An integrated nanoliter DNA analysis device

A device was developed that uses microfabricated fluidic channels, heaters, temperature sensors, and fluorescence detectors to analyze nanoliter-size DNA samples. The device is capable of measuring aqueous reagent and DNA-containing solutions, mixing the solutions together, amplifying or digesting the DNA to form discrete products, and separating and detecting those products. No external lenses, heaters, or mechanical pumps are necessary for complete sample processing and analysis. Because all of the components are made using conventional photolithographic production techniques, they operate as a single closed system. The components have the potential for assembly into complex, low-power, integrated analysis systems at low unit cost. The availability of portable, reliable instruments may facilitate the use of DNA analysis in applications such as rapid medical diagnostics and point-of-use agricultural testing.

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

An integrated microfluidic device for influenza and other genetic analyses

An integrated microfluidic device capable of performing a variety of genetic assays has been developed as a step towards building systems for widespread dissemination. The device integrates fluidic and thermal components such as heaters, temperature sensors, and addressable valves to control two nanoliter reactors in series followed by an electrophoretic separation. This combination of components is suitable for a variety of genetic analyses. As an example, we have successfully identified sequence-specific hemagglutinin A subtype for the A/LA/1/87 strain of influenza virus. The device uses a compact design and mass production technologies, making it an attractive platform for a variety of widely disseminated applications.

Fibrinogen acts as a bridging molecule in the adherence of Staphylococcus aureus to cultured human endothelial cells

The propensity of Staphylococcus aureus to cause acute endovascular infections during transient bacteremia is poorly understood. To examine the events leading to the attachment of staphylococci to endothelium, adherence assays were developed to study the role of blood factors in the mediation of staphylococcal adherence to cultured human umbilical vein endothelium in vitro. Results indicate that the preferential attachment of S. aureus to endothelial cells is mediated by fibrinogen adsorbed from plasma onto the endothelial surface. The binding is apparently specific because it could be blocked by goat anti-human fibrinogen antibody in a dose-dependent fashion while nonimmune goat IgG, mouse MAb against AG-1 (a platelet antigen found on the endothelial cell surface), nonspecific mouse MAb and rabbit antibodies to human vitronectin and fibronectin were not inhibitory. Our data also indicate that fibrinogen is a necessary but not the only blood constituent in the mediation of binding of S. aureus to endothelium. This was supported by the finding that fibrinogen alone, at a concentration equivalent to that in plasma, did not potentiate staphylococcal adherence as much as plasma while afibrinogenemic plasma reconstituted with fibrinogen did. Because fibrinogen is known to bind to endothelial cells, our data is consistent with the hypothesis that fibrinogen and additional plasma factor(s), possibly activated during inflammation, promote staphylococcal adherence to endothelium. In addition, the role of the fibrinogen binding receptor of S. aureus as an adherence factor to native endothelium is also suggested.

HDAC inhibitors regulate claudin-1 expression in colon cancer cells through modulation of mRNA stability

Expression and cellular distribution of claudin-1, a tight junction protein, is dysregulated in colon cancer and its overexpression in colon cancer cells induced dedifferentiation and increased invasion. However, the molecular mechanism(s) underlying dysregulated claudin-1 expression in colon cancer remains poorly understood. Histone deacetylase (HDAC)-dependent histone acetylation is an important mechanism of the regulation of cancer-related genes and inhibition of HDACs induces epithelial differentiation and decreased invasion. Therefore, in this study, we examined the role of HDAC-dependent epigenetic regulation of claudin-1 in colon cancer. In this study, we show that sodium butyrate and Trichostatin A (TSA), two structurally different and widely used HDAC inhibitors, inhibited claudin-1 expression in multiple colon cancer cell lines. Further studies revealed modulation of claudin-1 mRNA stability by its 3'-UTR as the major mechanism underlying HDAC-dependent claudin-1 expression. In addition, overexpression of claudin-1 abrogated the TSA-induced inhibition of invasion in colon cancer cells suggesting functional crosstalk. Analysis of mRNA expression in colon cancer patients, showed a similar pattern of increase in claudin-1 and HDAC-2 mRNA expression throughout all stages of colon cancer. Inhibition of claudin-1 expression by HDAC-2-specific small interfering RNA further supported the role of HDAC-2 in this regulation. Taken together, we report a novel post-transcriptional regulation of claudin-1 expression in colon cancer cells and further show a functional correlation between claudin-1 expression and TSA-mediated regulation of invasion. As HDAC inhibitors are considered to be promising anticancer drugs, these new findings will have implications in both laboratory and clinical settings.

Opines stimulate induction of the vir genes of the Agrobacterium tumefaciens Ti plasmid

Upon incubation of Agrobacterium tumefaciens A348 with acetosyringone, the vir genes encoded by the Ti (tumor-inducing) plasmid are induced. The addition of certain opines, including octopine, nopaline, leucinopine, and succinamopine, enhanced this induction 2- to 10-fold. The compounds mannopine, acetopine, arginine, pyruvate, and leucine did not stimulate the induction of the vir genes to such an extent. The enhancement of vir gene induction by opines depended on acetosyringone and the genes virA and virG. Opines stimulated the activity of the vir genes, the double-stranded cleavage of the T (transferred)-DNA at the border repeat sequences, and the production of T-strands by the bacterium. The transformation efficiency of cotton shoot tips was markedly increased by the addition of acetosyringone and nopaline at the time of infection.

Microfabricated reaction and separation systems

Over the past year there have been a number of recent advances in the fields of miniaturized reaction and separation systems, including the construction of fully integrated 'lab-on-a-chip' systems. Microreactors, which initially targeted DNA-based reactions such as the polymerase chain reaction, are now used in several other chemical and biochemical assays. Miniaturized separation columns are currently employed for analyzing a wide variety of samples including DNA, RNA, proteins and cells. Although significant advances have been made at the component level, the realization of an integrated analysis system still remains at the early stages of development.

Production of Enzymes From Agricultural Wastes and Their Potential Industrial Applications

Enzymatic hydrolysis is the significant technique for the conversion of agricultural wastes into valuable products. Agroindustrial wastes such as rice bran, wheat bran, wheat straw, sugarcane bagasse, and corncob are cheapest and plentifully available natural carbon sources for the production of industrially important enzymes. Innumerable enzymes that have numerous applications in industrial processes for food, drug, textile, and dye use have been produced from different types of microorganisms from agricultural wastes. Utilization of agricultural wastes offers great potential for reducing the production cost and increasing the use of enzymes for industrial purposes. This chapter focuses on economic production of actinobacterial enzymes from agricultural wastes to make a better alternative for utilization of biomass generated in million tons as waste annually.

Abdominal thrombotic and ischemic manifestations of the antiphospholipid antibody syndrome: CT findings in 42 patients

PURPOSE

To determine the abdominal computed tomographic (CT) findings in patients with antiphospholipid antibody syndrome (APS).

MATERIALS AND METHODS

Retrospective review of medical records from two university medical centers from 1994 through 1997 revealed 215 patients who had a hypercoagulable state attributed to primary or secondary APS. Abdominal CT findings in these patients were reviewed for evidence of large-vessel occlusion or visceral ischemia.

RESULTS

In 42 (19.5%) of 215 patients with APS (age range, 32-65 years; mean age, 42 years), abdominal thromboses or ischemic events were detected at CT. Twenty-two (52%) had major vascular thromboses, including those in the inferior vena cava (n = 10), portal and superior mesenteric veins (n = 7), splenic vein (n = 4), and aorta (n = 1). Thirty-six (86%) patients had abdominal visceral ischemia resulting in renal infarction (n = 22), bowel ischemia (n = 13), splenic infarction (n = 6), pancreatitis (n = 3), hepatic infarction (n = 1), and/or hepatic dysfunction with portal hypertension (n = 1). In some patients, more than one abdominal organ and/or vessel was involved.

CONCLUSION

Patients who have circulating antiphospholipid antibodies are at risk for major abdominal vascular thromboses and organ infarction. Radiologists must be familiar with this syndrome; they may be the first physicians to suggest the diagnosis on the basis of findings of unusual or recurrent sites of thrombosis, especially in young patients.

Cospeciation and horizontal transmission of avian sarcoma and leukosis virus gag genes in galliform birds

In a study of the evolution and distribution of avian retroviruses, we found avian sarcoma and leukosis virus (ASLV) gag genes in 26 species of galliform birds from North America, Central America, eastern Europe, Asia, and Africa. Nineteen of the 26 host species from whom ASLVs were sequenced were not previously known to contain ASLVs. We assessed congruence between ASLV phylogenies based on a total of 110 gag gene sequences and ASLV-host phylogenies based on mitochondrial 12S ribosomal DNA and ND2 sequences to infer coevolutionary history for ASLVs and their hosts. Widespread distribution of ASLVs among diverse, endemic galliform host species suggests an ancient association. Congruent ASLV and host phylogenies for two species of Perdix, two species of Gallus, and Lagopus lagopus and L. mutus also indicate an old association with vertical transmission and cospeciation for these ASLVs and hosts. An inference of horizontal transmission of ASLVs among some members of the Tetraoninae subfamily (grouse and ptarmigan) is supported by ASLV monophyletic groups reflecting geographic distribution and proximity of hosts rather than host species phylogeny. We provide a preliminary phylogenetic taxonomy for the new ASLVs, in which named taxa denote monophyletic groups.

Aspergillus fumigatus peptides differentially express Th1 and Th2 cytokines

Relevant allergens from Aspergillus fumigatus associated with allergic bronchopulmonary aspergillosis (ABPA) have been cloned and expressed. The pathogenesis of ABPA probably depends on specific cytokines and immunoglobulins secreted by lymphocytes on stimulation with different epitopes of those allergens. In the present study, we synthesized peptides of 12-16 amino acids from the sequence of Asp fI and compared their immunological responses in four mice strains (BALB/c, C57BL/6, AKR, and CBA). Of the five peptides studied for their cytokine profile, one showed a clear Th1, whereas another showed a Th2 response. The remaining three peptides varied in their immunoreactivity. The results suggest that a number of epitopes of diverse activities are present in individual molecules and may be involved in the pathogenesis of ABPA through differential cytokine secretions.

The murine clan V(H) III related 7183, J606 and S107 and DNA4 families commonly encode for binding to a bacterial B cell superantigen

Superantigens, by virtue of their unconventional binding interactions with Ag receptors, can simulate a large subset of mature lymphocytes in the repertoire. Recent studies have documented that in vivo exposure to the model bacterial B cell superantigen, Staphylococcal protein A (SpA), induces large scale effects on murine B-cell clonal selection by mechanism(s) that include deletion of supra-clonal sets. While the structural bases for the immunomodulatory properties of several T-cell superantigens have been well characterized, the requirements for murine Fab-binding of SpA remain incompletely defined. To investigate these structural requirements, a series of direct binding and inhibition studies were performed with a large panel of Moabs of diverse variable region gene usage. These studies confirm previous reports that superantigen binding is completely restricted to the products of clan V(H) III-related families, that include the small S107 and J606 families, and we also demonstrated that usage of the related small DNA4 family commonly correlates with weaker binding activity. Furthermore, our results document that genes from the largest clan V(H) III family, 7183, commonly encode for Fab-mediated binding of SpA, while antibodies from five other VH families, J558, Q52, Sm7, VH11 and VH12, did not display Fab-mediated SpA binding activity. By contributing to the essential foundation for understanding of the structural basis for binding interactions, these findings will aid interpretation of evolving observations regarding the clonal fates induced by in vivo B-cell superantigen exposure.

Antibodies to liver/kidney microsome1 in chronic active hepatitis recognize specific forms of hepatic cytochrome P-450

Anti-liver/kidney microsome1-positive sera from children with chronic active hepatitis were studied in an effort to identify the microsomal antigens selected during induction and progression of this autoimmune disease. Immunoblot analysis of sodium dodecyl sulfate gel-resolved microsomal proteins from human and rat liver using anti-liver/kidney microsome1-positive sera revealed a single polypeptide of 48 kilodaltons (human microsomes) or 50 kilodaltons (rat microsomes). Levels of the 50-kilodalton rat microsomal polypeptide were suppressed in vivo by several drugs known to modulate expression of individual forms (enzymes) of hepatic cytochrome P-450, with the largest decrease effected by phenobarbital. Dot blot analysis using a panel of 10 electrophoretically homogeneous rat liver cytochrome P-450 forms under nondenaturing conditions established that the two methylcholanthrene-inducible forms, P-450 BNF-B and P-450 ISF-G (P-450 gene subfamily IA), are selectively recognized by the anti-liver/kidney microsome1 antibodies. These findings demonstrate that sera associated with autoimmune (anti-liver/kidney microsome1) chronic active hepatitis are specifically reactive with select rat hepatic P-450 forms and suggest that these autoantibodies may be principally directed against one or more constitutive forms of the corresponding human liver cytochromes.

Immunodominant peptide epitopes of allergen, Asp f 1 from the fungus Aspergillus fumigatus

Aspergillus fumigatus ribotoxin Asp f 1 is a major allergen with IgE binding activity to serum of a majority of patients with allergic bronchopulmonary aspergillosis (ABPA). The IgE binding epitopes or the T-cell stimulatory peptides of this molecule have not been studied. In the present investigation, we have synthesized linear decapeptides spanning the whole molecule of Asp f 1 and analyzed their IgE binding properties. We have also synthesized peptides based on their possible T-cell stimulatory properties and studied the stimulation of peripheral blood mononuclear cells from ABPA patients and normal controls. Several peptides demonstrated distinct IgE antibody binding response against sera from ABPA patients and proliferative response against peripheral blood mononuclear cells from the patients. From the results, it can be concluded that the carboxy-terminal region of Asp f 1 representing amino acid residues 115-149 involved in both humoral and cell mediated immunoresponses in ABPA.

Heat shock protein synthesis and thermal tolerance in wheat

Plants respond to high temperature stress by the synthesis of an assortment of heat shock proteins that have been correlated with an acquired thermal tolerance to otherwise lethal temperatures. This study was conducted to determine whether genotypic differences in acquired thermal tolerance were associated with changes in the pattern of heat shock protein synthesis. The pattern of heat shock protein synthesis was analyzed by (35)S-methionine incorporation in wheat (Triticum aestivum L.) varieties exhibiting distinct levels of acquired thermal tolerance. Significant quantitative differences between the cultivars Mustang and Sturdy were observed in the HSP exhibiting apparent molecular weights of 16, 17, 22, 26, 33, and 42 Kilodaltons. Genotypic differences in the synthesis of the small subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase were observed at 34 degrees C. Two-dimensional electrophoretic analysis revealed unique proteins (16, 17, and 26 kilodaltons) in the thermal tolerant variety Mustang that were absent in the more thermal sensitive variety Sturdy. These results provide a correlation between the synthesis of specific low molecular weight heat shock proteins and the degree of thermal tolerance expressed following exposure to elevated temperatures.

Cytochrome p4501A1 gene variants as susceptibility marker for prostate cancer

CYP1A1 activates environmental procarcinogens and catalyzes oxidative metabolism of estrogens and is likely to play an important role in the etiology of prostate cancer. To evaluate this phenomenon, the association between two single nucleotide polymorphisms (A to G transition in exon7 leading to amino acid substitution Ile462Val and T3801C at 3'UTR) of CYP1A1 gene in prostate cancer were analyzed in a case-control study of 100 individuals in South Indian population. The estimated relative risk was significantly high for individuals with w1/m1 genotype at 3'UTR of CYP1A1 gene (OR-4.64; 95%CI = 1.51-14.86; P < 0.01) whereas the CYP1A1 Ile/Val genotype (w2/m2) on exon 7 was found to be associated with a decreased risk for prostate cancer (OR-0.17; 95%CI = 0.02-0.89; P=0.03). A Stratified analysis of the genotypes with age of onset and tumor grade showed the w1/m1 genotype to be significantly associated with an early age of onset; however the tumor grades did not have significant association with the variant genotypes. Thus the present study indicates that individuals with the variant w1/m1 genotype exhibit an increased risk while those with w2/m2 genotype exhibit a decreased risk for prostate cancer.

A simple model for electrical charge in globular macromolecules and linear polyelectrolytes in solution

We present a model for calculating the net and effective electrical charge of globular macromolecules and linear polyelectrolytes such as proteins and DNA, given the concentration of monovalent salt and pH in solution. The calculation is based on a numerical solution of the non-linear Poisson-Boltzmann equation using a finite element discretized continuum approach. The model simultaneously addresses the phenomena of charge regulation and renormalization, both of which underpin the electrostatics of biomolecules in solution. We show that while charge regulation addresses the true electrical charge of a molecule arising from the acid-base equilibria of its ionizable groups, charge renormalization finds relevance in the context of a molecule’s interaction with another charged entity. Writing this electrostatic interaction free energy in terms of a local electrical potential, we obtain an “interaction charge” for the molecule which we demonstrate agrees closely with the “effective charge” discussed in charge renormalization and counterion-condensation theories. The predictions of this model agree well with direct high-precision measurements of effective electrical charge of polyelectrolytes such as nucleic acids and disordered proteins in solution, without tunable parameters. Including the effective interior dielectric constant for compactly folded molecules as a tunable parameter, the model captures measurements of effective charge as well as published trends of pKa shifts in globular proteins. Our results suggest a straightforward general framework to model electrostatics in biomolecules in solution. In offering a platform that directly links theory and experiment, these calculations could foster a systematic understanding of the interrelationship between molecular 3D structure and conformation, electrical charge and electrostatic interactions in solution. The model could find particular relevance in situations where molecular crystal structures are not available or rapid, reliable predictions are desired.

Photocatalytic dye degradation and photoexcited anti-microbial activities of green zinc oxide nanoparticles synthesized via Sargassum muticum extracts

Drug-resistant superbugs (DRS) were isolated from hospital sewage waste and confirmed by a 16S rDNA molecular technique as B. filamentosus, B. flexus, P. stutzeri, and A. baumannii. Green nanotechnologies provide a new promising alternative pathway that was found to be much safer, eco-friendly, and has economic benefits over physical/chemical methods. Sargassum muticum (SM) mediated zinc oxide nanoparticles (ZnO-NPs) were proved to be photocatalytic and anti-microbial agents. Anti-microbial action was demonstrated by a maximal growth inhibition activity of 18 mm against A. baumannii and a minimal of 12 mm against B. flexus at 80 μg mL-1 concentrations. The anti-microbial mechanism of SMZnO-NPs employed a biphasic phenomenon persuaded by an osmotic shock that can attack the DRS bacterial cells directly and lead to death. In addition, photocatalytic activity was investigated by SMZnO-NPs for the degradation of methylene blue (MB) dye under different light conditions. Natural sunlight irradiation shows effective enhancement with the highest efficiencies of 96% being achieved within 60 min compared to UV-light and visible-light. The reusability of SMZnO-NPs provides up to 6 consecutive cycles towards MB decolorization for environmental water cleansing.