Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease

More than 1,000 susceptibility loci have been identified through genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings have not yet been defined. Here we used pooled next-generation sequencing to study 56 genes from regions associated with Crohn's disease in 350 cases and 350 controls. Through follow-up genotyping of 70 rare and low-frequency protein-altering variants in nine independent case-control series (16,054 Crohn's disease cases, 12,153 ulcerative colitis cases and 17,575 healthy controls), we identified four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association with a protective splice variant in CARD9 (P < 1 × 10(-16), odds ratio ≈ 0.29) and additional associations with coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by identifying new, rare and probably functional variants that could aid functional experiments and predictive models.     

Molecular functions and cellular roles of the ChlR1 (DDX11) helicase defective in the rare cohesinopathy Warsaw breakage syndrome

In 2010, a new recessive cohesinopathy disorder, designated Warsaw breakage syndrome (WABS), was described. The individual with WABS displayed microcephaly, pre- and postnatal growth retardation, and abnormal skin pigmentation. Cytogenetic analysis revealed mitomycin C (MMC)-induced chromosomal breakage; however, an additional sister chromatid cohesion defect was also observed. WABS is genetically linked to bi-allelic mutations in the ChlR1/DDX11 gene which encodes a protein of the conserved family of Iron–Sulfur (Fe–S) cluster DNA helicases. Mutations in the budding yeast ortholog of ChlR1, known as Chl1, were known to cause sister chromatid cohesion defects, indicating a conserved function of the gene. In 2012, three affected siblings were identified with similar symptoms to the original WABS case, and found to have a homozygous mutation in the conserved Fe–S domain of ChlR1, confirming the genetic linkage. Significantly, the clinically relevant mutations perturbed ChlR1 DNA unwinding activity. In addition to its genetic importance in human disease, ChlR1 is implicated in papillomavirus genome maintenance and cancer. Although its precise functions in genome homeostasis are still not well understood, ongoing molecular studies of ChlR1 suggest the helicase plays a critically important role in cellular replication and/or DNA repair.     

Cloning and expression of HIV-1 p24 gene in insect cells by using BAC-TO-BAC system

Recombinant transposing vector pFHIV24 was constructed by cloning the HIV-1 p24 gene into the Multiple cloning site (MCS) of the transposing vector pFastBac1 in the correct orientation with respect to the polyhedrin promoter. Recombinant bacmid bHIV24 was obtained by transposing a mini-att Tn7 element from the recombinant pFHIV24 to the mini-att Tn7 attachment site on the bacmid by Tn7 transposition functions provided by the helper plasmid. Minipreparation of recombinant bacmid DNA was transfected intoSpodoptera frugiperda (Sf9) cells to get the recombinant virus. Fresh insect Sf9 cells were infected with the recombinant virus containing p24 to express the target protein. The target protein expressed was analyzed on a 15% polyacrylamide gels and then used as antigen to check HIV-1 positive serum by ELISA. Our positive result shows that the expressed p24 protein could be used as standard antigen for HIV-1 diagnosis by ELISA and other reliable diagnostic methods of HIV-1 infection. Supported by the World Bank Boan Program Mallam Nock Joshua: born in 1967, Master of Science To whom correspondence should be addressed (027-7882712-2938)     

Nucleotide sequence of polyhedrin gene of LsNPV and analysis of baculovirus polyhedron proteins

The intact 741 bp polyhedrin gene of LsNPV was sequenced by Silver, Sequencing System, and shares 90.6% and 97.0% nucleotide identity, 97.2% and 97.6% amino acid identity with PfNPV and MdNPV polh genes respectively. The 14 bp conservative sequence with the core element GTAAG, is located in the 5′untranslated region of the gene. The polh gene was predicted to encodes a 246 amino acid residures with molecular weight of 29.0 kd, in which the number of acidic amino acids and alkaline amino acids was roughly equal resulting in almost no charges in polyhedrin protein molecule and hence occlusion body. It gives a valuable implication that ionic bonds as well as hydrophobic bonds and hydrogen bond may play an important role in the crystallization of polyhedrin, by comparing amino acid variation of twenty—one polyhedrin. The comparsion of promoter regions of polyhedrin gene and class II gene shown that they are very similar, but also have differences in GC content. This could explain that both categories of gene are highly expressed, and polyhedrin genes are expressed more higher than class II gene. Wang Jiawang: born in 1962, Doctor of science. Present address: Cancer Institute, CAMS, Beijing 100005     

Control of segment number in vertebrate embryos

The vertebrate body axis is subdivided into repeated segments, best exemplified by the vertebrae that derive from embryonic somites. The number of somites is precisely defined for any given species but varies widely from one species to another. To determine the mechanism controlling somite number, we have compared somitogenesis in zebrafish, chicken, mouse and corn snake embryos. Here we present evidence that in all of these species a similar 'clock-and-wavefront' mechanism operates to control somitogenesis; in all of them, somitogenesis is brought to an end through a process in which the presomitic mesoderm, having first increased in size, gradually shrinks until it is exhausted, terminating somite formation. In snake embryos, however, the segmentation clock rate is much faster relative to developmental rate than in other amniotes, leading to a greatly increased number of smaller-sized somites.     

Peroxidase and phospholipid deficiency in human eosinophilic granulocytes — A marker in population genetics

Summary A large scale investigation was carried out in order to establish the frequency of peroxidase and phospholipid deficiency of eosinophilic granulocytes among various ethnic groups in Israel. The simplicity of the method for staining eosinophilic peroxidase renders it a useful marker for the study of population genetics.     

Nano-bio interfaces probed by advanced optical spectroscopy: From model system studies to optical biosensors

Research in biology and medicine is a rapidly expanding field incorporating some of the most fundamental questions concerning structure, function, and purpose. The forefront of new research demands access to advanced techniques and instrumentation capable of probing these unanswered questions. Over the past several decades, nano-scale materials and devices ranging from quasione dimensional quantum dots to two dimensional graphene sheets have been engineered and have found applications in nano-bio imaging and spectroscopy. In this review, the incorporation of nanomaterials into three influential spectroscopic and microscopic techniques including fluorescence microscopy, surface plasmon resonance, and sum frequency generation will be introduced. Fluorescence imaging has visualized nanomaterials as compliments or replacements to comparable organic fluorphores, act as a quencher for FRET-based sensing, and serve as a nanoscaffold for molecular beacons. Their versatility in coating materials makes nanomaterials an excellent targeting molecule for any cellular macromolecule or structure. In addition to the targeting capabilities of nanomaterials in fluorescence imaging, surface plasmon resonance has incorporated nanomaterials for applications in signal enhancement, selectivity of target molecules, and the development of more refined and accurate detection. Functionalized nano-particles enhance the capabilities of sum frequency generation vibrational spectroscopy by providing unique surface chemistry which alters target molecule interactions and orientations. In summary, the incorporation of nanomaterials has greatly enhanced the field of biology and medicine and has allowed for the continual advancement of not only research but instrument development.     

The influence of homologous plasma and fetal calf serum on human lymphocytic cortisol metabolism.

The influence of a) tissue culture medium (RPMI), b) homologous plasma (HP), and c) fetal calf serum (FCS) on lymphocytic cortisol metabolism was compared to that of phosphate buffered saline alone. RPMI was found to enhance the conversion rate 1.71 times, whereas HP and FCS enhanced it about 3.2 times. Raising the temperature of the HP and FCS to 100 degrees C before incubation reduced the enhancing effect to the level of that obtained with RPMI.