Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups

BACKGROUND

Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based on chip or exome genotyping data. Such studies have limitations regarding whole genome-wide association analysis, making it crucial to have genome-to-phenome association information with the largest possible whole genome and matched phenome data to conduct further population-genome studies and develop health care services based on population genomics.

RESULTS

Here, we present 4,157 whole genome sequences (Korea4K) coupled with 107 health check-up parameters as the largest genomic resource of the Korean Genome Project. It encompasses most of the variants with allele frequency >0.001 in Koreans, indicating that it sufficiently covered most of the common and rare genetic variants with commonly measured phenotypes for Koreans. Korea4K provides 45,537,252 variants, and half of them were not present in Korea1K (1,094 samples). We also identified 1,356 new genotype-phenotype associations that were not found by the Korea1K dataset. Phenomics analyses further revealed 24 significant genetic correlations, 14 pleiotropic associations, and 127 causal relationships based on Mendelian randomization among 37 traits. In addition, the Korea4K imputation reference panel, the largest Korean variants reference to date, showed a superior imputation performance to Korea1K across all allele frequency categories.

CONCLUSIONS

Collectively, Korea4K provides not only the largest Korean genome data but also corresponding health check-up parameters and novel genome-phenome associations. The large-scale pathological whole genome-wide omics data will become a powerful set for genome-phenome level association studies to discover causal markers for the prediction and diagnosis of health conditions in future studies.

Identification and validation of six acute myocardial infarction-associated variants, including a novel prognostic marker for cardiac mortality

Background

Acute myocardial infarction (AMI) is one of the leading causes of death worldwide, and approximately half of AMI-related deaths occur before the affected individual reaches the hospital. The present study aimed to identify and validate genetic variants associated with AMI and their role as prognostic markers.

Materials and methods

We conducted a replication study of 29 previously identified novel loci containing 85 genetic variants associated with early-onset AMI using a new independent set of 2,920 Koreans [88 patients with early- and 1,085 patients with late-onset AMI, who underwent percutaneous coronary intervention (PCI), and 1,747 healthy controls].

Results

Of the 85 previously reported early-onset variants, six were confirmed in our genome-wide association study with a false discovery rate of less than 0.05. Notably, rs12639023, a cis-eQTL located in the intergenic region between LINC02005 and CNTN3, significantly increased longitudinal cardiac mortality and recurrent AMI. CNTN3 is known to play a role in altering vascular permeability. Another variant, rs78631167, located upstream of PLAUR and known to function in fibrinolysis, was moderately replicated in this study. By surveying the nearby genomic region around rs78631167, we identified a significant novel locus (rs8109584) located 13 bp downstream of rs78631167. The present study showed that six of the early-onset variants of AMI are applicable to both early- and late-onset cases.

Conclusion

Our results confirm markers that can potentially be utilized to predict, screen, prevent, and treat candidate patients with AMI and highlight the potential of rs12639023 as a prognostic marker for cardiac mortality in AMI.

Effect of synthetic cholesterol (Synthechol) supplementation in an egg yolk-free extender on dog sperm cryopreservation

BACKGROUND

SyntheChol is a new synthetic, non-animal-derived cholesterol that is easily dissolved in ethanol, ready to use, and behaves in a similar way as natural cholesterol. Therefore, it could be used as a substitute of natural cholesterol in dog sperm freezing extender.

OBJECTIVE

To evaluate the effect of supplementing an egg yolk-free (EY-free) extender with synthetic cholesterol (SyntheChol) on cryopreserved dog sperm.

MATERIALS AND METHODS

Spermatozoa (1 × 10⁸ sperm/mL) were suspended in EY-free extender supplemented with 0 % (control), 0.25, 0.5, 1, 2, 4, or 6 % SyntheChol (Extender 1), cooled at 4 degree C for 1 h, and diluted (1:1, v/v) with Extender 1 containing 1 M glycerol. The spermatozoa were then cooled to 4 degree C for 30 min. Sperm-containing straws were frozen using LN2 vapor. Sperm motility (computer-assisted sperm analysis, CASA), sperm membrane integrity (SYBR-14 and PI staining), and acrosome integrity (FITC-PSA) were evaluated after thawing. Thereafter, optimal concentrations were determined (0.25, 0.5, 1, or 2 %) and used to evaluate reactive oxygen species (ROS) generation, apoptosis, and the gene expression of motility-related sperm mitochondria-associated cysteine-rich protein, apoptosis-related B-cell lymphoma 2 (BCL2), and BCL2-associated X protein (BAX) in cryopreserved sperm.

RESULTS

Sperm progressive motility, membrane integrity, and acrosome integrity were markedly greater in the SyntheChol-supplemented groups (0.25, 0.5, 1, or 2 %) than in the control group. Only BAX expression was significantly reduced in the SyntheChol groups (0.25, 1, or 2 %) compared with the control group. However, there were no significant effects on the ROS generation or apoptosis index.

CONCLUSION

SyntheChol (0.25, 1, or 2 %) proved to be effective in reducing the BAX gene expression level and improving sperm progressive motility, and membrane and acrosome integrity. doi.org/10.54680/fr22210110212.

Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates

Coronavirus disease, COVID-19 (coronavirus disease 2019), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has a higher case fatality rate in European countries than in others, especially East Asian ones. One potential explanation for this regional difference is the diversity of the viral infection efficiency. Here, we analyzed the allele frequencies of a nonsynonymous variant rs12329760 (V197M) in the TMPRSS2 gene, a key enzyme essential for viral infection and found a significant association between the COVID-19 case fatality rate and the V197M allele frequencies, using over 200,000 present-day and ancient genomic samples. East Asian countries have higher V197M allele frequencies than other regions, including European countries which correlates to their lower case fatality rates. Structural and energy calculation analysis of the V197M amino acid change showed that it destabilizes the TMPRSS2 protein, possibly negatively affecting its ACE2 and viral spike protein processing.

The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences

Koreans are thought to be an ethnic group of admixed northern and southern subgroups. However, the exact genetic origins of these two remain unclear. In addition, the past admixture is presumed to have taken place on the Korean peninsula, but there is no genomic scale analysis exploring the origin, composition, admixture, or the past migration of Koreans. Here, 88 Korean genomes compared with 91 other present-day populations showed two major genetic components of East Siberia and Southeast Asia. Additional paleogenomic analysis with 115 ancient genomes from Pleistocene hunter-gatherers to Iron Age farmers showed a gradual admixture of Tianyuan (40 ka) and Devil’s gate (8 ka) ancestries throughout East Asia and East Siberia up until the Neolithic era. Afterward, the current genetic foundation of Koreans may have been established through a rapid admixture with ancient Southern Chinese populations associated with Iron Age Cambodians. We speculate that this admixing trend initially occurred mostly outside the Korean peninsula followed by continuous spread and localization in Korea, corresponding to the general admixture trend of East Asia. Over 70% of extant Korean genetic diversity is explained to be derived from such a recent population expansion and admixture from the South.

Identifying molecular targets for reverse aging using integrated network analysis of transcriptomic and epigenomic changes during aging

Aging is associated with widespread physiological changes, including skeletal muscle weakening, neuron system degeneration, hair loss, and skin wrinkling. Previous studies have identified numerous molecular biomarkers involved in these changes, but their regulatory mechanisms and functional repercussions remain elusive. In this study, we conducted next-generation sequencing of DNA methylation and RNA sequencing of blood samples from 51 healthy adults between 20 and 74 years of age and identified aging-related epigenetic and transcriptomic biomarkers. We also identified candidate molecular targets that can reversely regulate the transcriptomic biomarkers of aging by reconstructing a gene regulatory network model and performing signal flow analysis. For validation, we screened public experimental data including gene expression profiles in response to thousands of chemical perturbagens. Despite insufficient data on the binding targets of perturbagens and their modes of action, curcumin, which reversely regulated the biomarkers in the experimental dataset, was found to bind and inhibit JUN, which was identified as a candidate target via signal flow analysis. Collectively, our results demonstrate the utility of a network model for integrative analysis of omics data, which can help elucidate inter-omics regulatory mechanisms and develop therapeutic strategies against aging.

Welfare Genome Project: A Participatory Korean Personal Genome Project With Free Health Check-Up and Genetic Report Followed by Counseling

The Welfare Genome Project (WGP) provided 1,000 healthy Korean volunteers with detailed genetic and health reports to test the social perception of integrating personal genetic and healthcare data at a large-scale. WGP was launched in 2016 in the Ulsan Metropolitan City as the first large-scale genome project with public participation in Korea. The project produced a set of genetic materials, genotype information, clinical data, and lifestyle survey answers from participants aged 20–96. As compensation, the participants received a free general health check-up on 110 clinical traits, accompanied by a genetic report of their genotypes followed by genetic counseling. In a follow-up survey, 91.0% of the participants indicated that their genetic reports motivated them to improve their health. Overall, WGP expanded not only the general awareness of genomics, DNA sequencing technologies, bioinformatics, and bioethics regulations among all the parties involved, but also the general public’s understanding of how genome projects can indirectly benefit their health and lifestyle management. WGP established a data construction framework for not only scientific research but also the welfare of participants. In the future, the WGP framework can help lay the groundwork for a new personalized healthcare system that is seamlessly integrated with existing public medical infrastructure.

Polygenic risk score validation using Korean genomes of 265 early-onset acute myocardial infarction patients and 636 healthy controls

Background

The polygenic risk score (PRS) developed for coronary artery disease (CAD) is known to be effective for classifying patients with CAD and predicting subsequent events. However, the PRS was developed mainly based on the analysis of Caucasian genomes and has not been validated for East Asians. We aimed to evaluate the PRS in the genomes of Korean early-onset AMI patients (n = 265, age ≤50 years) following PCI and controls (n = 636) to examine whether the PRS improves risk prediction beyond conventional risk factors.

Results

The odds ratio of the PRS was 1.83 (95% confidence interval [CI]: 1.69–1.99) for early-onset AMI patients compared with the controls. For the classification of patients, the area under the curve (AUC) for the combined model with the six conventional risk factors (diabetes mellitus, family history of CAD, hypertension, body mass index, hypercholesterolemia, and current smoking) and PRS was 0.92 (95% CI: 0.90–0.94) while that for the six conventional risk factors was 0.91 (95% CI: 0.85–0.93). Although the AUC for PRS alone was 0.65 (95% CI: 0.61–0.69), adding the PRS to the six conventional risk factors significantly improved the accuracy of the prediction model (P = 0.015). Patients with the upper 50% of PRS showed a higher frequency of repeat revascularization (hazard ratio = 2.19, 95% CI: 1.47–3.26) than the others.

Conclusions

The PRS using 265 early-onset AMI genomes showed improvement in the identification of patients in the Korean population and showed potential for genomic screening in early life to complement conventional risk prediction.

Cryopreservation of Dog Spermatozoa Using Essential and Non-Essential Amino Acids Solutions in An Egg Yolk-Free Polyvinyl Alcohol Extender

BACKGROUND

Amino acids (AAs) have been indicated to have cryoprotective and antioxidative effects on sperm freezing using egg yolk (EY)-based extender. However, EY-based extender is difficult to be standardized for the effect of amino acids because the EY composition varies with the animal's diet.

OBJECTIVE

To test the effect of AAs in EY-free polyvinyl alcohol (EY-free PVA) extender and develop a chemically defined extender for dog sperm cryopreservation.

MATERIALS AND METHODS

In the first experiment (E1), dog spermatozoa (1ｘ10⁸ sperms/mL) were frozen with EY-free PVA extender without AAs or supplemented with essential (EAAs, 50 x: 1, 2, 4 %) or non-essential amino acids (NEAAs, 100 x: 1, 2, 4 %). In the second experiment (E2), spermatozoa were frozen with EY-free PVA extender supplemented with 0, 0.5, 1 or 2 % of an EAA-NEAA mixture. Motility, viability and acrosome integrity were evaluated after thawing in E1 and E2. In the third experiment (E3), spermatozoa were frozen using an extender supplemented with 2 % EAAs, 2 % NEAAs or a 0.5 % EAA-NEAA mixture. Reactive oxygen species (ROS) and phosphatidylserine (PS) translocation were assessed. Expression of genes for motility-related sperm mitochondrial-associated cysteine-rich protein (SMCP), apoptosis-related B-cell lymphoma 2 (BCL2) and BCL2 associated X protein (BAX) was measured.

RESULTS

Addition of EAAs, NEAAs or an EAA-NEAA mixture to EY-free PVA extender significantly increased sperm motility without affecting viability. Only 1 % NEAAs significantly increased the acrosome membrane. EAA-NEAA mixture (0.5 %) significantly increased SMCP, BCL2 and BAX expression compared to the control group without significant effect on PS translocation or ROS.

CONCLUSION

EAAs and NEAAs addition in EY-free PVA extender improved sperm motility, with limited effect on acrosome integrity and gene expression of SMCP, BCL2 and BAX during dog sperm cryopreservation.

Complete genome sequence and bioinformatics analysis of nine Egyptian females with clinical information from different geographic regions in Egypt

Egyptians are at a crossroad between Africa and Eurasia, providing useful genomic resources for analyzing both genetic and environmental factors for future personalized medicine. Two personal Egyptian whole genomes have been published previously by us and here nine female whole genome sequences with clinical information have been added to expand the genomic resource of Egyptian personal genomes. Here we report the analysis of whole genomes of nine Egyptian females from different regions using Illumina short-read sequencers. At 30x sequencing coverage, we identified 12 SNPs that were shared in most of the subjects associated with obesity which are concordant with their clinical diagnosis. Also, we found mtDNA mutation A4282G is common in all the samples and this is associated with chronic progressive external ophthalmoplegia (CPEO). Haplogroup and Admixture analyses revealed that most Egyptian samples are close to the other north Mediterranean, Middle Eastern, and European, respectively, possibly reflecting the into-Africa influx of human migration. In conclusion, we present whole-genome sequences of nine Egyptian females with personal clinical information that cover the diverse regions of Egypt. Although limited in sample size, the whole genomes data provides possible geno-phenotype candidate markers that are relevant to the region's diseases.

Korean Genome Project: 1094 Korean personal genomes with clinical information

We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31×), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.

Decoding a highly mixed Kazakh genome

We provide a Kazakh whole genome sequence (MJS) and analyses with the largest comparative Kazakh genomic data available to date. We found 102,240 novel SNVs and a high level of heterozygosity. ADMIXTURE analysis confirmed a significant proportion of variations in this individual coming from all continents except Africa and Oceania. A principal component analysis showed neighboring Kalmyk, Uzbek, and Kyrgyz populations to have the strongest resemblance to the MJS genome which reflects fairly recent Kazakh history. MJS's mitochondrial haplogroup, J1c2, probably represents an early European and Near Eastern influence to Central Asia. This was also supported by the heterozygous SNPs associated with European phenotypic features and strikingly similar Kazakh ancestral composition inferred by ADMIXTURE. Admixture (f3) analysis showed that MJS's genomic signature is best described as a cross between the Neolithic East Asian (Devil's Gate1) and the Bronze Age European (Halberstadt_LBA1) components rather than a contemporary admixture.

Depression and suicide risk prediction models using blood-derived multi-omics data

More than 300 million people worldwide experience depression; annually, ~800,000 people die by suicide. Unfortunately, conventional interview-based diagnosis is insufficient to accurately predict a psychiatric status. We developed machine learning models to predict depression and suicide risk using blood methylome and transcriptome data from 56 suicide attempters (SAs), 39 patients with major depressive disorder (MDD), and 87 healthy controls. Our random forest classifiers showed accuracies of 92.6% in distinguishing SAs from MDD patients, 87.3% in distinguishing MDD patients from controls, and 86.7% in distinguishing SAs from controls. We also developed regression models for predicting psychiatric scales with R² values of 0.961 and 0.943 for Hamilton Rating Scale for Depression-17 and Scale for Suicide Ideation, respectively. Multi-omics data were used to construct psychiatric status prediction models for improved mental health treatment.

The Draft Genome of an Octocoral, Dendronephthya gigantea

Coral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities of octocorallian species, appear more resilient. The genomes of several cnidarians species have been published, including from stony corals, sea anemones, and hydra. To fill the phylogenetic gap for octocoral species of cnidarians, we sequenced the octocoral, Dendronephthya gigantea, a nonsymbiotic soft coral, commonly known as the carnation coral. The D. gigantea genome size is ∼276 Mb. A high-quality genome assembly was constructed from PacBio long reads (29.85 Gb with 108× coverage) and Illumina short paired-end reads (35.54 Gb with 128× coverage) resulting in the highest N50 value (1.4 Mb) reported thus far among cnidarian genomes. About 12% of the genome is repetitive elements and contained 28,879 predicted protein-coding genes. This gene set is composed of 94% complete BUSCO ortholog benchmark genes, which is the second highest value among the cnidarians, indicating high quality. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence times were estimated at 544 MYA. There is a clear difference in Hox gene composition between these species: unlike hexacorals, the Antp superclass Evx gene was absent in D. gigantea. Here, we present the first genome assembly of a nonsymbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including stony and soft corals, both symbiotic and nonsymbiotic. The D. gigantea genome may also provide clues to mechanisms of differential coping between the soft and stony corals in response to scenarios of global warming.

Protective effect of a brown algae, Sargassum horneri on particulate matter-induced oxidative stress and inflammation in MLE-12 cells

The constant exposure to fine particulate matter (PM) induces oxidative stress and proinflammatory cytokine production. The ROS formed by oxidative stress is related to activate NF-κB signal pathway for inflammation. Sargassum horneri, a brown algae found in East Asia, is known to be an excellent source for bioactive components. In this study, the antioxidant and anti-inflammation effects of Sargassum horneri ethanol extract (SHE) on the PM-induced oxidative stress in MLE-12, a type II alveolar epithelial cell line were investigated. As the exposure concentration of PM increased to 1,000 μg/mL, the cell viability was reduced; however, it was increased when treated with SHE. The ROS generation and lipid peroxidation of MLE-12 cells were increased from the PM concentration of 125 μg/mL and they were reduced after treatment of SHE at 62.5 and 125 μg/mL. The expressions of antioxidant enzymes, catalase (CAT) and superoxide dismutase (SOD2), in MLE-12 cells exposed to PM were lower than those exposed to PM with SHE. The PM was proved to increase the expression of 8-OHdG, one of DNA oxidative damage markers, and OGG1, the repair enzyme of 8-OHdG, while SHE protected the DNA damage of cell. The expression of NF-κB signaling was reduced by SHE. These results suggest that SHE can adjust the expression of antioxidant enzymes, help to suppress the oxidative stress induced by PM, and attenuate its oxidative damage and NF-κB pathway to lung epithelial cells by eliminating over-produced ROS.

This research is part of a project titled ‘Development of functional food products with natural materials derived from marine resources’ funded by the Ministry of Oceans and Fisheries, Republic of Korea in 2017 (Project NO. 20172085).

The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation

BACKGROUND

Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura's jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations.

RESULTS

We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura's jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation).

CONCLUSIONS

Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators.

A New Technique to Determine the Size of Double-lumen Endobronchial Tubes by the Two Perpendicularly Measured Bronchial Diameters

The cross-section of the mainstem bronchi is not completely round. For preoperative selection of a double-lumen endobronchial tube size, it may be necessary to measure the mediolateral and the anteroposterior bronchial diameters, which can be measured respectively on chest radiograph and computed tomography. With Internal Review Board approval and patients’ informed consent, 105 elective thoracic surgical patients who needed left-sided double-lumen tubes were enrolled. Double-lumen tube size was selected depending on the arithmetic mean of the mediolateral and anteroposterior bronchial diameters. Moreover, the outer diameters of the bronchial tube should be smaller than both mediolateral and anteroposterior diameters. The recommended bronchial diameter for each double-lumen tube size was chosen so that the mean of the two bronchial diameters was 0 to 2.0 mm larger than the upper limit of 95% confidence interval of the averaged outer diameter of the bronchial tube of the selected double-lumen tube. In no case was the predicted double-lumen tube size inappropriate. Generally, anteroposterior bronchial diameters appeared to be different from mediolateral diameters (P=0.001). The double-lumen tube size to be selected based on only one bronchial diameter was different from the one selected based on two perpendicularly measured bronchial diameters in 54.3% of patients (57/105). Preoperative selection of the double-lumen tube size based on the anteroposterior, mediolateral and mean bronchial diameters seems to be useful in that this may obviate the need to change an inappropriately sized double-lumen tube and may be helpful in reducing the related complications.

Intraoperative Management of a Patient With Impaired Cardiac Function Undergoing Simultaneous ABO-Compatible Liver and ABO-Incompatible Kidney Transplant From 2 Living Donors: A Case Report

BACKGROUND

Combined liver and kidney transplant is a very complex surgery. To date, there has been no report on the intraoperative management of patients with impaired cardiac function undergoing simultaneous ABO-compatible liver and ABO-incompatible kidney transplant from 2 living donors.

CASE REPORT

A 60-year-old man underwent simultaneous ABO-compatible liver and ABO-incompatible kidney transplant from 2 living donors because of IgA nephropathy and alcoholic liver cirrhosis. The preoperative cardiac findings revealed continuous aggravation, shown by large left atrial enlargement, severe left ventricular hypertrophy, a very prolonged QT interval, and a calcified left anterior descending coronary artery. Severe hypotension with very weak pulsation and severe bradycardia developed, with an irregular junctional rhythm noted immediately after the liver graft was reperfused. Although epinephrine was administered as a rescue drug, hemodynamics did not improve, and central venous pressure and mean pulmonary arterial pressure increased to potentially fatal levels. Emergency phlebotomy via the central line was performed. Thereafter, hypotension and bradycardia recovered gradually as the central venous pressure and mean pulmonary arterial pressure decreased. The irregular junctional rhythm returned to a sinus rhythm, but the QTc interval was slightly more prolonged. Because of poor cardiac capacity, the volume and rate of fluid infusion were increased aggressively to maintain appropriate kidney graft perfusion after confirming vigorous urine production of the graft.

CONCLUSIONS

A heart with impaired function due to both end-stage liver and kidney diseases may be less able to withstand surgical stress. Further study on cardiac dysfunction will be helpful for the management of patients undergoing complex transplant surgery.

Performance of the Minto model for the target-controlled infusion of remifentanil during cardiopulmonary bypass

We studied the predictive performance of the Minto pharmacokinetic model during cardiopulmonary bypass in patients undergoing cardiac surgery. Patients received remifentanil target-controlled infusion using the Minto model during total intravenous anaesthesia with propofol. From 56 patients, 275 arterial blood samples were drawn before, during and after bypass to determine the plasma concentration of remifentanil, and the predicted concentrations were recorded at each time. For pooled data, the median prediction error and median absolute prediction error were 21.3% and 21.8%, respectively, and 22.1% and 22.3% during bypass. Both were 148.4% during hypothermic circulatory arrest and measured concentrations were more than three times greater than predicted (26.9 (17.0) vs. 7.1 (1.6) ng.ml^-1 ). The Minto model showed considerable bias but overall acceptable precision during bypass. The target concentration of remifentanil should be reduced when using the Minto model during hypothermic circulatory arrest.

Myotis rufoniger genome sequence and analyses: M. rufoniger's genomic feature and the decreasing effective population size of Myotis bats

Myotis rufoniger is a vesper bat in the genus Myotis. Here we report the whole genome sequence and analyses of the M. rufoniger. We generated 124 Gb of short-read DNA sequences with an estimated genome size of 1.88 Gb at a sequencing depth of 66× fold. The sequences were aligned to M. brandtii bat reference genome at a mapping rate of 96.50% covering 95.71% coding sequence region at 10× coverage. The divergence time of Myotis bat family is estimated to be 11.5 million years, and the divergence time between M. rufoniger and its closest species M. davidii is estimated to be 10.4 million years. We found 1,239 function-altering M. rufoniger specific amino acid sequences from 929 genes compared to other Myotis bat and mammalian genomes. The functional enrichment test of the 929 genes detected amino acid changes in melanin associated DCT, SLC45A2, TYRP1, and OCA2 genes possibly responsible for the M. rufoniger's red fur color and a general coloration in Myotis. N6AMT1 gene, associated with arsenic resistance, showed a high degree of function alteration in M. rufoniger. We further confirmed that the M. rufoniger also has bat-specific sequences within FSHB, GHR, IGF1R, TP53, MDM2, SLC45A2, RGS7BP, RHO, OPN1SW, and CNGB3 genes that have already been published to be related to bat's reproduction, lifespan, flight, low vision, and echolocation. Additionally, our demographic history analysis found that the effective population size of Myotis clade has been consistently decreasing since ~30k years ago. M. rufoniger's effective population size was the lowest in Myotis bats, confirming its relatively low genetic diversity.

The genetics of an early Neolithic pastoralist from the Zagros, Iran

The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding, ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting those of the Central Zagros were somewhat isolated from other populations of the Fertile Crescent. Runs of homozygosity are of a similar length to those from Neolithic farmers, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity between early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct.

Needs assessment for master of nursing programmes among Bangladesh nurses

AIM

This study aimed to assess the intent to enrol in a master of nursing programme among Bangladesh nurses, identify preferred programme options and measure the association among intent to enrol in the programme, clinical competency and job satisfaction.

BACKGROUND

Personal and professional aspects of potential students pursuing graduate education are beneficial in devising educational strategies. However, considering the pressing needs for higher nursing education, there are no masters of nursing programmes in Bangladesh.

METHODS

This study used a descriptive correlational design. Nurses working in Bangladesh public sector were recruited to participate in a self-administered survey (n = 260). The questionnaire consisted of perception of job satisfaction, clinical competency and the need for educational options, including the intent to enrol in a master of nursing programme, preferred specialty area, curriculum content and career goals after graduation. Data were analysed using descriptive statistics and point-biserial correlation.

RESULTS

Ninety per cent of the respondents reported that they intended to enrol in a master of nursing programme. Intention was significantly correlated with clinical competency but not with job satisfaction. The most preferred specialty areas were nursing management and education. Half of the respondents responded that teaching at nursing schools was a career goal after graduation.

DISCUSSION

The results of the needs assessment for the programme reflected the unique interest and priorities of the current status of Bangladesh.

CONCLUSIONS

The results indicate a strong motivation to enrol in a master of nursing programme, confidence in clinical competence and high demand for programme in nursing management and education. These findings should be considered to design the programme in order to meet the interest of Bangladesh nurses.

IMPLICATIONS FOR NURSING AND HEALTH POLICY

Educational needs assessments should take precedence to ensure the best possible educational outcome and to produce competent nurses who will contribute in achieving the Millennium Development Goals of Bangladesh.

Effects of Palonosetron on Perioperative Cardiovascular Complications in Patients Undergoing Noncardiac Surgery With General Anesthesia: A Retrospective Cohort Study

We retrospectively investigated whether palonosetron administered during the induction of general anesthesia is associated with an increased risk of perioperative cardiovascular complications in a single tertiary center cohort consisting of 4,517 palonosetron-exposed patients and 4,517 propensity score-matched patients without palonosetron exposure. The primary endpoint was a composite of perioperative cardiovascular complications, including intraoperative cardiac arrhythmia, intraoperative cardiac death, and myocardial injury within the first postoperative week, and there was no significant difference between the groups (odds ratio [OR] = 1.04; 95% confidence interval [CI] = 0.92-1.19). As secondary endpoints, intraoperative cardioversion, cardiac compression, use of cardiovascular drugs, postoperative hospital stay, and in-hospital mortality showed no differences between the groups. However, the palonosetron group showed decreased intraoperative hypotension (OR = 0.88; 95% CI = 0.79-0.97) and length of postoperative intensive care unit (ICU) stay (4.26 ± 9.86 vs. 6.14 ± 16.75; P = 0.026). Palonosetron did not increase the rate of perioperative cardiovascular complications, and can therefore be used safely during anesthetic induction.

295 EFFECT OF TREHALOSE DURING IN VITRO MATURATION OF PIG OOCYTES ON OOCYTE MATURATION AND EMBRYONIC DEVELOPMENT AFTER PARTHENOGENESIS

Autophagy is a critical process for the maintenance of cellular homeostasis and mammalian early embryogenesis. Autophagy can be regulated by various chemical inducers. However, there are few reports about effect of autophagy inducer in vitro maturation (IVM) of porcine oocyte. The present study investigated the effects of supplementary trehalose, a novel mTOR-independent autophagy enhancer, on oocyte maturation and embryonic development after parthenogenetic activation (PA). Immature oocytes were treated with various concentrations (0, 25, 50, and 100 mM) of trehalose in M-199 (Invitrogen, Carlsbad, CA) supplemented with 10 ng mL–1 of epidermal growth factor (EGF; Sigma-Aldrich Corp.), 1 ug mL–1 of insulin (Sigma-Aldrich Corp.), 4 IU mL–1 of pregnant mare serum gonadotropin (PMSG; Intervet, Boxmeer, Holland), 4 IU mL–1 of human chorionic gonadotropin (hCG; Intervet), and 10% (vol/vol) porcine follicular fluid (pFF) for 10 h, and transferred to another IVM medium without trehalose. Osmolality of each groups (0, 25, 50, and 100 mM trehalose) was in the 290 to 295, 310 to 315, 330 to 335, and 375 to 380 osmol range, respectively. After 44 h of IVM, trehalose treatment during IVM did not improve nuclear maturation rates of oocytes in any group (90.7, 92.1, 92.7, and 90.1%, respectively). The developmental competence of oocytes matured with different trehalose concentrations was evaluated after PA. There were no significant differences in cleavage rates. However, blastocyst (BL) formation was different. Oocytes treated with 25 mM of trehalose during IVM had a significantly higher (P < 0.05) BL formation rate (64.2%) after PA compared with the control (52.0%). The BL quality was also improved in the 25 mM trehalose-treated group. Early BL rate significantly reduced in the 25 mM trehalose-treated group as compared to control (19.6 v. 29.9%, P < 0.05). By contrast, expanded BL rate significantly increased in the 25 mM trehalose-treated group than of control (27.7 v. 11.0%, P < 0.05). Total cell numbers of BL were significantly higher (P < 0.05) in the 25 mM trehalose-treated group compared to those in the control group (52.2 v. 36.8). However, BL rate and quality of oocytes treated with 50 and 100 mM trehalose were similar with control group. In conclusion, these results indicate that 25 mM trehalose during IVM improved the developmental potential of porcine embryos. Trehalose will be useful for large-scale production of BL with good quality in porcine in vitro production.This work was supported by a grant from the Next-Generation Bio Green 21 Program (No. PJ009563032014), Rural Development Administration, Republic of Korea.