C<Subscript>1</Subscript>-/C<Subscript>2</Subscript>-aromatic-imino-glyco-conjugates: experimental and computational studies of binding,inhibition and docking aspects towards glycosidases isolated from soybean and jack bean

Several C₁-imino conjugates of d-galactose, d-lactose and d-ribose, where the nitrogen center was substituted by the salicylidene or naphthylidene, were synthesized and characterized. Similar C₂-imino conjugates of d-glucose have also been synthesized. All the glyco-imino-conjugates, which are transition state analogues, exhibited 100% inhibition of the activity towards glycosidases extracted from soybean and jack bean meal. Among these, a galactosyl-napthyl-imine-conjugate (1c) showed 50% inhibition of the activity of pure α-mannosidase from jack bean at 22 ± 2.5 μM, and a ribosyl-naphthyl-imine-conjugate (3c) showed at 31 ± 5.5 μM and hence these conjugates are potent inhibitors of glycosidases. The kinetic studies suggested non-competitive inhibition by these conjugates. The studies are also suggestive of the involvement of aromatic, imine and carbohydrate moieties of the glyco-imino-conjugates in the effective inhibition. The binding of glyco-imino-conjugate has been established by extensive studies carried out using fluorescence emission and isothermal titration calorimetry. The conformational changes resulted in the enzyme upon interaction of these derivatives has been established by studying the fluorescence quench of the enzyme by KI as well as from the secondary structural changes noticed in CD spectra. All these studies revealed the difference in the binding strengths of the naphthylidene vs. salicylidene as well as galactosyl vs. lactosyl moieties present in these conjugates. The differential inhibition of these glyco-conjugates has been addressed by quantifying the specific interactions present between the glyco-conjugates and the enzyme by using rigid docking studies. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Complete reduction of 2H-pyran-2-one moiety of coumarin and 6-methyl coumarin by Colletotrichum capsici

The microbial transformation of coumarin (1) and 6-methyl coumarin (2) using Colletotrichum capsici gave 2-(3'-hydroxypropyl) phenol (3) and 2-(3'-hydroxypropyl)-4-methyl phenol (4). The phytopathogenic fungi effectively reduced the 2H-pyran-2-one moiety of both parent coumarins to respective alcohols.     

Activated renal macrophages are markers of disease onset and disease remission in lupus nephritis

Costimulatory blockade with CTLA4Ig and anti-CD40L along with a single dose of cyclophosphamide induces remission of systemic lupus erythematosus nephritis in NZB/W F(1) mice. To understand the mechanisms for remission and for impending relapse, we examined the expression profiles of 61 inflammatory molecules in the perfused kidneys of treated mice and untreated mice at different stages of disease. Further studies using flow cytometry and immunohistochemistry allowed us to determine the cellular origins of several key markers. We show that only a limited set of inflammatory mediators is expressed in the kidney following glomerular immune complex deposition but before the onset of proteinuria. Formation of a lymphoid aggregate in the renal pelvis precedes the invasion of the kidney by inflammatory cells. Regulatory molecules are expressed early in the disease process and during remission but do not prevent the inevitable progression of active inflammation. Onset of proliferative glomerulonephritis and proteinuria is associated with activation of the renal endothelium, expression of chemokines that mediate glomerular cell infiltration, and infiltration by activated dendritic cells and macrophages that migrate to different topographical areas of the kidney but express a similar profile of inflammatory cytokines. Increasing interstitial infiltration by macrophages and progressive tubular damage, manifested by production of lipocalin-2, occur later in the disease process. Studies of treated mice identify a type II (M2b)-activated macrophage as a marker of remission induction and impending relapse and suggest that therapy for systemic lupus erythematosus nephritis should include strategies that prevent both activation of monocytes and their migration to the kidney.     

Biosorption of radionuclides by Rhizopus arrhizus

The sorption of various radionuclides viz. 233U, 239Pu, 241Am, 144Ce, 147Pm, 152+154Eu and 95Zr from aqueous nitrate medium has been studied using biomass Rhizopus arrhizus. The biosorption of 233U and 239Pu was found to be maximum at pH 6-7 whereas for other trivalent actinides and fission products viz. 241Am, 144Ce, 147Pm, 152+154Eu and tetravalent 95Zr, it was more effective at pH 2. This biomass is a promising sorbant for the treatment of radioactive effluents from nuclear industry. © Rapid Science Ltd. 1998     

Mixing time in a down-flow jet loop bioreactor

Mixing time was determined in a down-flow jet loop bioreactor with Newtonian and non-Newtonian fluids. It was observed that the mixing time decreased with an increase in linear liquid velocity, superficial gas velocity, draft tube to column diameter ratio, nozzle diameter and shear thinning of media. The optimum draft tube to column diameter ratio was found to be about 0.44. Correlations were presented for prediction of mixing time.List of Symbols A m² cross sectional area of the column - C kmol/m³ local tracer concentration - A _D m² flow area,A _D =/4 (D _Z ² -D _TO ² ) - D m column diameter - D _E m draft tube diameter - D _TO m outside diameter of the air tube - D _TFL m equivalent flow diameter,D _TFL =(D _Z ² -D _TO ² )^0.5 - D _z m nozzle diameter - g m/s² gravitational acceleration - h % inhomogeneity - H m height of the column - H _B m distance between the lower edge of the draft tube and the impact plate - H _T m distance between the upper edge of the draft tube and the liquid nozzle - K Pa.sⁿ consistency index in power-law model - L _E m length of the draft tube - n flow index in the power-law model - Re _j jet Reynolds number,Re _j =(D _TFL×w₁×_L)/ _eff - t _M s mixing time - t _sg m/s superficial gas velocity based onA - W _l m/s linear liquid velocity based onD _D Greek Letters N/m² shear stress - s shear rate - kg/m³ density of liquid - N/m surface tension of the liquid - Pa.sⁿ viscosity of liquid Indices X concentration at infinite time maximum value of tracer concentration - eff effective - L Liquid - obs observed - pred Predicted     

Fast gel electrophoresis to analyze DNA-protein interactions

A rapid method for electrophoresis of DNA-protein complexes is described. Popular "gel-shift" assays are performed using Pharmacia PhastSystem with its convenience of pre-cast gels and buffer strips and microprocessor-controlled high-resolution separation. Using this system, the products of a DNA binding reaction (DNA-protein complexes) can be separated from "free" DNA in less than one hour. DNA fragments as well as oligonucleotides have been used as targets with partially purified extracts containing sequence-specific DNA binding proteins. We present here a comparison of results of gel-shift assays obtained by conventional techniques and by our rapid "PhastShift" method which reduces the time, effort and technical expertise necessary to obtain reproducible results.     

Iterative cloning, overexpression, purification and isotopic labeling of an engineered dimer of a Ca(2+)-binding protein of the βγ-crystallin superfamily from Methanosarcina acetivorans

βγ-Crystallins are a large superfamily of proteins found in vertebrate eye lens. They are hetero-dimers (linked in tandem by a specific peptide) and are shown to bind calcium. The monomers possess two β-strand rich greek-key motifs. Recently, a structurally closest member to the family of lens βγ-crystallins has been described, for the first time, from the archaea Methanosarcina acetivorans, which is named as M-crystallin. Unlike lens βγ-crystallins, M-crystallin exits as a monomer. Here, we synthesized a dimeric gene of M-crystallin in which two monomers are linked by a 10-amino acid residue coding sequence. The linker sequence in the target protein is long and flexible enough to reduce the proximity between the individual crystallins in the dimer. This methodology would be highly beneficial in designing polyproteins (two or more proteins linked in tandem to aid mechanical stretching studies) that are regularly used in single-molecule force spectroscopy. The dimer of M-crystallin was overexpressed in Escherichia coli BLR(DE3) strain. The overexpressed protein containing an N-terminal hexa-histidine tag was purified using nickel affinity chromatography and then by size-exclusion chromatography. Further, a method to purify isotopically ((15)N) labeled protein with high yield for NMR studies is reported. The uniformly (15)N-labeled M-crystallin dimer thus produced has been characterized by recording sensitivity enhanced 2D [(15)N-(1)H] HSQC and other optical spectroscopy techniques. Observation of only one set of peaks in the HSQC, along with the structural characterization using optical spectroscopy, suggests that the domains in the dimer possess similar structure as that of the monomer.     

Selective deacetylation of zaluzanin D using transformed Escherichia coli cultures

The use of conventional and unconventional reaction methodology for the hydrolysis of the acetate group in zaluzanin D resulted in hydration of the 11,13 exocyclic bond along with deacetylation. But the microorganism E. coli selectively cleaved the acetate group to yield zaluzanin C.     

Hydrodynamics and mixing in down flow jet loop bioreactor with a non-Newtonian fluid

Gas holdup and liquid circulation time were measured in a down flow jet loop bioreactor with a non-Newtonian fluid. It was observed that the circulation time decreases with increase in nozzle diameter, draft tube to column diameter ratio and shear thinning of the media. The gas holdup increases with increase in gas and liquid velocities. The optimum draft tube to column diameter ratio was found to be 0.438. Correlations for gas holdup and circulation time involving operational and geometrical variables were presented.     

DA-TC: a novel application execution model in multicluster systems

The availability of a large number of separate clusters has given rise to the field of multicluster systems in which these resources are coupled to obtain their combined benefits to solve large-scale compute-intensive applications. However, it is challenging to achieve automatic load balancing of the jobs across these participating autonomic systems. We developed a novel user space execution model named DA-TC to address the workload allocation techniques for the applications with large number of sequential jobs in multicluster systems. Through this model, we can achieve dynamic load balancing for task assignment, and slower resources become beneficial factors rather than bottlenecks for application execution. The effectiveness of this strategy is demonstrated through theoretical analysis. This model is also evaluated through extensive experimental studies and the results show that when compared with the traditional method, the proposed DA-TC model can significantly improve the performance of application execution in terms of application turnaround time and system reliability in multicluster circumstances.