulated by phosphorylation or methylation reactions. Although the majority of database entries are from prokaryotic systems, eukaroytic proteins with bacterial-like signal transduction domains are also included. Currently SENTRA contains signal transduction proteins in 34 complete and almost completely sequenced prokaryotic genomes, as well as sequences from 243 organisms available in public databases (SWISS-PROT and EMBL). The analysis was carried out within the framework of the WIT2 system, which is designed and implemented to support genetic sequence analysis and comparative analysis of sequenced genomes.

Animals↗
PubMed2000

Microspheres containing neutralizing antibodies to tumor necrosis factor-alpha and interleukin-1 beta protect rats from Staphylococcus aureus-induced peritonitis.

Previous studies using microencapsulated neutralizing antibodies (NA) to tumor necrosis factor (TNF) and interleukin-1 (IL-1) in combination with gentamicin have demonstrated improved survival in a peritonitis model of gram-negative septic shock. Microencapsulation has been shown to improve the effectiveness of NA by delivering them intracellularly, taking advantage of the natural phagocytic activity of the macrophage. It is the purpose of this study to see if microencapsulated NA to TNF and IL-1 in combination with vancomycin can improve survival compared with NA in solution in Staphlococcus aureus-induced septic shock. Groups of 10 rats received the following treatments: (1) S. aureus plus no treatment, (2) S. aureus plus blank microspheres, (3) S. aureus plus vancomycin, (4) S. aureus plus a microsphere form of NA and vancomycin, (5) S. aureus plus a solution form of NA and vancomycin, (6) S. aureus plus a microsphere form of NA, and (7) S. aureus plus a solution form of NA. Survival was monitored for 5 days, and plasma TNF and IL-1 levels were measured for 48 h after S. aureus administration. All (100%) animals that received the microsphere form of NA plus vancomycin, 20%-70% of the animals that received the microsphere form of NA alone, and 20% of the animals that received antibiotics alone survived for 5 days or more. None of the animals in the no treatment group or blank microsphere treatment group and only 10% of the animals in the solution form of NA plus or minus vancomycin group survived for more than 5 days. Plasma TNF and IL-1 levels were significantly increased after S. aureus treatment. Simultaneous and delayed treatment with the microsphere form of NA plus or minus vancomycin significantly reduced TNF and IL-1 levels, and the solution form of NA significantly reduced only TNF levels after immediate treatment. The survival rate was higher in animals with lower TNF levels and IL-1 levels. The results demonstrate that the microsphere form of cytokine NA is 100% effective in combination with vancomycin in protecting rats from S. aureus-induced peritonitis. The microsphere form was also more efficient in attenuating both TNF and IL-1 levels.

Animals↗
PubMed2000

PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance.

MOTIVATION: The identification of sequence patterns involved in gene regulation and expression is a major challenge in molecular biology. In this paper we describe a novel algorithm and the software for searching nucleotide and protein sequences for complex nucleotide patterns including potential secondary structure elements, also allowing for mismatches/mispairings below a user-fixed threshold, and assessing the statistical significance of their occurrence through a Markov chain simulation. RESULTS: The application of the proposed algorithm allowed the identification of some functional elements, such as the Iron Responsive Element, the Histone stem-loop structure and the Selenocysteine Insertion Sequence, located in the mRNA untranslated regions of post-transcriptionally regulated genes with the assessment of sensitivity and selectivity of the searching method. AVAILABILITY: A Web interface is available at: http://bigarea.area.ba.cnr.it:8000/EmbIT/Pats earch.html.

3' Untranslated Regions↗
PubMed1999

The use of gene clusters to infer functional coupling.

Previously, we presented evidence that it is possible to predict functional coupling between genes based on conservation of gene clusters between genomes. With the rapid increase in the availability of prokaryotic sequence data, it has become possible to verify and apply the technique. In this paper, we extend our characterization of the parameters that determine the utility of the approach, and we generalize the approach in a way that supports detection of common classes of functionally coupled genes (e.g., transport and signal transduction clusters). Now that the analysis includes over 30 complete or nearly complete genomes, it has become clear that this approach will play a significant role in supporting efforts to assign functionality to the remaining uncharacterized genes in sequenced genomes.

Databases, Factual↗
PubMed1999

Targeting macrophages with microspheres containing cytokine-neutralizing antibodies prevents lethality in gram-negative peritonitis.

Macrophages release proinflammatory cytokines in response to infection that play a critical role in the pathophysiology of septic shock. We propose that targeting cytokine-neutralizing antibodies using albumin microspheres to macrophages will be more beneficial than the soluble form in reducing mortality related to peritonitis. In this study, we compared the distribution pattern of microspheres in infected and noninfected animals, evaluated the amount of microsphere taken up by peritoneal macrophages in vitro, and compared the efficacy of soluble and microsphere forms of cytokine-neutralizing antibodies in preventing lethality caused by Escherichia coli-induced peritonitis. The results indicate that twice the amount of microspheres accumulates near the site of infection (the peritoneal cavity), and 70% of the microspheres exposed to peritoneal macrophages were phagocytosed in 1 h. Treatment with the microsphere form of cytokine-neutralizing antibodies was more efficacious than using the soluble form in preventing lethality induced by E. coli. Immediate treatment was more efficacious than delayed treatment in the absence of gentamicin, whereas immediate and delayed treatment were equally efficacious in the presence of gentamicin. The combination of microspheres containing neutralizing antibodies to tumor necrosis factor-alpha (TNF-alpha) and interleukin-1beta (IL-1beta) protected 100% of the animals, whereas either one alone protected only 60%-90% of the animals from lethality caused by E. coli-induced peritonitis. In conclusion, the microsphere form of neutralizing antibodies to TNF-alpha IL-1beta may be an effective therapeutic agent in the treatment of septic shock caused by peritonitis.

Albumins↗