The protein kinase complement of the human genome

We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.     

Chromosome mapping and expression of a putative testis-determining gene in mouse

Isolation and mapping of a mouse complementary DNA sequence (mouse Y-finger) encoding a multiple, potential zinc-binding, finger protein homologous to the candidate human testis-determining factor gene is reported. Four similar sequences were identified in Hind III-digested mouse genomic DNA. Two (7.2 and 2.0 kb) were mapped to the Y chromosome. Only the 2.0-kb fragment, however, was correlated with testis determination. Polymerase chain reaction analysis suggests both Y loci are transcribed in adult testes. A 3.6-kb fragment was mapped to the X chromosome between the T16H and T6R1 translocation breakpoints, and a fourth (6.0 kb) was mapped to chromosome 10. Hence, mYfin sequences have been duplicated several times in the mouse, although they are not duplicated in humans.     

Segregation of loci for C-type virus induction in strains of mice with high and low incidence of leukemia

Multiple genetic loci for induction of murine leukemia viruses are demonstrated in cells of the high leukemic incidence C58 mouse strain. The biologic properties of viruses at C58 inducibility loci are clearly distinguishable from those of viruses activated from mouse cells containing a locus for virus induction of the low leukemia incidence BALB/c strain. These findings are consistent with the hypothesis that the genes for virus induction in normal mouse embryo cells represent viral structural information.     

Adaptation to climate across the Arabidopsis thaliana genome

Understanding the genetic bases and modes of adaptation to current climatic conditions is essential to accurately predict responses to future environmental change. We conducted a genome-wide scan to identify climate-adaptive genetic loci and pathways in the plant Arabidopsis thaliana. Amino acid-changing variants were significantly enriched among the loci strongly correlated with climate, suggesting that our scan effectively detects adaptive alleles. Moreover, from our results, we successfully predicted relative fitness among a set of geographically diverse A. thaliana accessions when grown together in a common environment. Our results provide a set of candidates for dissecting the molecular bases of climate adaptations, as well as insights about the prevalence of selective sweeps, which has implications for predicting the rate of adaptation.     

大菱鲆微卫星标记的分离及其多态性位点检测

以生物素标记的（CA）12为探针进行杂交,借助磁珠筛选出含微卫星的Mbo I酶切片段,构建了大菱鲆Scophthalmus maximus微卫星富集文库,用同位素γ-^23P标记的探针（CA）12进行二次筛选,获得1600个阳性克隆,占59．3％。测序347个序列,得到335个（96．54％）含有微卫星序列的克隆,其中含有微卫星座位378个。完美型的微卫星序列有236个（62．4％）,非完美型的有121个（32．0％）,复合型的有21个（5．6％）,从所得序列中分离和鉴定了32对微卫星标记。利用31尾大菱鲆养殖个体评价微卫星位点,分析表明,10个位点具有多态性。不同位点等位基因数目为3～11不等,期望杂合度（He）和多态信息含量（PIC）变动范围分别为0．5061—0．8995和0．4133～0．8742。本研究中开发的微卫星多态性较高,将为大菱鲆养殖品系的优化、遗传多样性的检测及遗传图谱的构建等打下基础。     

Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus

Genomic imprinting causes parental origin-specific monoallelic gene expression through differential DNA methylation established in the parental germ line. However, the mechanisms underlying how specific sequences are selectively methylated are not fully understood. We have found that the components of the PIWI-interacting RNA (piRNA) pathway are required for de novo methylation of the differentially methylated region (DMR) of the imprinted mouse Rasgrf1 locus, but not other paternally imprinted loci. A retrotransposon sequence within a noncoding RNA spanning the DMR was targeted by piRNAs generated from a different locus. A direct repeat in the DMR, which is required for the methylation and imprinting of Rasgrf1, served as a promoter for this RNA. We propose a model in which piRNAs and a target RNA direct the sequence-specific methylation of Rasgrf1.     

Distribution of hydrogen in the near surface of Mars: evidence for subsurface ice deposits

Using the Gamma-Ray Spectrometer on the Mars Odyssey, we have identified two regions near the poles that are enriched in hydrogen. The data indicate the presence of a subsurface layer enriched in hydrogen overlain by a hydrogen-poor layer. The thickness of the upper layer decreases with decreasing distance to the pole, ranging from a column density of about 150 grams per square centimeter at -42 degrees latitude to about 40 grams per square centimeter at -77 degrees. The hydrogen-rich regions correlate with regions of predicted ice stability. We suggest that the host of the hydrogen in the subsurface layer is ice, which constitutes 35 +/- 15% of the layer by weight.     

Regulation of X-chromosome counting by Tsix and Xite sequences

In mammals, X-inactivation establishes X-chromosome dosage parity between males and females. How X-chromosome counting regulates this process remains elusive, because neither the hypothesized inactivation "blocking factor" nor the required cis-elements have been defined. Here, a mouse knockout and transgenic analysis identified DNA sequences within the noncoding Tsix and Xite genes as numerators. Homozygous deficiency of Tsix resulted in "chaotic choice" and a variable number of inactive X's, whereas overdosage of Tsix/Xite inhibited X-inactivation. Thus, counting was affected by specific Tsix/Xite mutations, suggesting that counting is genetically separable from but molecularly coupled to choice. The mutations affect XX and XY cells differently, demonstrating that counting and choice are regulated not by one "blocking factor," but by both a "blocking" and a "competence" factor.     

A family of three mouse potassium channel genes with intronless coding regions

To understand the molecular mechanisms responsible for generating physiologically diverse potassium channels in mammalian cells, mouse genomic clones have been isolated with a potassium channel complementary DNA, MBK1, that is homologous to the Drosophila potassium channel gene, Shaker. A family of three closely related potassium channel genes (MK1, MK2, and MK3) that are encoded at distinct genomic loci has been isolated. Sequence analysis reveals that the coding region of each of these three genes exists as a single uninterrupted exon in the mouse genome. This organization precludes the generation of multiple forms of the protein by alternative RNA splicing, a mechanism known to characterize the Drosophila potassium channel genes Shaker and Shab. Thus, mammals may use a different strategy for generating diverse K+ channels by encoding related genes at multiple distinct genomic loci, each of which produces only a single protein.     

Discovery of ancient silicate stardust in a meteorite

We have discovered nine presolar silicate grains from the carbonaceous chondrite Acfer 094. Their anomalous oxygen isotopic compositions indicate formation in the atmospheres of evolved stars. Two grains are identified as pyroxene, two as olivine, one as a glass with embedded metal and sulfides (GEMS), and one as an Al-rich silicate. One grain is enriched in 26Mg, which is attributed to the radioactive decay of 26Al and provides information about mixing processes in the parent star. This discovery opens new means for studying stellar processes and conditions in various solar system environments.     

Proteomic analysis of pathogen-responsive proteins from maize stem apoplast triggered by Fusarium verticillioides

During the attack of a pathogen, a variety of defense-associated proteins are released by the host plant in the apoplast to impede the perceived attack. This study utilized the mass spectrometry(LC-MS/MS) and label-free quantification method to analyze the apoplastic fluid(APF) from maize stalk and identified the proteins responsive to the Fusarium verticillioides infection. We have identified 742 proteins, and among these, 119 proteins were differentially accumulated(DAPs), i.e., 35 up-regulate...     

Evidence for selective advantage of pathogenic FGFR2 mutations in the male germ line

Observed mutation rates in humans appear higher in male than female gametes and often increase with paternal age. This bias, usually attributed to the accumulation of replication errors or inefficient repair processes, has been difficult to study directly. Here, we describe a sensitive method to quantify substitutions at nucleotide 755 of the fibroblast growth factor receptor 2 (FGFR2) gene in sperm. Although substitution levels increase with age, we show that even high levels originate from infrequent mutational events. We propose that these FGFR2 mutations, although harmful to embryonic development, are paradoxically enriched because they confer a selective advantage to the spermatogonial cells in which they arise.     

Duplication, deletion, and polymorphism in the sex-determining region of the mouse Y chromosome

The ZFY gene in the sex-determining region of the human Y chromosome encodes a "zinc-finger" protein that may be the testis-determining factor, TDF. Although the Y chromosomes of most placental mammals carry a single homolog of ZFY, the mouse Y chromosome has two homologs, both in the sex-determining (Sxr) region. Zfy-1 alone may suffice to determine maleness; Zfy-2 is dispensable, as it was deleted in an Sxr variant that retains sex-determining function but has lost other genes. Both loci mapped near the centromere of the mouse Y chromosome. The Y chromosomes of the subspecies Mus musculus musculus and M. m. domesticus were distinguishable by a Zfy-1 restriction fragment polymorphism, which can be used to study their differing interactions with autosomal sex-determining genes.     

Genetic and immunological complexity of major histocompatibility regions

There are genetic differences within the major histocompatibility complex of the mouse which lead to skin graft rejection but which cannot be detected serologically. When confronted with these differences on allogeneic cells, lymphocytes proliferate in vitro. In other cases, in vitro lymphocyte proliferation but no skin graft rejection is associated with loci that are linked to but genetically separable from the loci controlling the serologically defined antigens.     

鸡脾脏重全基因组关联分析

【目的】利用全基因组关联分析（genome-wide association study, GWAS）技术解析产蛋后期母鸡脾脏重的分子机制和遗传特征,为改善产蛋后期母鸡的健康状况提供理论依据。【方法】利用东乡绿壳蛋鸡和白来航蛋鸡构建资源群体,以72周龄F2代501只母鸡脾脏重为研究材料。首先利用高密度600 K 基因芯片对试验群体基因组进行SNPs检测。其次利用APT软件进行质控、BEAGLE软件进行基因型填充、PLINK软件进行主成分分析,GEMMA软件进行全基因组关联分析,最终获得脾脏重的显著和潜在显著关联位点。然后利用GCTA软件计算基于SNP数据的脾脏重遗传力以及染色体遗传力,并利用Haploview软件对显著或潜在关联位点进行连锁不平衡分析。最后通过显著位点区域的相关基因功能注释来筛选影响母鸡产蛋后期脾脏重的候选基因。【结果】由72周龄母鸡脾脏重的表型数据可知,在蛋鸡产蛋后期存在较大的变异系数,脾脏重的遗传力为0.236。通过基因型分析得到43万个高质量的SNP进行进一步分析。群体结构分析发现基因膨胀系数为1.042,表明试验群体没有群体分层的现象,避免了关联分析中假阳性结果的出现。利用单变量混合线性模型分析共发现了412和281个SNPs位点与脾脏重显著和潜在显著关联,位于1、4、16、28号染色体上。显著性关联位点在1号染色体161-174 Mb区间和28号染色体0.47-1.27 Mb区间,潜在性显著位点在4号染色体76 Mb区间和16号染色体175kb区间。由于显著区域可能存在的连锁不平衡,对显著性位点进行了条件分析和连锁不平衡检验,以1号染色体位点rs314001986和28号染色体上位点rs312729296进行条件分析,经分析后原先显著关联的位点均不显著,即以rs314001986和rs312729296作为候选SNP进行基因注释分析。对4号染色体和16号染色体潜在显著位点进行连锁不平衡分析,结果显示潜在性显著位点间存在强的连锁不平衡,即以性状表型方差贡献率最大的SNP rs315270535和rs314065899为候选位点进行进一步分析。参考鸡的galgal4基因组,对各显著及潜在性显著位点及区间初步筛选到KCTD4、LDB2、HEP21和PCASP2候选基因,鉴定的候选基因可能参与了脾脏生长以及免疫应答等过程。此外,将显著位点的基因型与群体的表型数据进行关联分析,发现rs314001986和rs312729296在基因型为GG时对脾脏均有增重效应。此外,基于群体的基因型数据得到1号染色体解释的遗传力为9.25%,28号染色体为4.55%。【结论】初步揭示了母鸡产蛋后期脾脏重的遗传特征,脾脏重的遗传力和染色体遗传力为首次报道。生物信息学分析鉴定到影响脾脏重的区域为新的发现,并初步筛选出4个候选基因。     

抗白粉病小偃麦衍生品系高分子量麦谷蛋白亚基分析

采用聚丙烯酰胺电泳技术(SDS-PAGE)分析了64个抗白粉病八倍体小偃麦衍生品系的高分子量麦谷蛋白亚基(HMW-GS)组成。结果表明,在供试材料中亚基组成类型极其丰富。在Glu-A1,Glu-B1和Glu-D1这3个位点上分别检测到3,5,2种不同的亚基组成类型。其中,在Glu-A1位点上大多数品种都具有null亚基,占该位点亚基的90%;在Glu-B1位点上的变异类型最丰富,7+8亚基出现频率最高,为50%;在Glu-D1位点上,劣质亚基2+12出现的频率最高,为78%,被世界公认的优质亚基5+10出现的频率为22%。这些抗白粉病小麦种质可为育种工作者提供优点突出而无突出缺点的亲本。