Identification of functional elements and regulatory circuits by Drosophila modENCODE

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation

Clostridium butyricum Bacteremia Associated with Probiotic Use, Japan

Clostridium butyricum, a probiotic commonly prescribed in Asia, most notably as MIYA-BM (Miyarisan Pharmaceutical Co., Ltd.; https://www.miyarisan.com), occasionally leads to bacteremia. The prevalence and characteristics of C. butyricum bacteremia and its bacteriologic and genetic underpinnings remain unknown. We retrospectively investigated patients admitted to Osaka University Hospital during September 2011–February 2023. Whole-genome sequencing revealed 5 (0.08%) cases of C. butyricum bacteremia among 6,576 case-patients who had blood cultures positive for any bacteria. Four patients consumed MIYA-BM, and 1 patient consumed a different C. butyricum-containing probiotic. Most patients had compromised immune systems, and common symptoms included fever and abdominal distress. One patient died of nonocclusive mesenteric ischemia. Sequencing results confirmed that all identified C. butyricum bacteremia strains were probiotic derivatives. Our findings underscore the risk for bacteremia resulting from probiotic use, especially in hospitalized patients, necessitating judicious prescription practices

Transcutaneous Carbon Dioxide Induces Mitochondrial Apoptosis and Suppresses Metastasis of Oral Squamous Cell Carcinoma <i>In Vivo</i>

<div><p>Squamous cell carcinoma (SCC) is the main histological type of oral cancer. Its growth rate and incidence of metastasis to regional lymph nodes is influenced by various factors, including hypoxic conditions. We have previously reported that transcutaneous CO₂ induces mitochondrial apoptosis and decreases lung metastasis by reoxygenating sarcoma cells. However, previous studies have not determined the sequential mechanism by which transcutaneous CO₂ suppresses growth of epithelial tumors, including SCCs. Moreover, there is no report that transcutaneous CO₂ suppresses lymphogenous metastasis using human cell lines xenografts. In this study, we examined the effects of transcutaneous CO₂ on cancer apoptosis and lymphogenous metastasis using human SCC xenografts. Our results showed that transcutaneous CO₂ affects expressions of PGC-1α and TFAM and protein levels of cleavage products of caspase-3, caspase-9 and PARP, which relatives mitochondrial apoptosis. They also showed that transcutaneous CO₂ significantly inhibits SCC tumor growth and affects expressions of HIF-1α, VEGF, MMP-2 and MMP-9, which play essential roles in tumor angiogenesis, invasion and metastasis. In conclusion, transcutaneous CO₂ suppressed tumor growth, increased mitochondrial apoptosis and decreased the number of lymph node metastasis in human SCC by decreasing intra-tumoral hypoxia and suppressing metastatic potential with no observable effect <i>in vivo</i>. Our findings indicate that transcutaneous CO₂ could be a novel therapeutic tool for treating human SCC.</p></div

The effect of transcutaneous CO₂ on HSC-3 tumor growth.

<p>Tumor growth (A) and body weight (B) was monitored for 4 weeks in the CO₂-treated and control groups (*P<0.05).</p

Procedure for administering transcutaneous CO₂ in animal model of human SCC.

<p>The area of skin around the implanted tumor was covered with CO₂ hydrogel and sealed with a polyethylene bag, through which 100% CO₂ gas was administered. Treatment commenced 7 days after HSC-3 cell implantation, and was performed twice a week for 3 weeks.</p

The effect of transcutaneous CO₂ on HSC-3 cell apoptotic pathway.

<p>(A) The mRNA expressions of PGC-1α and TFAM gene were evaluated using real-time PCR (*P<0.05). (B) Mitochondrial DNA (mtDNA) content was also measured; differences were not statically significant. (C) Immunoblot analysis of expressions of the cleavage products of caspase-3, caspase-9 and PARP. β-actin was used as an endogenous loading control. (D) At the end of experiment, the numbers of apoptotic cells in tumors of both groups were assessed by FACS.</p

The effect of transcutaneous CO₂ on the metastatic potential of HSC-3.

<p>(A) The mRNA expressions of VEGF, MMP-2 and MMP-9 gene were measured using real-time PCR (*P<0.05). (B) Immunohistochemical staining for HIF-1α, VEGF, MMP-2 and MMP-9 in implanted tumors from both groups.</p

The effect of transcutaneous CO₂ on metastasis of HSC-3 to the regional lymph nodes.

<p>(A) Detection of micrometastases in the axillary lymph nodes by hematoxylin and eosin staining. (B, C) Human β-globin gene expression in the axillary lymph nodes was assessed by PCR analysis to detect metastasis.</p