Comparisons of eukaryotic genomic sequences.

A method for assessing genomic similarity based on relative abundances of short oligonucleotides in large DNA samples is introduced. The method requires neither homologous sequences nor prior sequence alignments. The analysis centers on (i) dinucleotide (and tri- and tetra-) relative abundance extremes in genomic sequences, (ii) distances between sequences based on all dinucleotide relative abundance values, and (iii) a multidimensional partial ordering protocol. The emphasis in this paper is on assessments of general relatedness of genomes as distinguished from phylogenetic reconstructions. Our methods demonstrate that the relative abundance distances almost always differ more for genomic interspecific sequence comparisons than for genomic intraspecific sequence comparisons, indicating congruence over different genome sequence samples. The genomic comparisons are generally concordant with accepted phylogenies among vertebrate and among fungal species sequences. Several unexpected relationships between the major groups of metazoa, fungal, and protist DNA emerge, including the following. (i) Schizosaccharomyces pombe and Saccharomyces cerevisiae in dinucleotide relative abundance distances are as similar to each other as human is to bovine. (ii) S. cerevisiae, although substantially far from, is significantly closer to the vertebrates than are the invertebrates (Drosophila melanogaster, Bombyx mori, and Caenorhabditis elegans). This phenomenon may suggest variable evolutionary rates during the metazoan radiations and slower changes in the fungal divergences, and/or a polyphyletic origin of metazoa. (iii) The genomic sequences of D. melanogaster and Trypanosoma brucei are strikingly similar. This DNA similarity might be explained by some molecular adaptation of the parasite to its dipteran (tsetse fly) host, a host-parasite gene transfer hypothesis. Robustness of the methods may be due to a genomic signature of dinucleotide relative abundance values reflecting DNA structures related to dinucleotide stacking energies, constraints of DNA curvature, and mechanisms attendant to replication, repair, and recombination.     

Leukemic reticuloendotheliosis: A study of the origin of the malignant cell

A highly pure preparation of neoplastic cells from the spleen of a patient with leukemic reticuloendotheliosis was studied for function, membrane characteristics and glucose metabolism. Glass adherence and phagocytosis of small particles (latex and carbon black) were demonstrated with phase contrast microscopy. Staphylocidal activity was similar to that of normal monocytes. Immunofluorescent assays revealed nonspecific uptake of antiserums to immunoglobulkis G (IgG), M (IgM), A (IgA) and kappa and lambda light chains. Rosette assays Indicated the presence of receptors for IgG on the surface of all cells but no receptors for complement (C3) or sheep red blood cells. Glucose metabolic studies revealed a pattern that differed from that of normal monocytes or lymphocytes with intermediate values for glycolysls, low hexose monophosphate shunt activity and high Krebs cycle activity. Increments in tritiated (³H)-thymldine uptake and glucose metabolism in response to phytohemagglutinin stimulation were minimal (5 per cent of normal lymphocyte values) and no response was noted with pokeweed mitogen stimulation. These findings suggest that the leukemic reticuloendotheliosis cell most closely resembles cells of the monocyte-histiocyte series.     

Ribonucleoprotein-masked nicks at 50-kbp intervals in the eukaryotic genomic DNA

By using a microscopic approach, field inversion single-cell gel electrophoresis, we show that preformed single-strand discontinuities are present in the chromatin of resting and proliferating mammalian and yeast cells. These single-strand breaks are primarily nicks positioned at approximately 50-kbp intervals throughout the entire genome that could be efficiently labeled in situ by DNA polymerase I holoenzyme but not by Klenow fragment and terminal transferase unless after ribonucleolytic treatments. The RNA molecules involved appear to comprise R-loops, recognized by the S9.6 RNA/DNA hybrid-specific antibody. By using the breakpoint cluster region of the Mixed Lineage Leukemia (MLL) gene as a model, we have found that the number of manifest nicks detected by FISH performed after field inversion single-cell gel electrophoresis depends on epigenetic context, but the difference between germ-line and translocated MLL alleles is abolished by protease treatment. Our data imply that the double-stranded genomic DNA is composed of contiguous rather than continuous single strands and reveal an aspect of higher-order chromatin organization with ribonucleoprotein-associated persistent nicks defining approximately 50-kbp domains.     

Interspecific introgressive origin of genomic diversity in the house mouse

We report on a genome-wide scan for introgression between the house mouse (Mus musculus domesticus) and the Algerian mouse (Mus spretus), using samples from the ranges of sympatry and allopatry in Africa and Europe. Our analysis reveals wide variability in introgression signatures along the genomes, as well as across the samples. We find that fewer than half of the autosomes in each genome harbor all detectable introgression, whereas the X chromosome has none. Further, European mice carry more M. spretus alleles than the sympatric African ones. Using the length distribution and sharing patterns of introgressed genomic tracts across the samples, we infer, first, that at least three distinct hybridization events involving M. spretus have occurred, one of which is ancient, and the other two are recent (one presumably due to warfarin rodenticide selection). Second, several of the inferred introgressed tracts contain genes that are likely to confer adaptive advantage. Third, introgressed tracts might contain driver genes that determine the evolutionary fate of those tracts. Further, functional analysis revealed introgressed genes that are essential to fitness, including the Vkorc1 gene, which is implicated in rodenticide resistance, and olfactory receptor genes. Our findings highlight the extent and role of introgression in nature and call for careful analysis and interpretation of house mouse data in evolutionary and genetic studies.Classical laboratory mouse strains, as well as newly established wild-derived ones, are widely used by geneticists for answering a diverse array of questions (1). Understanding the genome contents and architecture of these strains is important for studies of natural variation and complex traits, as well as evolutionary studies in general (2). Mus spretus, a sister species of Mus musculus, impacts the findings in M. musculus investigations for at least two reasons. First, it was deliberately interbred with laboratory M. musculus strains to introduce genetic variation (3). Second, Mus musculus domesticus is partially sympatric (naturally cooccurring) with M. spretus (Fig. 1).Open in a separate windowFig. 1.Species ranges and samples used in our study. The species range of M. spretus is shown in green (4), and the species range of M. m. domesticus includes the blue regions, the range of M. spretus, and beyond (1). M. m. domesticus and M. spretus samples were obtained from locations marked with red circles and purple diamonds, respectively. The samples originated from within and outside the area of sympatry between the two species. (SI Appendix, Table S1, provides additional details about the samples used in our study.)Recent studies have examined admixture between subspecies of house mice (5–8), but have not studied introgression with M. spretus. In at least one case (5), the introgressive descent of the mouse genome was hidden due to data postprocessing that masked introgressed genomic regions as missing data. In another study reporting whole-genome sequencing of 17 classical laboratory strains (6), M. spretus was used as an outgroup for phylogenetic analysis. The authors were surprised to find that 12.1% of loci failed to place M. spretus as an outgroup to the M. musculus clade. The authors concluded that M. spretus was not a reliable outgroup but did not pursue their observation further. On the other hand, in a 2002 study (9), Orth et al. compiled data on allozyme, microsatellite, and mitochondrial variation in house mice from Spain (sympatry) and nearby countries in western and central Europe. Interestingly, allele sharing between the species was observed in the range of sympatry but not outside in the range of allopatry. The studies demonstrated the possibility of natural hybridization between these two sister species. Further, the study of Song et al. (10) demonstrated a recent adaptive introgression from M. spretus into some M. m. domesticus populations in the wild, involving the vitamin K epoxide reductase subcomponent 1 (Vkorc1) gene, which was later shown to be more widespread in Europe, albeit geographically restricted to parts of southwestern and central Europe (11).Major, unanswered questions arise from these studies. First, is the vicinity around the Vkorc1 gene an isolated case of adaptive introgression in the house mouse genome, or do many other such regions exist? Second, is introgression between M. spretus and M. m. domesticus common outside the range of sympatry? Third, have there been other hybridization events, and, in particular, more ancient ones? Fourth, what role do introgressed genes, and, more generally, genomic regions, play?To investigate these open questions, we used genome-wide variation data from 20 M. m. domesticus samples (wild and wild-derived) from the ranges of sympatry and allopatry, as well as two M. spretus samples. For detecting introgression, we used PhyloNet-HMM (12), a newly developed method for statistical inference of introgression in genomes while accounting for other evolutionary processes, most notably incomplete lineage sorting (ILS).Our analysis provides answers to the questions posed above. First, we find signatures of introgression between M. spretus and each of the M. m. domesticus samples. The amount of introgression varies across the autosomes of each genome, with a few chromosomes harboring all detectable introgression, and most of the chromosomes have none. We detected no introgression on the X chromosome. Further, the amount of introgression varied widely across the samples. Our analyses demonstrate introgression outside the range of sympatry. In fact, our results show more signatures of introgression in the genomes of allopatric samples from Europe than in sympatric samples from Africa. For the third question, we used the length distribution and sharing patterns of introgressed regions across the samples to show support for at least three hybridization events: an ancient hybridization event that predates the colonization of Europe by M. m. domesticus and two more recent events, one of which presumably occurred about 50 y ago and is related to warfarin resistance selection (10). For the fourth question, our functional analysis of the introgressed genes shows enrichment for certain categories, most notably olfaction—an essential trait for the fitness of rodents. Understanding the genomic architecture and evolutionary history of the house mouse has broad implications on various aspects of evolutionary, genetic, and biomedical research endeavors that use this model organism. The PhyloNet-HMM method (12) can be used to detect introgression in other eukaryotic species, further broadening the impact of this work.     

A progenitor cell origin of myeloid malignancies

All cancers rely on cells that have properties of long-term self-renewal or “stemness” to maintain and propagate the tumor, but the cell of origin of most cancers is still unknown. Here, we design a stochastic mathematical model of hematopoietic stem and progenitor cells to study the evolutionary dynamics of cancer initiation. We consider different evolutionary pathways leading to cancer-initiating cells in JAK2V617F-positive myeloproliferative neoplasms (MPN): (i) the JAK2V617F mutation may arise in a stem cell; (ii) a progenitor cell may first acquire a mutation conferring self-renewal, followed by acquisition of the JAK2V617F mutation; (iii) the JAK2V617F mutation may first emerge in a progenitor cell, followed by a mutation conferring self-renewal; and (iv) a mutation conferring self-renewal to progenitors may arise in the stem cell population without causing a change in the stem cell''s phenotype, followed by the JAK2V617F mutation emerging in a progenitor cell. We find mathematical evidence that a progenitor is the most likely cell of origin of JAK2V617F-mutant MPN. These results may also have relevance to other tumor types arising in tissues that are organized as a differentiation hierarchy.     

Dendritic cell ontogeny: A human dendritic cell lineage of myeloid origin

Dendritic cells (DC) have been thought to represent a family of closely related cells with similar functions and developmental pathways. The best-characterized precursors are the epidermal Langerhans cells, which migrate to lymphoid organs and become activated DC in response to inflammatory stimuli. Here, we demonstrate that a large subset of DC in the T cell-dependent areas of human lymphoid organs are nonactivated cells and belong to a separate lineage that can be identified by high levels of the interleukin 3 receptor α chain (IL-3Rα^hi). The CD34⁺IL-3Rα^hi DC progenitors are of myeloid origin and are distinct from those that give rise to Langerhans cells in vitro. The IL-3Rα^hi DC furthermore appear to migrate to lymphoid organs independently of inflammatory stimuli or foreign antigens. Thus, DC are heterogeneous with regard to function and ontogeny.     

Pyrexia of unknown origin: causes,investigation and management

Pyrexia of unknown origin (PUO) is a syndrome that has long tested the skills of physicians to achieve a diagnosis in affected patients. By definition, patients included in this syndrome will be more difficult to diagnose as they have already resisted classification during baseline investigations. Furthermore, investigation of PUO requires knowledge of many diseases across a range of clinical specialties, as well as knowledge of less commonly used investigative tools. As both society and medicine continue to change, the aetiology and epidemiology of the diseases that cause PUO also change. For these reasons, it is important for physicians to approach PUO in a logical manner, and for the causes and approach to PUO to be continuously reviewed. In this article, we review the aetiology of PUO and the diagnostic strategies that may be used to investigate it.     

树突状细胞与肠源性感染

树突状细胞(DC)广泛分布于整个肠道,是体内功能较强的抗原呈递细胞,在肠黏膜屏障中扮演着重要的角色。肠源性感染一般认为是肠黏膜屏障失常后细菌移位所致。因此,DC可能参与了肠源性感染的发生,对DC进一步深入研究,有助于发现新的肠源性感染治疗方法。     

Reproduction,symbiosis, and the eukaryotic cell

This paper develops a conceptual framework for addressing questions about reproduction, individuality, and the units of selection in symbiotic associations, with special attention to the origin of the eukaryotic cell. Three kinds of reproduction are distinguished, and a possible evolutionary sequence giving rise to a mitochondrion-containing eukaryotic cell from an endosymbiotic partnership is analyzed as a series of transitions between each of the three forms of reproduction. The sequence of changes seen in this “egalitarian” evolutionary transition is compared with those that apply in “fraternal” transitions, such as the evolution of multicellularity in animals.     

Construction of genomic libraries of mycobacterial origin: identification of recombinants encoding mycobacterial-specific proteins

A complete genomic library from Mycobacterium vaccae (2785 recombinants) and a partial genomic library of M. leprae and BCG (300 and 1750 clones, respectively) were constructed in the plasmid pBR322. Bam HI was selected as the restriction endonuclease for obtaining DNA cleavage products. Evidence was obtained for limited expression of the cloned mycobacterial DNA inserts in Escherichia coli. A recombinant has been identified which codes for antigen immunoreactive with rabbit anti-M. leprae antibody but not with anti-H37Rv antibody.     

A logical approach to the investigation of red cell enzymopathies

This relatively rare group of disorders may cause quite marked morbidity and occasionally be life-threatening. As their inheritance is largely known accurate information in one family member has obvious benefits to other family members as well as the patient. The identification of the defect is dependent on an accurate clinical story which can be used to guide both the use and the interpretation of the various laboratory tests available. From the clinical aspect the enzymopathies can be divided into various broad groups. First, those involving the main glycolysis which produces the red cell's energy requirements in the form of ATP. Defects of this pathway generally cause a non-spherocytic haemolytic anaemia. Second, those involving the pentose phosphate shunt which maintains the redox potential of the cell necessary for its protection against oxidant stress. The commonest enzyme deficiency world wide, G6PD, is in this pathway and is characterized by stress-induced haemolytic crises. Third, defects of the various linked reactions. The most important of these are the methaemoglobin reductases which catalyse the reduction of methaemoglobin to functional haemoglobin and the enzymes in the Rapoport-Luebering shunt which can modulate the 2,3-DPG level. Whilst defects of these metabolic pathways make up the majority of cases associated with haemolysis, defects of other enzymes, on the whole less critical to the red cell's survival, must occasionally be considered. The red cell, because of its relatively easy availability, can be used as a 'biopsy tool' in the diagnosis of some systemic disorders in which the red cell enzymopathy is not the main feature of the disease. Such considerations are particularly important owing to the technological advances that have occurred in the last 10-15 years which have enabled correct assignment of an increased number of difficult cases. Not only is it possible to characterise the variant enzymes more accurately but it is now possible to have a 'metabolic window' on the red cell and examine it for the derangements of metabolism that characterise the various enzyme deficiencies.     

非小细胞肺癌化疗疗效预测基因ERCC1的研究进展

非小细胞肺癌（non-smallcelllungcancer,NSCLC）是现今世界范围内最常见的恶性肿瘤之一。手术及化疗是其治疗的主要方法,研究和确定临床上NSCLC化疗敏感性预测的靶向分子和指标将有利于NSCLC患者的个体化治疗。该文就核苷酸切除修复交叉互补组1（excision repair CROSS complementation group1,ERCCl）基因作为NSCLC化疗疗效预测指标的研究现状作一综述。     

A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication

During pre-replication complex (pre-RC) formation, origin recognition complex (ORC), Cdc6, and Cdt1 cooperatively load the 6-subunit mini chromosome maintenance (MCM2-7) complex onto DNA. Loading of MCM2-7 is a prerequisite for DNA licensing that restricts DNA replication to once per cell cycle. During S phase MCM2-7 functions as part of the replicative helicase but within the pre-RC MCM2-7 is inactive. The organization of replicative DNA helicases before and after loading onto DNA has been studied in bacteria and viruses but not eukaryotes and is of major importance for understanding the MCM2-7 loading mechanism and replisome assembly. Lack of an efficient reconstituted pre-RC system has hindered the detailed mechanistic and structural analysis of MCM2-7 loading for a long time. We have reconstituted Saccharomyces cerevisiae pre-RC formation with purified proteins and showed efficient loading of MCM2-7 onto origin DNA in vitro. MCM2-7 loading was found to be dependent on the presence of all pre-RC proteins, origin DNA, and ATP hydrolysis. The quaternary structure of MCM2-7 changes during pre-RC formation: MCM2-7 before loading is a single hexamer in solution but is transformed into a double-hexamer during pre-RC formation. Using electron microscopy (EM), we observed that loaded MCM2-7 encircles DNA. The loaded MCM2-7 complex can slide on DNA, and sliding is not directional. Our results provide key insights into mechanisms of pre-RC formation and have important implications for understanding the role of the MCM2-7 in establishment of bidirectional replication forks.     

Somatic cell origin of teratocarcinomas

Malignant teratocarcinomas arise from developmentally totipotent normal stem cells. Whether the targets are embryonal somatic cells or germinal cells has long been a matter of controversy. Past experiments on teratocarcinoma induction by ectopic grafting of early rodent embryos or fetal germinal ridges have remained ambiguous because embryos ordinarily soon form germ cells, and parthenogenetic germ cells form "embryos." In order to interrupt the developmental cycle at its most telling point, day 6 (egg-cylinder stage) mouse embryos of genetically sterile types were grafted; in such grafts, only a terminal residue of totipotent embryonal somatic ("ectoderm") cells is available, and subsequent germ cell development is severely impaired. One graft series, from S1(J)/+ matings, comprised 25% S1(J)/S1(J) presumptive sterile embryos; these grafts formed tumors containing embryonal carcinoma cells as often (47%) as did control +/+ grafts (41%) on the same genetic background. In another series, from W/+ matings, tumors of the sterile W/W genotype were individually identified by means of a closely linked marker, phosphoglucomutase (PGM, EC 2.7.5.1; Pgm-1 locus), coding for electrophoretic enzyme variants and incorporated into the stock. Four tumors were obtained (out of 16) that had the PGM-1D phenotype diagnostic for W/W, and that also contained embryonal carcinoma cells. Therefore, the malignancy arises here in susceptible somatic embryonal stem cells at the terminal stage of their capacity for totipotency. Other teratocarcinomas-whether induced or spontaneous-of ostensible germ-cell origin by parthenogenesis may also depend upon development of the same somatic target cells before neoplastic conversion can occur. A general model based on these experiments is proposed for all malignancies: Malignant transformation of a particular kind of normal stem cell may be possible only when that stem cell has progressed to the threshold of further differentiation.