Identification of hydrogen bonds to the Rieske cluster through the weakly coupled nitrogens detected by electron spin echo envelope modulation spectroscopy

The interaction of the reduced[2Fe-2S] cluster of isolated Rieske fragment from the bc1 complex of Rhodobacter sphaeroides with nitrogens (14N and 15N) from the local protein environment has been studied by X- and S-band pulsed EPR spectroscopy. The two-dimensional electron spin echo envelope modulation spectra of uniformly 15N-labeled protein show two well resolved cross-peaks with weak couplings of approximately 0.3-0.4 and 1.1 MHz in addition to couplings in the range of 6-8 MHz from two coordinating Ndelta of histidine ligands. The quadrupole coupling constants for weakly coupled nitrogens determined from S-band electron spin echo envelope modulation spectra identify them as Nepsilon of histidine ligands and peptide nitrogen (Np), respectively. Analysis of the line intensities in orientation-selected S-band spectra indicated that Np is the backbone N-atom of Leu-132 residue. The hyperfine couplings from Nepsilon and Np demonstrate the predominantly isotropic character resulting from the transfer of unpaired spin density onto the 2s orbitals of the nitrogens. Spectra also show that other peptide nitrogens in the protein environment must carry a 5-10 times smaller amount of spin density than the Np of Leu-132 residue. The appearance of the excess unpaired spin density on the Np of Leu-132 residue indicates its involvement in hydrogen bond formation with the bridging sulfur of the Rieske cluster. The configuration of the hydrogen bond therefore provides a preferred path for spin density transfer. Observation of similar splittings in the 15N spectra of other Rieske-type proteins and [2Fe-2S] ferredoxins suggests that a hydrogen bond between the bridging sulfur and peptide nitrogen is a common structural feature of [2Fe-2S] clusters.     

福建省3种维管植物新记录

报道3种福建省新分布维管植物,分别为四川石杉Huperzia sutchueniana (Herter) Ching、金发石杉Huperzia quasipolytrichoides (Hayata) Ching、山柳菊Hieracium umbellatum L.。标本存放于福建生物工程职业技术学院标本馆。     

Array CGH data modeling and smoothing in Stationary Wavelet Packet Transform domain

Background

Array-based comparative genomic hybridization (array CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci and the reliable detection of local one-copy-level variations. Characterization of these DNA copy number changes is important for both the basic understanding of cancer and its diagnosis. In order to develop effective methods to identify aberration regions from array CGH data, many recent research work focus on both smoothing-based and segmentation-based data processing. In this paper, we propose stationary packet wavelet transform based approach to smooth array CGH data. Our purpose is to remove CGH noise in whole frequency while keeping true signal by using bivariate model.

Results

In both synthetic and real CGH data, Stationary Wavelet Packet Transform (SWPT) is the best wavelet transform to analyze CGH signal in whole frequency. We also introduce a new bivariate shrinkage model which shows the relationship of CGH noisy coefficients of two scales in SWPT. Before smoothing, the symmetric extension is considered as a preprocessing step to save information at the border.

Conclusion

We have designed the SWTP and the SWPT-Bi which are using the stationary wavelet packet transform with the hard thresholding and the new bivariate shrinkage estimator respectively to smooth the array CGH data. We demonstrate the effectiveness of our approach through theoretical and experimental exploration of a set of array CGH data, including both synthetic data and real data. The comparison results show that our method outperforms the previous approaches.

     

The contemporary refugee crisis: an overview of mental health challenges

There has been an unprecedented upsurge in the number of refugees worldwide, the majority being located in low‐income countries with limited resources in mental health care. This paper considers contemporary issues in the refugee mental health field, including developments in research, conceptual models, social and psychological interventions, and policy. Prevalence data yielded by cross‐sectional epidemiological studies do not allow a clear distinction to be made between situational forms of distress and frank mental disorder, a shortcoming that may be addressed by longitudinal studies. An evolving ecological model of research focuses on the dynamic inter‐relationship of past traumatic experiences, ongoing daily stressors and the background disruptions of core psychosocial systems, the scope extending beyond the individual to the conjugal couple and the family. Although brief, structured psychotherapies administered by lay counsellors have been shown to be effective in the short term for a range of traumatic stress responses, questions remain whether these interventions can be sustained in low‐resource settings and whether they meet the needs of complex cases. In the ideal circumstance, a comprehensive array of programs should be provided, including social and psychotherapeutic interventions, generic mental health services, rehabilitation, and special programs for vulnerable groups. Sustainability of services, ensuring best practice, evidence‐based approaches, and promoting equity of access must remain the goals of future developments, a daunting challenge given that most refugees reside in settings where skills and resources in mental health care are in shortest supply.     

Association between the Polymorphism rs3217927 of CCND2 and the Risk of Childhood Acute Lymphoblastic Leukemia in a Chinese Population

CyclinD proteins, the ultimate recipients of mitogenic and oncogenic signals, play a crucial role in cell-cycle regulation. CyclinD2, one of the cyclinD family, is overexpressed in T-acute lymphoblastic leukemia (ALL) and B-cell chronic lymphocytic leukemia and involved in the pathogenesis of leukemias. Recent reports indicated that CCND2 polymorphisms are associated with human cancer risk, thusly we hypothesized that CCND2 gene polymorphisms may contribute to childhood ALL susceptibility. We selected the polymorphism rs3217927 located in the 3′UTR region of CCND2 to assess its associations with childhood ALL risk in a case-control study. A significant difference was found in the genotype distributions of rs3217927 polymorphism between cases and controls (P = 0.019) and homozygous GG genotype may be an increased risk factor for childhood ALL (adjusted OR  =  1.84, 95% CI  =  1.14 —2.99). Furthermore, this increased risk was more pronounced with GG genotype among high-risk ALL (adjusted OR  = 1.95, 95% CI  =  1.04–3.67), low-risk ALL (adjusted OR  =  2.09, 95% CI  =  1.13–3.87), B-phenotype ALL patients (adjusted OR  =  1.78, 95% CI  =  1.08–2.95) and T-phenotype ALL patients (adjusted OR  =  2.87, 95% CI  =  1.16–7.13). Our results provide evidence that CCND2 polymorphism rs3217927 may be involved in the etiology of childhood ALL, and the GG genotype of rs3217927 may modulate the genetic susceptibility to childhood ALL in the Chinese population. Further functional studies and investigations in larger populations should be conducted to validate our findings.     

外用红色诺卡氏菌细胞壁骨架效力测试实验方法的研究

摸索改进外用红色诺卡氏菌(Nocardia rubra)细胞壁骨架的两种效力测试方法,即流式细胞术-荧光微球法、流式细胞术-免疫双标法(荧光微球+荧光抗体),并与国家食品药品监督管理局原审批方法进行比较,经过统计学评估,评价两种方法的可行性.通过抽取小鼠免疫后获得的腹腔液注入到流式细胞仪,在发射光的荧光通路中,检测巨噬...     

Crystal and solution structures of methyltransferase RsmH provide basis for methylation of C1402 in 16S rRNA

RsmH is a specific AdoMet-dependent methyltransferase (MTase) responsible for N(4)-methylation of C1402 in 16S rRNA and conserved in almost all species of bacteria. The methylcytidine interacts with the P-site codon of the mRNA and increases ribosomal decoding fidelity. In this study, high resolution crystal structure (2.25?) of Escherichia coli RsmH in complex with AdoMet and cytidine (the putative rRNA binding site) was determined. The structural analysis demonstrated that the complex consists of two distinct but structurally related domains: the typical MTase domain and the putative substrate recognition and binding domain. A deep pocket was found in the conserved AdoMet binding domain. It was also found that the cytidine bound far from AdoMet with the distance of 25.9?. It indicates that the complex is not in a catalytically active state, and structural rearrangement of RsmH or the nucleotides neighboring C1402 may be necessary to trigger catalysis. Although there is only one molecule in the asymmetric unit of the crystals, RsmH can form a compact dimer across a crystallographic twofold axis. Further analysis of RsmH by small-angle X-ray scattering (SAXS) also revealed the dimer in solution, but with a more flexible conformation than that in crystal, likely resulting from the absence of the substrate. It implies that an active status of RsmH in vivo is achieved by a formation of the dimeric architecture. In general, crystal and solution structural analysis provides new information on the mechanism of the methylation of the fine-tuning ribosomal decoding center by the RsmH.     

Characterization of Fusarium species section Liseola by restriction analysis of the IGS region

Fusarium species section Liseola namely F. fujikuroi, F. proliferatum, F. andiyazi, F. verticillioides, and F. sacchari are well-known plant pathogens on rice, sugarcane and maize. In the present study, restriction analysis of the intergenic spacer regions (IGS) was used to characterize the five Fusarium species isolated from rice, sugarcane and maize collected from various locations in Peninsular Malaysia. From the analysis, and based on restriction patterns generated by the six restriction enzymes, Bsu151, BsuRI, EcoRI, Hin6I, HinfI, and MspI, 53 haplotypes were recorded among 74 isolates. HinfI showed the most variable restriction patterns (with 11 patterns), while EcoRI showed only three patterns. Although a high level of variation was observed, it was possible to characterize closely related species and isolates from different species. UPGMA cluster analysis showed that the isolates of Fusarium from the same species were grouped together regardless of the hosts. We conclude that restriction analysis of the IGS regions can be used to characterize Fusarium species section Liseola and to discriminate closely related species as well as to clarify their taxonomic position.     

Ethnic variations of a retinoblastoma susceptibility gene (RB1) polymorphism in eight Asian populations

An A → G single nucleotide polymorphism (SNP) at nucleotide 153,104 in the retinoblastoma susceptibility locus (RB1) at 13q14 was previously reported to be present only in Asians. In this study, we determined the distribution of this SNP in normal Southeast Asian populations (Chinese, Malay, Javanese, Thai, Filipino), in South Asian populations (Bangladeshi, Pakistani Pushtun and Indian) and in Chinese retinoblastoma cases and control subjects. TheRB1 SNP was present in all populations at an overall frequency of ≤0.18. Heterozygosity was higher in the Southeast Asian groups (0.14–0.34) than in the South Asian groups (Bangladeshi and Indian) (0.04–0.06). Significant differences in allele frequencies were found between the two population groups. Interestingly, our Pakistani population comprised of ethnic Pushtuns from northwest Pakistan was significantly different from the neighbouring Bangladeshi and Indian populations. No significant difference was found between Chinese case patients and control subjects. ThisRB1 SNP appears to be an ethnic variant prevalent in Southeast Asian populations and may be useful for studyingRB1 inheritance by pedigree analysis.