Non-pathogenic microbiota accelerate age-related CpG Island methylation in colonic mucosa

DNA methylation is an epigenetic process altered in cancer and ageing. Age-related methylation drift can be used to estimate lifespan and can be influenced by extrinsic factors such as diet. Here, we report that non-pathogenic microbiota accelerate age-related methylation drift in the colon when compared with germ-free mice. DNA methylation analyses showed that microbiota and IL10KO were associated with changes in 5% and 4.1% of CpG sites, while mice with both factors had 18% alterations. Microbiota, IL10KO, and their combination altered 0.4%, 0.4%, and 4% of CpG island methylation, respectively. These are comparable to what is seen in colon cancer. Ageing changes were accelerated in the IL10KO mice with microbiota, and the affected genes were more likely to be altered in colon cancer. Thus, the microbiota affect DNA methylation of the colon in patterns reminiscent of what is observed in ageing and colorectal cancer.

Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer

IMPORTANCE

Epstein-Barr virus (EBV) latency is controlled by epigenetic silencing by DNA methylation [5-methyl cytosine (5mC)], histone modifications, and chromatin looping. However, how they dictate the transcriptional program in EBV-associated gastric cancers remains incompletely understood. EBV-associated gastric cancer displays a 5mC hypermethylated phenotype. A potential treatment for this cancer subtype is the DNA hypomethylating agent, which induces EBV lytic reactivation and targets hypermethylation of the cellular DNA. In this study, we identified a heterogeneous pool of EBV epialleles within two tumor-derived gastric cancer cell lines that are disrupted with a hypomethylating agent. Stochastic DNA methylation patterning at critical regulatory regions may be an underlying mechanism for spontaneous reactivation. Our results highlight the critical role of epigenetic modulation on EBV latency and life cycle, which is maintained through the interaction between 5mC and the host protein CCCTC-binding factor.

DNA methylation entropy as a measure of stem cell replication and aging

BACKGROUND

Epigenetic marks are encoded by DNA methylation and accumulate errors as organisms age. This drift correlates with lifespan, but the biology of how this occurs is still unexplained. We analyze DNA methylation with age in mouse intestinal stem cells and compare them to nonstem cells.

RESULTS

Age-related changes in DNA methylation are identical in stem and nonstem cells, affect most prominently CpG islands and correlate weakly with gene expression. Age-related DNA methylation entropy, measured by the Jensen-Shannon Distribution, affects up to 25% of the detectable CpG sites and is a better measure of aging than individual CpG methylation. We analyze this entropy as a function of age in seven other tissues (heart, kidney, skeletal muscle, lung, liver, spleen, and blood) and it correlates strikingly with tissue-specific stem cell division rates. Thus, DNA methylation drift and increased entropy with age are primarily caused by and are sensors for, stem cell replication in adult tissues.

CONCLUSIONS

These data have implications for the mechanisms of tissue-specific functional declines with aging and for the development of DNA-methylation-based biological clocks.

The nuclear lamina binds the EBV genome during latency and regulates viral gene expression

The Epstein Barr virus (EBV) infects almost 95% of the population worldwide. While typically asymptomatic, EBV latent infection is associated with several malignancies of epithelial and lymphoid origin in immunocompromised individuals. In latently infected cells, the EBV genome persists as a chromatinized episome that expresses a limited set of viral genes in different patterns, referred to as latency types, which coincide with varying stages of infection and various malignancies. We have previously demonstrated that latency types correlate with differences in the composition and structure of the EBV episome. Several cellular factors, including the nuclear lamina, regulate chromatin composition and architecture. While the interaction of the viral genome with the nuclear lamina has been studied in the context of EBV lytic reactivation, the role of the nuclear lamina in controlling EBV latency has not been investigated. Here, we report that the nuclear lamina is an essential epigenetic regulator of the EBV episome. We observed that in B cells, EBV infection affects the composition of the nuclear lamina by inducing the expression of lamin A/C, but only in EBV+ cells expressing the Type III latency program. Using ChIP-Seq, we determined that lamin B1 and lamin A/C bind the EBV genome, and their binding correlates with deposition of the histone repressive mark H3K9me2. By RNA-Seq, we observed that knock-out of lamin A/C in B cells alters EBV gene expression. Our data indicate that the interaction between lamins and the EBV episome contributes to the epigenetic control of viral gene expression during latency, suggesting a restrictive function of the nuclear lamina as part of the host response against viral DNA entry into the nucleus.

Epstein-Barr virus (EBV) is a common herpesvirus that establishes a lifelong latent infection in a small fraction of B cells of the infected individuals. In most cases, EBV infection is asymptomatic; however, especially in the context of immune suppression, EBV latent infection is associated with several malignancies. In EBV+ cancer cells, latent viral gene expression plays an essential role in sustaining the cancer phenotype. We and others have established that epigenetic modifications of the viral genome are critical to regulating EBV gene expression during latency. Understanding how the EBV genome is epigenetically regulated during latent infection may help identify new specific therapeutic targets for treating EBV+ malignancies. The nuclear lamina is involved in regulating the composition and structure of the cellular chromatin. In the present study, we determined that the nuclear lamina binds the EBV genome during latency, influencing viral gene expression. Depleting one component of the nuclear lamina, lamin A/C, increased the expression of latent EBV genes associated with cellular proliferation, indicating that the binding of the nuclear lamina with the viral genome is essential to control viral gene expression in infected cells. Our data show for the first time that the nuclear lamina may be involved in the cellular response against EBV infection by restricting viral gene expression.

The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity

Epstein-Barr virus (EBV) persists in human B-cells by maintaining its chromatinized episomes within the nucleus. We have previously shown that cellular factor Poly [ADP-ribose] polymerase 1 (PARP1) binds the EBV genome, stabilizes CTCF binding at specific loci, and that PARP1 enzymatic activity correlates with maintaining a transcriptionally active latency program. To better understand PARP1's role in regulating EBV latency, here we functionally characterize the effect of PARP enzymatic inhibition on episomal structure through in situ HiC mapping, generating a complete 3D structure of the EBV genome. We also map intragenomic contact changes after PARP inhibition to global binding of chromatin looping factors CTCF and cohesin across the EBV genome. We find that PARP inhibition leads to fewer total unique intragenomic interactions within the EBV episome, yet new chromatin loops distinct from the untreated episome are also formed. This study also illustrates that PARP inhibition alters gene expression at the regions where chromatin looping is most effected. We observe that PARP1 inhibition does not alter cohesin binding sites but does increase its frequency of binding at those sites. Taken together, these findings demonstrate that PARP has an essential role in regulating global EBV chromatin structure and latent gene expression.

TET2 and DNMT3A Mutations Exert Divergent Effects on DNA Repair and Sensitivity of Leukemia Cells to PARP Inhibitors

Somatic variants in TET2 and DNMT3A are founding mutations in hematological malignancies that affect the epigenetic regulation of DNA methylation. Mutations in both genes often co-occur with activating mutations in genes encoding oncogenic tyrosine kinases such as FLT3ITD, BCR-ABL1, JAK2V617F , and MPLW515L , or with mutations affecting related signaling pathways such as NRASG12D and CALRdel52 . Here, we show that TET2 and DNMT3A mutations exert divergent roles in regulating DNA repair activities in leukemia cells expressing these oncogenes. Malignant TET2-deficient cells displayed downregulation of BRCA1 and LIG4, resulting in reduced activity of BRCA1/2-mediated homologous recombination (HR) and DNA-PK-mediated non-homologous end-joining (D-NHEJ), respectively. TET2-deficient cells relied on PARP1-mediated alternative NHEJ (Alt-NHEJ) for protection from the toxic effects of spontaneous and drug-induced DNA double-strand breaks. Conversely, DNMT3A-deficient cells favored HR/D-NHEJ owing to downregulation of PARP1 and reduction of Alt-NHEJ. Consequently, malignant TET2-deficient cells were sensitive to PARP inhibitor (PARPi) treatment in vitro and in vivo, whereas DNMT3A-deficient cells were resistant. Disruption of TET2 dioxygenase activity or TET2-Wilms' tumor 1 (WT1)-binding ability was responsible for DNA repair defects and sensitivity to PARPi associated with TET2 deficiency. Moreover, mutation or deletion of WT1 mimicked the effect of TET2 mutation on DSB repair activity and sensitivity to PARPi. Collectively, these findings reveal that TET2 and WT1 mutations may serve as biomarkers of synthetic lethality triggered by PARPi, which should be explored therapeutically. SIGNIFICANCE: TET2 and DNMT3A mutations affect distinct DNA repair mechanisms and govern the differential sensitivities of oncogenic tyrosine kinase-positive malignant hematopoietic cells to PARP inhibitors.

Attitudes of a group of primary school teachers towards the educational inclusion of hearing-impaired learners in regular classrooms

Research has clearly demonstrated a link between the attitudes of regular education teachers and the success of inclusion of learners with special educational needs. Therefore, the present study aimed to investigate the attitudes of a group of junior primary school teachers from the Gauteng area towards the inclusion of hearing-impaired children into regular classes. A survey research design was employed which utilized a questionnaire as the research tool. Analysis of results indicated that the teachers surveyed were relatively positive in their attitudes towards inclusion. Greater exposure to disability in terms of training and experience was related to more positive attitudes. Similarly, more positive attitudes were related to greater perceived competence in teaching hearing-impaired pupils. All of the teachers surveyed felt that speech-language pathologists and audiologists (SLPs & As) should be involved in facilitating inclusion of hearing-impaired children. Many of the respondents expressed concern regarding their lack of training, knowledge and skills. The findings from the research project highlight the need for an adequate training and support system for teachers prior to the implementation of an inclusive educational policy, and the potential role of SLPs & As in this regard.

The Drosophila Medea gene is required downstream of dpp and encodes a functional homolog of human Smad4

The Transforming Growth Factor-beta superfamily member decapentaplegic (dpp) acts as an extracellular morphogen to pattern the embryonic ectoderm of the Drosophila embryo. To identify components of the dpp signaling pathway, we screened for mutations that act as dominant maternal enhancers of a weak allele of the dpp target gene zerknLllt. In this screen, we recovered new alleles of the Mothers against dpp (Mad) and Medea genes. Phenotypic analysis of the new Medea mutations indicates that Medea, like Mad, is required for both embryonic and imaginal disc patterning. Genetic analysis suggests that Medea may have two independently mutable functions in patterning the embryonic ectoderm. Complete elimination of maternal and zygotic Medea activity in the early embryo results in a ventralized phenotype identical to that of null dpp mutants, indicating that Medea is required for all dpp-dependent signaling in embryonic dorsal-ventral patterning. Injection of mRNAs encoding DPP or a constitutively activated form of the DPP receptor, Thick veins, into embryos lacking all Medea activity failed to induce formation of any dorsal cell fates, demonstrating that Medea acts downstream of the thick veins receptor. We cloned Medea and found that it encodes a protein with striking sequence similarity to human SMAD4. Moreover, injection of human SMAD4 mRNA into embryos lacking all Medea activity conferred phenotypic rescue of the dorsal-ventral pattern, demonstrating conservation of function between the two gene products.

fusca3: A Heterochronic Mutation Affecting Late Embryo Development in Arabidopsis

Molecular studies of late embryogenesis and seed development have emphasized differential gene expression as a means of identifying discrete stages of embryogenesis. Little has been done to identify factors that regulate the length of a given developmental stage or the degree of overlap between adjacent developmental programs. We designed a genetic screen to identify mutations that disrupt late embryo development in Arabidopsis without loss of hormonal responses. One such mutation, fusca3 (fus3), alters late embryo functions, such as the establishment of dormancy and desiccation tolerance, and reduces storage protein levels. fus3 cotyledons bear trichomes, and their ultrastructure is similar to that of leaf primordia. Immature fus3 embryos enter germinative development, and the shoot apical meristems develop leaf primordia before seed desiccation begins. The cotyledons resemble leaf primordia, yet retain some cotyledon characteristics; thus, cotyledon- and leaf-specific functions are expressed simultaneously. Together, these observations are consistent with a heterochronic interpretation of the fus3 mutation.

fusca3: A Heterochronic Mutation Affecting Late Embryo Development in Arabidopsis

Molecular studies of late embryogenesis and seed development have emphasized differential gene expression as a means of identifying discrete stages of embryogenesis. Little has been done to identify factors that regulate the length of a given developmental stage or the degree of overlap between adjacent developmental programs. We designed a genetic screen to identify mutations that disrupt late embryo development in Arabidopsis without loss of hormonal responses. One such mutation, fusca3 (fus3), alters late embryo functions, such as the establishment of dormancy and desiccation tolerance, and reduces storage protein levels. fus3 cotyledons bear trichomes, and their ultrastructure is similar to that of leaf primordia. Immature fus3 embryos enter germinative development, and the shoot apical meristems develop leaf primordia before seed desiccation begins. The cotyledons resemble leaf primordia, yet retain some cotyledon characteristics; thus, cotyledon- and leaf-specific functions are expressed simultaneously. Together, these observations are consistent with a heterochronic interpretation of the fus3 mutation.

Isolation of an internal deletion mutant of the Arabidopsis thaliana ABI3 gene

An Arabidopsis thaliana mutant that produces green seeds that are highly insensitive to exogenous ABA, non-dormant and severely desiccation intolerant was isolated from a population of fast neutron-irradiated seeds. Molecular and genetic analysis of this mutant shows that these phenotypes are caused by an internal deletion of approximately one third of the ABI3 gene. Therefore abi3 mutants with the above phenotypes are representative of null alleles at this locus.

Trypanosoma brucei: characterization of protein kinases that are capable of autophosphorylation in vitro

Autophosphorylation by protein kinases has been implicated as an important control mechanism in signal transduction and growth regulatory pathways in mammalian cells. We have set out to investigate whether any such autophosphorylating protein kinase activities can be found in Trypanosoma brucei. In order to do this, we have developed a system for characterizing such protein kinase activities using an in vitro assay. This assay was carried out by fractionation of trypanosome lysates using isoelectric focusing gel electrophoresis followed by incubation of the gel in gamma 32P-labelled nucleotide triphosphate and subsequent autoradiography. We have identified two classes of autophosphorylating protein kinase activities. In the first class all were dependent on ATP as the phosphate donor substrate and were all found to have a molecular size of 60 kDa. Differences in the activity of these protein kinases were observed between the bloodstream and procyclic life-cycle stages. Furthermore, the addition of mammalian epidermal growth factor to bloodstream stage lysates stimulated an additional activity. The second class of autophosphorylating protein kinases utilized GTP as the phosphate donor and were all found to be 90 kDa in size. Stage-specific differences were also observed in the activity of these protein kinases.

Characterisation of protein kinase C like activities in Trypanosoma brucei

Protein kinase activities in bloodstream and procyclic forms of Trypanosoma brucei have been partially purified and characterised. Cytosolic extracts were separated on DEAE-cellulose and assayed for the ability to phosphorylate histone in the presence of Ca2+ and diacylglycerol. Five peaks of activity were identified in bloodstream T. brucei and only three in procyclic lysates. One of the kinases present in bloodstream T. brucei shares may characteristics with mammalian protein kinase C. Further characterisation of the kinases using an in situ assay after separating proteins by isoelectric focussing confirmed that the kinases present in bloodstream and procyclic stages differed in properties and either bloodstream kinases are more stable or greater in number than procyclic kinases. A protein present in bloodstream T. brucei was shown by Western blot analysis to contain an epitope recognized by a monoclonal antibody raised against mammalian protein kinase C. We thus conclude that the protein kinases are differentially regulated between the two stages of the parasite and that the bloodstream stage has a protein kinase C homologue. The implications of these findings in relation to a cellular signalling pathway in trypanosomes is discussed.

Wheelchair use by ambulatory nursing home residents

In a survey of wheelchair use in two nursing homes, the authors found a substantial number of cognitively intact nursing home residents who walked, but who also used a wheelchair. Using chart review and interviews with the residents, it was found that multiple physical factors, including pain, strength, endurance, vision and balance, and multiple social and environmental factors, including the fear of falling, were related to the resident's decision to use a wheelchair as an alternative means of mobility. A physical examination focused on aspects of mobility was completed on each resident and was intended to characterize the physical limitations in groups studied. In the nursing home environment, use of the wheelchair is viewed by the residents as a self-initiated choice which the residents believed significantly enhanced their sense of well-being. Finally, there was minimal recognition of mobility as a problem on the part of the medical and nursing staff. The study raises a number of important issues concerning walking versus wheelchair use in the nursing home.

Variation in arbovirus infection rates in species of birds sampled in a serological survey during an encephalitis epidemic in the Murray Valley of South-eastern Australia, February 1974

There was extensive and exuberant breeding of waterbirds before and during an epidemic of arboviral encephalitis in the Murray Valley of south eastern Australia in 1974. As estimated by haemagglutination inhibition tests on 432 bird sera collected between 4th and 13th February, 1974, infection with Murray Valley encephalitis virus, Kunjin virus and possibly other flaviviruses was concentrated in species of the Order Ciconiiformes (55% positive) and Pelecaniformes (41%), compared with only 5% in Anseriformes. Although Sindbis virus infections were also highest in these 2 Orders (56% and 46%, respectively), the incidence of antibodies was spread more uniformly through other Orders than with the flaviviruses: e.g. Anseriformes, 33%, Podicipitiformes, 27%. As viruses were recovered virtually only from Culex annulirostris mosquitoes, the different patterns of infection seem unrelated to host preference by mosquito species or behavioural response to mosquito attack, and suggest a specific relationship between MVE/KUN and Ciconiiformes and Pelecaniformes. The highest infection rate was 22/25 in mature rufous night herons (formerly nankeen night herons) Nycticorax calendonicus, and here tolerance to mosquito attack was probably a contributing factor. Assays of sera from 13 horses indicated high infection rates both alphaviruses and flaviviruses.

The Occurence of the Dusky Field-rat, Rattus sordidus (Rodentia : Muridae), in New South Wales

Description and measurements are given of two young female R. sordidus trapped near Evans Head, N.S.W., in 1968 and 1970.

Macquarie Island: the introduction of the European rabbit flea Spilopsyllus cuniculi (Dale) as a possible vector for myxomatosis

The European rabbit flea Spilopsyllus cuniculi (Dale) was first released on Macquarie Island in December 1968. The flea has survived and bred on the island and about 30% of the rabbits sampled from the original release area in January 1972 were flea-infested.