Quantitative structure-activity relationship study on sulfanilamide schiff's bases: carbonic anhydrase (CA) inhibitors

The paper deals with quantitative structure–activity studies on a group of sulfanilamide Schiff's base inhibitors of carbonic anhydrase (CA) using distance-based topological indices. The regression analysis of the data has shown that the activities of the compounds used in inhibiting Carbonic AnhydraseII (CAII) activity can be modeled excellently in multi-parametric model in that some indicator parameters are also involved. The results are discussed critically.     

Biological systems of the host cell involved in Agrobacterium infection

Genetic transformation of plants by Agrobacterium, which in nature causes neoplastic growths, represents the only known case of trans‐kingdom DNA transfer. Furthermore, under laboratory conditions, Agrobacterium can also transform a wide range of other eukaryotic species, from fungi to sea urchins to human cells. How can the Agrobacterium virulence machinery function in such a variety of evolutionarily distant and diverse species? The answer to this question lies in the ability of Agrobacterium to hijack fundamental cellular processes which are shared by most eukaryotic organisms. Our knowledge of these host cellular functions is critical for understanding the molecular mechanisms that underlie genetic transformation of eukaryotic cells. This review outlines the bacterial virulence machinery and provides a detailed discussion of seven major biological systems of the host cell–cell surface receptor arrays, cellular motors, nuclear import, chromatin targeting, targeted proteolysis, DNA repair, and plant immunity – thought to participate in the Agrobacterium‐mediated genetic transformation.     

In the Multi-domain Protein Adenylate Kinase,Domain Insertion Facilitates Cooperative Folding while Accommodating Function at Domain Interfaces

Having multiple domains in proteins can lead to partial folding and increased aggregation. Folding cooperativity, the all or nothing folding of a protein, can reduce this aggregation propensity. In agreement with bulk experiments, a coarse-grained structure-based model of the three-domain protein, E. coli Adenylate kinase (AKE), folds cooperatively. Domain interfaces have previously been implicated in the cooperative folding of multi-domain proteins. To understand their role in AKE folding, we computationally create mutants with deleted inter-domain interfaces and simulate their folding. We find that inter-domain interfaces play a minor role in the folding cooperativity of AKE. On further analysis, we find that unlike other multi-domain proteins whose folding has been studied, the domains of AKE are not singly-linked. Two of its domains have two linkers to the third one, i.e., they are inserted into the third one. We use circular permutation to modify AKE chain-connectivity and convert inserted-domains into singly-linked domains. We find that domain insertion in AKE achieves the following: (1) It facilitates folding cooperativity even when domains have different stabilities. Insertion constrains the N- and C-termini of inserted domains and stabilizes their folded states. Therefore, domains that perform conformational transitions can be smaller with fewer stabilizing interactions. (2) Inter-domain interactions are not needed to promote folding cooperativity and can be tuned for function. In AKE, these interactions help promote conformational dynamics limited catalysis. Finally, using structural bioinformatics, we suggest that domain insertion may also facilitate the cooperative folding of other multi-domain proteins.     

Chemometrics applications in biotechnology processes: Predicting column integrity and impurity clearance during reuse of chromatography resin

Separation media, in particular chromatography media, is typically one of the major contributors to the cost of goods for production of a biotechnology therapeutic. To be cost‐effective, it is industry practice that media be reused over several cycles before being discarded. The traditional approach for estimating the number of cycles a particular media can be reused for involves performing laboratory scale experiments that monitor column performance and carryover. This dataset is then used to predict the number of cycles the media can be used at manufacturing scale (concurrent validation). Although, well accepted and widely practiced, there are challenges associated with extrapolating the laboratory scale data to manufacturing scale due to differences that may exist across scales. Factors that may be different include: level of impurities in the feed material, lot to lot variability in feedstock impurities, design of the column housing unit with respect to cleanability, and homogeneity of the column packing. In view of these challenges, there is a need for approaches that may be able to predict column underperformance at the manufacturing scale over the product lifecycle. In case such an underperformance is predicted, the operators can unpack and repack the chromatography column beforehand and thus avoid batch loss. Chemometrics offers one such solution. In this article, we present an application of chemometrics toward the analysis of a set of chromatography profiles with the intention of predicting the various events of column underperformance including the backpressure buildup and inefficient deoxyribonucleic acid clearance. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Folding circular permutants of IL-1β: route selection driven by functional frustration

Interleukin-1β (IL-1β) is the cytokine crucial to inflammatory and immune response. Two dominant routes are populated in the folding to native structure. These distinct routes are a result of the competition between early packing of the functional loops versus closure of the β-barrel to achieve efficient folding and have been observed both experimentally and computationally. Kinetic experiments on the WT protein established that the dominant route is characterized by early packing of geometrically frustrated functional loops. However, deletion of one of the functional loops, the β-bulge, switches the dominant route to an alternative, yet, as accessible, route, where the termini necessary for barrel closure form first. Here, we explore the effect of circular permutation of the WT sequence on the observed folding landscape with a combination of kinetic and thermodynamic experiments. Our experiments show that while the rate of formation of permutant protein is always slower than that observed for the WT sequence, the region of initial nucleation for all permutants is similar to that observed for the WT protein and occurs within a similar timescale. That is, even permutants with significant sequence rearrangement in which the functional-nucleus is placed at opposing ends of the polypeptide chain, fold by the dominant WT "functional loop-packing route", despite the entropic cost of having to fold the N- and C- termini early. Taken together, our results indicate that the early packing of the functional loops dominates the folding landscape in active proteins, and, despite the entropic penalty of coalescing the termini early, these proteins will populate an entropically unfavorable route in order to conserve function. More generally, circular permutation can elucidate the influence of local energetic stabilization of functional regions within a protein, where topological complexity creates a mismatch between energetics and topology in active proteins.     

Plant diversity and dry-matter dynamics of peri-urban plant communities in an Indian dry tropical region

The emergence of variety of land-use changes due to continuous anthropogenic pressure in peri-urban areas may concomitantly result in modification of the structure of associated plant communities for their sustainable growth. In the present study, plant diversity, and above- and belowground biomass distribution among species were investigated to understand their dynamics across different season, soil, and site conditions in a dry tropical peri-urban region in India. From four study sites that covered contrasting land uses: abandoned brick kiln (ABK), grazing land (GL), Kali river bank (KRB), and agricultural land (AL), a total of 360 monoliths were randomly extracted in three seasons, and dry weights were estimated for aboveground and belowground parts of species individuals. Seasonal soil samples of the sites were analyzed for physico-chemical characteristics. Of the total 87 recorded species that were mainly annual weeds and ruderals, 77% were forbs and 23% grasses. The ranges of plant biomass recorded across all sites and seasons were: aboveground 228–738 g m⁻², belowground 83–288 g m⁻², and a total of 344–1,026 g m⁻². The dominance of species differed between above- and belowground; some species dominated only above- or belowground, and others dominated in both layers. Above- and belowground biomass of the sites, differential community-biomass allocation to above- and belowground parts and species dominants varied significantly with site and season. ABK and AL sites showed lower species diversity and soil nutrients compared to GL and KRB sites. Belowground biomass significantly declined with increasing soil organic C and total N, indicating altered dry matter allocation under resource-scarce habitat conditions. Higher diversity occurred at both low- and high-biomass sites, reflective of enhanced ability of these plant communities to exploit resources maximally in spatio-temporal pattern.     

Giant lipoma of the adrenal gland: a case report

Introduction

Lipoma of the adrenal gland is rare with a reported incidence of between 2% to 4%. Improved imaging techniques have helped in the diagnosis of these lesions.

Case presentation

We report an incidentally detected giant adrenal lipoma in a 43-year-old Asian man with a six year history of hypertension. He had a myocardial infarction one year earlier, for which he was taking an antiplatelet agent in addition to antihypertensive medication.The tumor was detected by computed tomography and magnetic resonance imaging, and was a large, well-defined, altered signal intensity lesion 12 cm in size in the right suprarenal region. The tumor was resected laparoscopically and sent for histopathologic evaluation. It measured 15 cm × 11.5 cm × 6.5 cm on gross examination, weighed 810 g and had a homogenous yellow cut surface. The postoperative course was smooth. Microscopy revealed mature adipose tissue with myxoid degeneration. Over the course of a four month follow-up the patient recovered.

Conclusion

Giant lipoma of the adrenal gland, a benign tumor, is rare compared with myelolipoma. Improved radiologic modalities have led to increased reporting of these benign tumors. Laparoscopic removal of the tumor has helped in early recovery and in reinstating patients to normal lives.

     

Understanding the Folding-Function Tradeoff in Proteins

When an amino-acid sequence cannot be optimized for both folding and function, folding can get compromised in favor of function. To understand this tradeoff better, we devise a novel method for extracting the “function-less” folding-motif of a protein fold from a set of structurally similar but functionally diverse proteins. We then obtain the β-trefoil folding-motif, and study its folding using structure-based models and molecular dynamics simulations. CompariA protein sequence serves two purpson with the folding of wild-type β-trefoil proteins shows that function affects folding in two ways: In the slower folding interleukin-1β, binding sites make the fold more complex, increase contact order and slow folding. In the faster folding hisactophilin, residues which could have been part of the folding-motif are used for function. This reduces the density of native contacts in functional regions and increases folding rate. The folding-motif helps identify subtle structural deviations which perturb folding. These may then be used for functional annotation. Further, the folding-motif could potentially be used as a first step in the sequence design of function-less scaffold proteins. Desired function can then be engineered into these scaffolds.     

Calcitriol attenuates TLR2/IL-33 signaling pathway to repress Th9 cell differentiation and potentially limits the pathophysiology of rheumatoid arthritis

There is limited information regarding the TLR2 signaling pathway involved in Th9 cell differentiation. The role of calcitriol in regulating TLR2-mediated Th9 cell development is unknown. Thus, we aimed to unravel the TLR2 signaling pathway in Th9 cells and its regulation by calcitriol. We have used n?=?5–6 animals for each murine experiment. Human studies involved five healthy volunteers. Moreover, ten healthy individuals and ten RA patients were included in the study. Murine and human Th9 cells were treated with Calcitriol (100 nM) and Pam₃CSK₄ (2 µg/mL). The number of IL-9+ve cells was determined by flow cytometry. Real-time PCR was used to assess the gene expression. Serum 25(OH)D₃ levels were determined by HPLC. We observed that TLR2 signals via IL-33/ST2 in Th9 cells. Increased TLR2 expression associated with increased IL9 expression and augmented disease severity in RA patients. Calcitriol attenuated TLR2 signaling in murine and human Th9 cells. Low serum vitamin D3 level negatively associated with increased IL-9 and TLR2 expression and disease severity in RA patients. Our data suggest a potential role of calcitriol to ameliorate the disease severity of RA patients.

     

Two rhizobacterial strains,individually and in interactions with Rhizobium sp., enhance fusarial wilt control,growth, and yield in pigeon pea

A Pseudomonas aeruginosa strain, RRLJ 04, and a Bacillus cereus strain, BS 03, were tested both individually and in combination with a Rhizobium strain, RH 2, for their ability to enhance plant growth and nodulation in pigeon pea (Cajanus cajan L.) under gnotobiotic, greenhouse and field conditions. Both of the rhizobacterial strains exhibited a positive effect on growth in terms of shoot height, root length, fresh and dry weight, nodulation and yield over the non-treated control. Co-inoculation of seeds with these strains and Rhizobium RH 2 also reduced the number of wilted plants, when grown in soil infested with Fusarium udum. Gnotobiotic studies confirmed that the suppression of wilt disease was due to the presence of the respective PGPR strains. Seed bacterization with drug-marked mutants of RRLJ 04 and BS 03 confirmed their ability to colonize and multiply along the roots. The results suggest that co-inoculation of these strains with Rhizobium strain RH 2 can be further exploited for enhanced growth, nodulation and yield in addition to control of fusarial wilt in pigeon pea.