SBOL Visual: A Graphical Language for Genetic Designs

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.     

Triglyceride-Increasing Alleles Associated with Protection against Type-2 Diabetes

Elevated plasma triglyceride (TG) levels are an established risk factor for type-2 diabetes (T2D). However, recent studies have hinted at the possibility that genetic risk for TG may paradoxically protect against T2D. In this study, we examined the association of genetic risk for TG with incident T2D, and the interaction of baseline TG with TG genetic risk on incident T2D in 13,247 European-Americans (EA) and 3,238 African-Americans (AA) from three prospective cohort studies. A TG genetic risk score (GRS) was calculated based on 31 validated single nucleotide polymorphisms (SNPs). We considered several baseline covariates, including body- mass index (BMI) and lipid traits. Among EA and AA, we find, as expected, that baseline levels of TG are strongly positively associated with incident T2D (p<2 x 10^-10). However, the TG GRS is negatively associated with T2D (p=0.013), upon adjusting for only race, in the full dataset. Upon additionally adjusting for age, sex, BMI, high-density lipoprotein cholesterol and TG, the TG GRS is significantly and negatively associated with T2D incidence (p=7.0 x 10^-8), with similar trends among both EA and AA. No single SNP appears to be driving this association. We also find a significant statistical interaction of the TG GRS with TG (p_interaction=3.3 x 10^-4), whereby the association of TG with incident T2D is strongest among those with low genetic risk for TG. Further research is needed to understand the likely pleiotropic mechanisms underlying these findings, and to clarify the causal relationship between T2D and TG.     

Pyrimidine Pool Disequilibrium Induced by a Cytidine Deaminase Deficiency Inhibits PARP-1 Activity,Leading to the Under Replication of DNA

Genome stability is jeopardized by imbalances of the dNTP pool; such imbalances affect the rate of fork progression. For example, cytidine deaminase (CDA) deficiency leads to an excess of dCTP, slowing the replication fork. We describe here a novel mechanism by which pyrimidine pool disequilibrium compromises the completion of replication and chromosome segregation: the intracellular accumulation of dCTP inhibits PARP-1 activity. CDA deficiency results in incomplete DNA replication when cells enter mitosis, leading to the formation of ultrafine anaphase bridges between sister-chromatids at “difficult-to-replicate” sites such as centromeres and fragile sites. Using molecular combing, electron microscopy and a sensitive assay involving cell imaging to quantify steady-state PAR levels, we found that DNA replication was unsuccessful due to the partial inhibition of basal PARP-1 activity, rather than slower fork speed. The stimulation of PARP-1 activity in CDA-deficient cells restores replication and, thus, chromosome segregation. Moreover, increasing intracellular dCTP levels generates under-replication-induced sister-chromatid bridges as efficiently as PARP-1 knockdown. These results have direct implications for Bloom syndrome (BS), a rare genetic disease combining susceptibility to cancer and genomic instability. BS results from mutation of the BLM gene, encoding BLM, a RecQ 3’-5’ DNA helicase, a deficiency of which leads to CDA downregulation. BS cells thus have a CDA defect, resulting in a high frequency of ultrafine anaphase bridges due entirely to dCTP-dependent PARP-1 inhibition and independent of BLM status. Our study describes previously unknown pathological consequences of the distortion of dNTP pools and reveals an unexpected role for PARP-1 in preventing DNA under-replication and chromosome segregation defects.     

Endothelial Nitric Oxide Synthase Deficient Mice Are Protected from Lipopolysaccharide Induced Acute Lung Injury

Lipopolysaccharide (LPS) derived from the outer membrane of gram-negative bacteria induces acute lung injury (ALI) in mice. This injury is associated with lung edema, inflammation, diffuse alveolar damage, and severe respiratory insufficiency. We have previously reported that LPS-mediated nitric oxide synthase (NOS) uncoupling, through increases in asymmetric dimethylarginine (ADMA), plays an important role in the development of ALI through the generation of reactive oxygen and nitrogen species. Therefore, the focus of this study was to determine whether mice deficient in endothelial NOS (eNOS^-/-) are protected against ALI. In both wild-type and eNOS^-/- mice, ALI was induced by the intratracheal instillation of LPS (2 mg/kg). After 24 hours, we found that eNOS^-/-mice were protected against the LPS mediated increase in inflammatory cell infiltration, inflammatory cytokine production, and lung injury. In addition, LPS exposed eNOS^-/- mice had increased oxygen saturation and improved lung mechanics. The protection in eNOS^-/- mice was associated with an attenuated production of NO, NOS derived superoxide, and peroxynitrite. Furthermore, we found that eNOS^-/- mice had less RhoA activation that correlated with a reduction in RhoA nitration at Tyr³⁴. Finally, we found that the reduction in NOS uncoupling in eNOS^-/- mice was due to a preservation of dimethylarginine dimethylaminohydrolase (DDAH) activity that prevented the LPS-mediated increase in ADMA. Together our data suggest that eNOS derived reactive species play an important role in the development of LPS-mediated lung injury.     

Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies

Puerto Rico and the surrounding islands rest on the eastern fringe of the Caribbean's Greater Antilles, located less than 100 miles northwest of the Lesser Antilles. Puerto Ricans are genetic descendants of pre‐Columbian peoples, as well as peoples of European and African descent through 500 years of migration to the island. To infer these patterns of pre‐Columbian and historic peopling of the Caribbean, we characterized genetic diversity in 326 individuals from the southeastern region of Puerto Rico and the island municipality of Vieques. We sequenced the mitochondrial DNA (mtDNA) control region of all of the samples and the complete mitogenomes of 12 of them to infer their putative place of origin. In addition, we genotyped 121 male samples for 25 Y‐chromosome single nucleotide polymorphism and 17 STR loci. Approximately 60% of the participants had indigenous mtDNA haplotypes (mostly from haplogroups A2 and C1), while 25% had African and 15% European haplotypes. Three A2 sublineages were unique to the Greater Antilles, one of which was similar to Mesoamerican types, while C1b haplogroups showed links to South America, suggesting that people reached the island from the two distinct continental source areas. However, none of the male participants had indigenous Y‐chromosomes, with 85% of them instead being European/Mediterranean and 15% sub‐Saharan African in origin. West Eurasian Y‐chromosome short tandem repeat haplotypes were quite diverse and showed similarities to those observed in southern Europe, North Africa and the Middle East. These results attest to the distinct, yet equally complex, pasts for the male and female ancestors of modern day Puerto Ricans. Am J Phys Anthropol 155:352–368, 2014. © 2014 Wiley Periodicals, Inc.     

Anthropometric characteristics of Indian cycle rickshaw pullers

In India, about 0.86 million people is engaged in pulling cycle rickshaws as occupation. There is no anthropometric data of cycle rickshaw pullers although data is available for Indian population. The objective of the study was to collect anthropometric data of the cycle rickshaw pullers so that these could be utilized for redesigning a cycle rickshaw. Anthropometric data for 34 body measurements were recorded from 880 rickshaw pullers (age 18 to 66 years) of four different places in India. The mean values of different standing heights, different lengths and breadths of cycle rickshaw pullers were significantly lower compared with Indian population. However, there was no significant difference in erect sitting height. The outcome of the research project is beneficial for the manufacturers of cycle rickshaws and similar products well as users of such products, including rickshaw pullers. The manufacturers would be able to use the data for fabricating newer models of cycle rickshaws which would be more compatible for rickshaw pullers as well as passengers.     

Removal of Heavy Metals from Soil Polluted with Effluents from a Paint Industry Using Helianthus annuus L. and Tithonia diversifolia (Hemsl.) as Influenced by Fertilizer Applications

Contamination of soils by effluents from industries is on the increase. There is the possibility of remediating these contaminated soils through the use of certain plants. This work investigated the remediating ability of Helianthus annuus and Tithonia diversifolia on the soil polluted with effluents from a paint industry in Ibadan, Nigeria. The experiment consisted of three treatments (H. annuus, T. diversifolia, and control) each replicated three times in a factorial combination of four different fertility managements, viz mineral fertilizer (MF); Grade A organomineral fertilizer (OMF); control₁, plants without fertilizer application; and control₂, where no fertilizer and no crop was planted using randomized complete block design. A total of 12 plots of 2 × 4 m² each per phytoplant were obtained. Each plot was planted with the viable seeds of the phytoplant at a spacing of 60 × 30 cm² and at the seed rate of four seeds per hole. The seedlings were thinned to two stands per hole 2 weeks after planting (WAP) and also weeded two times (2 and 5 WAP). After in situ second successive cultivation, percentage removal of heavy metals by Helianthus annuus with MF and OMF, respectively, were Cu 32.5 and 41.6; Pb 30.3 and 42.8; and Cd 44.5 and 56.7. Tithonia diversifolia, similarly, removed, respectively, Cu 16.9 and 23.4; Pb 36.9 and 43.7; and Cd 20.1 and 35.1. Lower percentages were removed in the controls where no fertilizer was applied. In the shoot of H. annuus with OMF, significantly (p< .05) higher values of 0.27, 1.72, and 0.11 mg kg^?1 of Cu, Pb, and Cd, respectively, were removed and stored at second cultivation as against 0.21, 3.39 and 0.08 mg kg^?1 in the shoot of T diversifolia. Lower values of Cu, Pb, and Cd were removed with MF, and also at first cultivation with OMF and MF. This study therefore recommends the use of sunflower plants, whether hybrids or wild-types along with the application of OMF for the effective remediation of soils contaminated with heavy metals, particularly in tropical climate.