Impact of Health Workers' Choice of COVID-19 Vaccine Booster on Immunization Levels in Istanbul, Turkey

BACKGROUND

There are limited data regarding short- and medium-term IgG antibody levels after the CoronaVac and BNT162b2 vaccines. This study aimed to investigate the antibody responses of health workers who initially received two doses of CoronaVac one month apart followed by a booster dose of either CoronaVac or BNT162b2, as well as determine whether either vaccine provided superior results.

METHODS

This research represents the second phase of a mixed-methods vaccine cohort study and was conducted between July 2021 and February 2022. The participants (n = 117) were interviewed in person and blood samples were collected before and at 1 and 6 months after the booster vaccination.

RESULTS

BNT162b2 was found to have greater immunogenic potential than CoronaVac (p < 0.001). Health workers without chronic disease exhibited statistically significant increases in antibody levels after both vaccines (p < 0.001), whereas only BNT162b2 caused a significant increase in antibody levels in participants with chronic disease (p < 0.001). Samples obtained before and at 1 and 6 months after the booster vaccination revealed no age- or sex-based differences in IgG-inducing potential for either vaccine (p > 0.05). Antibody levels were comparable in both vaccine groups before the booster regardless of COVID-19 history (p > 0.05); however, antibody levels were significantly higher after the BNT162b2 booster at 1 month (<0.001) and at 6 months, except among participants who had a positive history of COVID-19 infection (p < 0.001).

CONCLUSIONS

Our results suggest that even a single booster dose of BNT162b2 after initial vaccination with CoronaVac provides a protective advantage against COVID-19, especially for risk groups such as health workers and those with chronic diseases.

Cr[Formula: see text]AlN and the search for the highest temperature superconductor in the M[Formula: see text]AX family

We have developed a high-throughput computational method to predict the superconducting transition temperature in stable hexagonal M[Formula: see text]AX phases, and applied it to all the known possible choices for M (M: Sc, Ti, V, Cr, Mn, Fe, Y, Zr, Nb, Mo, Lu, Hf and Ta). We combine this with the best candidates for A (A: Al, Cu, Ge and Sn ) and X (X: C and N) from our previous work, and predict T[Formula: see text] for 60 M[Formula: see text]AX-phase materials, 53 of which have never been studied before. From all of these, we identify Cr[Formula: see text]AlN as the best candidate for the highest T[Formula: see text], and confirm its high T[Formula: see text] with more detailed density functional theory electron-phonon coupling calculations. Our detailed calculations predict [Formula: see text] = 14.8 K for Cr[Formula: see text]AlN, which is significantly higher than any [Formula: see text] value known or predicted for any material in the M[Formula: see text]AX family to date.

Seroprevalence of Toxoplasma, Rubella and Cytomegalovirus in Women of Fertility Age in Our Region

Objective

Toxoplasma gondii (T. gondii), Rubella and Cytomegalovirus (CMV) infections can cause severe morbidity in the fetus when transmissed during pregnancy. In our study, it was aimed to examine the seropositivity rates for T. gondii, Rubella and CMV infections in women of childbearing age who applied to our hospital.

Methods

Anti-Toxoplasma IgG, anti-Toxoplasma IgM, anti-Rubella IgG, anti-Rubella IgM, anti-CMV IgG and anti-CMV were studied in women of childbearing age (18-49 years old) who applied to our hospital's outpatient clinics between January 2018 and December 2020. The tests were performed in our microbiology laboratory using the ELISA method on Architect i2000 (Abbott, USA) and COBAS e601 (Roche, Germany) devices.

Results

As a result of the data obtained, the percentages of IgM and IgG positivity for anti-Toxoplasma were calculated as 1.4% and 30.9%, respectively. Anti-Rubella IgM positivity was 0.7%, anti-Rubella IgG positivity was 91%, anti-CMV IgG positivity was 98.8%, and anti-CMV IgM positivity was 2%.

Conclusion

Having its own seroprevalence for each region has is important in terms of planning pregnancy screenings. The seropositivity rates in our region are in line with other studies in the country. Since CMV seropositivity is very high in the population and there is no effective treatment or vaccine, screening may not be not necessary. T. gondii and Rubella screenings can be recommended due to the lower immunity rates and the availability of vaccine and treatment options.

Prediction of phonon-mediated superconductivity in new Ti-based M[Formula: see text]AX phases

A high-throughput computational method is used to predict 39 new superconductors in the Ti-based M[Formula: see text]AX phases, and the best candidates are then studied in more detail using density functional theory electron-phonon coupling calculations. The detailed calculations agree with the simple predictions, and Ti[Formula: see text]AlX (X: B, C and N) materials are predicted to have higher values of [Formula: see text] than any currently known hexagonal M[Formula: see text]AX phases. The electronic states at the Fermi level are dominated by the Ti 3d states. The choice of X (X: B, C and N) has a significant impact on the electronic density of states but not on the phonon characteristics. The electron-phonon coupling parameter for Ti[Formula: see text]AlX (X: B, C and N) was determined to be 0.685, 0.743 and 0.775 with a predicted [Formula: see text] of 7.8 K, 10.8 K and 13.0 K, respectively.

Investigation of diagnostic use of serum anti-Müllerian hormone concentration in dioestrus and anoestrus bitches before and after ovariohysterectomy and the relationship with ovarian follicle numbers

The aims of the study were to (1) compare the serum concentration of anti-Müllerian hormone (AMH) with the number of follicles in ovaries and (2) determine the serum AMH con- centration before and after ovariohysterectomy in dioestrus and anoestrus bitches. Sixteen bitches were divided into two groups: Group I (n=8) consisted of dioestrus and group II (n=8) anoestrus bitches. The blood samples for AMH assesment were taken before ovariohysterectomy (day 0) and on day 1, 5 and 10. Both in group I and II, serum AMH concentrations on day 1 and 5 were significantly different compared to day 0 (p⟨0.05). However, the concentrations at day 10 were under the minimum detectable concentration (1.0 ng/mL) and this finding revealed that ovaries are the only source of AMH synthesis. Follicle counts were not statistically different between the groups (p>0.05). Significantly positive correlation in serum AMH with secondary follicle num- bers (r=.942, p⟨0.01), as well as negative correlation with antral follicle numbers (r=-.765, p⟨0.05) were determined in the group I. In the group II, positive correlations between serum AMH concentration and secondary follicle numbers (r=.960, p⟨0.01) and early antral follicles (r=.726, p⟨0.05) were noted. Assesment of AMH concentration seems to not only provide the diagnosis of the presence of ovaries but also correlate with the number of secondary follicles in young dioestrus and anoestrus bitches.

Evaluation of Nigella sativa oil loaded electrospun polyurethane nanofibrous mat as wound dressing

Electrospun nanofibers have a natural wound healing effect due to their similarity to the extracellular matrix (ECM). Nigella sativa oil, which has therapeutic properties, is used for a wide variety of applications in traditional medicine. The aim of this study was to investigate the release characteristic and wound healing performance of Nigella sativa oil (NSO) loaded polyurethane (PU) electrospun nanofibrous mats in wound dressing applications. In addition, the antibacterial activity and cytotoxicity of the electrospun mats were studied. Analyses using a scanning electron microscope (SEM) showed that PU/NSO nanofibrous mat with an average fiber diameter of 416 ± 66 nm were successfully fabricated. NSO was released at a maximum ratio of 30% from the electrospun mat, and the Korsmeyer-Peppas model was identified as best for determining the release mechanism. Significant antibacterial activity was observed against Staphylococcus aureus (90.26%) and Escherichia coli (95.75%). The developed PU/NSO nanofibrous mat increased the cell viability more than 100% in human umbilical vein endothelial cell line (HUVEC) cell line. The NSO loaded PU nanofibrous mat significantly promoted the wound healing process on a rat wound model, and its wound closure reached approximately 85% compared to the control groups on the 9^th day (p < 0.01). The results indicated PU/NSO nanofibrous mat is a suitable candidate for a wound dressing.

Primary Unilateral Small Cell Neuroendocrine Carcinoma of the Kidney in a Dog

Primary small cell carcinomas are rare in domestic animals. A mass measuring 15 × 20 × 9 cm was detected in the left abdominal cavity of a 7.5-year-old female golden retriever. The cut surface of the excised mass showed a tumour replacing the left kidney. Microscopically, the mass was composed of polymorphic, small basophilic cells with a high nuclear to cytoplasmic ratio and round, oval or short slender fusiform nuclei with condensed or finely granular chromatin, absent or inconspicuous nucleoli, and scant, faintly eosinophilic cytoplasm with poorly defined cytoplasmic borders. Immunohistochemically, most of the neoplastic cells were immunoreactive for thyroid transcription factor 1 and CD56, moderately positive for vimentin and weakly or sparsely labelled for chromogranin A, synaptophysin, Wilms' tumour 1 protein, neuron-specific enolase, pan-cytokeratin (CK) AE1/AE3 and epithelial membrane antigen. The tumour cells were negative for glial fibrillary acidic protein (GFAP), ionized calcium-binding adapter molecule 1, CK7, CK20, CD3, CD45 and CD99. These findings indicated a neuroendocrine origin of the tumour. To the best of author's knowledge, this is the first report of a small cell neuroendocrine carcinoma originating as a primary tumour in the kidney of a dog.

The corepressor CtBP2 is required for proper development of the mouse cerebral cortex

The development of the cerebral cortex depends on numerous parameters, including extracellular cues and microenvironmental factors that also affect gene expression. C-Terminal Binding Proteins (CtBPs) 1 and 2 are transcriptional co-repressors which have been shown to be critically involved in embryonic development. CtBPs are oxygen sensing molecules, and we have previously demonstrated an important role for CtBP1 in integrating oxygen levels and BMP-signaling to influence neural progenitor fate choice. In turn, CtBP2 has been associated with neurodevelopment and neurological disease, and we have shown that CtBP2 acetylation and dimerization, required for proper transcriptional activity, are regulated by microenvironmental oxygen levels. Yet, the putative function of CtBP2 in mammalian cortical development and neurogenesis in vivo is still largely unknown. Here we show that CtBP2 was widely expressed by neural stem and progenitor cells (NSPCs) as well as neurons during cortical development in mice. By using in utero electroporation of siRNA to reduce the levels of CtBP2 mRNA and protein in the developing mouse brain, we found that the NSPC proliferation and migration were largely perturbed, while glial differentiation under these conditions remained unchanged. Our study provides evidence that CtBP2 is required for the maintenance and migration of the NSPCs during mouse cortical development.

Effects of partial and complete replacement of added phosphates with encapsulated phosphates on lipid oxidation inhibition in cooked ground meat during storage

The objective of this research was to investigate the influence of various levels (0.0, 0.1, 0.2, 0.3, 0.4, 0.5%) of added encapsulated polyphosphates (sodium tripolyphosphate; sodium pyrophosphate) combined with unencapsulated polyphosphate to total 0.5% on the inhibition of lipid oxidation in cooked ground meat (beef, chicken) during refrigerated storage (0, 1, 7 d). The use of sodium tripolyphosphate (encapsulated sodium tripolyphosphate, unencapsulated sodium tripolyphosphate) led to lower cooking loss compared to sodium pyrophosphate in both meat species (p < 0.05). Increasing encapsulated sodium tripolyphosphate up to 0.3% decreased cooking loss in ground beef (p < 0.05). Added encapsulated polyphosphate at 0.5% had the same effect on pH as 0.5% unencapsulated polyphosphate in the cooked ground beef and chicken. A higher accumulation of orthophosphate was determined in the samples with sodium tripolyphosphate compared to those with sodium pyrophosphate (p < 0.05). Inclusion of a minimum of 0.1% encapsulated polyphosphate decreased thiobarbituric acid reactive substances and lipid hydroperoxides on 7 d. Increasing encapsulated sodium tripolyphosphate and encapsulated sodium pyrophosphate up to 0.2% in beef decreased thiobarbituric acid reactive substances at 7 d. Addition of 0.4% encapsulated sodium tripolyphosphate and 0.3% encapsulated sodium pyrophosphate in chicken prevented any increase in TBARS during storage. Incorporating encapsulated sodium pyrophosphate at 0.3% inhibited lipid hydroperoxide formation in beef and chicken. The meat industry could achieve enhanced lipid oxidation inhibition by replacing some of the unencapsulated polyphosphate with encapsulated polyphosphate in their product formulations.

Multicellular Interactions in 3D Engineered Myocardial Tissue

Cardiovascular disease is a leading cause of death in the US and many countries worldwide. Current cell-based clinical trials to restore cardiomyocyte (CM) health by local delivery of cells have shown only moderate benefit in improving cardiac pumping capacity. CMs have highly organized physiological structure and interact dynamically with non-CM populations, including endothelial cells and fibroblasts. Within engineered myocardial tissue, non-CM populations play an important role in CM survival and function, in part by secreting paracrine factors and cell-cell interactions. In this review, we summarize the progress of engineering myocardial tissue with pre-formed physiological multicellular organization, and present the challenges toward clinical translation.

Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1

Our information-driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in the CAPRI community-wide experiment. This sustained performance is due, in part, to its ability to integrate experimental data and/or bioinformatics information into the modelling process, and also to the overall robustness of the scoring function used to assess and rank the predictions. In the CASP-CAPRI Round 1 scoring experiment we successfully selected acceptable/medium quality models for 18/14 of the 25 targets - a top-ranking performance among all scorers. Considering that for only 20 targets acceptable models were generated by the community, our effective success rate reaches as high as 90% (18/20). This was achieved using the standard HADDOCK scoring function, which, thirteen years after its original publication, still consists of a simple linear combination of intermolecular van der Waals and Coulomb electrostatics energies and an empirically derived desolvation energy term. Despite its simplicity, this scoring function makes sense from a physico-chemical perspective, encoding key aspects of biomolecular recognition. In addition to its success in the scoring experiment, the HADDOCK server takes the first place in the server prediction category, with 16 successful predictions. Much like our scoring protocol, because of the limited time per target, the predictions relied mainly on either an ab initio center-of-mass and symmetry restrained protocol, or on a template-based approach whenever applicable. These results underline the success of our simple but sensible prediction and scoring scheme. Proteins 2017; 85:417-423. © 2016 Wiley Periodicals, Inc.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.

EVALUATION OF PREIMPLANTATION GENETIC ANEUPLOIDY SCREENING CASES AT A REFERENCE GENETICS CENTER: 10 YEARS' EXPERIENCE

The aim of this study is to review and evaluate our preimplantation genetic screening (PGS) records in terms of their demographic data, indications, cytogenetic results, pregnancy outcomes and discuss these findings in different aspects. PGS was performed in a total of 84 couples (87 cycles) between the period 2005 to 2015. Biopsied blastomeres from embryos on day 3 were fixed and fluorescence in situ hybridization was carried out for chromosomes 13, 16, 18, 21, 22, X and Y depending on the indication. The diagnostic and clinical data were retrospectively evaluated. A total of 450 blastomeres were biopsied. Ninety-eight of them were found to be suitable for transfer. They were transferred to 72 patients in 75 cycles resulting in 23 pregnancies and 20 healthy births. The most common indication was unexplained infertility. The implantation rate was calculated as 23.4% whereas the take-home baby rate was 26.6% per transfer. The highest rate of healthy living births is achieved in patients having low grade maternal mosaic sex chromosomal aneuploidy. All living births achieved by PGS had normal chromosomal structure which we can propose it as an alternative test for couples at risk to select normal embryos to improve the outcomes of assisted reproductive procedures and to avoid the transfer of chromosomally unbalanced and multiple embryos.

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.

TWINS WITH KLEEFSTRA SYNDROME DUE TO CHROMOSOME 9q34.3 MICRODELETION

Kleefstra or 9q subtelomeric deletion syndrome (9qSTDS) is a rare microdeletion syndrome. The most prominent phenotypic features include hypotonia, developmental retardation, as well as typical dysmorphic face. It has been shown that terminal deletions of the chromosome 9q34.3 region, or EHMT1 gene mutations, lead to Kleefstra syndrome. We present 16-month-old twin sisters, one of whom had originally been referred for Down syndrome screening due to hypotonia, growth and development retardation, dysmorphic facial signs, and accompanying congenital heart disease. They were subsequently diagnosed as Kleefstra syndrome based on subtelomeric FISH analysis. In conclusion, Kleefstra syndrome should be considered in the differential diagnosis of Down syndrome because it presents with very similar phenotypic features.

CtBPs sense microenvironmental oxygen levels to regulate neural stem cell state

Bone morphogenetic proteins (BMPs) secreted by the dorsal neural tube and overlying ectoderm are key signals for the specification of the roof plate and dorsal interneuron populations. However, the signals that confer nonneurogenic character to the roof plate region are largely unknown. We report that the roof plate region shows elevated oxygen levels compared to neurogenic regions of the neural tube. These high oxygen levels are required for the expression of the antineuronal transcription factor Hes1 in the roof plate region. The transcriptional corepressor CtBP is a critical mediator of the oxygen-sensing response. High oxygen promotes a decrease in the CtBP occupancy of the promoter of Hes1. Furthermore, under conditions of high oxygen and BMP, CtBP associates with HES1 and represses neurogenesis. We propose that CtBP integrates signals originating from microenvironmental levels of oxygen and BMP to confer nonneurogenic character to the roof plate region.

A twin sibling with Prader-Willi syndrome caused by uniparental disomy conceived after in vitro fertilization

The use of assisted reproductive technologies (ART) has increased gradually in the treatment of infertility worldwide. On the other hand ART has been found to be associated with an increased risk of congenital malformations including imprinting defects as well. Although a number of imprinting syndromes have been reported to be related with ART, no case with uniparental disomy (UPD) caused Prader-Willi syndrome (PWS) [OMIM ID: 176270] has been reported in the literature. Here we present a dizygotic twin in which one of them was born with maternal UPD15 following ART. The proband was a 2-year-old boy who had feeding difficulties, generalized hypotonia, frontal bossing, broad forehead, small hands and feet. Laboratory investigations revealed minimal dilatation in 3rd and 4th ventricles and corpus callosum hypoplasia in magnetic resonance imaging, supravalvular pulmonary stenosis in echocardiography and pelvicaliectasia in the USG examinations. Methylation and microsatellite markers analyses showed maternal UPD for chromosome 15. Here we report, for the first time UPD caused PWS patient born after ART.

Defining the limits of homology modeling in information-driven protein docking

Information-driven docking is currently one of the most successful approaches to obtain structural models of protein interactions as demonstrated in the latest round of CAPRI. While various experimental and computational techniques can be used to retrieve information about the binding mode, the availability of three-dimensional structures of the interacting partners remains a limiting factor. Fortunately, the wealth of structural information gathered by large-scale initiatives allows for homology-based modeling of a significant fraction of the protein universe. Defining the limits of information-driven docking based on such homology models is therefore highly relevant. Here we show, using previous CAPRI targets, that out of a variety of measures, the global sequence identity between template and target is a simple but reliable predictor of the achievable quality of the docking models. This indicates that a well-defined overall fold is critical for the interaction. Furthermore, the quality of the data at our disposal to characterize the interaction plays a determinant role in the success of the docking. Given reliable interface information we can obtain acceptable predictions even at low global sequence identity. These results, which define the boundaries between trustworthy and unreliable predictions, should guide both experts and nonexperts in defining the limits of what is achievable by docking. This is highly relevant considering that the fraction of the interactome amenable for docking is only bound to grow as the number of experimentally solved structures increases.

Subtelomeric rearrangements in patients with idiopathic intellectual disabilitiy/ multiple congenital anomalies and recurrent miscarriages: seven years' experience

Cryptic subtelomeric anomalies are a significant cause of idiopathic intellectual disability and/or multiple congenital anomalies (ID/MCA) and multiple miscarriages (MM). Effective preselection of patients is essential as the cost of subtelomeric testing is high and it is labor-intensive. Therefore, the aim of this study is to evaluate the frequency of subtelomeric anomalies by using commercial FISH probes in 151 patients of ID/MCA and 32 couples with MM who were referred to a genetic center during 7-year period and to determine whether performing subtelomeric testing is feasible for these groups of patients. We assessed the clinical information of all referrals including family history, physical examination, facial dysmorphism, congenital malformations and scored the ID/MCA patients according to the criteria suggested previously. The etiology was not elucidated and all patients had normal karyotypes. Subtelomeric deletions were found in 10 patients in ID/MCA group (6.62%). These were deletions of 14qter (2 patients), 18qter (2 patients), 18pter (2 patients), 15qter, 7pter, 8pter and 4qter. The clinical information of all patients having deletions has been summarized and confined with the current literature. No anomaly was detected in the MM group. In conclusion, the prevalence of subtelomeric anomalies in ID/MCA group in this study is consistent with the literature and subtelomeric FISH analysis is feasible in determining their etiology when a checklist is used. Besides, assessment of the genetic basis of ID/MCA had lead the prevention of the recurrence of such conditions in selected families as well as elucidating novel genetic causes of ID.

SPG4 gene promoter regulation via Elk1 transcription factor

The most common cause of autosomal dominant hereditary spastic paraplegia, that is characterized with axonal degeneration in corticospinal tracts and posterior columns, is known to be caused by mutations in the SPG4 gene which encodes spastin, a microtubule severing ATPase belonging to AAA family. Spastin promotes the formation of microtubule networks that are essential for axon growth and branching which are important for neuronal plasticity. Mutations observed in SPG4 gene of hereditary spastic paraplegia patients have been shown to cause reduced spastin levels. In addition to mutations, transcriptional regulation of spastin gene expression may also affect spastin level. ETS (E Twenty Six-specific)-domain transcription factor, Elk1, has been shown to be important for synaptic plasticity and interact with microtubules. In this study, we aimed to identify the critical promoter regions of SPG4 gene and effects of Elk on SPG4 gene expression. We identified 700 bp TATA-less promoter including a critical CpG island as an optimal promoter, and deletion of the CpG island gradually decreased the SPG4 promoter activity. In addition, we identified the binding sites of Elk1 on the SPG4 promoter by EMSA. Over-expression of Elk1 showed that it repressed the SPG4 promoter and also decreased spastin protein level in SHSY-5Y cells.

Sudden vision loss in a mucopolysaccharidosis I patient receiving enzyme replacement therapy

A 25-year-old female was referred for short stature and joint deformities. Except for previous corneal transplantation, her medical history was unremarkable. Initial physical examination revealed the presence of a coarse facies, short neck, kyphosis, restricted joint movements and deformities, and cardiac murmur besides a normal intellect. Urine glycosaminoglycan levels were high, and blood enzyme assay indicated significantly low alpha-L-iduronidase levels. Mucopolysaccharidosis I (MPS I) was diagnosed and prompted the onset of enzyme replacement therapy (ERT), which significantly improved articular complaints, while cardiac pathology remained stable. At the eighteenth month of ERT, sudden vision loss developed. She spontaneously recovered her vision in a month. MPS I is a progressive disease, in which tissue accummulation of heparan and dermatan sulphate result from defective activity or lack of alpha-L-iduronidase. ERT in MPS I usually presents favourable outcomes or at least stabilization of symptoms. This present case qualifies as the first report ofa MPS I patient developing sudden vision loss under ERT. We suggest that further research studies are warranted for defining the efficiency and possible limitations of ERT.

A new syndrome presenting with dysmorphic facies, oculocutaneous albinism, glaucoma, cryptorchidism and mental retardation

We report a case with a new syndrome that presents with glaucoma, cryptorchidism, oculocutaneous albinism, ataxia, hypotonia, autistic behaviour besides various major and minor craniofacial dysmorphic, skeletal, and neuroimaging findings, and suggest that this case represents a new syndrome not reported previously.

Effects of inherited thrombophilia in women with recurrent pregnancy loss

PURPOSE OF INVESTIGATION

To evaluate the prevalence and effects of inherited thrombophilia caused by factor V Leiden, prothrombin G20210A and methylenetetrahydrofolate reductase (MTHFR) C677T mutations in women with recurrent pregnancy loss.

METHODS

A study group of 97 women with recurrent miscarriages and a control group of 71 healthy pregnant women were included in the study. Genotype analyses for factor V Leiden, prothrombin G20210A and MTHFR C677T polymorphisms were performed by real-time polymerase chain reaction (RT-PCR).

RESULTS

The frequency of factor V Leiden, prothrombin G20210A and MTHFR C677T mutations were similar in both the study and control group. There were eight patients (8.2%) who had more than one gene mutation in the study group and one patient in the control group (1.4%). This difference was not statistically significant. Study group patients (n = 97) were compared in terms of the number of miscarriages and the abortion week, in addition to being a carrier of factor V Leiden and MTHFR C677T gene mutations. No statistically significant correlation was found between being a factor V Leiden and MTHFR C677T mutation carrier with either the number of miscarriages or the abortion week.

CONCLUSION

Factor V Leiden, prothrombin G20210A and MTHFR C677T gene mutations are not individually related with recurrent pregnancy loss. However, combined gene mutation status may be associated with recurrent miscarriages.

Effects of Manisa propolis on telomerase activity in leukemia cells obtained from the bone marrow of leukemia patients

Propolis is a resinous material collected by honeybees and obtained from beehives that has anticancer effects by inducing apoptosis. The aim of this study is to investigate the effect of propolis on human telomerase reverse transcriptase (hTERT) in the leukemia cells obtained from leukemia patients. Four different bone marrow cell cultures from each of four leukemia cases were prepared. The 60 ng/ml, 30 ng/ml and 15 ng/ml working concentrations of propolis were administered to three cultures of each patient, while one culture contained only culture medium. hTERT mRNA expression levels of cells were detected at 24 h, 48 h and 72 h using the LightCycler 2.0 instrument. A significant decrease in hTERT expression levels was observed in the 60 ng/ml concentration of propolis. In conclusion, Manisa propolis may also have a potential effect on the expression of hTERT in leukemia-particularly owing to its constituent chrysin.

Expanding CEP290 mutational spectrum in ciliopathies

Ciliopathies are an expanding group of rare conditions characterized by multiorgan involvement, that are caused by mutations in genes encoding for proteins of the primary cilium or its apparatus. Among these genes, CEP290 bears an intriguing allelic spectrum, being commonly mutated in Joubert syndrome and related disorders (JSRD), Meckel syndrome (MKS), Senior-Loken syndrome and isolated Leber congenital amaurosis (LCA). Although these conditions are recessively inherited, in a subset of patients only one CEP290 mutation could be detected. To assess whether genomic rearrangements involving the CEP290 gene could represent a possible mutational mechanism in these cases, exon dosage analysis on genomic DNA was performed in two groups of CEP290 heterozygous patients, including five JSRD/MKS cases and four LCA, respectively. In one JSRD patient, we identified a large heterozygous deletion encompassing CEP290 C-terminus that resulted in marked reduction of mRNA expression. No copy number alterations were identified in the remaining probands. The present work expands the CEP290 genotypic spectrum to include multiexon deletions. Although this mechanism does not appear to be frequent, screening for genomic rearrangements should be considered in patients in whom a single CEP290 mutated allele was identified.

Ligand-independent signaling by disulfide-crosslinked dimers of the p75 neurotrophin receptor

Dimerization is recognized as a crucial step in the activation of many plasma membrane receptors. However, a growing number of receptors pre-exist as dimers in the absence of ligand, indicating that, although necessary, dimerization is not always sufficient for signaling. The p75 neurotrophin receptor (p75(NTR)) forms disulfide-linked dimers at the cell surface independently of ligand binding through Cys257 in its transmembrane domain. Here, we show that crosslinking of p75(NTR) dimers by cysteine-scanning mutagenesis results in constitutive, ligand-independent activity in several pathways that are normally engaged upon neurotrophin stimulation of native receptors. The activity profiles of different disulfide-crosslinked p75(NTR) mutants were similar but not identical, suggesting that different configurations of p75(NTR) dimers might be endowed with different functions. Interestingly, crosslinked p75(NTR) mutants did not mimic the effects of the myelin inhibitors Nogo or MAG, suggesting the existence of ligand-specific activation mechanisms. Together, these results support a conformational model of p75(NTR) activation by neurotrophins, and reveal a genetic approach to generate gain-of-function receptor variants with distinct functional profiles.

Activation of the p75 neurotrophin receptor through conformational rearrangement of disulphide-linked receptor dimers

Ligand-mediated dimerization has emerged as a universal mechanism of growth factor receptor activation. Neurotrophins interact with dimers of the p75 neurotrophin receptor (p75(NTR)), but the mechanism of receptor activation has remained elusive. Here, we show that p75(NTR) forms disulphide-linked dimers independently of neurotrophin binding through the highly conserved Cys(257) in its transmembrane domain. Mutation of Cys(257) abolished neurotrophin-dependent receptor activity but did not affect downstream signaling by the p75(NTR)/NgR/Lingo-1 complex in response to MAG, indicating the existence of distinct, ligand-specific activation mechanisms for p75(NTR). FRET experiments revealed a close association of p75(NTR) intracellular domains that was transiently disrupted by conformational changes induced upon NGF binding. Although mutation of Cys(257) did not alter the oligomeric state of p75(NTR), the mutant receptor was no longer able to propagate conformational changes to the cytoplasmic domain upon ligand binding. We propose that neurotrophins activate p75(NTR) by a mechanism involving rearrangement of disulphide-linked receptor subunits.

Common MEFV mutations and polymorphisms in an elderly population: an association with E148Q polymorphism and rheumatoid factor levels

OBJECTIVES

To analyse the most common MEFV (Mediterranean fever gene) mutations and polymorphisms in an elderly population free of chronic inflammatory disease (n=164), and explore possible associations between hsCRP (high sensitive C-reactive protein) and RF (rheumatoid factor) levels with MEFV mutations and polymorphisms.

METHODS

An elderly group free of chronic inflammatory disease was chosen among the outpatients of the division of geriatric medicine. Total genomic DNA was isolated from blood, and PCR-RFLP analysis was performed using established protocols. Sera were analyzed for hsCRP and RF levels.

RESULTS

The frequencies for 694V (1.8%), 694I (1.8%), 680I (0.6%), 726A (2.1%) and 148Q (5%) alleles were found to be similar to Turkish historic controls, with a carrier frequency of 1/4. Further analyses with rheumatoid factor (RF) levels and mutations revealed a significant association between the presence of the E148Q polymorphism with increased RF levels (>15 mg/dl) (xi2= 7.358, p=0.007, OR=5.41 95% CI 1.41-20.64).

CONCLUSIONS

Common MEFV mutations and polymorphisms were similarly represented among the elderly population compared to historic controls. On the other hand, a significant association was found between the presence of E148Q polymorphism and increased RF levels. This suggests that the previously noted increased RF levels in elderly populations may somehow be related to the now described association of RF with MEFV E148Q polymorphism.

A new case of Martsolf syndrome

Martsolf syndrome is an autosomal recessive syndrome characterized by microcephaly, mental retardation, cataract, hypogonadism and short stature. A seven-year-old boy was admitted to the hospital with growth retardation and difficulties in walking. His parents were first cousins. Bilateral lens extraction was performed during infancy because of congenital cataract. On physical examination he had short stature, microcephaly, micropthalmia, hypogonadism, mental retardation. Brain magnetic resonance imaging revealed alterations in the white matter. Up to date very few cases with this syndrome have been reported. This is the first case described in the Turkish population and may add valuable information to the literature.

Duane anomaly, meningomyelocele, dextroposition of heart and localized vertebrocostal alterations with associated anomalies in a girl

Vertebral and rib anomalies occur because of defects at different stages of embryo development and result in different malformations. Developmental field defects are the term to describe the alterations in the biological units which occur because of defects in the pattern formation. Short trunk dwarfism associated with vertebral and rib anomalies is one of the well-known conditions described under various names. Here we report on a 20-month-old female with short trunk dwarfism involving an asymmetrically malformed thorax with kyphoscoliosis presenting skeletal anomalies of spine and ribs and additional multiple associated anomalies such as downslanting palpebral fissures, long philtrum, high palate, rocker bottom feet, dextroposition of heart, cascade stomach, retroposition of bulbi duodeni and bilateral renal cortical thinning. Ophthalmological examination revealed Duane anomaly. No mutation was detected in the analysis of the DLL3 gene. The malformations in the patient are related to different progenitor fields in the early development of the embryo and the presented combination of Duane anomaly with the associated anomalies has not been reported in the literature.

Chromosomal rearrangements in children with idiopathic mental retardation using subtelomeric fluorescent in situ hybridization

To screen a selected group of children with idiopathic mental retardation for subtelomeric abnormalities using the fluorescent in situ hybridization (FISH), which has been reported to be cost-effective in routine applications. We also aimed to assess the availability of the scoring system which is used for selection of those children for FISH analysis. A total of 30 children aged 3-16 years with idiopathic mental retardation (moderate to severe) and normal karyotypes were included in this study. The children whose parents had consanguineous marriages were excluded from the study. All cases were evaluated using the scoring system published by de Vries et al. (5) Forty-one subtelomeric regions for each case were analyzed by fluorescent in situ hybridization. One case with a score value 5 presented terminal deletion of chromosome 9p by FISH (3.3 %). Analyzing chromosomes of the same case with higher resolution G-banding showed the same abnormality. The frequency of subtelomeric abnormalities in our study group was much lower than the frequencies reported in other studies and the scoring criterions suggested by de Vries et al. have not effectively increased our subtelomeric deletion detection rates. Autosomal recessive disorders may be a more common reason compared to subtelomeric abnormalities in this group of patients in the countries where consanguinity rate is high. Laboratories may be encouraged to analyze high-resolution G-banded karyotypes in those cases. Moreover more effective selection criteria for FISH are suggested by establishing thorough genotype-phenotype correlations besides case reports with different subtelomeric abnormalities.

Trends in cytogenetic prenatal diagnosis in a reference hospital in Izmir/Turkey: a comparative study for four years

The aim of the study was to investigate the major changes in the indications, culture success and abnormality rate for conventional cytogenetic prenatal diagnosis on amniotic fluid samples between the period of January 1998 and December 2001 in Izmir. The cytogenetic laboratory provides a prenatal service to obstetrics-gynecology departments of different hospitals in Izmir. A limited number of patients (6-8 per week) is randomly accepted for prenatal cytogenetic study. Over the 4 years period 1190 prenatal cytogenetic tests were performed in our center. The most common indication was advanced maternal age for each year. However its rate has increased significantly within the years (35.68% in 1998, 61.38% in 2001), while the rate of both triple test and ultrasound scanning indications decreased. Culture success rates have improved (97.97% in 1998, 99.74% in 2001). Comparing the first two years to the last two years the rate of abnormal cytogenetic results decreased significantly (3.83% in 1998-99, 2.48% in 2000-01). The major reason for this decrease is probably related to the changes in indications throughout the years.