Early detection of colorectal cancer using aberrant circulating cell-free mitochondrial DNA fragmentomics.

Background: Early detection of colorectal cancer (CRC) is crucial for improving the survival rates of patients.

Objective: We aimed to develop a novel strategy for early CRC detection using the fragmentomic features of circulating cell-free mitochondrial DNA (ccf-mtDNA).

Design: Here, a total of 1147 participants, including 478 healthy controls (HCs), 112 patients with advanced adenomas (AAs) and 557 patients with CRC, were enrolled from five hospitals and plasma samples were collected for capture-based ccf-mtDNA sequencing.

OsbZIP23 delays flowering by repressing OsMADS14 expression in rice.

Flowering time is a fundamental factor determining the global distribution and final yield of rice (Oryza sativa L.). The initiation of the floral transition process signifies the beginning of the reproductive phase.

SCCA and CYFRA 21-1 Reference Intervals for Apparently Healthy Chinese Adults: a Multicenter Cross-Sectional Study.

Background: This study aimed to establish reference intervals for two biomarkers actively utilized in routine annual medical check-ups in China: squamous cell carcinoma antigen (SCCA) and cytokeratin 19 fragment (CYRFA 21-1), and to understand the influence of age, gender, and benign nodule(s) on their levels.

Methods: This prospective multicenter cross-sectional study continuously enrolled apparently healthy adults attending annual medical check-ups at three sites in 2019. Serum SCCA and CYFRA 21-1 levels were measured using electrochemiluminescence immunoassays.

Whole-genome sequencing of allotetraploid bermudagrass reveals the origin of Cynodon and candidate genes for salt tolerance.

Bermudagrass (Cynodon dactylon) is a globally distributed, extensively used warm-season turf and forage grass with high tolerance to salinity and drought stress in alkaline environments. However, the origin of the species and genetic mechanisms for salinity tolerance in the species are basically unknown. Accordingly, we set out to study evolution divergence events in the Cynodon genome and to identify genes for salinity tolerance.

Chromosome ends initiate homologous chromosome pairing during rice meiosis.

During meiotic prophase I, chromosomes undergo large-scale dynamics to allow homologous chromosome pairing, prior to which chromosome ends attach to the inner nuclear envelope and form a chromosomal bouquet. Chromosome pairing is crucial for homologous recombination and accurate chromosome segregation during meiosis. However, the specific mechanism by which homologous chromosomes recognize each other is poorly understood.

The roles of DNA methylation on pH dependent i-motif (iM) formation in rice.

I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences. The formation of iMs is sensitive to pH conditions and DNA methylation, although the extent of which is still unknown in both humans and plants. To investigate this, we here conducted iMab antibody-based immunoprecipitation and sequencing (iM-IP-seq) along with bisulfite sequencing using CK (original genomic DNA without methylation-related treatments) and hypermethylated or demethylated DNA at both pH 5.

Genome-Wide Effects on Gene Expression Between Parental and Filial Generations of Trisomy 11 and 12 of Rice.

Aneuploid refers to the gene dosage imbalance due to copy number alterations. Aneuploidy is generally harmful to the growth, development and reproduction of organisms according to the numerous research. However, it has rarely been reported on whether aneuploid have a relevant pattern of genome expression between the parental and its offspring generations.

Histone deacetylase OsHDA706 increases salt tolerance via H4K5/K8 deacetylation of OsPP2C49 in rice.

High salt is a major environmental factor that threatens plant growth and development. Increasing evidence indicates that histone acetylation is involved in plant responses to various abiotic stress; however, the underlying epigenetic regulatory mechanisms remain poorly understood. In this study, we revealed that the histone deacetylase OsHDA706 epigenetically regulates the expression of salt stress response genes in rice (Oryza sativa L.

Molecular manipulations of miR398 increase rice grain yield under different conditions.

Rice miR398 targets two stress-tolerant genes, -- and (copper chaperone of CSD), which usually boost plants' tolerance by inhibiting growth. So, how to accurately regulate the activities of miR398 targets and thus make rice better able to adapt to different conditions has great significances in producing rice yields under the current circumstances of shrinking arable lands resulting from global urbanization and increasing salty soil caused by irrigation. Through controlling the expressions of miR398 in different levels, we found down-regulated expression of miR398 targets can promote growth under good growth conditions while up-regulated expressions of the targets can help rice tolerate salt.

De novo centromere formation in pericentromeric region of rice chromosome 8.

Neocentromeres develop when kinetochores assemble de novo at DNA loci that are not previously associated with CenH3 nucleosomes, and can rescue rearranged chromosomes that have lost a functional centromere. The molecular mechanisms associated with neocentromere formation in plants have been elusive. Here, we developed a Xian (indica) rice line with poor growth performance in the field due to approximately 272 kb deletion that spans centromeric DNA sequences, including the centromeric satellite repeat CentO, in the centromere of chromosome 8 (Cen8).

Serology-Based Model for Personalized Epithelial Ovarian Cancer Risk Evaluation.

This study aimed to establish a prognosis-prediction model based on serological indicators in patients with epithelial ovarian cancer (EOC). Patients initially diagnosed as ovarian cancer and surgically treated in Fudan University Shanghai Cancer Center from 2014 to 2018 were consecutively enrolled. Serological indicators preoperatively were collected.

Liquid Biopsy and Tissue Biopsy Comparison with Digital PCR and IHC/FISH for HER2 Amplification Detection in Breast Cancer Patients.

Two hundred twenty-four breast cancer patients with paired tissue and plasma samples were enrolled from 3 clinical centers to evaluate sensitivity and specificity of a digital PCR HER2 amplification assay. All patients were histologically confirmed diagnosis of locally advanced and recurrent or metastatic breast cancer with stage III/IV and had tissue HER2 status determinations using IHC/FISH. For the whole 224 advanced breast cancer patients, the sensitivity between dPCR in plasma and IHC/FISH in tissue samples is 43.

Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories.

Motivation: The recent emergence of cloud laboratories-collections of automated wet-lab instruments that are accessed remotely, presents new opportunities to apply Artificial Intelligence and Machine Learning in scientific research. Among these is the challenge of automating the process of optimizing experimental protocols to maximize data quality.

Results: We introduce a new deterministic algorithm, called PaRallel OptimizaTiOn for ClOud Laboratories (PROTOCOL), that improves experimental protocols via asynchronous, parallel Bayesian optimization.

Research progress of plant cytogenetics in Jiangsu province.

Cytogenetics was established based on the "Chromosome theory of inheritance", proposed by Boveri and Sutton and evidenced by Morgan's lab in early stage of the 20 centrary. With rapid development of related research areas, especially molecular genetics, cytogenetics developed from traditional into a new era, molecular cytogenetics in late 1960s. Featured by an established technique named DNA in situ hybridization (ISH), molecular cytogenetics has been applied in various research areas.

Left atrial appendage exclusion is effective in reducing postoperative stroke after mitral valve replacement.

Objective: This study aimed to evaluate the role of surgical left atrial appendage (LAA) exclusion in the prevention of stroke after mitral valve replacement (MVR).

Methods: We retrospectively reviewed clinical data of 860 patients who received MVR in our center from January 2008 to January 2013. The patients were randomly assigned to two surgical groups, namely LAA exclusion group (n = 521) and LAA nonexclusion group (n = 339) according to whether concurrent surgical exclusion of the LAA was to be undertaken or not before surgery in a blind fashion.

Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa.

Background: Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed.

Results: In this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in rice (Oryza sativa) seedlings.

OsPP2C09, a negative regulatory factor in abscisic acid signalling, plays an essential role in balancing plant growth and drought tolerance in rice.

Plants maintain a dynamic balance between plant growth and stress tolerance to optimise their fitness and ensure survival. Here, we investigated the roles of a clade A type 2C protein phosphatase (PP2C)-encoding gene, OsPP2C09, in regulating the trade-off between plant growth and drought tolerance in rice (Oryza sativa L.).

Inferior Vena Cava Filter Broken and Migrated to Left Ventricle With Destruction of Mitral Valve.

Inferior vena cava filters are used for patients with pulmonary embolism or those with risk of embolization. Here we present a case of a 38-year-old man who underwent placement of an inferior vena cava filter because of deep vein thrombosis. The operating arm fractured and embolized to the posteromedial papillary muscle of mitral valve and the posterior inferior wall of the left ventricle through right atrium and atrioventricular septum, leading to large symptomatic mitral and tricuspid insufficiency and pericardial tamponade.

COM1, a factor of alternative non-homologous end joining, lagging behind the classic non-homologous end joining pathway in rice somatic cells.

The role of rice (Oryza sativa) COM1 in meiotic homologous recombination (HR) is well understood, but its part in somatic double-stranded break (DSB) repair remains unclear. Here, we show that for rice plants COM1 conferred tolerance against DNA damage caused by the chemicals bleomycin and mitomycin C, while the COM1 mutation did not compromise HR efficiencies and HR factor (RAD51 and RAD51 paralogues) localization to irradiation-induced DSBs. Similar retarded growth at the post-germination stage was observed in the com1-2 mre11 double mutant and the mre11 single mutant, while combined mutations in COM1 with the HR pathway gene (RAD51C) or classic non-homologous end joining (NHEJ) pathway genes (KU70, KU80, and LIG4) caused more phenotypic defects.

Genome-wide Profiling of Histone Lysine Butyrylation Reveals its Role in the Positive Regulation of Gene Transcription in Rice.

Background: Histone modifications play important roles in growth and development of rice (Oryza sativa L.). Lysine butyrylation (Kbu) with a four-carbon chain is a newly-discovered histone acylation modification in rice.

Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species.

Fluorescence in situ hybridization using probes based on oligonucleotides (oligo-FISH) is a useful tool for chromosome identification and karyotype analysis. Here we developed two oligo-FISH probes that allow the identification of each of the 12 pairs of chromosomes in rice (Oryza sativa). These two probes comprised 25 717 (green) and 25 215 (red) oligos (45 nucleotides), respectively, and generated 26 distinct FISH signals that can be used as a barcode to uniquely label each of the 12 pairs of rice chromosomes.