Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs

Background

Gene expression genetic studies in human tissues and cells identify cis- and trans-acting expression quantitative trait loci (eQTLs). These eQTLs provide insights into regulatory mechanisms underlying disease risk. However, few studies systematically characterized eQTL results across cell and tissues types. We synthesized eQTL results from >50 datasets, including new primary data from human brain, peripheral plaque and kidney samples, in order to discover features of human eQTLs.

Results

We find a substantial number of robust cis-eQTLs and far fewer trans-eQTLs consistent across tissues. Analysis of 45 full human GWAS scans indicates eQTLs are enriched overall, and above nSNPs, among positive statistical signals in genetic mapping studies, and account for a significant fraction of the strongest human trait effects. Expression QTLs are enriched for gene centricity, higher population allele frequencies, in housekeeping genes, and for coincidence with regulatory features, though there is little evidence of 5′ or 3′ positional bias. Several regulatory categories are not enriched including microRNAs and their predicted binding sites and long, intergenic non-coding RNAs. Among the most tissue-ubiquitous cis-eQTLs, there is enrichment for genes involved in xenobiotic metabolism and mitochondrial function, suggesting these eQTLs may have adaptive origins. Several strong eQTLs (CDK5RAP2, NBPFs) coincide with regions of reported human lineage selection. The intersection of new kidney and plaque eQTLs with related GWAS suggest possible gene prioritization. For example, butyrophilins are now linked to arterial pathogenesis via multiple genetic and expression studies. Expression QTL and GWAS results are made available as a community resource through the NHLBI GRASP database [http://apps.nhlbi.nih.gov/grasp/].

Conclusions

Expression QTLs inform the interpretation of human trait variability, and may account for a greater fraction of phenotypic variability than protein-coding variants. The synthesis of available tissue eQTL data highlights many strong cis-eQTLs that may have important biologic roles and could serve as positive controls in future studies. Our results indicate some strong tissue-ubiquitous eQTLs may have adaptive origins in humans. Efforts to expand the genetic, splicing and tissue coverage of known eQTLs will provide further insights into human gene regulation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-532) contains supplementary material, which is available to authorized users.     

A mutant Pfu DNA polymerase designed for advanced uracil-excision DNA engineering

Background  

The combined use of restriction enzymes with PCR has revolutionized molecular cloning, but is inherently restricted by the content of the manipulated DNA sequences. Uracil-excision based cloning is ligase and sequence independent and allows seamless fusion of multiple DNA sequences in simple one-tube reactions, with higher accuracy than overlapping PCR.     

Nonea pisidica (Boraginaceae-Boragineae), a new species from southwest Anatolia and its relationships inferred from karyology and cpDNA sequences

The new species Nonea pisidica (Boraginaceae-Boragineae) is described based on two collections by the authors from the region of Lake Burdur in southwest Anatolia, Turkey. It shows a combination of morphological characteristics concerning habit, flower, and fruit that distinguishes it from N. caspica and N. pallens, the two more similar taxa in Nonea sect. Nonea. Karyological analyses corroborate the separation of the three species, which have different chromosome complements and even base numbers. N. pisidica is characterised by 2n = 30, a complement previously unknown for west Asiatic species of Nonea. The dibasic haploid number x = 15 may have originated through amphidiploid hybridisation between two annual, diploid taxa with x = 7 and x = 8, such as N. lutea and N. caspica. The relationships of the new species were further analysed using trnL_UAA sequences of the chloroplast genome, which were obtained for 16 selected species of Nonea. The resulting phylogeny confirms that it is related to N. caspica and N. lutea, but not to N. pallens, in spite of morphological resemblance. Lack of relationship with the south Mediterranean N. vesicaria, the only other species of Nonea known to have 2n = 30, suggests that amphidiploidy may have played an important role in speciation processes through recurrent and polytopical occurrence.     

Total chemical synthesis of human activin beta(A)[12-116] and related large-loop polypeptides.

We report here the synthesis, purification, and characterization of several large polypeptides related to the human activin beta(A) subunit and their cyclic counterparts. In particular, we describe for the first time the total chemical synthesis of a 105-mer polypeptide, des[1-11] activin beta(A), and related large-loop polypeptide, by an optimized solid phase synthetic protocol based on 9-flouroenylmethyoxycarbonyl (Fmoc) chemistry. These studies show that automated chemical synthesis utilizing Fmoc-based solid phase synthetic strategies provides a practical alternative to recombinant DNA technology for the production of activin-related subunits, with the opportunity to rapidly provide different analogues and structural variants for subsequent structure-function and associated biophysical investigations.     

Engagement of ubiquitination and de-ubiquitination at rostral ventrolateral medulla in experimental brain death

Background

Whereas brain death is a vitally important clinical phenomenon, our contemporary understanding on its underlying cellular mechanisms remains elusive. This study evaluated whether the ubiquitin-proteasome system (UPS) in the rostral ventrolateral medulla (RVLM), a neural substrate that our laboratory identified previously to be intimately related to brain death, is engaged in this fatal process.

Methods

We performed proteomics, Western Blot, real-time PCR, ELISA and pharmacological experiments in conjunction with a clinically relevant experimental endotoxemia model of brain death based on intravenous administration of Escherichia coli lipopolysaccharide in adult male Sprague–Dawley rats.

Results

Proteomics, Western blot and enzyme activity analyses demonstrated that polyubiquitination was preserved and de-ubiquitination by ubiquitin C-terminal hydrolase isozyme-L1 (UCH-L1) was sustained, alongside increased monoubiquitin availability or proteasome activity in RVLM over the course of experimental endotoxemia. However, real-time PCR revealed no significant alteration in proteasome subunit alpha type-1, ubiquitin or UCH-L1 at mRNA level. Functionally, whereas microinjection into the bilateral RVLM of proteasome inhibitors (lactacystin or proteasome inhibitor II) potentiated survival, an inhibitor of ubiquitin-recycling (ubiquitin aldehyde) or an UCH-L1 inhibitor exacerbated mortality.

Conclusions

We proposed previously that the progression towards brain death entails a tug-of-war between pro-death and pro-life programs in RVLM. It is conceivable that ubiquitination or de-ubiquitination in RVLM participate in brain death by regulating the degradation of the proteins involved in those programs.     

Tpx-1 is a component of the outer dense fibers and acrosome of rat spermatozoa

Previously we reported the cloning of a member of the cysteine-rich secretory protein family, tpx-1, from a testis expression library using an outer dense fiber (ODF)-specific antiserum. Using immunohistochemical and immunoelectron microscopic techniques and Western blotting of purified sperm tail components, we have determined that tpx-1 exists as 25 and 27 kDa proteins in two components of rat spermatid: the ODFs and the acrosome. Tpx-1 mRNA is first expressed in the late pachytene spermatocytes, but the production of these tpx-1 proteins is translationally delayed for 4-5 days before being incorporated into the developing sperm acrosome, surrounding the elongating and condensing spermatid nucleus. Concurrent with sperm head formation, tpx-1 protein was incorporated into the developing sperm tail, and specifically the ODFs. The tpx-1 protein was seen within structures resembling granulated bodies in the cytoplasmic lobe of elongating spermatids and was incorporated subsequently into the growing tail in a manner consistent with ODF development. In addition, tpx-1 protein was localized at the ultrastructural level of the connecting piece of the neck and longitudinal columns of the fibrous sheath, suggesting common protein components in these cytoskeletal structures. As such, tpx-1 may have functional significance in the processes of sperm head development and tail function.     

Validation of Heart Failure Events in the Antihypertensive and Lipid Lowering Treatment to Prevent Heart Attack Trial (ALLHAT) Participants Assigned to Doxazosin and Chlorthalidone

BACKGROUND: The Antihypertensive and Lipid Lowering Treatment to Prevent Heart Attack Trial (ALLHAT) is a randomized, double-blind, active-controlled trial designed to compare the rate of coronary heart disease events in high-risk hypertensive participants initially randomized to a diuretic (chlorthalidone) versus each of three alternative antihypertensive drugs: alpha-adrenergic blocker (doxazosin), ACE-inhibitor (lisinopril), and calcium-channel blocker (amlodipine). Combined cardiovascular disease risk was significantly increased in the doxazosin arm compared to the chlorthalidone arm (RR 1.25; 95% CI, 1.17-1.33; P <.001), with a doubling of heart failure (fatal, hospitalized, or non-hospitalized but treated) (RR 2.04; 95% CI, 1.79-2.32; P <.001). Questions about heart failure diagnostic criteria led to steps to validate these events further. METHODS AND RESULTS: Baseline characteristics (age, race, sex, blood pressure) did not differ significantly between treatment groups (P <.05) for participants with heart failure events. Post-event pharmacologic management was similar in both groups and generally conformed to accepted heart failure therapy. Central review of a small sample of cases showed high adherence to ALLHAT heart failure criteria. Of 105 participants with quantitative ejection fraction measurements provided, (67% by echocardiogram, 31% by catheterization), 29/46 (63%) from the chlorthalidone group and 41/59 (70%) from the doxazosin group were at or below 40%. Two-year heart failure case-fatalities (22% and 19% in the doxazosin and chlorthalidone groups, respectively) were as expected and did not differ significantly (RR 0.96; 95% CI, 0.67-1.38; P = 0.83). CONCLUSION: Results of the validation process supported findings of increased heart failure in the ALLHAT doxazosin treatment arm compared to the chlorthalidone treatment arm.     

Defunct brain stem cardiovascular regulation underlies cardiovascular collapse associated with methamphetamine intoxication

Background  

Intoxication from the psychostimulant methamphetamine (METH) because of cardiovascular collapse is a common cause of death within the abuse population. For obvious reasons, the heart has been taken as the primary target for this METH-induced toxicity. The demonstration that failure of brain stem cardiovascular regulation, rather than the heart, holds the key to cardiovascular collapse induced by the pesticide mevinphos implicates another potential underlying mechanism. The present study evaluated the hypothesis that METH effects acute cardiovascular depression by dampening the functional integrity of baroreflex via an action on brain stem nuclei that are associated with this homeostatic mechanism.     

应用ARIMA模型预测宝安区某街道其它感染性腹泻发病率的探讨

目的:探讨应用ARIMA模型预测宝安区某街道其它感染性腹泻发病率的可行性。方法:应用SPSSl3.0软件对2005年～2009年宝安区某街道其它感染性腹泻逐月发病率进行ARIMA模型建模拟合,用所得到的模型对2010年各月发病率进行预测,并评价其预测效果。结果:宝安区桌街道其它感染性腹泻发病率每年11月为发病高峰,ARIMA(0,1,1)(0,1,0)12模型是其拟合的最佳模型,其预测结果和实际值绝对误差的绝对值最大为930.47,最小为1.96,平均值214.83,平均相对误差百分比39.04%。结论:模型虽然起到一定的预测效果,但预测精度仍存在误差,可通过积累新的周期数据对ARIMA模型进行修正和重新拟合,也可尝试新的预测方法或其他模型,才能加强和保证预测的精度。     

应用ARIMA模型预测宝安区某街道其它感染性腹泻发病率的探讨

目的：探讨应用ARIMA模型预测宝安区某街道其它感染性腹泻发病率的可行性。方法：应用SPSS13．0软件对2005年～2009年宝安区某街道其它感染性腹泻逐月发病率进行ARIMA模型建模拟合,用所得到的模型对2010年各月发病率进行预测,并评价其预测效果。结果：宝安区某街道其它感染性腹泻发病率每年11月为发病高峰,ARIMA（0,1,1）（0,1,0）12模型是其拟合的最佳模型,其预测结果和实际值绝对误差的绝对值最大为930．47,最小为1．96,平均值214．83,平均相对误差百分比39．04％。结论：模型虽然起到一定的预测效果,但预测精度仍存在误差,可通过积累新的周期数据对ARIMA模型进行修正和重新拟合,也可尝试新的预测方法或其他模型,才能加强和保证预测的精度。