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The well-established manifestation of mitochondrial mutations in functional cardiac disease (e.g., mitochondrial cardiomyopathy) prompted the hypothesis that mitochondrial DNA (mtDNA) sequence and/or copy number (mtDNAcn) variation contribute to cardiac defects in congenital heart disease (CHD). MtDNAcns were calculated and rare, non-synonymous mtDNA mutations were identified in 1,837 CHD-affected proband-parent trios, 116 CHD-affected singletons, and 114 paired cardiovascular tissue/blood samples. The variant allele fraction (VAF) of heteroplasmic variants in mitochondrial RNA from 257 CHD cardiovascular tissue samples was also calculated. On average, mtDNA from blood had 0.14 rare variants and 52.9 mtDNA copies per nuclear genome per proband. No variation with parental age at proband birth or CHD-affected proband age was seen. mtDNAcns in valve/vessel tissue (320 ± 70) were lower than in atrial tissue (1,080 ± 320, p = 6.8E-21), which were lower than in ventricle tissue (1,340 ± 280, p = 1.4E-4). The frequency of rare variants in CHD-affected individual DNA was indistinguishable from the frequency in an unaffected cohort, and proband mtDNAcns did not vary from those of CHD cohort parents. In both the CHD and the comparison cohorts, mtDNAcns were significantly correlated between mother-child, father-child, and mother-father. mtDNAcns among people with European (mean = 52.0), African (53.0), and Asian haplogroups (53.5) were calculated and were significantly different for European and Asian haplogroups (p = 2.6E-3). Variant heteroplasmic fraction (HF) in blood correlated well with paired cardiovascular tissue HF (r = 0.975) and RNA VAF (r = 0.953), which suggests blood HF is a reasonable proxy for HF in heart tissue. We conclude that mtDNA mutations and mtDNAcns are unlikely to contribute significantly to CHD risk.

BackgroundThe contribution of somatic mosaicism, or genetic mutations arising after oocyte fertilization, to congenital heart disease (CHD) is not well understood. Further, the relationship between mosaicism in blood and cardiovascular tissue has not been determined.MethodsWe developed a new computational method, EM-mosaic (Expectation-Maximization-based detection of mosaicism), to analyze mosaicism in exome sequences derived primarily from blood DNA of 2530 CHD proband-parent trios. To optimize this method, we measured mosaic detection power as a function of sequencing depth. In parallel, we analyzed our cohort using MosaicHunter, a Bayesian genotyping algorithm-based mosaic detection tool, and compared the two methods. The accuracy of these mosaic variant detection algorithms was assessed using an independent resequencing method. We then applied both methods to detect mosaicism in cardiac tissue-derived exome sequences of 66 participants for which matched blood and heart tissue was available.ResultsEM-mosaic detected 326 mosaic mutations in blood and/or cardiac tissue DNA. Of the 309 detected in blood DNA, 85/97 (88%) tested were independently confirmed, while 7/17 (41%) candidates of 17 detected in cardiac tissue were confirmed. MosaicHunter detected an additional 64 mosaics, of which 23/46 (50%) among 58 candidates from blood and 4/6 (67%) of 6 candidates from cardiac tissue confirmed. Twenty-five mosaic variants altered CHD-risk genes, affecting 1% of our cohort. Of these 25, 22/22 candidates tested were confirmed. Variants predicted as damaging had higher variant allele fraction than benign variants, suggesting a role in CHD. The estimated true frequency of mosaic variants above 10% mosaicism was 0.14/person in blood and 0.21/person in cardiac tissue. Analysis of 66 individuals with matched cardiac tissue available revealed both tissue-specific and shared mosaicism, with shared mosaics generally having higher allele fraction.ConclusionsWe estimate that ~ 1% of CHD probands have a mosaic variant detectable in blood that could contribute to cardiac malformations, particularly those damaging variants with relatively higher allele fraction. Although blood is a readily available DNA source, cardiac tissues analyzed contributed ~ 5% of somatic mosaic variants identified, indicating the value of tissue mosaicism analyses.

Multiple tools have been developed to identify copy number variants (CNVs) from whole exome (WES) and whole genome sequencing (WGS) data. Current tools such as XHMM for WES and CNVnator for WGS identify CNVs based on changes in read depth. For WGS, other methods to identify CNVs include utilizing discordant read pairs and split reads and genome-wide local assembly with tools such as Lumpy and SvABA, respectively. Here, we introduce a new method to identify deletion CNVs from WES and WGS trio data based on the clustering of Mendelian errors (MEs). Using our Mendelian Error Method (MEM), we identified 127 deletions (inherited and de novo) in 2,601 WES trios from the Pediatric Cardiac Genomics Consortium, with a validation rate of 88% by digital droplet PCR. MEM identified additional de novo deletions compared with XHMM, and a significant enrichment of 15q11.2 deletions compared with controls. In addition, MEM identified eight cases of uniparental disomy, sample switches, and DNA contamination. We applied MEM to WGS data from the Genome In A Bottle Ashkenazi trio and identified deletions with 97% specificity. MEM provides a robust, computationally inexpensive method for identifying deletions, and an orthogonal approach for verifying deletions called by other tools.

This study investigates the causal relationships between international tourism development and the economic growth of a global city–state – Singapore – drilling into the temporal details of the tourism-economy nexus in small countries. Many studies have examined whether the tourism-led growth hypothesis or the economy driven-tourism growth hypothesis holds in large developed and emerging countries. Still, relatively few studies examine small countries' tourism-economy nexus, and the temporal details of the nexus have not been adequately examined. We examine the tourism-economy nexus in Singapore using quarterly data from 1991Q1 to 2020Q4 and the Autoregressive Distributed Lag (ARDL) Model, with the long- and short-run dynamics and the feedback loop of the nexus considered. Our statistical findings show that international tourism development leads economic growth by two quarters in Singapore. Also, there are both 'consistent' and 'contemporaneous' positive feedback loops between tourism development and economic growth, but those loops cannot last for more than a quarter. From the economic perspective, our study reveals that improving tourism activities may accelerate the post-Covid economic recovery of some small countries that rely on tourism. Yet, continuous input is required to sustain the tourism-economy synergy. [ABSTRACT FROM AUTHOR]

The continuous emergence of drug-resistant strains of bacteria poses an urgent risk to human health and dictates the need for new antimicrobials. Along this line, we have been working on developing inhibitors of SecA, a key component of the bacterial Sec-dependent secretion machinery. Herein, we describe the synthesis and antimicrobial evaluation of 6-oxo-1,6-dihydropyrimidine-5-carbonitrile derivatives as potential SecA inhibitors.

Aberrant expression of viral-like repeat elements is a common feature of epithelial cancers, and the substantial diversity of repeat species provides a distinct view of the cancer transcriptome. Repeatome profiling across ovarian, pancreatic, and colorectal cell lines identifies distinct clustering independent of tissue origin that is seen with coding gene analysis. Deeper analysis of ovarian cancer cell lines demonstrated that human satellite II (HSATII) satellite repeat expression was highly associated with epithelial-mesenchymal transition (EMT) and anticorrelated with IFN-response genes indicative of a more aggressive phenotype. SATII expression--and its correlation with EMT and anticorrelation with IFN-response genes-- was also found in ovarian cancer RNA-Seq data and was associated with significantly shorter survival in a second independent cohort of patients with ovarian cancer. Repeat RNAs were enriched in tumor-derived extracellular vesicles capable of stimulating monocyte-derived macrophages, demonstrating a mechanism that alters the tumor microenvironment with these viral-like sequences. Targeting of HSATII with antisense locked nucleic acids stimulated IFN response and induced MHC I expression in ovarian cancer cell lines, highlighting a potential strategy of modulating the repeatome to reestablish antitumor cell immune surveillance., Introduction Repetitive elements make up approximately 50% of the human genome (1, 2), and their aberrant expression has been described across a wide range ofcancers (3-5). Repeat suppression is achieved [...]

Microwave hybrid heating (MHH) process is a unique and novel approach of joint materials. Several lightweight materials (medium and high melting point) such as nickel, copper and aluminum have been successfully joined in the past research. However, small dimensions and low melting point of light weight materials such as zinc (Zn) metal or zinc (Zn) powder were always being a challenging mere for creating bond via any joining techniques. The sheets of stainless steel SS304 (17 mm×7.9 mm×0.2 mm) have been fabricated and joined at lap joint by using novel Microwave hybrid heating technique with mini heat chamber of 2.45 GHz of frequency and 200 W–360 W of microwave power, using pure zinc powder (99.9 %) as an interface material. Epoxy rate and exposure time have been varied from 10 % to 20 % and 2 min to 4 min, respectively. A developed heat chamber has been set in domestic microwave oven properly as proposed. To evaluate the microstructure correlation and microhardness at joint interface, the field emission scanning electron microscopy (FESEM – EDS), x‐ray diffraction (XRD) and Vickers hardness were used. For the experimental studies, it had found an excellent bonding was produced at interface layer between the upper and lower sections with good penetration rate of 360 W of microwave power, 4 min of exposure time and 20 % of epoxy rate as the 183.1 HV 0.05 of excellent microhardness and the intermetallic phase of iron‐zinc (FeZn11), nickel‐zinc (NiZn) and nickel‐zinc (NiZn3) were observed at interface layer. [ABSTRACT FROM AUTHOR]

Metal bonding via joints of low melting point materials such as zinc and tin has been technically challenging. This paper presents a unique technique for bonding small dimensions and the low melting point of materials through the microwave hybrid heating (MHH) process. Joint of stainless steel SS304 was applied to the joint with the tin (Sn) powder with the application of microwave radiation by using domestic microwave oven at 2.45 GHz of constant frequency, 200–360 W of microwave power, 120–180 s of exposure time, and 10–20 % of the epoxy rate. A developed heat chamber was used as a susceptor and insulator in the microwave hybrid heating (MHH) process. The tin powder and parent metals were strongly bonded as lap position by the microwave hybrid heating (MHH) process at 360 W of microwave power, 180 s of constant exposure time, and 20 % of the constant epoxy rate. Characterization of the joint was evaluated through microhardness and x‐ray diffraction (XRD) analysis techniques. It was found that the intermetallic compounds (phase) of nickel tin (NiSn), iron tin (Fe1.84Sn), sulfur tin (SSn), chromium tin (Cr2Sn3), chromium tin (CrSn2), and tin phosphorus (SnP) at the joint surface with highest microhardness obtained at 498.4 HV 0.05 at 360 W of microwave power. [ABSTRACT FROM AUTHOR]