DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

Background  

Cloning of cattle by somatic cell nuclear transfer (SCNT) is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI).     

Gene rearrangement and sequence analysis of mitogenomes suggest polyphyly of Archaeobalanid and Balanid barnacles (Cirripedia: Balanomorpha)

The acorn barnacles (Cirripedia, Thoracica, Balanomorpha) are a diverse group of crustaceans found in virtually all marine and estuarine habitats. Barnacles are important model species in various biological researches, including evolution, intertidal ecology, larval biology and antifouling. However, there remains a lack of a thorough understanding of the phylogeny for this group of animals, particularly at higher taxonomic levels. In this study, we attempt to determine the phylogenetic relationships among balanomorphan families based on analysis of complete mitochondrial genome from various barnacle families and investigate the evolution of mitogenome in barnacles. Whole mitogenomes of six barnacles were newly sequenced, including Acasta sulcata (Archaeobalanidae), Armatobalanus allium (Archaeobalanidae), Chelonibia testudinaria (Chelonibiidae), Octomeris sp. (Chthamalidae), Savignium biporata (Pyrgomatidae) and Tetraclitella divisa (Tetraclitidae), which exhibit five different gene arrangements. Phylogenetic analysis on 15 complete mitochondrial genome sequences from major barnacle families supported Chthamalidae, Pyrgomatidae and Tetraclitidae formed monophyletic units, but suggested polyphyly of both Archaeobalanidae and Balanidae. Chthamalidae was the earliest diverged lineage in Balanomorpha. Chelonibiidae + Tetraclitidae formed the sister taxon to the monophyletic superfamily Balanoidea (Archaeobalanidae + Balanidae + Pyrgomatidae). The members of Archaeobalanidae and Balanidae intermingled in the inferred topology with the monophyletic Pyrgomatidae deeply nested within. Two Megabalanus species from the family Balanidae and A. sulcata from the family Archaeobalanidae share the same six‐gene‐cluster inversion as compared to the other ten balanomorphan barnacles, providing further evidence for the non‐monophyly for the two families. We showed here that the informativeness of the complete mitogenome sequence and rare genomic events in resolving various questions concerning Balanomorpha relationships. The non‐monophyletic status of Archaeobalanidae and Balanidae falsified many previous hypotheses concerning the complex evolution of Balanomorpha and call for further investigations and careful revision on the taxonomy of the group. Future study focusing on the enigmatic and tentatively basal lineages, for example, Chionelasmatoidea Pachylasmatoidea and Catophragmidae, would be most helpful in fully resolving the phylogeny and mitogenome evolutionary history of acorn barnacles.     

A semiparametric joint model for cluster size and subunit-specific interval-censored outcomes

Clustered data frequently arise in biomedical studies, where observations, or subunits, measured within a cluster are associated. The cluster size is said to be informative, if the outcome variable is associated with the number of subunits in a cluster. In most existing work, the informative cluster size issue is handled by marginal approaches based on within-cluster resampling, or cluster-weighted generalized estimating equations. Although these approaches yield consistent estimation of the marginal models, they do not allow estimation of within-cluster associations and are generally inefficient. In this paper, we propose a semiparametric joint model for clustered interval-censored event time data with informative cluster size. We use a random effect to account for the association among event times of the same cluster as well as the association between event times and the cluster size. For estimation, we propose a sieve maximum likelihood approach and devise a computationally-efficient expectation-maximization algorithm for implementation. The estimators are shown to be strongly consistent, with the Euclidean components being asymptotically normal and achieving semiparametric efficiency. Extensive simulation studies are conducted to evaluate the finite-sample performance, efficiency and robustness of the proposed method. We also illustrate our method via application to a motivating periodontal disease dataset.     

In vitro activity of oritavancin (LY333328), vancomycin, clindamycin, and metronidazole against Clostridium perfringens, Propionibacterium acnes, and anaerobic Gram-positive cocci

Using an agar dilution method, we determined the in vitro activity of oritavancin, vancomycin, clindamycin and metronidazole against 114 unique clinical isolates of Gram-positive anaerobes. MIC(90)s (microg/mL) for oritavancin were as follows: Clostridium perfringens 1.0, Propionibacterium acnes 0.25, Peptostreptococcus anaerobius 0.25, Peptoniphilus asaccharolyticus 0.5, Finegoldia magna 0.25, Micromonas. micros 0.25, and Anaerococcus prevotii 0.25. On a weight basis, oritavancin is slightly more active than vancomycin against the strains tested. The oritavancin MICs are comparable to those previously reported against staphylococci and enterococci. Oritavancin shows excellent potential for treatment of infections containing Gram-positive anaerobes such as these.     

Protective immunosurveillance of the central nervous system by Listeria-specific CD4 and CD8 T cells in systemic listeriosis in the absence of intracerebral Listeria

The invasion of the CNS by pathogens poses a major risk for damage of the highly vulnerable brain. The aim of the present study was to analyze immunological mechanisms that may prevent spread of infections to the CNS. Intraperitoneal application of Listeria monocytogenes to mice induced infection of the spleen, whereas pathogens remained absent from the brain. Interestingly, Listeria-specific CD4 and CD8 T cells homed to the brain and persisted intracerebrally for at least 50 days after both primary and secondary infection. CD4 and CD8 T cells resided in the leptomeninges, in the choroid plexus, and, in low numbers, in the brain parenchyma. CD4 and CD8 T cells isolated from the brain early after infection (day 7) were characterized by an activated phenotype with spontaneous IFN-gamma production, whereas at a later stage of infection (day 28) restimulation with Listeria-specific peptides was required for the induction of IFN-gamma production by CD4 and CD8 T cells. In contrast to splenic T cells, T cells in the brain did not exhibit cytotoxic activity. Adoptively transferred T cells isolated from the brains of Listeria-infected mice reduced the bacterial load in cerebral listeriosis. The frequency of intracerebral Listeria-specific T cells was partially regulated by the time of exposure to Listeria and cross-regulated by CD4 and CD8 T cells. Collectively, these data reveal a novel T cell-mediated pathway of active immunosurveillance of the CNS during bacterial infections.     

Proteome of Oriental ginseng Panax ginseng C. A. Meyer and the potential to use it as an identification tool

Oriental ginseng (Panax ginseng C. A. Meyer) and American ginseng (Panax quinquefolius) are two widely used valuable traditional Chinese medicines (TCM). Previously, the identification of ginseng was mainly performed by analyzing the ginsengnosides using high performance liquid chromatography and amplification of polymorphic DNA using polymerase chain reaction. However, these methods cannot be used to distinguish TCM samples which are from different parts (main root, lateral roots, rhizome head and skin) of ginseng and ginseng culture cells from wild-grown ginseng. The present study aimed to identify different species of ginseng, different parts of the same ginseng and cultured cells of ginseng using a proteomic approach. Two-dimensional electrophoresis (2-DE) maps were established from the American ginseng main root, different parts (main root, lateral roots, rhizome head and skins) of Oriental ginseng and Oriental ginseng culture cells. Our results show that the 2-DE maps of different ginseng samples contain sufficient differences to permit easy discrimination. We have also identified common and specific protein spots in the 2-DE maps of different ginseng samples. The use of these "marker proteins" may help to speed up the identification process.