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.

     

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.     

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.     

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     

Enzymatic dehalogenation of pentachlorophenol by Pseudomonas fluorescens of the microbial community from tannery effluent

Four different bacterial isolates obtained from a stable bacterial consortium were capable of utilizing pentachlorophenol (PCP) as sole carbon and energy source. The consortium was developed by continuous enrichment in the chemostat. The degradation of PCP by bacterial strain was preceded through an oxidative route as indicated by accumulation of tetrachloro-rho-hydroquinone and dichlorohydroquinone as determined by high performance liquid chromatography (HPLC). Among the four isolates, Pseudomonas fluorescens exhibited maximum degradation capability and enzyme production. PCP-monooxygenase enzyme was extracted from culture extract and fractionated by DEAE-cellulose ion exchange chromatography. The molecular weight of the enzyme, purified from Pseudomonas fluorescens, determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and gel filtration chromatography was found to be 24000 Da.     

<Emphasis Type="Italic">Escherichia coli</Emphasis> AlkB interacts with single-stranded DNA binding protein SSB by an intrinsically disordered region of SSB

Intrinsically disordered regions (IDRs) of proteins often regulate function through interactions with folded domains. Escherichia coli single-stranded DNA binding protein SSB binds and stabilizes single-stranded DNA (ssDNA). The N-terminal of SSB contains characteristic OB (oligonucleotide/oligosaccharide-binding) fold which binds ssDNA tightly but non-specifically. SSB also forms complexes with a large number proteins via the C-terminal interaction domain consisting mostly of acidic amino acid residues. The amino acid residues located between the OB-fold and C-terminal acidic domain are known to constitute an IDR and no functional significance has been attributed to this region. Although SSB is known to bind many DNA repair protein, it is not known whether it binds to DNA dealkylation repair protein AlkB. Here, we characterize AlkB SSB interaction and demonstrate that SSB binds to AlkB via the IDR. We have established that AlkB-SSB interaction by in vitro pull-down and yeast two-hybrid analysis. We mapped the site of contact to be the residues 152–169 of SSB. Unlike most of the SSB-binding proteins which utilize C-terminal acidic domain for interaction, IDR of SSB is necessary and sufficient for AlkB interaction.     

Efflux pump inhibition by 11H-pyrido[2,1-b]quinazolin-11-one analogues in mycobacteria

Mycobacterium tuberculosis infection causes 1.8 million deaths worldwide, of which half a million has been diagnosed with resistant tuberculosis (TB). Emergence of multi drug resistant and extensive drug resistant strains has made all the existing anti-TB therapy futile. The major involvement of efflux pump in drug resistance has made it a direct approach for therapeutic exploration against resistant M. tuberculosis. This study demarcates the role of 11H-pyrido[2,1-b]quinazolin-11-one (quinazolinone) analogues as efflux pump inhibitor in Mycobacterium smegmatis. Sixteen quinazolinone analogues were synthesized by treating 2-aminopyridine and 2-fluorobenzonitrile with K^tOBu. Analogues were tested, and 3a, 3b, 3c, 3g, 3j, 3l, 3m, and 3p were found to modulate EtBr MIC by >4 whereas 3a, 3g, 3i and 3o showed >4 modulation on norfloxacin MIC. 3l and 3o in addition to their very low toxicity they showed high EtBr and norfloxacin accumulation respectively. Time kill curve showed effective log reduction in colony forming unit in presence of these analogues, thus confirming their role as efflux pump inhibitor. Through docking and alignment studies, we have also shown that the LfrA amino acid residues that the analogues are interacting with are present in Rv2333c and Rv2846c of M. tuberculosis. This study have shown for the first time the possibility of developing the 11H-pyrido[2,1-b]quinazolin-11-one analogues as efflux pump inhibitors for M. smegmatis and hence unbolts the scope to advance this study against resistant M. tuberculosis as well.     

Enrichment and characterization of a microbial community from tannery effluent for degradation of pentachlorophenol

A bacterial community obtained by continuous enrichment from the microbial population of tannery effluent using pentachlorophenol (PCP) as sole source of carbon and energy, contained four different bacterial species including Serratia marcescens (three isolates, TE₁, TE₂ and TE₄) and Pseudomonas fluorescens (one isolate, TE₃). The members of the community grew separately on various chlorinated compounds, carbon and nitrogen sources and exhibited a remarkable ability to utilize PCP. Biodegradation studies revealed a time-dependent disappearance of PCP and its intermediary metabolites, tetrachloro-p-hydroquinone and chlorohydroquinone, and indicated the individual role of members of the community in the degradation of PCP.