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At least 397 records · Page 22Linked to original sources

Development of the central nervous system of the larva of the ascidian, Ciona intestinalis L. I. The early lineages of the neural plate.

The early lineages of the larval central nervous system (CNS) of the ascidian, Ciona intestinalis, have been traced using scanning electron microscopy (SEM) of embryos fixed at 12-min intervals. The CNS precursors lie superficially, exposed for a long portion (9.3 hr of 42%) of embryonic development, in the neural plate. In the 64-cell stage embryo the neural plate contains 10 cells; in all but the first vegetal division these divide with transverse cleavage planes. Synchrony is progressively lessened, but temporal sequence is always exact. Successive divisions occur initially at 30-min intervals. Our analysis confirms existing lineage descriptions for the neural plate up to the end of gastrulation and advances the lineage record through the crucial and temporally complex ninth cleavage, during which cells divide by the following rules: medial cells in each row divide first; the anterior row of vegetal daughter cells divides before their posterior siblings; the posterior row of animal daughter cells divide before their anterior siblings. All cells attain their 10th generation, but four cannot be followed by SEM. In preparation for neurulation the neural plate then comprises 76 cells, forming up to four rows each of eight vegetal hemisphere cells located on the dorsal surface of the embryo, anterior to the blastopore, and eight rows each of six animal hemisphere cells, located anterior to the rows of eight. The temporal and spatial patterns of early cleavage stages have been confirmed in vivo by observations using Nomarski optics.

Animals↗

The importance of maternal lineage on milk yield traits of dairy cattle.

Maternal lineage effects on milk yield traits, considered indicative of cytoplasmic inheritance, were evaluated with animal models. Cattle were from a selection experiment begun in 1968. Maternal pedigrees were traced to the first female member in the Holstein-Friesian Herdbook; purchased cows entering the herd, considered foundation females, were assigned to maternal lineage groups. All models accounted for year-season of calving, parity, and selection lines. Maternal lineage effects were included in a repeated records model with cow effects and preadjustment for sire and maternal grandsire transmitting abilities. Maternal lineage accounted for 5.2, 4.1, and 10.5% of phenotypic variation of preadjusted records of milk yield, fat yield, and fat percentage, respectively. Maternal lineage was evaluated as a fixed effect in an animal model including random animal and permanent environmental effects. Maternal lineage significantly affected fat percentage but not milk yield. Maternal genetic (nuclear) effects and their covariance with additive animal effects did not significantly account for additional variation nor did they influence maternal lineage estimates. Maternal lineage affected calculated net energy of milk but was not important for SNF yield or concentration. Maternal lineage influenced fat percentage, energy concentration, and, to a lesser extent, fat yield in milk of dairy cattle.

Animals↗

Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer.

Parallel collision-induced dissociation (CID) of peptides rather than serial, as is customary, results in loss of the obvious parent-fragment ion lineage available from CID on a single ion. We report proof-of-principle results suggesting the feasibility of parallel peptide CID, referred to here as shotgun CID, for protein identification when using the measured mass accuracies available from a time of flight mass analyzer and currently available search routines such as SEQUEST. Additionally, we report that parent-fragment ion lineage may be reconstructed from information encoded in the chromatographic single ion current traces of peptides.

Feasibility Studies↗

A HERV-K provirus in chimpanzees, bonobos and gorillas, but not humans.

Evidence from DNA sequencing studies strongly indicated that humans and chimpanzees are more closely related to each other than either is to gorillas [1-4]. However, precise details of the nature of the evolutionary separation of the lineage leading to humans from those leading to the African great apes have remained uncertain. The unique insertion sites of endogenous retroviruses, like those of other transposable genetic elements, should be useful for resolving phylogenetic relationships among closely related species. We identified a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome. Humans contain an intact preintegration site at this locus. These observations provide very strong evidence that, for some fraction of the genome, chimpanzees, bonobos, and gorillas are more closely related to each other than they are to humans. They also show that HERV-K replicated as a virus and reinfected the germline of the common ancestor of the four modern species during the period of time when the lineages were separating and demonstrate the utility of using HERV-K to trace human evolution.

Animals↗

Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion.

In Saccharomyces, an ancient whole-genome duplication (WGD) and widespread duplicate gene deletion resulted in extensive reorganization of adjacent gene relationships. We have studied the evolution of adjacent gene pairs' identity, orientation, and spacing following whole-genome duplication and deletion (WGD-D) using comparative genomic analyses and simulations. Surveying adjacent gene organization across the Saccharomyces species complex, we find a genome-wide bias toward divergently and convergently transcribed gene pairs in all species but a reduction in this bias in the species that underwent WGD-D. Among neutral models of WGD-D, only single-gene deletion can produce the appropriate reduction in orientation bias and recapitulate the pattern of short, highly dispersed deletions we observe in Saccharomyces cerevisiae. To characterize the dynamics of WGD-D, we trace the conservation and creation of adjacent gene pairs along the S. cerevisiae lineage. We find that newly created adjacencies have a tandem orientation bias, while adjacencies conserved from prior to WGD-D have the same divergent-convergent bias as found in the species that diverged before WGD. We also find that adjacent gene pairs produced by WGD-D gained greater intergenic spacing but that this is reduced in the older adjacencies. Given this, and the preponderance of short deleted blocks, we argue that the deletion phase of WGD-D occurred primarily by small inactivating mutations followed by numerous small deletions. Newly created adjacent gene pairs also have an initial increase in mean log2 expression ratios and maximal expression levels, suggesting that increased intergenic spacing caused a genome-wide reduction in transcriptional interference.

Evolution, Molecular↗

CD8alpha+ dendritic cells originate from the CD8alpha- dendritic cell subset by a maturation process involving CD8alpha, DEC-205, and CD24 up-regulation.

CD8alpha+ and CD8alpha- dendritic cells (DCs) have been considered as independent DC subpopulations both ontogenetically and functionally during recent years. However, it has been demonstrated that both DC subsets can be generated from a single precursor population, supporting the concept that they do not represent separate DC lineages. By using highly purified splenic CD8alpha- DCs, which were injected intravenously and traced by means of an Ly5.1/Ly5.2 transfer system, this study shows that CD8alpha- DCs acquired the phenotypic characteristics of CD8alpha+ DCs, by a differentiation process involving CD8alpha, DEC-205, and CD24 up-regulation, paralleled by the down-regulation of CD11b, F4/80, and CD4. These data demonstrate that CD8alpha+ DCs derive from CD8alpha- DCs, and strongly support that CD8alpha- and CD8alpha+ DCs represent different maturation or differentiation stages of the same DC population. Therefore, CD8alpha+ DCs would represent the last stage of DC differentiation, playing an essential role in the induction of T-cell responses, due to their antigen-presenting potential, cross-priming ability, and capacity to secrete large amounts of key cytokines such as interferon gamma and interleukin-12.

Animals↗

Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

BACKGROUND: The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. RESULTS: This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. CONCLUSION: This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome.

Animals↗

Fate diversity of primitive streak cells during heart field formation in ovo.

In amniote embryos, cells from a rostral portion of the primitive streak migrate anterolaterally and establish the heart field mesoderm, from which two cardiac cell lineages, cardiomyocytes and endocardial endothelial cells, differentiate. The endoderm underlying the heart field has been postulated as the source of several paracrine factors that may serve to induce each of these cell types. However, it has been unclear how these signal molecules, which are expressed broadly in the endoderm, instruct individual cells of the heart field mesoderm to enter either the cardiomyocyte lineage or the endocardial cell lineage. To clarify lineage relationships of these two cardiac cell types, the fate of chicken primitive streak cells was traced for the first time in ovo. By using replication-defective retroviral-mediated gene transfer, we demonstrate that cells in the rostral half of Hamburger and Hamilton (HH) stage 3 primitive streak generate a daughter population that proliferates and migrates into the heart field, differentiating into either endocardial or myocardial cells, but not both cell types. The results suggest that the rostral portion of the primitive streak at HH stage 3 consists of at least two distinct subpopulations, entering either the cardiomyocyte lineage or the endocardial cell lineage. Thus, in ovo these two cell lineages of the heart are already segregated within the primitive streak, significantly before their migration to the heart field. When the precardiomyocytes and pre-endocardial cells arrive at the heart field, each mesodermal cell subpopulation may be permissive to paracrine signal(s) from underlying endoderm to initiate their terminal differentiation into either muscle or endothelial cells.

Animals↗

Inhibition of human embryonic stem cell differentiation by mechanical strain.

Mechanical forces have been reported to induce proliferation and/or differentiation in many cell types, but the role of mechanotransduction during embryonic stem cell fate decisions is unknown. To ascertain the role of mechanical strain in human embryonic stem cell (hESC) differentiation, we measured the rate of hESC differentiation in the presence and absence of biaxial cyclic strain. Above a threshold of 10% cyclic strain, applied to a deformable elastic substratum upon which the hESC colonies were cultured, hESC differentiation was reduced and self-renewal was promoted without selecting against survival of differentiated or undifferentiated cells. Frequency of mechanical strain application had little effect on extent of differentiation. hESCs cultured under cyclic strain retained pluripotency, evidenced by their ability to differentiate to cell lineages in all three germ layers. Mechanical inhibition of hESC differentiation could not be traced to secretion of chemical factors into the media suggesting that mechanical forces may directly regulate hESC differentiation. Mechanical strain is not sufficient to inhibit differentiation, however, in unconditioned medium, hESCs grown under strain differentiated at the same rate as cells cultured in the absence of strain. Thus, while mechanical forces play a role in regulating hESC self-renewal and differentiation, they must act synergistically with chemical signals. These findings imply that application of mechanical forces may be useful, in combination with chemical and matrix-encoded signals, towards controlling differentiation of hESCs for therapeutic applications.

Cell Culture Techniques↗

Rapid discrimination of rabies viruses isolated from various host species in Brazil by multiplex reverse transcription-polymerase chain reaction.

Rabies is carried mainly by mammalian carnivores and vampire bats in Latin America. However, rabies virus (RV) has been isolated in recent years from not only vampire bats in rural areas but also from several non-vampire bat species in urban areas, respectively. Therefore, rapid molecular screening is necessary for efficient epidemiology of these RVs. In this study, we investigated the usefulness of multiplex reverse transcription-polymerase chain reaction (RT-PCR) for determining the origins of 54 RV isolates from various host species in Brazil. And to evaluate the multiplex RT-PCR as a potential diagnostic tool, we investigated the sensitivity of this method. In addition, we compared the results with a phylogenetic tree developed from sequences of the RV glycoprotein (G protein) gene. Multiplex RT-PCR products showed five different sizes of products, whereas the phylogenic tree showed six groups. Of these six groups, four corresponded with the four sizes of the multiplex RT-PCR products. The other two groups showed correspondance with another one size of the multiplex RT-PCR products, indicating that multiplex RT-PCR results reflected the lineage of the 54 isolates. This study also showed that this method can detect trace amounts of RNA. In conclusion, this multiplex RT-PCR method allows the rapid, specific, and simultaneous detection of RVs isolated from various host species in Brazil.

Animals↗

Cocirculation and evolution of two lineages of influenza B viruses in europe and Israel in the 2001-2002 season.

Forty-nine influenza B virus isolates collected in Belgium, Finland, Spain, and Israel during the 2001-2002 winter season were categorized into either of two lineages, B/Yamagata/16/88 or B/Victoria/2/87, based on the phylogenetic studies of HA1 sequences. The data trace the geographic spread of B/Victoria/2/87-like viruses and support the emergence of B/Hong Kong/1351/02-like viruses, possibly due to selective advantages of reassortment.

Amino Acid Sequence↗

Evolution of a triplet repeat in a conifer.

The opportunity to trace the evolution of a triplet repeat is rare, especially for seed-plant lineages with a well-defined fossil record. Microsatellite PtTX2133 sequences from 18 species in 2 conifer genera were used to calibrate the birth of a CAGn repeat, from its protomicrosatellite origins to its repeat expansion. Birth occurred in the hard-pine genome ~ 136 million years ago, or 14 million generations ago, then expanded as a polymorphic triplet repeat 136-100 million years before a major North American vicariance event. Calibration of the triplet-repeat birth and expansion is supported by the shared allelic lineages among Old and New World hard pines and the shared alleles solely among North American diploxylon or hard pines. Five CAGn repeat units appeared to be the expansion threshold for Old and New World diploxylon pines. Haploxylon pine species worldwide did not undergo birth and repeat expansion, remaining monomorphic, with a single imperfect 198-bp allele. A sister genus, Picea, had only a region of cryptic simplicity, preceding a proto-microsatellite region. The polymorphic triplet repeat in hard pines is older than some long-lived microsatellites reported for reptiles, yet younger than those reported for insects. Some cautionary points are raised about phylogenetic applications for this long-lived microsatellite.

Alleles↗

In vivo fate-tracing studies using the Scl stem cell enhancer: embryonic hematopoietic stem cells significantly contribute to adult hematopoiesis.

Evidence for the lineage relationship between embryonic and adult hematopoietic stem cells (HSCs) in the mouse is primarily indirect. In order to study this relationship in a direct manner, we expressed the tamoxifen-inducible Cre-ER(T) recombinase under the control of the stem cell leukemia (Scl) stem-cell enhancer in transgenic mice (HSC-SCL-Cre-ER(T)). To determine functionality, HSC-SCL-Cre-ER(T) transgenics were bred with Cre reporter mice. Flow cytometric and transplantation studies revealed tamoxifen-dependent recombination occurring in more than 90% of adult long-term HSCs, whereas the targeted proportion within mature progenitor populations was significantly lower. Moreover, the transgene was able to irreversibly tag embryonic HSCs on days 10 and 11 of gestation. These cells contributed to bone marrow hematopoiesis 5 months later. In order to investigate whether the de novo HSC generation is completed during embryogenesis, HSC-SCL-Cre-ER(T)-marked fetal liver cells were transplanted into adult recipients. Strikingly, the proportion of marked cells within the transplanted and the in vivo-remaining HSC compartment was not different, implying that no further HSC generation occurred during late fetal and neonatal stages of development. These data demonstrate for the first time the direct lineage relationship between midgestation embryonic and adult HSCs in the mouse. Additionally, the HSC-SCL-Cre-ER(T) mice will provide a valuable tool to achieve temporally controlled genetic manipulation of HSCs.

Age Factors↗

Phylogenetically distant intracellular symbionts in termites.

Cockroaches are known to harbour intracellular bacteria in specialised cells (mycetocytes, or bacteriocytes) of the fat body. In termites, mycetocyte bacteria have been observed only in Mastotermes darwiniensis. These symbionts are thought to have originated from a bacterium that infected an ancestor common to cockroaches and termites. Thus, loss of the infection should have occurred during evolution in all termite lineages, with the exception of that leading to M. darwiniensis. One might suspect that traces of the ancient infection may be present in some termites, in the form of non-mycetocyte intracellular bacteria (e.g. a small number of bacteria within normal cells). Indeed, circumstantial evidence for the presence of intracellular bacteria in two termite species has been reported. However, no data are available on the actual distribution of these bacteria in termites, or on their relationships with the mycetocyte bacteria of cockroaches and M. darwiniensis. In this paper we report results indicating that non-mycetocyte intracellular bacteria are widespread in termites. These results were obtained by electron microscopy on representatives of nine termite species. In addition, sequence analysis of the 16S rRNA genes indicated that the non-mycetocyte bacteria of termites belong to the wolbachia group of the alpha-2 subclass of the proteobacteria. These latter bacteria are not related to the mycetocyte bacteria of cockroaches and M. darwiniensis, which belong to the blattabacterium group of the flavobacteria-bacteroides. PCR analyses with primers specific for wolbachia or blattabacterium provided further support for the identification of the observed non-mycetocyte bacteria as members of the wolbachia group.

Animals↗

Usefulness of genetic typing methods to trace epidemiologically Salmonella serotype Ohio.

Different genetic typing procedures were applied in an epidemiological study of Salmonella serotype Ohio. Isolates that generated identical DNA fingerprints (HinclI ribotypes, ERIC and RAPD profiles) were clustered into the same lineage, and the addition of data from plasmid, integron and resistance profiles was used to differentiate types. Results led to the determination of the endemic and the emergent epidemic types at specific times, and to ascertain the clinical and epidemiological impact of each type. In the series analysed (47 clinical isolates and 3 non-clinical isolates) 11 lineages and 32 types were found. Two lineages were considered prevalent and endemic, and during an epidemiological alert (Spain, 1998) a re-emergence and spread of organisms mainly from the most frequent lineage had occurred. The combination of H-ribotype with ERIC profile, as primary markers, and resistance profile with plasmid profile, as secondary markers, was shown to be the most useful tool to trace epidemiologically Ohio.

Adolescent↗

Combination of growth factors enhances remyelination in a cuprizone-induced demyelination mouse model.

Loss of oligodendrocytes (OLs) is often associated with demyelination. PDGF-AA, bFGF, NT3 and IGF-1 are known to regulate OL proliferation, survival and/or differentiation. Following cuprizone-induced demyelination in mice a combination of above four growth factors (GF) was intracranially injected to stimulate remyelination in vivo. Activation of cell signaling and transcription factors involved in cell proliferation, survival and differentiation was observed in response to GF. Increased cell proliferation and migration occurred in corpus callosum, lateral ventricles, rostral migratory stream and cerebri at 2-5 days post injection (dpi) of GF cocktail. The fate of these newly formed nestin or bromodeoxyuridine (BrdU) positive progenitors was traced to proteoglycan NG2 and glutathione transferase (GST) pi positive cells, early and mature OL lineage markers, respectively. Immunostaining for myelin showed the presence of more myelinated fibers in GF-injected brains at 21 dpi. Remyelination in response to GF was confirmed by electron microscopy. In conclusion, this combination of GF is a promising tool to consider for remyelination strategies.

Animals↗

Ornithinimicrobium humiphilum gen. nov., sp. nov., a novel soil actinomycete with L-ornithine in the peptidoglycan.

A Gram-positive bacterium originating from garden soil was taxonomically studied. Cells are non-motile, non-sporulating, irregular rods and cocci. The cell wall peptidoglycan contains L-ornithine as diagnostic diamino acid and an interpeptide bridge consisting of L-Orn<--L-Ala<--Gly<--D-Asp. The major menaquinone is MK-8(H4). 13-Methyl tetradecanoic acid and 14-methyl pentadecanoic acid are the predominant fatty acids. The polar lipids are phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, three unknown glycolipids and three unknown phospholipids. Mycolic acids are absent. The DNA G+C composition is 70 mol%. The acyl type of the glycan chain of peptidoglycan is acetyl. Glucose is the dominating whole cell sugar; arabinose, rhamnose and xylose are present in traces. Results of 16S rDNA sequence comparisons revealed that strain HKI 0124T represents a novel lineage within the suborder Micrococcineae of the order Actinomycetales adjacent to the recently described genus Ornithinicoccus. On the basis of the clearly pronounced morphological, physiological, chemotaxonomic and phylogenetic differences between strain HKI 0124T and all members of the suborder Micrococcineae, it is proposed to assign strain HKI 0124T to a new genus and species, Ornithinimicrobium humiphilum gen. nov., sp. nov. The type and only strain is HKI 0124T (= DSM 12362T = CIP 106634T).

Actinomycetales↗

Restriction endonuclease-fragment polymorphisms of oral viridans streptococci, compared by conventional and field-inversion gel electrophoresis.

Oral streptococci formerly classified as Streptococcus sanguis or Streptococcus mitis have recently been divided into four species. Two additional species have also been proposed for this group. Each species is genetically distinct, but they have many traits in common, which makes it difficult for clinical isolates to be identified by phenotypic tests. Genotypic comparison may provide an alternative approach. This study used DNA fingerprint analysis for comparison of genotypes of 21 reference strains--classified as Streptococcus gordonii, Streptococcus sanguis, Streptococcus oralis, "Streptococcus parasanguis", or "Streptococcus crista" in previous DNA hybridization studies--and 17 clinical and laboratory strains placed in those groups on the basis of phenotypic tests. HinDIII and PvuII digests were run in conventional horizontal agarose gels. SfiI digests of reference strains and two laboratory strains were run in field-inversion gels. Fingerprint patterns were compared by visual examination, cluster analysis of densitometric traces, and lane-matching software. Only two "S. crista" strains and two parent mutant lineages showed fingerprint patterns that were identical by visual examination. Fingerprint patterns of all other strains were unique. Cluster analysis results could not be considered valid, since replicate lanes in different gels were not grouped together. HinDIII and PvuII digests contained too many bands for correct matching by lane-matching software. SfiI digests were correctly matched by computer, with the same results as visual examination. Results indicate that the diversity of strains within these streptococcal species was too great to permit species identification by DNA fingerprint patterns. This genotypic diversity suggests that isolates from unrelated hosts may have been separate for long periods of time.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Proteins↗