Regionally Specific and Genome-Wide Analyses Conclusively Demonstrate the Absence of CpG Methylation in Human Mitochondrial DNA

Although CpG methylation clearly distributes genome-wide in vertebrate nuclear DNA, the state of methylation in the vertebrate mitochondrial genome has been unclear. Several recent reports using immunoprecipitation, mass spectrometry, and enzyme-linked immunosorbent assay methods concluded that human mitochondrial DNA (mtDNA) has much more than the 2 to 5% CpG methylation previously estimated. However, these methods do not provide information as to the sites or frequency of methylation at each CpG site. Here, we have used the more definitive bisulfite genomic sequencing method to examine CpG methylation in HCT116 human cells and primary human cells to independently answer these two questions. We found no evidence of CpG methylation at a biologically significant level in these regions of the human mitochondrial genome. Furthermore, unbiased next-generation sequencing of sodium bisulfite treated total DNA from HCT116 cells and analysis of genome-wide sodium bisulfite sequencing data sets from several other DNA sources confirmed this absence of CpG methylation in mtDNA. Based on our findings using regionally specific and genome-wide approaches with multiple human cell sources, we can definitively conclude that CpG methylation is absent in mtDNA. It is highly unlikely that CpG methylation plays any role in direct control of mitochondrial function.     

Proinflammatory cytokine responses induced by influenza A (H5N1) viruses in primary human alveolar and bronchial epithelial cells

Background

Fatal human respiratory disease associated with influenza A subtype H5N1 has been documented in Hong Kong, and more recently in Vietnam, Thailand and Cambodia. We previously demonstrated that patients with H5N1 disease had unusually high serum levels of IP-10 (interferon-gamma-inducible protein-10). Furthermore, when compared with human influenza virus subtype H1N1, the H5N1 viruses in 1997 (A/Hong Kong/483/97) (H5N1/97) were more potent inducers of pro-inflammatory cytokines (e.g. tumor necrosis factor-a) and chemokines (e.g. IP-10) from primary human macrophages in vitro, which suggests that cytokines dysregulation may play a role in pathogenesis of H5N1 disease. Since respiratory epithelial cells are the primary target cell for replication of influenza viruses, it is pertinent to investigate the cytokine induction profile of H5N1 viruses in these cells.

Methods

We used quantitative RT-PCR and ELISA to compare the profile of cytokine and chemokine gene expression induced by H5N1 viruses A/HK/483/97 (H5N1/97), A/Vietnam/1194/04 and A/Vietnam/3046/04 (both H5N1/04) with that of human H1N1 virus in human primary alveolar and bronchial epithelial cells in vitro.

Results

We demonstrated that in comparison to human H1N1 viruses, H5N1/97 and H5N1/04 viruses were more potent inducers of IP-10, interferon beta, RANTES (regulated on activation, normal T cell expressed and secreted) and interleukin 6 (IL-6) in primary human alveolar and bronchial epithelial cells in vitro. Recent H5N1 viruses from Vietnam (H5N1/04) appeared to be even more potent at inducing IP-10 than H5N1/97 virus.

Conclusion

The H5N1/97 and H5N1/04 subtype influenza A viruses are more potent inducers of proinflammatory cytokines and chemokines in primary human respiratory epithelial cells than subtype H1N1 virus. We suggest that this hyper-induction of cytokines may be relevant to the pathogenesis of human H5N1 disease.     

Levels of Thermostable Direct Hemolysin Produced by Vibrio parahaemolyticus O3:K6 and Other Serovars Grown Anaerobically with the Presence of a Bile Acid

Twenty-three V. parahaemolyticus strains, including 12 pandemic O3:K6 strains, were examined for their growth and production of thermostable direct hemolysin (TDH) under an anaerobic culture condition with or without presence of a bile acid, taurocholic acid (TCA). Both bacterial growth and TDH production were markedly enhanced by TCA for a majority of the strains, but the scale of the TDH production was disproportionately greater than that of the corresponding growth for 14 strains. Such enhancement was, however, not specific to the pandemic strains. Received: 27 August 2001 / Accepted: 15 October 2001     

Occurrence of urease-positive Vibrio parahaemolyticus in Kanagawa, Japan, with specific reference to presence of thermostable direct hemolysin (TDH) and the TDH-related-hemolysin genes.

A total of 132 strains of V. parahaemolyticus isolated from patients and from the suspected causal food items of past food poisoning cases occurring in Kanagawa Prefecture, Japan, were examined for the ability to hydrolyze urea, with specific reference to the presence of the thermostable direct hemolysin gene (tdh) and the gene for thermostable direct hemolysin-related hemolysin (trh). Ten strains belonging to five different O-antigen serotypes were positive for urea hydrolysis (UH+), and four of these strains did not carry tdh. A total of 106 strains carried tdh, but less than 6% of them were UH+, whereas all trh-carrying strains were UH+. The evidence suggests that urea hydrolysis is not a reliable marker for identifying tdh-carrying V. parahaemolyticus strains in Japan (the Pacific Northeast) but may be a marker for trh-carrying strains.     

Effects of fetal calf serum in culture medium on development of bovine oocytes matured and fertilized in vitro

Bovine oocytes matured and fertilized in vitro were cultured in a chemically defined bovine embryo culture medium (BECM) or polyvinylalcohol (PVA)-free BECM supplemented with 10% heat-treated or unheated fetal calf serum (FCS). When PVA in BECM was replaced with FCS 8 h postinsemination, the proportion of >/=-cell-stage embryos 48 h postinsemination was significantly lower in heat-treated FCS (74%) than in PVA (91%) medium, but the value (84%) in unheated FCS was not different from the values in PVA and heat-treated FCS. However, the addition of either heat-treated FCS or unheated FCS to PVA-free BECM did not depress or increase the proportions (63 to 70%) of >/=-cell-stage embryos 96 h postinsemination and stimulated blastocyst formation 144 (21 to 28%) and 192 (47 to 54%) h postinsemination. Blastocyst formation was also stimulated when heattreated FCS or unheated FCS was added to PVA-free BECM 120 h postinsemination. The mean cell number of blastocysts developed in PVA-free BECM with heat-treated FCS (150 cells) or unheated FCS (152 cells) significantly increased compared with that (119 cells) developed without FCS. These results indicate that, although BECM can support bovine embryo development, a high proportion (about 50%) of morphologically normal blastocysts can be produced from oocytes matured and fertilized in vitro when they are cultured in PVA-free BECM containing FCS.     

A Guyon's canal ganglion presenting as occupational overuse syndrome: A case report

We report a case of severe weight loss secondary to anorexia nervosa causing bilateral superficial peroneal nerve entrapment in a young female patient who was treated successfully by bilateral surgical decompression.     

Estimating the spawning activity of fish species using nuclear and mitochondrial environmental DNA concentrations and their ratios

1. During spawning activity, fish release large amounts of sperm and eggs into the water, which has been assumed to cause an increase in environmental DNA (eDNA) levels and nuclear DNA/mitochondrial DNA ratios. To test whether these assumptions are valid and whether nuclear and mitochondrial eDNA analysis can be used to monitor the spawning activity of freshwater fish, we conducted field eDNA surveys and traditional surveys using common carp (Cyprinus carpio), largemouth bass (Micropterus salmoides) and bluegill sunfish (Lepomis macrochirus) as model species.
2. Fish spawning periods were estimated based on age, as estimated using the body lengths of juveniles collected in the Miharu reservoir in Fukushima, Japan. The results showed that the main spawning periods of largemouth bass and bluegill sunfish were from April to July and from July to August, respectively.
3. Field eDNA surveys were conducted in the Hebisawagawa front reservoir, which is connected to the Miharu reservoir. From March to August 2019 and 2020, weekly eDNA sampling was conducted at three sites, and daily sampling was conducted at six sites from 23 June to 3 July 2020. The eDNA concentrations of the nuclear internal transcribed spacer 1 (ITS1) and mitochondrial cytochrome B (CytB), as well as the ITS1/CytB ratio, were measured for each of the three fish in each water sample. Water temperature had a statistically significant effect on eDNA concentration, probably reflecting the relationship between water temperature and spawning.
4. We created generalised additive mixed models to estimate spawning activity periods based on weekly eDNA data. The estimated periods of spawning activity for common carp, largemouth bass and bluegill sunfish were March to May, May to July, and May to August, respectively. The estimated spawning periods coincided with known fish ecology or the results of traditional methods. This method also has been applied to daily eDNA samples, showing the feasibility of high-resolution estimation of spawning activity.
5. For common carp and bluegill sunfish, we were able to estimate the spawning period using this method. Although the method is affected by biomass and the diffusion and degradation of eDNA, it has the potential to accurately estimating spawning activities. These then can be estimated without conducting laborious traditional surveys, facilitating the monitoring of reproduction by rare, invasive or important fishery species. Further research on the diffusion distance and degradation time of the eDNA concentration peak caused by fish spawning activity may improve the accuracy of monitoring.

     

Calicivirus

Caliciviruses represented by norovirus and sapovirus exist not only in human but also in other animal species. Clinical manifestations are gastroenteritis, respiratory infections, vesicles and hemorrhagic skin diseases and others symptoms depended on the viruses. Inapparent symptom of calicivirus infection is also recognized. Calicivirus is stable in the environment and found sometimes in contaminated food or water sources. In addition to intragenomic mutation, intragenomic recombination is the common phenomenon that usually found in calicivirus genome. The genomic recombinations have been reported among the strains within the same animal species. For diagnosis and molecular epidemiological study, several laboratory methods are available, such as genetic molecular analysis, enzyme immunoassay and immunochromatography, which developed by using the antibody against virus-like particles. The reactivity between virus and host immunity is type specific and the titer of cross reaction is not so high. There are evidences that the new variant strains are emerged and spread quickly year by year. Histo-blood group antigen (HBGA) is one of the specific host cells receptor for calicivirus. Infectivity of the virus depends on specificity of the HBGA on the host cells. Because of the inability to culture human norovirus and sapovirus, pathogenesis and immunological data are limited. So far, only feline calicivirus and mouse norovirus are cultivable. Animal model studies for calicivirus by gnotobiotic pigs with human calicivirus and mouse with mouse norovirus are mainly used for experiments of pathobiological study, treatment and vaccine development.