Comparative genome sequence analysis of Sulfolobus acidocaldarius and 9 other isolates of its genus for factors influencing codon and amino acid usage

In the present study, major constraints for codon and amino acid usage of Sulfolobus acidocaldarius, Sulfolobus solfataricus, Sulfolobus tokodali, Sulfolobus islandis and 6 other isolates from islandicus species of genus Sulfolobus were investigated. Correspondence analysis revealed high significant correlation between the major trend of synonymous codon usage and gene expression level, as assessed by the “Codon Adaptation Index” (CAI). There is a significant negative correlation between Nc (Effective number of codons) and CAI demonstrating role of codon bias as an important determinant of codon usage. The significant correlation between major trend of synonymous codon usage and GC3s (G + C at third synonymous position) indicated dominant role of mutational bias in codon usage pattern. The result was further supported from SCUO (synonymous codon usage order) analysis. The amino acid usage was found to be significantly influenced by aromaticity and hydrophobicity of proteins. However, translational selection which causes a preference for codons that are most rapidly translated by current tRNA with multiple copy numbers was not found to be highly dominating for all studied isolates. Notably, 26 codons that were found to be optimally used by genes of S. acidocaldarius at higher expression level and its comparative analysis with 9 other isolates may provide some useful clues for further in vivo genetic studies on this genus.     

Molecular dynamics simulation of neuropeptide B and neuropeptide W in the dipalmitoylphosphatidylcholine membrane bilayer

GPR7 and GPR8 are recently deorphanized G-protein-coupled receptors that are implicated in the regulation of neuroendocrine function, feeding behavior, and energy homeostasis. Neuropeptide B (NPB) and neuropeptide W (NPW) are two membrane-bound hypothalamic peptides, which specifically antagonize GPR7 and GPR8. Despite years of research, an accurate estimation of structure and molecular recognition of these neuropeptide systems still remains elusive. Herein, we investigated the structure, orientation, and interaction of NPB and NPW in a dipalmitoylphosphatidylcholine bilayer using long-range molecular dynamics (MD) simulation. During 30-ns simulation, membrane-embedded helical axes of NPB and NPW tilted 30 and 15°, respectively, from the membrane normal in order to overcome possible hydrophobic mismatch with the lipid bilayer. The calculation of various structural parameters indicated that NPW is more rigid and compact as compared to NPB. Qualitatively, the peptides exhibited flexible N-terminal (residues 1–12) and rigid C-terminal α-helical parts (residues 13–21), confirming previous NMR data. A strong electrostatic attraction between C-termini and headgroup atoms caused translocation of the peptides towards lower leaflet of the bilayer. The stabilizing hydrogen bonds (H-bonds) between phosphate groups and Trp1, Lys3, and Arg15 of the peptides played important roles for membrane anchoring. MD simulations of Alanine (Ala) mutants revealed that WYK->Ala variant of NPB/NPW lacked crucial H-bond interactions with phospholipid headgroups and also caused severe misfolding in NPB. Altogether, the knowledge of preferred structural fold and interaction of neuropeptides within the membrane bilayer will be useful to develop synthetic agonist or antagonist peptides for GPR7 and GPR8.     

Cation-Mediated Interplay of Loops in Chaperonin-10

Abstract

The ubiquitously occurring chaperonins consist of a large tetradecameric Chaperonin-60, forming a cylindrical assembly, and a smaller heptameric Chaperonin-10. For a functional protein folding cycle, Chaperonin-10 caps the cylindrical Chaperonin-60 from one end forming an asymmetric complex. The oligomeric assembly of Chaperonin-10 is known to be highly plastic in nature. In Mycobacterium tuberculosis, the plasticity has been shown to be modulated by reversible binding of divalent cations. Binding of cations confers rigidity to the metal binding loop, and also promotes stability of the oligomeric structure. We have probed the conformational effects of cation binding on the Chaperonin-10 structure through fluorescence studies and molecular dynamics simulations. Fluorescence studies show that cation binding induces reduced exposure and flexibility of the dome loop. The simulations corroborate these results and further indicate a complex landscape of correlated motions between different parts of the molecule. They also show a fascinating interplay between two distantly spaced loops, the metal binding “dome loop” and the GroEL-binding “mobile loop”, suggesting an important cation-mediated role in the recognition of Chaperonin-60. In the presence of cations the mobile loop appears poised to dock onto the Chaperonin-60 structure. The divalent metal ions may thus act as key elements in the protein folding cycle, and trigger a conformational switch for molecular recognition.     

Identification of interactions involved in the generation of nucleophilic reactivity and of catalytic competence in the catalytic site Cys/His ion pair of papain

Understanding the roles of noncovalent interactions within the enzyme molecule and between enzyme and substrate or inhibitor is an essential goal of the investigation of active center chemistry and catalytic mechanism. Studies on members of the papain family of cysteine proteinases, particularly papain (EC 3.4.22.2) itself, continue to contribute to this goal. The historic role of the catalytic site Cys/His ion pair now needs to be understood within the context of multiple dynamic phenomena. Movement of Trp177 may be necessary to expose His159 to solvent with consequent decrease in its degree of electrostatic solvation of (Cys25)-S(-). Here we report an investigation of this possibility using computer modeling of quasi-transition states and pH-dependent kinetics using 3,3'-dipyridazinyl disulfide, its n-propyl and phenyl derivatives, and 4,4'-dipyrimidyl disulfide as reactivity probes that differ in the location of potential hydrogen-bonding acceptor atoms. Those interactions that influence ion pair geometry and thereby catalytic competence, including by transmission of the modulatory effect of a remote ionization with pK(a) 4, were identified. A key result is the correlation between the kinetic influence of the modulatory trigger of pK(a) 4 and disruption of the hydrogen bond donated by the indole N-H of Trp177, the hydrophobic shield of the initial "intimate" ion pair. This hydrogen bond is accepted by the amide O of Gln19-a component of the oxyanion hole that binds the tetrahedral species formed from the substrate during the catalytic act. The disruption would be expected to contribute to the mobility of Trp177 and possibly to the effectiveness of the binding of the developing oxyanion.     

Adrenomedullin 2/intermedin regulates HLA-G in human trophoblasts

Adrenomedullin 2 (ADM2), also referred to as intermedin (IMD), is expressed in trophoblast cells in human placenta and enhances the invasion and migration of first-trimester HTR-8SV/neo cells. Further infusion of ADM2 antagonist in pregnant rat causes fetoplacental growth restriction, suggesting a role for ADM2 in maintaining a successful pregnancy. This study was undertaken to assess whether ADM2 protein is present in decidual tissue and colocalized with HLA-G-positive cytotrophoblast cells and natural killer cells; to assess whether ADM2 regulates expression of HLA-G in trophoblast cells; and to identify whether mitogen-activated protein kinase (MAPK) signaling pathway is involved in ADM2-induced trophoblast cell invasion and migration. Using immunohistochemical methods and RT-PCR, this study shows that ADM2 protein is colocalized with HLA-G-expressing cytotrophoblast cells as well as with NCAM1 (CD56) immunoreactivity in human first-trimester decidual tissue, and that ADM2 mRNA is expressed in peripheral blood natural killer cells. Further, ADM2 dose dependently increases the expression of HLA-G antigen in HTR-8SV/neo cells as well as in term placental villi explants, suggesting involvement of ADM2 in the regulation of HLA-G in trophoblast cells. In addition, interference with the activity of RAF and MAPK3/1 by their inhibitors, manumycin and U0126, respectively, reduces ADM2-induced HTR-8SV/neo cell invasion and migration. In summary, this study suggests a potential involvement for ADM2 in regulating HLA-G antigen at the maternal-fetal interface in human pregnancy and facilitating trophoblast invasion and migration via MAPK3/1 phosphorylation.     

Aluminium Rhizotoxicity in Cicer arietinum

Russian Journal of Plant Physiology - The effects of aluminium (Al)-induced alterations on elongating radicles of Cicer arietinum L. were studied in relation to growth and biochemical markers of...     

Impact of forest plantation on methane emissions from tropical peatland

Tropical peatlands are a known source of methane (CH₄) to the atmosphere, but their contribution to atmospheric CH₄ is poorly constrained. Since the 1980s, extensive areas of the peatlands in Southeast Asia have experienced land‐cover change to smallholder agriculture and forest plantations. This land‐cover change generally involves lowering of groundwater level (GWL), as well as modification of vegetation type, both of which potentially influence CH₄ emissions. We measured CH₄ exchanges at the landscape scale using eddy covariance towers over two land‐cover types in tropical peatland in Sumatra, Indonesia: (a) a natural forest and (b) an Acacia crassicarpa plantation. Annual CH₄ exchanges over the natural forest (9.1 ± 0.9 g CH₄ m^?2 year^?1) were around twice as high as those of the Acacia plantation (4.7 ± 1.5 g CH₄ m^?2 year^?1). Results highlight that tropical peatlands are significant CH₄ sources, and probably have a greater impact on global atmospheric CH₄ concentrations than previously thought. Observations showed a clear diurnal variation in CH₄ exchange over the natural forest where the GWL was higher than 40 cm below the ground surface. The diurnal variation in CH₄ exchanges was strongly correlated with associated changes in the canopy conductance to water vapor, photosynthetic photon flux density, vapor pressure deficit, and air temperature. The absence of a comparable diurnal pattern in CH₄ exchange over the Acacia plantation may be the result of the GWL being consistently below the root zone. Our results, which are among the first eddy covariance CH₄ exchange data reported for any tropical peatland, should help to reduce the uncertainty in the estimation of CH₄ emissions from a globally important ecosystem, provide a more complete estimate of the impact of land‐cover change on tropical peat, and develop science‐based peatland management practices that help to minimize greenhouse gas emissions.     

Performance of DHI Score as a Predictor of Benign Paroxysmal Positional Vertigo in Geriatric Patients with Dizziness/Vertigo: A Cross-Sectional Study

Background

Dizziness/vertigo is one of the most common complaint and handicapping condition among patients aged 65 years and older (Geriatric patients). This study was conducted to assess the impact of dizziness/vertigo on the quality of life in the geriatric patients attending a geriatric outpatient clinic.

Settings and Design

A cross-sectional study was performed in a geriatric outpatient clinic of a rural teaching tertiary care hospital in central India.

Materials and Methods

In all consecutive geriatric patients with dizziness/vertigo attending geriatric outpatient clinic, DHI questionnaire was applied to assess the impact of dizziness/vertigo and dizziness associated handicap in the three areas of a patients’ life: physical, functional and emotional domain. Later, each patient was evaluated and underwent Dix-Hallpike maneuver by the physician who was blind of the DHI scoring of the patient.

Statistical Analysis Used

We compared means and proportions of variables across two categories of benign paroxysmal positional vertigo (BPPV) and non-BPPV. For these comparisons we used Student’s t-test to test for continuous variables, chi-square test for categorical variables and Fisher’s exact test in the case of small cell sizes (expected value<5).

Results

The magnitude of dizziness/vertigo was 3%. Of the 88 dizziness/vertigo patients, 19 (22%) and 69(78%) cases, respectively, were attributed to BPPV and non-BPPV group. The association of DHI score ≥50 with the BPPV was found to be statistically significant with x² value = 58.2 at P<0.01.

Conclusion

DHI Score is a useful tool for the prediction of benign paroxysmal positional vertigo. Correct diagnosis of BPPV is 16 times greater if the DHI Score is greater than or equal to 50. The physical, functional and emotional investigation of dizziness, through the DHI, has demonstrated to be a valuable and useful instrument in the clinical routine.     

LRRK2 and RIPK2 Variants in the NOD 2-Mediated Signaling Pathway Are Associated with Susceptibility to Mycobacterium leprae in Indian Populations

In recent years, genome wide association studies have discovered a large number of gene loci that play a functional role in innate and adaptive immune pathways associated with leprosy susceptibility. The immunological control of intracellular bacteria M. leprae is modulated by NOD2-mediated signaling of Th1 responses. In this study, we investigated 211 clinically classified leprosy patients and 230 ethnically matched controls in Indian population by genotyping four variants in NOD2 (rs9302752A/G), LRRK2 (rs1873613A/G), RIPK2 (rs40457A/G and rs42490G/A). The LRRK2 locus is associated with leprosy outcome. The LRRK2 rs1873613A minor allele and respective rs1873613AA genotypes were significantly associated with an increased risk whereas the LRRK2 rs1873613G major allele and rs1873613GG genotypes confer protection in paucibacillary and leprosy patients. The reconstructed GA haplotypes from RIPK2 rs40457A/G and rs42490G/A variants was observed to contribute towards increased risk whereas haplotypes AA was observed to confer protective role. Our results indicate that a possible shared mechanisms underlying the development of these two clinical forms of the disease as hypothesized. Our findings confirm and validates the role of gene variants involved in NOD2-mediated signalling pathways that play a role in immunological control of intracellular bacteria M. leprae.