Genetic and molecular characteristics of a new natural haplotype twMP1 of the house mouse (Mus domesticus R.) from Peru

A new natural haplotype, twWP1, found in a population of house mouse Mus domesticus from Peru, was subjected to genetic and molecular analyses. Experiments were performed to study the complementation of the new haplotype, fertility of twMP1/tx heterozygotes, and transmission ratio distortion (TRD) of the t-carrying chromosome in the progeny of heterozygous males. Molecular analysis included blot hybridization with t-specific probes Tu48, Tu66, and Tu119. The results were collated with the structure and properties of the t complex, and the new haplotype was identified as a complete lethal one.     

Genetic and Molecular Characterization of New Natural Haplotype t wMP1 Found in House Mouse Mus domesticus R. from Peru

A new natural haplotype, t ^wMP1, found in a population of house mouse Mus domesticus from Peru, was subjected to genetic and molecular analyses. Experiments were performed to study the complementation of the new haplotype, fertility of t ^wMP1/t ^x heterozygotes, and transmission ratio distortion (TRD) of the t-carrying chromosome in the progeny of heterozygous males. Molecular analysis included blot hybridization with t-specific probes Tu48, Tu66, and Tu119. The results were collated with the structure and properties of the t complex, and the new haplotype was identified as a complete lethal one.     

Polymorphisms distinguishing different mouse species and t haplotypes.

Three anonymous chromosome 17 DNA markers, D17Tu36, D17Tu43, and D17Le66B, differentiate between house mouse species and/or between t chromosomes. The D17Tu36 probe, which maps near the Fu locus and to the In(17)4 on t chromosomes, identifies at least 15 haplotypes, each haplotype characterized by a particular combination of DNA fragments obtained after digestion with the Taq I restriction endonuclease. Ten of these haplotypes occur in Mus domesticus, while the remaining five occur in M. musculus. In each of these two species, one haplotype is borne by t chromosomes while the other haplotypes are present on non-t chromosomes. The D17Tu43 probe, which maps near the D17Leh122 locus and to the In(17)3 on t chromosomes, also identifies at least 15 haplotypes in Taq I DNA digests, of which nine occur in M. domesticus and six in M. musculus. One of the nine M. domesticus haplotypes is borne by t chromosomes, the other haplotypes are borne by non-t chromosomes; two of the six M. musculus haplotypes are borne by t chromosomes and the remaining four by non-t chromosomes. Some of the D17Tu43 haplotypes are widely distributed in a given species, while others appear to be population-specific. Exceptions to species-specificity are found only in a few mice captured near the M. domesticus-M. musculus hybrid zone or in t chromosomes that appear to be of hybrid origin. The D17Leh66B probe, which maps to the In(17)2, distinguishes three haplotypes of M. domesticus-derived t chromosomes and one haplotype of M. musculus-derived t chromosomes. Because of these characteristics, the three markers are well suited for the study of mouse population genetics in general and of t chromosome population genetics in particular. A preliminary survey of wild M. domesticus and M. musculus populations has not uncovered any evidence of widespread introgression of genes from one species to the other; possible minor introgressions were found only in the vicinity of the hybrid zone. Typing of inbred strains has revealed the contribution of only M. domesticus DNA to the chromosome 17 of the laboratory mouse.     

A novel maternal lineage revealed in sheep (Ovis aries)

It is generally believed that domestic sheep have two maternal lineages (haplotypes A and B), based on mitochondrial DNA analysis. In the present study, we provide evidence that a novel maternal lineage (haplotype C) is exhibited in Chinese native sheep. To verify this finding, 231 samples were collected from six Chinese local breeds, which cover the vast geographical region of sheep inhabitation in China. For comparison, 50 samples were collected from two Western breeds collected in China. Mitochondrial DNA was screened by PCR single-strand conformational polymorphism (SSCP), leading to the identification of novel band patterns in ND2 and ND4 genes in the Chinese breeds. Interestingly, mutations at the two loci were in strong linkage disequilibrium. Direct sequencing of the DNA fragments revealed a non-synonymous substitution in ND2. Furthermore, two synonymous mutations were identified by comparisons of the novel type (haplotype C) and the established types (haplotypes A and B). The entire mitochondrial control region for 55 samples was then sequenced to construct a phylogenetic tree and median joining network. Both the tree and network demonstrated a topology of three groups, which is in consistent with the SSCP analysis. Unlike Western breeds, Chinese breeds are composed mainly of haplotypes A and B, but with a small fraction of haplotype C. According to Fu's test and mismatch distribution, haplotype C has not been subject to a recent population expansion. Based on these results, we propose a novel origin for Chinese sheep.     

Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins

We characterized two novel 7SL RNA-derived short interspersed nuclear element (SINE) families (Tu types I and II) and a novel tRNA-derived SINE family (Tu type III) from the tree shrew (Tupaia belangeri). Tu type I contains a monomer unit of a 7SL RNA-derived Alu-like sequence and a tRNA-derived region that includes internal RNA polymerase III promoters. Tu type II has a similar hybrid structure, although the monomer unit of the 7SL RNA-derived sequence is replaced by a dimer. Along with the primate Alu, the galago Alu type II, and the rodent B1, these two families represent the fourth and fifth 7SL RNA-derived SINE families to be identified. Furthermore, comparison of the Alu domains of Tu types I and II with those of other 7SL RNA-derived SINEs reveals that the nucleotides responsible for stabilization of the Alu domain have been conserved during evolution, providing the possibility that these conserved nucleotides play an indispensable role in retropositional activity. Evolutionary relationships among these 7SL RNA-derived SINE families, as well as phylogenetic relationships of their host species, are discussed.     

(13)C, (31)P and (15)N NMR studies of the ligand exchange reactions of auranofin and chloro(triethylphosphine)gold(I) with thiourea.

The interaction of thiourea (Tu) with auranofin (Et(3)PAuSATg) and its analogue, Et(3)PAuCl has been studied using (13)C, (31)P and (15)N NMR spectroscopy. It is observed that Tu is able to replace both the ligands, Et(3)P and SATg(-) simultaneously from gold(I) in auranofin, forming [Et(3)P-Au-Tu](+) and Tu-Au-SATg complexes. However, no separate resonances for these species were observed either due to their rapid exchange with auranofin and thus giving only the average resonances or because the chemical shifts of either two species are same so that they cannot be resolved. The displaced SATg(-) is oxidized to its disulfide, (SATg)(2). However, some of the displaced Et(3)P is oxidized to Et(3)PO while the remaining reacts with Tu to form Et(3)P-Tu species, characterized by delta 31P of 1.0 ppm, assigned after an independent reaction between Et(3)P and Tu. In an experiment using a 0.05 M solution of auranofin, the Et(3)PO resonance appeared in auranofin spectrum after 4 days of addition of 1.0 equivalent of Tu, showing that the reaction is slow. A resonance for free Et(3)P is also detected in 31P NMR on the addition of CN(-). It is also observed that Tu reacts with Et(3)PAuCl to form [Et(3)P-Au-Tu](+) via displacement of Cl(-), consistent with an upfield shift of 6.2 ppm in >C [double bond] S resonance of Tu in (13)C NMR. In (15)N NMR, a smaller downfield, instead of an upfield shift, in NH(2) resonance of Tu on its addition to auranofin and Et(3)PAuCl indicates that it is not binding to gold(I) through nitrogen.     

A novel splicing variant of CADM2 as a protective transcript of psoriasis

CADM2, a candidate gene for psoriasis, was identified by a genome-wide association study using microsatellites in the Japanese population (561 cases and 561 controls). Moreover, haplotype analysis included an additional 68 SNPs and indicated that a 110-kb haplotype block was detected for the protective risk haplotype of psoriasis. We also identified an initial exon of novel splicing variants in this haplotype block. A functional analysis by qRT-PCR using RNAs from the blood of 56 cases and 64 controls significantly demonstrated an inverse correlation between expression frequencies in a novel splicing variant and the number of alleles associated with psoriasis. To confirm these results, we must perform replication studies using other ethnic groups and more functional analysis particularly for skin tissues.     

土族生物资源利用相关的传统知识多样性

生物资源利用相关的传统知识是对生物资源进行识别和利用的传统知识系统。随着现代生物技术的发展, 这类传统知识显示出其在科学、经济、文化乃至粮食安全战略方面的价值。本研究根据《生物多样性相关传统知识分类、调查与编目技术规定(试行)》, 对我国青海省土族聚集区的土族生物资源利用相关的传统知识进行了系统调查与编目, 并借鉴生物多样性测度方法, 创建了传统知识多样性指数计算方法, 对土族生物资源利用相关传统知识多样性进行分析。结果如下: (1)编目现存的土族生物资源利用相关的传统知识词条共424条; (2)土族传统知识的α多样性指数D_TK = 0.67, 表明其传统知识多样性较高; 土族传统知识的β_wtk多样性指数在不同的县域差异较大, 表明其在县域之间存在差异, 在空间上分布不连续、不均匀。本研究利用生物多样性指数验证了传统知识的定量研究方法, 说明传统知识多样性指数不仅可用于定量研究表征区域传统知识的多样性, 揭示不同空间区域内的分布特征, 还可为未来构建传统知识的定量研究体系提供重要的参考依据。     

我国几个民族中毛发根葡糖磷酸变位酶—1的亚型分布

本文报道了利用等电聚焦的方法,从毛发根鞘细胞分析了我国汉、苗、土家、撒拉、土、达斡尔和赫哲等民族的葡糖磷酸变位酶-1(PGM_1)10亚型的分布,并且与其他人群的基因频率作了比较。     

Structure and evolution of the D17LeH80-like locus in the murine t-complex]

The t complex in the proximal part of chromosome 17 is one of the most thoroughly studied regions of the mouse genome. We determined the sequence of Tu80, a molecular clone derived from microdissected fragments of chromosome 17. The sequence data demonstrated that the total length being 324 bp, Tu80 contains an open-reading frame (ORF) of 204 bp. Two fragments were detected within the ORF, one homologous to the LINE1-element, the other to the first intron of the C epsilon gene of mouse immunoglobin. A sequence designated NOV1 was isolated from the genomic library of mouse chromosome 17. NOV1 was found to contain a B2 insert, making in structurally different from Tu80. The sequences of Tu80 and NOV1 were compared with those of LINE1 and the first intron of the C epsilon gene. The results suggested that the ancestor of the Tu80-like sequence might have arisen through illegitimate recombination between the fragments of LINE1 and the C epsilon gene. It is concluded that Tu80 and NOV1 might have resulted from duplication of the ancestral sequence and following divergence. The comparative analysis also demonstrated high degree of conservation of the LINE1 fragments in Tu80 and NOV1, as well as in the LINE1 in a number of mammalian species. Based on the structure of human, rat, rabbit and mouse LINE1 fragments, and also on that of NOV1 and Tu80, phylogenetic tree has been constructed. Its topology is consistent with the accepted phylogenetic relationships among the species studied. The data available tend to support the assumption that the ancestor for the Tu80-like sequence might have arisen not later than 27-33 million years ago.     

Repetitive sequences of the tree shrew genome (Mammalia, Scandentia)

Copies of two repetitive elements of the genome of common tree shrew (Tupaia glis) were cloned and sequenced. The first element, Tu III, is a approximately 260 bp long short interspersed element (SINE) with the 5'-end derived from glycine RNA. Tu III carries long polypurine- and polypyrimidine-rich tracts, which may contribute to the specific secondary structure of Tu III RNA. This SINE was also found in the genome of smooth-tailed tree shrew of another genus (Dendrogale). Tu III seems to be confined to the order Scandentia (tree shrews) since it was not found in DNA of other tested mammals. The second element Tu-SAT1 is a tandem repeat with a monomer length of 365 bp. Some properties of its nucleotide sequence suggest that Tu-SAT1 is a centromeric satellite.     

Identification of a cryptic lethal mutation in the mouse t(w73) haplotype

t haplotypes are naturally occurring, variant forms of the t complex on mouse chromosome 17, characterized by the presence of four inversions with respect to wild-type. They harbour mutations causing male sterility, male transmission ratio distortion (TRD) and embryonic lethality. Mice carrying t haplotypes have been found throughout the world, and genetic studies of the lethal mutations have identified at least 16 complementation groups. The embryonic lethal phenotypes of many t haplotypes have been characterized in detail, and are thought to be the consequence of homozygosity for single gene mutations. However, the existence of additional mutations in genes that function at later stages of development would be obscured. Here we investigated the possibility of multiple mutations in t haplotypes by screening the t(w73) haplotype for the presence of novel mutations. Since genetic analysis of t haplotype mutations is hindered by recombination suppression due to the inversions, deletion complexes covering the proximal two-thirds of the t complex were used to uncover the presence of any new lethal alleles. This analysis revealed a novel mutation between D17Jcs41 and D17Mit100, causing mice carrying both t(w73) and selected deletions to die at birth, prior to feeding. The finding of a new, cryptic lethal mutation in t haplotypes is an indication that these recombinationally isolated chromosomes, which already contain at least one lethal mutation that prevents homozygosity, may serve as sinks for the accumulation of additional recessive mutations.     

Repetitive sequences of the tree shrew genome (Mammalia, Scandentia)

Copies of two repetitive elements of the common tree shrew (Tupaia glis) genome were cloned and sequenced. The first element, Tu III, is a ～260 bp long short interspersed element (SINE) with the 5′ end derived from glycine RNA. Tu III carries long polypurine-and polypyrimidine-rich tracts, which may contribute to the specific secondary structure of Tu III RNA. This SINE was also found in the genome of the smooth-tailed tree shrew of another genus (Dendrogale). Tu III appears to be confined to the order Scandentia since it was not found in the DNA of other tested mammals. The second element, Tu-SAT1, is a tandem repeat with a monomer length of 365 bp. Some properties of its nucleotide sequence suggest that Tu-SAT1 is a centromeric satellite.     

青海撒拉族侧面部几何形态测量分析

采用基于标志点的几何形态学测量方法对青海循化撒拉族自治县的撒拉族男性82人侧面轮廓形状进行了分析。撒拉族人群额部的变异主要体现在第7、8特征点区域(鼻凹点之上区域),额部其他区域的形态变异较小,而鼻区、嘴唇及下巴区域的形态变异较大,这些特征与土族较相似。同时,撒拉族也显示出明显区别于土族、藏族的形态。如撒拉族额部比较突出,显得前倾,额部相对较长,唇部相对土族较回缩。撒拉族额部特征点集的面积较大,可能反映了撒拉族额部的变异大于土族、藏族。聚类分析显示,男性两类侧面轮廓的差异主要集中在额部,与土族的类别间差异有相似之处。异速生长分析显示,尺寸大小能够解释形状变异的5.51%,随着CS值的增大,额部和下巴部变化明显,额度由陡直趋向于变得平缓,下巴部也随CS值的增大由较突出变为明显回缩。土族、藏族也是随着CS值的增大,额部由陡直趋向于变得平缓,下巴部由较突出变为明显回缩,似乎提示撒拉族、土族、藏族有相似的面部形态变化规律:长面型者的额部较低平,下巴部较回缩。     

High frequency of MIC null haplotype (HLA-B48-MICA-del-MICB*0107 N) in the Angaite Amerindian community in Paraguay

We describe a high frequency of the MIC null haplotype, HLA-B48-MICA-del-MICB*0107 N, in the Angaite Amerindian community in Paraguay. Of the 16 unrelated subjects, 9 (56.5%) had this haplotype. The structural analyses revealed this haplotype was similar to the previously reported Asian haplotype in that they had a large-scale deletion including the entire MICA gene and linked to MICB*0107 N and HLA-B*48. The novel recombination haplotype between this MIC null haplotype and HLA-B15, HLA-B15-MICA-del-MICB*0107 N, was also found in this community.     

Genetic Evidence for Two T Complex Tail Interaction (Tct) Loci in T Haplotypes

The t complex on chromosome 17 of the house mouse is an exceptional model for studying the genetic control of transmission ratio, gametogenesis, and embryogenesis. Partial haplotypes derived through rare recombination between a t haplotype and its wild-type homolog have been essential in the genetic analysis of these various properties of the t complex. A new partial t haplotype, which was derived from the complete tw71 haplotype and which is called tw71Jr1, was shown to have unexpected effects on tail length and unique recombination breakpoints. This haplotype, either when homozygous or when heterozygous with the progenitor tw71 haplotype, produced short-tailed rather than normal-tailed mice on certain genetic backgrounds. Genetic analysis of this exceptional haplotype showed that the recombination breakpoints were different from those leading to any other partial t haplotype. Based on this haplotype, a model is proposed that accounts for genetic interactions between the brachyury locus (T), the t complex tail interaction (tct) locus, and their wild-type homolog(s) that determine tail length. An important part of this model is the hypothesis that the tct locus, which enhances the tail-shortening effect of T mutations, is in fact at least two, genetically separable genes with different genetic activities. Genetic analysis of parental and recombinant haplotypes also suggests that intrachromosomal recombination involving an inverted duplicated segment can account for the variable orientation of loci within an inverted duplication on wild-type homologs of the t haplotype.     

Molecular analysis of the Retinoic Acid Induced 1 gene (RAI1) in patients with suspected Smith-Magenis syndrome without the 17p11.2 deletion

Smith-Magenis syndrome (SMS) is a complex neurobehavioral disorder characterized by multiple congenital anomalies. The syndrome is primarily ascribed to a ～3.7 Mb de novo deletion on chromosome 17p11.2. Haploinsufficiency of multiple genes likely underlies the complex clinical phenotype. RAI1 (Retinoic Acid Induced 1) is recognized as a major gene involved in the SMS phenotype. Extensive genetic and clinical analyses of 36 patients with SMS-like features, but without the 17p11.2 microdeletion, yielded 10 patients with RAI1 variants, including 4 with de novo deleterious mutations, and 6 with novel missense variants, 5 of which were familial. Haplotype analysis showed two major RAI1 haplotypes in our primarily Caucasian cohort; the novel RAI1 variants did not occur in a preferred haplotype. RNA analysis revealed that RAI1 mRNA expression was significantly decreased in cells of patients with the common 17p11.2 deletion, as well as in those with de novo RAI1 variants. Expression levels varied in patients with familial RAI1 variants and in non-17p11.2 deleted patients without identified RAI1 defects. No correlation between SNP haplotype and RAI1 expression was found. Two clinical features, ocular abnormalities and polyembolokoilomania (object insertion), were significantly correlated with decreased RAI1 expression. While not significantly correlated, the presence of hearing loss, seizures, hoarse voice, childhood onset of obesity and specific behavioral aspects and the absence of immunologic abnormalities and cardiovascular or renal structural anomalies, appeared to be specific for the de novo RAI1 subgroup. Recognition of the combination of these features will assist in referral for RAI1 analysis of patients with SMS-like features without detectable microdeletion of 17p11.2. Moreover, RAI1 expression emerged as a genetic target for development of therapeutic interventions for SMS.     

Elongation factor Tu can reduce translation errors in poly(U)-directed cell-free systems

Rates of incorporation of [³H]phenylalanine and [¹⁴C]leucine from the aminoacylated transfer-RNA into polypeptides synthesized on poly(U) programmed Escherichia coli ribosomes have been determined in cell-free translation systems containing either elongation factors Tu and G with GTP, or just elongation factor Tu or G with GTP, or none of the elongation factors. The presence of elongation factor Tu with GTP has been shown to reduce the leucine to phenylalanine ratio in the product at relatively low concentrations of Mg²⁺. This error-reducing effect of elongation factor Tu has not been observed at high concentrations of Mg²⁺, although the factor still contributed to the speed of elongation. The results are discussed in terms of the kinetic proof-reading mechanism proposed by Hopfield (1974).     

A glutathione-S-transferase (TuGSTd05) associated with acaricide resistance in Tetranychus urticae directly metabolizes the complex II inhibitor cyflumetofen

Cyflumetofen is a recently introduced acaricide with a novel mode of action, acting as an inhibitor of complex II of mitochondrial electron transport chain. It is activated by hydrolysis and the resulting de-esterified metabolite is a much stronger inhibitor. Cyflumetofen represents a great addition for the control of mite species including Tetranychus urticae, a major agricultural pest, which has the ability to develop resistance to most classes of pesticides rapidly. A resistant strain (Tu008R) was recently described and synergism experiments pointed towards the involvement of GSTs. Here, we conducted genome-wide gene expression analysis, comparing Tu008R with its parental susceptible strain, and identified the delta GST TuGSTd05 as the prime resistance-conferring candidate. Docking analysis suggests that both cyflumetofen and its de-esterified metabolite are potential substrates for conjugation by TuGSTd05. Several amino acids were identified that might be involved in the interaction, with Y107 and N103 possibly having an important role. To further investigate interaction as well as the role of Y107 and N103 in vitro, we recombinantly expressed and kinetically characterized the wild type TuGSTd05, TuGSTd05 Y107F and TuGSTd05 N103L mutants. While cyflumetofen was not found to act as a strong inhibitor, the de-esterified metabolite showed strong affinity for TuGSTd05 (IC₅₀ = 4 μM), which could serve as a mechanism of rapid detoxification. Y107 and N103 might contribute to this interaction. HPLC-MS analysis provided solid indications that TuGSTd05 catalyzes the conjugation of ionized glutathione (GS⁻) to cyflumetofen and/or its de-esterified metabolite and the resulting metabolite and possible site of attack were identified.