Chromosome duplications and deletions and their mechanisms of origin.

Duplications and deletions of the same gene loci or chromosome regions are known to produce different clinical manifestations and are significant factors in human morbidity and mortality. Extensive cytogenetic and molecular cytogenetic studies with cosmid and YAC probes in two patients with unique mosaicism for reciprocal duplication-deletion allowed us to further understand the origin of these abnormalities. The first patient's mosaic karyotype was 46,XX, inv dup(11) (q23q13)/46,XX,del(11)(q13q23). The second patient had a 46,XY,dup(7)(p11.2p13)/46,XY,del(7)(p11.2p13)/46,XY karyotype. Fluorescence in situ hybridization studies on the first patient placed the two breakpoints near the folate-sensitive fragile sites FRA11A and FRA11B. The presence of repeated sequences responsible for these fragile sites may have been involved in the patient's duplication-deletion. Our investigation leads us to conclude that, in addition to known mechanisms (such as unequal crossovers between homologs, unequal sister chromatid exchanges, excision of intrachromatid loops, and meiotic recombination within a single chromatid), duplication-deletion can also arise by the formation of an overlying loop followed by an uneven crossover at the level of the DNA strand.     

Independent contrasts and regression through the origin

Following the pioneering work of Felsenstein and Garland, phylogeneticists have been using regression through the origin to analyze comparative data using independent contrasts. The reason why regression through the origin must be used with such data was revisited. The demonstration led to the formulation of a permutation test for the coefficient of determination and the regression coefficient estimates in regression through the origin. Simulations were carried out to measure type I error and power of the parametric and permutation tests under two models of data generation: regression models I and II (correlation model). Although regression through the origin assumes model I data, in independent contrast data error is present in the explanatory as well as the response variables. Two forms of permutations were investigated to test the regression coefficients: permutation of the values of the response variable y, and permutation of the residuals of the regression model. The simulations showed that the parametric tests or any of the permutation tests can be used when the error is normal, which is the usual assumption in independent contrast studies; only the test by permutation of y should be used when the error is highly asymmetric; and the parametric tests should be used when extreme values are present in covariables. Two examples are presented. The first one concerns non-specificity in fish parasites of the genus Lamellodiscus, the second the richness in parasites in 78 species of mammals.     

The tricho-rhino-phalangeal syndromes: frequency and parental origin of 8q deletions

The tricho-rhino-phalangeal syndromes type I (TRPS I) and type II (TRPS II) result from the deletion of overlapping sets of genes within the Langer-Giedion syndrome chromosomal region (LGCR) on chromosome 8. In contrast to TRPS I patients, most TRPS II patients have cytogenetically visible deletions and are often mentally retarded. Using Southern blot and fluorescence in situ hybridization analysis, we searched for submicroscopic deletions in 12 patients with TRPS I and an apparently normal karyotype. One patient of normal intelligence was found to have a deletion of approximately 5 Mb. This suggests that mental retardation in TRPS is caused by genes outside the 5-Mb region. Using three LGCR microsatellite markers, we determined the parental origin of this TRPS I deletion and of eight TRPS II deletions. In six patients, the deletion was of paternal origin and in three patients it was of maternal origin. Received: 6 September 1996 / Revised: 20 November 1996     

Multiple deletions of mtDNA remove the light strand origin of replication

Idiopathic inflammatory myopathies are progressive, debilitating muscle diseases. The pathogenesis of these disorders is multifactorial and appears to include mutations of the mitochondrial genome, which are usually indicated by morphological changes of mitochondria. The vast majority of all mitochondrial DNA deletions found are located between the origins of replication in the "major region" between nt5760-nt190. Using long distance PCR and sequencing techniques, we detected deletions which were unusually large (ca. 10500-12800 bp) and show uncommon 5'-breakpoints between nt800 and nt3326. Unlike most other deletions, their breakpoints are far upstream of the "major region." The atypical location of these deletions suggests a different pathomechanism. The impact of the mitochondrial DNA deletions in the pathogenetic cascade remains uncertain.     

In vitro characteristics of metastatic variant subclones of restricted genetic origin

We have studied several metastatic variant cell lines derived from a common clonal origin and their transformed and untransformed parental cell lines. A number of in vitro characteristics were examined for each tumor line and these properties were correlated with the ability of the tumor cells to form pulmonary nodules in an experimental metastasis assay. Direct correlations with metastatic behavior in the lung colony assay were found to exist with the amount of cell-bound Concanavalin A and the procoagulant activities of cell lysates. In vitro parameters that did not correlate with the metastatic phenotype were: population doubling times in culture, saturation density achieved in culture, the number of colony-forming cells shed from confluent cultures, rates of cellular attachment to homotypic or heterotypic cell monolayers, plasminogen-activator production and procoagulant activity produced in serum-free conditioned medium.     

Different molecular mechanisms causing 9p21 deletions in acute lymphoblastic leukemia of childhood

Deletion of chromosome 9p21 is a crucial event for the development of several cancers including acute lymphoblastic leukemia (ALL). Double strand breaks (DSBs) triggering 9p21 deletions in ALL have been reported to occur at a few defined sites by illegitimate action of the V(D)J recombination activating protein complex. We have cloned 23 breakpoint junctions for a total of 46 breakpoints in 17 childhood ALL (9 B- and 8 T-lineages) showing different size deletions at one or both homologous chromosomes 9 to investigate which particular sequences make the region susceptible to interstitial deletion. We found that half of 9p21 deletion breakpoints were mediated by ectopic V(D)J recombination mechanisms whereas the remaining half were associated to repeated sequences, including some with potential for non-B DNA structure formation. Other mechanisms, such as microhomology-mediated repair, that are common in other cancers, play only a very minor role in ALL. Nucleotide insertions at breakpoint junctions and microinversions flanking the breakpoints have been detected at 20/23 and 2/23 breakpoint junctions, respectively, both in the presence of recombination signal sequence (RSS)-like sequences and of other unspecific sequences. The majority of breakpoints were unique except for two cases, both T-ALL, showing identical deletions. Four of the 46 breakpoints coincide with those reported in other cases, thus confirming the presence of recurrent deletion hotspots. Among the six cases with heterozygous 9p deletions, we found that the remaining CDKN2A and CDKN2B alleles were hypermethylated at CpG islands.     

Independent spontaneous mitochondrial malate dehydrogenase null mutants in soybean are the result of deletions

The mitochondrial malate dehydrogenase-1 (Mdh1) gene of soybean [Glycine max (L.) Merr.] spontaneously mutates to a null phenotype at a relatively high rate. To determine the molecular basis for the instability of the Mdh1 gene, the gene was cloned and sequenced. The null phenotype correlated with the deletion of specific genomic restriction fragments that encode the Mdh1 gene. The composition of the Mdh1 gene and its environs were compared with those of the more stable MDH2 gene. Several possible causes of the observed instability were found, including duplications, repeats, and two regions with similarity to a soybean catalase. The most likely cause of instability, however, appeared to be a 1233 bp region with 58.9% identity to the Cyclops retrotransposons. Translation of a 714 bp segment of this region produced a peptide composed of 238 amino acid residues that showed 35-40% identity and 55-60% similarity to several putative Cyclops gag-pol proteins (group-specific antigen polyprotein). This short peptide also contained a segment that corresponded to the protease active site of the gag-pol protein. Thus in an appropriate genetic background, a retrotransposon, whether whole or fractured, could promote genetic rearrangements.     

丁香属植物的地理分布及其起源演化

木犀科丁香属植物主要分布在中国、朝鲜、日本以及欧洲东南部。中国是丁香属的自然分布中心,丁香主要分布在中国西南、西北、华北、东北等地区。根据植物区系的演化规律,作者认为丁香属起源于中国西南,并以此为中心主要沿中国西南-西北-华北-东北-朝鲜半岛-日本和中国西南-中亚-欧洲的路径散布。近缘种之间存在着遥远的地理隔离,中国原产的华丁香与分布在我国西北及中亚的花叶丁香、欧洲特有种欧洲丁香均为近缘种,表明欧洲丁香的散布与中国西北的种类有着密切的联系。近年分子生物学试验表明羽叶性状是演化中的过渡类型,在研究该属系统演化中具有重要作用。化石记录华北紫丁香在中新世时的华中地区已有存在,说明该属至少在中新世时完成了由西南向华中的演化、辐射。     

Exon size distribution and the origin of introns

Since it was first recognised that eukaryotic genes are fragmented into coding segments (exons) separated by non-coding segments (introns), the reason for this phenomenon has been debated. There are two dominant theories: that the piecewise arrangement of genes allows functional protein domains, represented by exons, to recombine by shuffling to form novel proteins with combinations of functions; or that introns represent parasitic DNA that can infest the eukaryotic genome because it does not interfere grossly with the fitness of its host. Differing distributions of exon lengths are predicted by these two theories. In this paper we examine distributions of exon lengths for six different organisms and find that they offer empirical evidence that both theories may in part be correct.     

Parental origin of de novo constitutional deletions of chromosomal band 11p13.

One-half of all cases of Wilms tumor (WT), a childhood kidney tumor, show loss of heterozygosity at chromosomal band 11p13 loci, suggesting that mutation of one allele and subsequent mutation or loss of the homologous allele are important events in the development of these tumors. The previously reported nonrandom loss of maternal alleles in these tumors implied that the primary mutation occurred on the paternally derived chromosome and that it was "unmasked" by loss of the normal maternal allele. This, in turn, suggests that the paternally derived allele is more mutable than the maternal one. To investigate whether germinal mutations are seen with equal frequency in maternally versus paternally inherited chromosomes, we determined the parental origin of the de novo germinal 11p13 deletions in eight children by typing lymphocyte DNA from these children and from their parents for 11p13 RFLPs. In seven of the eight cases, the de novo deletion was of paternal origin. The one case of maternal origin was unremarkable in terms of the size or extent of the 11p13 deletion, and the child did develop WT. Transmission of 11p13 deletions by both maternal and paternal carriers of balanced translocations has been reported, although maternal inheritance predominates. These data, in addition to the general preponderance of paternally derived, de novo mutations at other loci, suggest that the increased frequency of paternal deletions we observed is due to an increased germinal mutation rate in males.     

Parental origin and germline mosaicism of deletions and duplications of the dystrophin gene: a European study

Summary Knowledge about the parental origin of new mutations and the occurrence of germline mosaicism is important for estimating recurrence risks in Duchenne (DMD) and Becker muscular dystrophy (BMD). However, there are problems in resolving these issues partly because not all mutations can as yet be directly detected, and additionally because genetic ratios are very sensitive to ascertainment bias. In the present study, therefore, analysis was restricted to currently detectable mutations (deletions and duplications) in particular types of families which tend to be rare. In order to obtain sufficient data we pooled results from 25 European centers. In mothers of affected patients who were the first in their family with a dystrophin gene deletion or duplication, the ratio between the paternal and the maternal origin of this new mutation was 32:49 (binomial test P = 0.075) for DMD. In five BMD families the ratio between paternal and maternal origin of new mutations was 32. Recurrence risk because of maternal germline mosaicism was studied in sisters or subsequent sibs of isolated cases with an apparently new detectable mutation. In 12 out of 59 (0.20; 95% CI 0.10–0.31) transmissions of the risk haplotype the DMD mutation was transmitted as well. No recurrences were found in nine BMD families.     

Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle

In order to clarify the origin and genetic diversity of cattle in North Eastern Asia, this study examined mitochondrial displacement loop sequence variation and frequencies of Bos taurus and Bos indicus Y chromosome haplotypes in Japanese, Mongolian, and Korean native cattle. In mitochondrial analyses, 20% of Mongolian cattle carried B. indicus mitochondrial haplotypes, but Japanese and Korean cattle carried only B. taurus haplotypes. In contrast, all samples revealed B. taurus Y chromosome haplotypes. This may be due to the import of zebu and other cattle during the Mongol Empire era with subsequent crossing with native taurine cattle. B. taurus mtDNA sequences fall into several geographically distributed haplogroups and one of these, termed here T4, is described in each of the test samples, but has not been observed in Near Eastern, European or African cattle. This may have been locally domesticated from an East Eurasian strain of Bos primigenius.     

Independent maternal origin of Chinese swamp buffalo (Bubalus bubalis)

To obtain more knowledge on the origin and genetic diversity of the swamp buffalo (Bubalus bubalis) in China, the complete mitochondrial D-loop sequences of 119 samples representing seven native types were compared. Two mitochondrial DNA (mtDNA) lineages (lineages A and B) were determined for the Chinese swamp buffalo. Examination of the diversity patterns suggest that lineage A has undergone a population expansion event. Divergence of lineages A and B was estimated at 18,000 years ago. Combined analyses of mtDNA sequences from Chinese, Indian, Brazilian/Italian and Southeast Asian/Australian buffalo samples showed independent domestication events in the swamp buffalo from China and the river buffalo from the India subcontinent. The spread of swamp and river buffalo from China and India respectively to mainland Southeast Asia suggests that Southeast Asia is a hybrid zone for buffalo. Our data support the hypothesis of the evolution of domesticated swamp and river buffalo from ancestral swamp-like animals. These ancestral animals were extensively distributed across mainland Asia and most likely are represented today by the wild Asian buffalo (Bubalus arnee).     

2014年泌尿道感染病原菌分布及药敏性分析

摘要：目的 分析并了解泌尿道感染病原菌的分布及药敏性,为临床合理有效的抗菌治疗提供参考依据。方法 收集宁波市医疗中心李惠利医院2014年住院及门诊部送检的中段尿标本分离的1 187株病原菌,对其菌群分布和药敏结果进行回顾性分析。结果 1 187株尿培养病原菌中,细菌占82.8%（983/1 187）,真菌占17.2%（204/1 187）。检出率前四位的细菌分别是大肠埃希菌（31.2%）、屎肠球菌（10.5%）、肺炎克雷伯菌（9.6%）和粪肠球菌（9.2%）,其中大肠埃希菌和肺炎克雷伯菌产超广谱β-内酰胺酶的阳性率分别是61.2%和26.9%,对头孢菌素类、青霉素类和单环酰胺类抗生素的敏感率普遍较低,对碳青霉烯类药物的敏感率>85%。屎肠球菌和粪肠球菌对抗菌药物的敏感性存在较大差异,且表现出较高的多药耐药性,屎肠球菌对万古霉素和利奈唑胺的敏感率分别为100.0%和95.1%,粪肠球菌对青霉素G和氨苄西林完全敏感。检出率前两位的真菌分别是白色假丝酵母菌（9.0%）和光滑假丝酵母菌（6.2%）,两者对5-氟胞嘧啶和两性霉素B近乎100.0%敏感。结论 本院引起泌尿道感染的病原菌种类繁多,对不同抗菌药物的敏感性差异较大,临床应根据药敏试验结果权衡利弊后合理使用抗菌药物,预防和控制耐药菌株的形成。     

The origin and distribution of feral mink in Scotland

A result of the post-war boom in mink farming was the escape of mink which are now well established in the wild. Feral mink are known to be present in all Scottish mainland counties, except Sutherland and Caithness, and are also found on the islands of Arran and Lewis. Populations are thriving on most of the main river systems. The existence of suitable habitat and adequate food supplies suggests that mink will continue to increase and spread in Scotland.     

Geographic distribution and origin of CFTR mutations in Germany

The geographic distribution and origin of CFTR mutations in Germany was evaluated in 658 three-generation families with cystic fibrosis (CF). Fifty different mutations were detected on 1305 parental CF chromosomes from 22 European countries and overseas. The major mutation ΔF508 was identified on 71.5% of all CF chromosomes, followed by R553X (1.8%), N1303K (1.3%), G542X (1.1%), G551D (0.8%) and R347P (0.8%). According to the grandparents’ birthplace, 74% of CF chromosomes had their origin in Germany; the ΔF508 percentage was 77%, 75%, 70% and 62% in northern, southern, western and eastern Germany, respectively. Ten or more mutant alleles in the investigated CF gene pool originated from Austria, the Czech Republic, Poland, Russia, Turkey and the Ukraine. This widespread geographic origin of CFTR mutations in today’s Germany reflects the many demographic changes and migrations in Central Europe during the 20th century. Received: 10 October 1995 / Revised: 9 January 1995