MitoScape: A big-data,machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data

The growing number of next-generation sequencing (NGS) data presents a unique opportunity to study the combined impact of mitochondrial and nuclear-encoded genetic variation in complex disease. Mitochondrial DNA variants and in particular, heteroplasmic variants, are critical for determining human disease severity. While there are approaches for obtaining mitochondrial DNA variants from NGS data, these software do not account for the unique characteristics of mitochondrial genetics and can be inaccurate even for homoplasmic variants. We introduce MitoScape, a novel, big-data, software for extracting mitochondrial DNA sequences from NGS. MitoScape adopts a novel departure from other algorithms by using machine learning to model the unique characteristics of mitochondrial genetics. We also employ a novel approach of using rho-zero (mitochondrial DNA-depleted) data to model nuclear-encoded mitochondrial sequences. We showed that MitoScape produces accurate heteroplasmy estimates using gold-standard mitochondrial DNA data. We provide a comprehensive comparison of the most common tools for obtaining mtDNA variants from NGS and showed that MitoScape had superior performance to compared tools in every statistically category we compared, including false positives and false negatives. By applying MitoScape to common disease examples, we illustrate how MitoScape facilitates important heteroplasmy-disease association discoveries by expanding upon a reported association between hypertrophic cardiomyopathy and mitochondrial haplogroup T in men (adjusted p-value = 0.003). The improved accuracy of mitochondrial DNA variants produced by MitoScape will be instrumental in diagnosing disease in the context of personalized medicine and clinical diagnostics.     

肝素的抗肿瘤转移活性及其与选凝素的关系

肝素作为传统抗凝剂,常用来治疗癌症患者静脉血栓。临床和实验数据证实,肝素具有抗肿瘤活性。同时也有大量研究发现,肝素有抗肿瘤转移的作用。肝素可以通过各种机制抑制肿瘤转移,包括抑制细胞间的相互作用;抑制肝素酶的表达;调节各种生长因子以及调节机体凝血功能等。选凝素(seletin)是介导肿瘤转移初始阶段的重要因子,而肝素能够抑制选凝素介导的的肿瘤细胞与白细胞、血小板及内皮细胞的相互作用,从而达到抗转移的效果。本文综述了肝素抑制选凝素介导的肿瘤转移的作用机制,为肝素在抗肿瘤转移方面的临床应用提供参考。     

Mutations in TBC1D24, a Gene Associated With Epilepsy,Also Cause Nonsyndromic Deafness DFNB86

Inherited deafness is clinically and genetically heterogeneous. We recently mapped DFNB86, a locus associated with nonsyndromic deafness, to chromosome 16p. In this study, whole-exome sequencing was performed with genomic DNA from affected individuals from three large consanguineous families in which markers linked to DFNB86 segregate with profound deafness. Analyses of these data revealed homozygous mutation c.208G>T (p.Asp70Tyr) or c.878G>C (p.Arg293Pro) in TBC1D24 as the underlying cause of deafness in the three families. Sanger sequence analysis of TBC1D24 in an additional large family in which deafness segregates with DFNB86 identified the c.208G>T (p.Asp70Tyr) substitution. These mutations affect TBC1D24 amino acid residues that are conserved in orthologs ranging from fruit fly to human. Neither variant was observed in databases of single-nucleotide variants or in 634 chromosomes from ethnically matched control subjects. TBC1D24 in the mouse inner ear was immunolocalized predominantly to spiral ganglion neurons, indicating that DFNB86 deafness might be an auditory neuropathy spectrum disorder. Previously, six recessive mutations in TBC1D24 were reported to cause seizures (hearing loss was not reported) ranging in severity from epilepsy with otherwise normal development to epileptic encephalopathy resulting in childhood death. Two of our four families in which deafness segregates with mutant alleles of TBC1D24 were available for neurological examination. Cosegregation of epilepsy and deafness was not observed in these two families. Although the causal relationship between genotype and phenotype is not presently understood, our findings, combined with published data, indicate that recessive alleles of TBC1D24 can cause either epilepsy or nonsyndromic deafness.     

Evidence for a freezing tolerance-growth rate trade-off in the live oaks (Quercus series Virentes) across the tropical-temperate divide

? It has long been hypothesized that species are limited to the north by minimum temperature and to the south by competition, resulting in a trade-off between freezing tolerance and growth rate. We investigated the extent to which the climatic origins of populations from four live oak species (Quercus series Virentes) were associated with freezing tolerance and growth rate, and whether species fitted a model of locally adapted populations, each with narrow climatic tolerances, or of broadly adapted populations with wide climatic tolerances. ? Acorns from populations of four species across a tropical-temperate gradient were grown under common tropical and temperate conditions. Growth rate, seed mass, and leaf and stem freezing traits were compared with source minimum temperatures. ? Maximum growth rates under tropical conditions were negatively correlated with freezing tolerance under temperate conditions. The minimum source temperature predicted the freezing tolerance of populations under temperate conditions. The tropical species Q. oleoides was differentiated from the three temperate species, and variation among species was greater than among populations. ? The trade-off between freezing tolerance and growth rate supports the range limit hypothesis. Limited variation within species indicates that the distributions of species may be driven more strongly by broad climatic factors than by highly local conditions.     

不同种类可吸收性外科缝线的体外降解性能评价

目的研究3种不同种类的可吸收性缝线的体外降解性能,分析其体外降解产物。方法将3种可吸收性缝线分别按比例浸入Sorensen缓冲液中进行体外降解实验,设3个降解周期组,每组设3个重复,分别过滤分离试样、碎片和溶液,计算试样的质量损耗率。并对其体外降解产物进行定性定量分析。结果3种试样体外降解的质量损耗率均逐期增大;不同种类缝线的体外降解液成分不同,且其主要成份含量逐期增加。结论：不同种类的可吸收性缝线应采用不同的定性定量分析方法,根据产物推断缝线的生物安全性。     

Prevalence of Hypertension in China: A Cross-Sectional Study

Aims

The present study aimed to assess the prevalence of hypertension among Chinese adults.

Methods

Data were obtained from sphygmomanometer measurements and a questionnaire administered to 46239 Chinese adults ≥20 years of age who participated in the 2007–2008 China National Diabetes and Metabolic Disorders Study. Hypertension was defined as blood pressure ≥140/90 mm Hg or use of antihypertensive medication.

Results

A total of 26.6% of Chinese adults had hypertension, and a significantly greater number of men were hypertensive than women (29.2% vs 24.1%, p<0.001). The age-specific prevalence of hypertension was 13.0%, 36.7%, and 56.5% among persons aged 20 to 44 years (young people), 45 to 64 years (middle-aged people), and ≥65 years (elderly people), respectively. In economically developed regions, the prevalence of hypertension was significantly higher among rural residents than among urban residents (31.3% vs 29.2%, p = 0.001). Among women or individuals who lived in the northern region, the disparity in the prevalence of hypertension between urban and rural areas disappeared (women: 24.0% vs. 24.0%, p = 0.942; northern region: 31.6% vs. 31.2%, p = 0.505). Among hypertensive patients, 45.0% were aware of their condition, 36.2% were treated, and 11.1% were adequately controlled.

Conclusions

The prevalence of hypertension in China is increasing. The trend of an increase in prevalence is striking in young people and rural populations. Hypertension awareness, treatment, and control are poor. Public health efforts for further improving awareness and enhancing effective control are urgently needed in China, especially in emerging populations.     

Monitoring of Antiretroviral Therapy and Mortality in HIV Programmes in Malawi,South Africa and Zambia: Mathematical Modelling Study

Objectives

Mortality in patients starting antiretroviral therapy (ART) is higher in Malawi and Zambia than in South Africa. We examined whether different monitoring of ART (viral load [VL] in South Africa and CD4 count in Malawi and Zambia) could explain this mortality difference.

Design:

Mathematical modelling study based on data from ART programmes.

Methods

We used a stochastic simulation model to study the effect of VL monitoring on mortality over 5 years. In baseline scenario A all parameters were identical between strategies except for more timely and complete detection of treatment failure with VL monitoring. Additional scenarios introduced delays in switching to second-line ART (scenario B) or higher virologic failure rates (due to worse adherence) when monitoring was based on CD4 counts only (scenario C). Results are presented as relative risks (RR) with 95% prediction intervals and percent of observed mortality difference explained.

Results

RRs comparing VL with CD4 cell count monitoring were 0.94 (0.74–1.03) in scenario A, 0.94 (0.77–1.02) with delayed switching (scenario B) and 0.80 (0.44–1.07) when assuming a 3-times higher rate of failure (scenario C). The observed mortality at 3 years was 10.9% in Malawi and Zambia and 8.6% in South Africa (absolute difference 2.3%). The percentage of the mortality difference explained by VL monitoring ranged from 4% (scenario A) to 32% (scenarios B and C combined, assuming a 3-times higher failure rate). Eleven percent was explained by non-HIV related mortality.

Conclusions

VL monitoring reduces mortality moderately when assuming improved adherence and decreased failure rates.     

Hematopoietic stem cell-derived adipocytes and fibroblasts in the tumor microenvironment

The tumor microenvironment(TME) is complex and constantly evolving. This is due, in part, to the crosstalk between tumor cells and the multiple cell types that comprise the TME, which results in a heterogeneous population of tumor cells and TME cells. This review will focus on two stromal cell types, the cancerassociated adipocyte(CAA) and the cancer-associated fibroblast(CAF). In the clinic, the presence of CAAs and CAFs in the TME translates to poor prognosis in multiple tumor types. CAAs and CAFs have an activated phenotype and produce growth factors, inflammatory factors, cytokines, chemokines, extracellular matrix components, and proteases in an accelerated and aberrant fashion. Through this activated state, CAAs and CAFs remodel the TME, thereby driving all aspects of tumor progression, including tumor growth and survival, chemoresistance, tumor vascularization, tumor invasion, and tumor cell metastasis. Similarities in the tumorpromoting functions of CAAs and CAFs suggest that a multipronged therapeutic approach may be necessary to achieve maximal impact on disease. While CAAs and CAFs are thought to arise from tissues adjacent to the tumor, multiple alternative origins for CAAs and CAFs have recently been identified. Recent studies from our lab and others suggest that the hematopoietic stem cell, through the myeloid lineage, may serve as a progenitor for CAAs and CAFs. We hypothesize that the multiple origins of CAAs and CAFs may contribute to the heterogeneity seen in the TME. Thus, a better understanding of the origin of CAAs and CAFs, how this origin impacts their functions in the TME, and thetemporal participation of uniquely originating TME cells may lead to novel or improved anti-tumor therapeutics.     

Human immunodeficiency virus type 1 envelope glycoprotein oligomerization requires the gp41 amphipathic alpha-helical/leucine zipper-like sequence.

Human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) oligomerization was investigated by coexpressing wild-type and truncated envelope glycoproteins to determine the minimum sequence required for mutant-wild-type hetero-oligomerization. The gp41 putative amphipathic alpha-helix, Leu-550 to Leu-582, was essential for hetero-oligomer formation. Alanine substitution of 9 of the 10 residues composing the gp41 amphipathic alpha-helix 4-3 hydrophobic repeat sequence was required to inhibit mutant-wild-type hetero-oligomerization and to render the envelope glycoprotein precursor, gp160, monomeric. This indicates that multiple hydrophobic contacts contribute to the stable envelope glycoprotein oligomeric structure. Single alanine substitutions within the hydrophobic repeat sequence did not affect gp160 oligomeric structure but abolished syncytium-forming function. Some mutations also diminished gp160 processing efficiency and the association between gp120 and gp41 in a position-dependent manner. These results indicate that the gp41 amphipathic alpha-helix 4-3 hydrophobic repeat sequence plays a central role in HIV-1 envelope glycoprotein oligomerization and fusion function.     

酸性磷酸酶参与大豆子叶磷转运和利用

本文以磷效率不同的两个大豆品种为材料,研究大豆幼苗期子叶酸性磷酸酶活性和同工酶谱对外源磷有效性的响应,及其参与子叶磷高效转运和利用的过程。结果表明：在幼苗生长前期,子叶酸性磷酸酶活性及其同工酶谱组成变化明显,而且不受外源磷有效性的调控;在幼苗生长的前8天,子叶全磷含量随着酸性磷酸酶的活性增加而显著降低,而且磷高效大豆品种比磷低效大豆品种具有较高的酸性磷酸酶活性和植株全磷含量。以上结果说明在大豆幼苗生长前期,由于大粒种子不仅具有较高的磷含量,而且具有较高子叶酸性磷酸酶活性,促进子叶有机磷的水解和转运是磷高效大豆品种适应低磷胁迫的生理机制之一。