Recognition pliability is coupled to structural heterogeneity: a calmodulin intrinsically disordered binding region complex

Protein interactions within regulatory networks should adapt in a spatiotemporal-dependent dynamic environment, in order to process and respond to diverse and versatile cellular signals. However, the principles governing recognition pliability in protein complexes are not well understood. We have investigated a region of the intrinsically disordered protein myelin basic protein (MBP(145-165)) that interacts with calmodulin, but that also promiscuously binds other biomolecules (membranes, modifying enzymes). To characterize this interaction, we implemented an NMR spectroscopic approach that calculates, for each conformation of the complex, the maximum occurrence based on recorded pseudocontact shifts and residual dipolar couplings. We found that the MBP(145-165)-calmodulin interaction is characterized by structural heterogeneity. Quantitative comparative analysis indicated that distinct conformational landscapes of structural heterogeneity are sampled for different calmodulin-target complexes. Such structural heterogeneity in protein complexes could potentially explain the way that transient and promiscuous protein interactions are optimized and tuned in complex regulatory networks.     

Isolation, identification and application of novel bacterial consortium TJ-1 for the decolourization of structurally different azo dyes

A novel bacterial consortium (TJ-1), which could decolorize Acid Orange 7 (AO7) and manyother azo dyes, was developed. In TJ-1 three bacterial strains were identified as Aeromonas caviae, Proteus mirabilis and Rhodococcus globerulus by 16S rRNA gene sequence analysis. AO7 decolorization was significantly higher with the use of consortium as compared to the use of individual strains, indicating complementary interactions among these strains. AO7 decolorization was observed under microaerophilic condition in the presence of organic carbon source. Either yeast extract (YE) alone or a combination of YE and glucose resulted in much higher decolorization of AO7 as compared to glucose alone, peptone or starch. Kinetic studies with different initial AO7 concentrations showed that more than 90% decolorization could be achieved even at 200mg/l within 16h. Fed-batch studies showed that AO7 decolorization required 10h during the first cycle and 5h in the second and third cycles, showing that bacterial cells could be used for multiple cycles. The consortium also decolorized fifteen other azo dyes individually as well as a simulated wastewater containing a mixture of all the sixteen azo dyes, thus, conferring the possibility of application of TJ-1 for the treatment of industrial wastewaters.     

Comparative organic growth factor requirements of nine Candida species

Nine Candida species isolated from fleshy fruits have been examined for their organic growth factor requirements. Complete or partial deficiencies for thiamine, biotin, pyridoxine, inositol, pantothenic acid, ascorbic acid and xanthine have been reported in C. catenuclta, C. curiosa, C. curvata, C. humicola, C. rhagii, C. steatolytica and C. tropicalis. Only two species, namely, C. fragicola and C. ishiwadea were prototrophic for the growth factors. Concentrations of essential growth factors higher than the optimum have been found inhibitory for the growth of yeasts.     

Double-minute chromatin bodies in HL-60 leukemia cells sensitive and resistant to differentiation inducing agents

We studied the chromosome characteristics of HL-60 promyelocytic leukemia cells sensitive and resistant to differentiation inducing agents (DI). The karyotypic analysis of sensitive (HL-60 S) and resistant (HL-60 R) cells revealed the presence of identical chromosome abnormalities such as loss of chromosomes 5, 9, 10, 14, 16, 17 and X; and gain of chromosome 18. HL-60 S and HL-60 R cells also share five common markers. The difference between the two cell lines consisted essentially of the loss of an unidentifiable chromosome segment in the HL-60 R cell line. In addition, the two sublines showed marked differences in the content of double-minute chromatin bodies (DM), which were abundant in HL-60 S but rarely found in HL-60 R cells. Contrary to a previous report by others, there was no evidence of chromosome rearrangement of the DM as homogeneously stained regions (HSR) or abnormally banding regions (ABR) in the resistant HL-60 R cells. The presence of DM as an expression of gene amplification may be of relevance in the determination of susceptibility of HL-60 cells to DI.     

Fluorescence analysis of late DNA replication in mouse metaphase chromosomes using BUdR and 33258 Hoechst

A late replicating X or Y chromosome can be detected by 33258 Hoechst staining and fluorescence microscopy in a large proportion of female or male mouse embryo cells, respectively, which have been cultured in medium containing 5-bromodeoxyuridine (BUdR) for part of one DNA synthesis period, The observed distribution of late replicating chromosome regions also includes centromeric heterochromatin and some quinacrine positive bands.     

Coping with ethnicity in South Asia: Bangladesh,Punjab and Kashmir compared

In the anthropological and sociological studies of India the terms ‘tribe’ and ‘caste’, have been in use for almost two hundred years. The related notions of ‘tribalism’ and ‘casteism’ were brought in to replace a static (structural) by a dynamic (organizational, processual) approach. Since the 1970s, ‘ethnic group’ and ‘ethnicity’ have gained currency. After defining the terms, three cases of ethnicity are examined, namely East Bengali Muslim, Punjabi Sikh and Kashmiri Muslim. It is argued that, while the first is a success story, the second seems more like a retreat at present, and the third is at best nascent. The reasons for this difference are explored. Ethnicity, it is argued, is not only characterization of identity, but also a set of strategies to establish a new state. This objective is opposed by competing ethnic groups and the existing state. Ethnic movements therefore involve violence and their outcome is dependent upon a variety of factors and therefore contingent.     

Sequence and Structural Features of Subsite Residues in GH10 and GH11 Xylanases

Xylanases are the enzymes that breakdown complex plant cell wall polysaccharide xylan into xylose by hydrolysing the β-(1→4) glycosidic linkage between xylosides. They mainly belong to the families GH10 and GH11 of the glycoside hydrolase claβs of enzymes. GH10 xylanases have (α/β)₈-barrel type of fold whereas GH11 xylanases have β-jelly roll type of fold. Both enzymes have several substrate binding subsites. This study analysed in detail the sequence and structural conservation of subsites residues by examining their 3D structures crystallized with homoxylan or its non-hydrolysable form as substrate. A total of 19 structures from GH10 and 6 structures from GH11 were analysed. It was found that in GH10 the subsites -3 to -1 consisted of conserved residues, whereas in GH11 subsites -1, -3 and +1 were found to be conserved. The substrate and subsite interaction analysed based on the presence of h-bonds and CH-π interactions showed that Face-to-Face or Edge-to-Face CH-π interactions are formed in the subsites of GH10, whereas such specific CH-π interactions were no at all observed in case of GH11 xylanases. The spatial conservation of subsite residues was also analysed using a distance matrix based approach. It was found that in GH10 xylanases conserved residues have conserved spatial position of those residues as opposed to GH11 enzymes where in subsites -2 and +2 conserved residues showed non-conservation in their spatial positions. The results presented in this study can be used in discovering new xylanases and in the engineering highly efficient xylanases.     

Evaluation of adaptability to different seasons in goat breeds of semi-arid region in India through differential expression pattern of heat shock protein genes

The present study was conducted to examine differential expression pattern of HSP genes and adaptability in Indian goat breeds of semi-arid region. The study was conducted in five animals from each breed viz. Barbari, Sirohi, and Jhakrana during winter, thermo-neutral and summer seasons. The respiratory rate (RR) and rectal temperature (RT) of the goats were recorded at 09:00 h during the study period. The blood samples were collected for RNA isolation, cDNA synthesis, and quantitative analysis of HSP genes expression by quantitative RT-PCR. The RR increased significantly (p < 0.01) during summer as compared to winter and thermo-neutral season however, RT did not change (p > 0.05) during different seasons. The expression of HSP genes was significantly (p < 0.01) increased during summer (high THI) as compared to thermo-neutral season in all the goat breeds. Among HSPs, only HSP90 was upregulated (p < 0.01) in Jhakrana goats during winter as compared to thermo-neutral season. The deviation in expression of HSP genes during summer and winter with respect to thermo-neutral season was minimum in Barbari goats. Therefore, it can be concluded that Barbari goats possessed better adaptability during summer and winter as compared to Sirohi and Jhakrana goats in semi-arid climatic conditions of India.     

Seed traits,fatty acid profile and genetic diversity assessment in <Emphasis Type="Italic">Pongamia pinnata</Emphasis> (L.) Pierre germplasm

Phenotypic variation of important seed traits like seed length, seed breadth, seed thickness, 100 seed weight and seed oil content were recorded in a total of 157 collected accessions of Pongamia. Out of these, fatty acid profiles of 38 accessions selected based on their high and low oil content was analyzed. Fatty acid profile revealed high variability in stearic, oleic and linoleic acid which varied from 0.42 to 10.61 %, 34.34 to 74.58 %, and 7.00 to 31.28 % respectively. Variations in palmitic and linolenic acid were small. Iodine value, saponification number and cetane number (CN) of fatty acid methyl esters (FAME) of seed oil ranges from 186.99 to 201.25, 81.13 to 108.19 and 46.16 to 56.47 respectively. Fatty acid compositions, degree of unsaturation and CN are the important parameters, which are used to determine quality of FAME were used as biodiesel. Some of the Pongamia accessions identified were higher in oil content while some accessions showed higher degree of unsaturation and a few of them had CN values higher than 55. Genetic diversity analysis with six TE-AFLP primers generated a total of 334 bands out of which 174 (52.10 %) were polymorphic. The genetic similarity ranged from 0.11 to 0.47. These findings clearly showed high level of genetic diversity and all economically desirable traits were not present in a single genotype of Pongamia. All these traits could be selected from these CPTs and transfer to a single elite variety through selection and breeding programme and could be utilized for large scale multiplication and plantation to produce high quantity and quality biodiesel in future.