Comparison of the Intrinsic Dynamics of Aminoacyl-tRNA Synthetases

Aminoacyl-tRNA synthetases (AARSs) are an important family of enzymes that catalyze tRNA aminoacylation reaction (Ibba and Soll in Annu Rev Biochem 2000, 69:617–650) [1]. AARSs are grouped into two broad classes (class I and II) based on sequence/structural homology and mode of their interactions with the tRNA molecule (Ibba and Soll in Annu Rev Biochem 2000, 69:617–650) [1]. As protein dynamics play an important role in enzyme function, we explored the intrinsic dynamics of these enzymes using normal mode analysis and investigated if the two classes and six subclasses (Ia–c and IIa–c) of AARSs exhibit any distinct patterns of motion. The present study found that the intrinsic dynamics-based classification of these enzymes is similar to that obtained based on sequence/structural homology for most enzymes. However, the classification of seryl-tRNA synthetase was not straightforward; the internal mobility patterns of this enzyme are comparable to both IIa and IIb AARSs. This study revealed only a few general mobility patterns in these enzymes—(1) the insertion domain is generally engaged in anticorrelated motion with respect to the catalytic domain for both classes of AARSs and (2) anticodon binding domain dynamics are partly correlated and partly anticorrelated with respect to other domains for class I enzymes. In most of the class II AARSs, the anticodon binding domain is predominately engaged in anticorrelated motion with respect to the catalytic domain and correlated to the insertion domain. This study supports the notion that dynamic-based classification could be useful for functional classification of proteins.     

Over-Expression of Cysteine Leucine Rich Protein Is Related to SAG Resistance in Clinical Isolates of Leishmania donovani

Background

Resistance emergence against antileishmanial drugs, particularly Sodium Antimony Gluconate (SAG) has severely hampered the therapeutic strategy against visceral leishmaniasis, the mechanism of resistance being indistinguishable. Cysteine leucine rich protein (CLrP), was recognized as one of the overexpressed proteins in resistant isolates, as observed in differential proteomics between sensitive and resistant isolates of L. donovani. The present study deals with the characterization of CLrP and for its possible connection with SAG resistance.

Methodology and Principal Findings

In pursuance of deciphering the role of CLrP in SAG resistance, gene was cloned, over-expressed in E. coli system and thereafter antibody was raised. The expression profile of CLrP and was found to be over-expressed in SAG resistant clinical isolates of L. donovani as compared to SAG sensitive ones when investigated by real-time PCR and western blotting. CLrP has been characterized through bioinformatics, immunoblotting and immunolocalization analysis, which reveals its post-translational modification along with its dual existence in the nucleus as well as in the membrane of the parasite. Further investigation using a ChIP assay confirmed its DNA binding potential. Over-expression of CLrP in sensitive isolate of L. donovani significantly decreased its responsiveness to SAG (SbV and SbIII) and a shift towards the resistant mode was observed. Further, a significant increase in its infectivity in murine macrophages has been observed.

Conclusion/Significance

The study reports the differential expression of CLrP in SAG sensitive and resistant isolates of L. donovani. Functional intricacy of CLrP increases with dual localization, glycosylation and DNA binding potential of the protein. Further over-expressing CLrP in sensitive isolate of L. donovani shows significantly decreased sensitivity towards SAG and increased infectivity as well, thus assisting the parasite in securing a safe niche. Results indicates the possible contribution of CLrP to antimonial resistance in L. donovani by assisting the parasite growth in the macrophages.     

Perceived Morbidity,Healthcare-Seeking Behavior and Their Determinants in a Poor-Resource Setting: Observation from India

BackgroundTo control the double burden of communicable and non-communicable diseases (NCDs), in the developing world, understanding the patterns of morbidity and healthcare-seeking is critical. The objective of this cross-sectional study was to determine the distribution, predictors and inter-relationship of perceived morbidity and related healthcare-seeking behavior in a poor-resource setting.MethodsBetween October 2013 and July 2014, 43999 consenting subjects were recruited from 10107 households in Malda district of West Bengal state in India, through multistage random sampling, using probability proportional-to-size. Information on socio-demographics, behaviors, recent ailments, perceived severity and healthcare-seeking were analyzed in SAS-9.3.2.ResultsRecent illnesses were reported by 55.91% (n=24600) participants. Among diagnosed ailments (n=23626), 50.92% (n=12031) were NCDs. Respiratory (17.28%,n=7605)), gastrointestinal (13.48%,n=5929) and musculoskeletal (6.25%,n=2749) problems were predominant. Non-qualified practitioners treated 53.16% (n=13074) episodes. Older children/adolescents [adjusted odds ratio for private healthcare providers(AOR_Pri)=0.76, 95% confidence interval=0.71-0.83) and for Govt. healthcare provider(AOR_Govt)=0.80(0.68-0.95)], females [AOR_Govt=0.80(0.73-0.88)], Muslims [AOR_Pri=0.85(0.69-0.76) and AOR_Govt=0.92(0.87-0.96)], backward castes [AOR_Govt=0.93(0.91-0.96)] and rural residents [AOR_Pri=0.82(0.75-0.89) and AOR_Govt=0.72(0.64-0.81)] had lower odds of visiting qualified practitioners. Apparently less severe NCDs [acid-peptic disorders: AOR_Pri=0.41(0.37-0.46) & AOR_Govt=0.41(0.37-0.46), osteoarthritis: AOR_Pri=0.72(0.59-0.68) & AOR_Govt=0.58(0.43-0.78)], gastrointestinal [AOR_Pri=0.28(0.24-0.33) & AOR_Govt=0.69(0.58-0.81)], respiratory [AOR_Pri=0.35(0.32-0.39) & AOR_Govt=0.46(0.41-0.52)] and skin infections [AOR_Pri=0.65(0.55-0.77)] were also less often treated by qualified practitioners. Better education [AOR_Pri=1.91(1.65-2.22) for ≥graduation], sanitation [AOR_Pri=1.58(1.42-1.75)] and access to safe water [AOR_Pri=1.33(1.05-1.67)] were associated with healthcare-seeking from qualified private practitioners. Longstanding NCDs [chronic obstructive pulmonary diseases: AOR_Pri=1.80(1.46-2.23), hypertension: AOR_Pri=1.94(1.60-2.36), diabetes: AOR_Pri=4.94(3.55-6.87)] and serious infections [typhoid: AOR_Pri=2.86(2.04-4.03)] were also more commonly treated by qualified private practitioners. Potential limitations included temporal ambiguity, reverse causation, generalizability issues and misclassification.ConclusionIn this poor-resource setting with high morbidity, ailments and their perceived severity were important predictors for healthcare-seeking. Interventions to improve awareness and healthcare-seeking among under-privileged and vulnerable population with efforts to improve the knowledge and practice of non-qualified practitioners probably required urgently.     

Stacking interactions in RNA and DNA: Roll‐slide energy hyperspace for ten unique dinucleotide steps

Understanding dinucleotide sequence directed structures of nuleic acids and their variability from experimental observation remained ineffective due to unavailability of statistically meaningful data. We have attempted to understand this from energy scan along twist, roll, and slide degrees of freedom which are mostly dependent on dinucleotide sequence using ab initio density functional theory. We have carried out stacking energy analysis in these dinucleotide parameter phase space for all ten unique dinucleotide steps in DNA and RNA using DFT‐D by ωB97X‐D/6‐31G(2d,2p), which appears to satisfactorily explain conformational preferences for AU/AU step in our recent study. We show that values of roll, slide, and twist of most of the dinucleotide sequences in crystal structures fall in the low energy region. The minimum energy regions with large twist values are associated with the roll and slide values of B‐DNA, whereas, smaller twist values correspond to higher stability to RNA and A‐DNA like conformations. Incorporation of solvent effect by CPCM method could explain the preference shown by some sequences to occur in B‐DNA or A‐DNA conformations. Conformational preference of BII sub‐state in B‐DNA is preferentially displayed mainly by pyrimidine–purine steps and partly by purine–purine steps. The purine–pyrimidine steps show largest effect of 5‐methyl group of thymine in stacking energy and the introduction of solvent reduces this effect significantly. These predicted structures and variabilities can explain the effect of sequence on DNA and RNA functionality. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 134–147, 2015.     

Ligand-to-ligand electron transfer and temperature induced valence tautomerism in o-dioxolene chelated manganese complexes

Three polymeric o-dioxolene chelated manganese(III) complexes, {[Mn^III(H₂L¹)(Cl₄Cat)₂][Mn^III(Cl₄Cat)₂(H₂O)₂]}_∞ (1) (L¹ = N,N′-bis(2-pyridylmethyl)-1,4-butanediamine, Cl₄Cat = tetrachlorocatecholate dianion], {[Mn^III(H₂L¹)(Br₄Cat)₂][Mn^III(Br₄Cat)₂(H₂O)₂]·4DMF}_∞, (2) and {[Mn^III(H₂L²)(Br₄Cat)₂][Mn^III(Br₄Cat)₂(DMF)₂]}_∞ (3) (L² = N,N′-bis(2-pyridylmethyl)-1,6-hexanediamine, Br₄Cat = tetrabromocatecholate dianion) have been synthesized and structures were determined by X-ray crystallography. All the complexes were fully characterized by various spectroscopic techniques and their electronic properties are described. It was found that the simple protonation or deprotonation of the bridging ligand (L¹ or L²) coordinated to metal-dioxolene chromophore induce a change in the oxidation state of the coordinated dioxolene ligand without affecting the metal oxidation state. As a result, drastic change in the optical absorption properties of the complexes is observed in the visible and near-IR region as the transformation involves semiquinone-catecholate ligands. Moreover, all three complexes undergo thermally induced valence tautomerism in solution. For all the complexes, on increasing the temperature, the intensity of the lower energy Inter Valence Charge Transfer (IVCT) band at about 1930 nm increases with corresponding decrease of 600 nm band with an isosbestic point at 1820 nm due to the formation of mixed valence species Mn^II(X₄SQ)(X₄Cat)⁻ from (X = Cl or Br) by the transfer of one electron from Cat²⁻ to Mn^III center.     

Hematopoietic Recovery and Amelioration of Radiation-Induced Lethality by the Vitamin E Isoform δ-Tocotrienol

δ-Tocotrienol (DT3), a vitamin E isoform, is associated with strong antioxidant and immunomodulatory properties. We confirmed the potent antioxidant activity in membrane systems and showed that DT3 is an effective radiation protector and mitigator. DT3 (4 μM, P < 0.001) inhibited lipid peroxidation in mouse liver microsomes and nitric oxide (NO) formation (20 μM DT3, P < 0.01) in RAW264.7 cells, a murine alveolar macrophage line. In CD2F1 mice exposed to lethal total-body radiation from a (60)Co γ-radiation source, a single subcutaneous (s.c.) injection of DT3 before or after irradiation produced a significant increase in 30-day survival. DT3 was effective from 18.75 to 300 mg/kg (--24 h, P < 0.001). A single dose of 150 or 300 mg/kg DT3 given 24 h before irradiation (radioprotection) resulted in dose reduction factors (DRFs) of 1.19 and 1.27, respectively (P < 0.001). Further, DT3 reduced radiation lethality when administered 2, 6 or 12 h after irradiation, and 150 mg/kg DT3 administered 2 h after exposure conferred a DRF of 1.1 (mitigation). The optimum schedule of 300 mg/kg DT3 24 h prior to 7 Gy significantly reduced pancytopenia compared to irradiated controls (P < 0.05). The large therapeutic potential of and multi-lineage hematopoietic recovery for DT3 warrants further studies.     

Variations of scalp, pubic and axillary hair

Hair examinations and comparisons conducted by forensic scientists often provide investigative and associative information. Apart from its length and its natural color, hair displays a morphologic diversity both macroscopically and microscopically. Pseudogenization of 相似文献