The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights.

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.

Global marine microbial diversity and its potential in bioprospecting.

The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.

Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA.

Ribosomal deoxyribonucleic acid (DNA) (rDNA) repeats are tandemly located on five acrocentric chromosomes with up to hundreds of copies in the human genome. DNA methylation, the most well-studied epigenetic mechanism, has been characterized for most genomic regions across various biological contexts. However, rDNA methylation patterns remain largely unexplored due to the repetitive structure. In this study, we designed a specific mapping strategy to investigate rDNA methylation patterns at each CpG site across various physiological and pathological processes. We found that CpG sites on rDNA could be categorized into two types. One is within or adjacent to transcribed regions; the other is distal to transcribed regions. The former shows highly variable methylation levels across samples, while the latter shows stable high methylation levels in normal tissues but severe hypomethylation in tumors. We further showed that rDNA methylation profiles in plasma cell-free DNA could be used as a biomarker for cancer detection. It shows good performances on public datasets, including colorectal cancer [area under the curve (AUC) = 0.85], lung cancer (AUC = 0.84), hepatocellular carcinoma (AUC = 0.91) and in-house generated hepatocellular carcinoma dataset (AUC = 0.96) even at low genome coverage (<1×). Taken together, these findings broaden our understanding of rDNA regulation and suggest the potential utility of rDNA methylation features as disease biomarkers.

Oxidants Controlled C-H Bond Functionalization of N-Aryltetrahydroisoquinolines: The Construction of the Quaternary Carbon Center and Cleavage of the C-N Bond.

Initiated by triarylamine radical cation salt (TBPA), the direct C-H bond functionalization of α-N-aryltetrahydroisoquinoline esters was smoothly realized, giving a series of α-hydroxylated derivatives with a quaternary carbon center in good yields. Differently, in the presence of tert-butyl nitrite (TBN), the C-N single bond was cleaved to keto esters. The mechanistic study revealed that these reactions were mediated by a similar mechanism, in which the N-nitrosation might provide a driving force to the C-N bond cleavage.

CBr4 as a Mild Oxidant-Enabled Oxidation of a sp3 C-H Bond: A Facile Synthesis of the Persistent Iminium Salts of Tetrahydroisoquinolines.

Using CBr4 as a mild oxidant, the direct C-H bond oxidation of N-aryltetrahydroisoquinolines was achieved, giving a series of the corresponding iminium salts in high yields under metal- and photo-free reaction conditions. This reaction is superior in high yields and good functional group tolerance, and the late-stage derivatization showed that these iminium salts can readily be applied to the synthesis of the functionalized THIQs.

Organic Bases as the Organic Electron Donors (OED) Promoted Reductive Coupling of Diarylhalomethanes: Halogens Controlled Construction of Tetraarylethylenes and Tetraarylethanes.

Using the organic base as the organic electron donors, the reductive coupling of diaryhalomethanes was smoothly achieved under transition-metal-free reaction conditions, giving a series of synthetically important tetraarylethylenes and tetraarylethanes in high yields. The mechanistic study revealed that the organic bases acting as the electron donor initiated the generation of a radical intermediate, realizing the construction of tetraarylethylene and tetraarylethane skeletons.

Single-Electron Reduction of "Push-Pull" C-C Single Bond and Decyanation Using Tertiary Amines as the Organic Electron Donor.

Using commercially available tertiary amines as an organic electron donor (OED), the reduction of "push-pull" C-C single bond and reductive decyanation of tetrahydroisoquinolines were realized. These reactions exhibited higher reaction efficiency and better functional group tolerance compared with those of metallic reductants, and the mechanistic study indicated that a radical intermediate was involved in the reduction of the C-C single bond, which provides a new way to the OED-enabled mild reduction.

Indium Promotes Direct Sulfonamidation of Unactivated Alcohols.

An improved protocol has been developed for the direct sulfonamidation of unactivated alkyl alcohols using In(OTf)3 as a Lewis acid catalyst. Although the established methods using Lewis or Brønsted acids have been well-studied for the direct functionalization of alcohols, their substrate scope mainly focuses on the π-activated alcohols. In this reaction, unactivated aliphatic alcohols were evaluated and afforded the desired sulfonamide products with good to excellent yields.

Development and validation of a clinical prediction model for the risk of distal metastasis in intrahepatic cholangiocarcinoma: a real-world study.

BACKGROUND: Cholangiocarcinoma (CCA) is a highly malignant and easily metastatic bile duct tumor with poor prognosis. We aimed at studying the associated risk factors affecting distal metastasis of CCA and using nomogram to guide clinicians in predicting distal metastasis of CCA. METHODS: Based on inclusion and exclusion criteria, 345 patients with CCA were selected from the Fifth Medical Center of Chinese PLA General Hospital and were divided into distal metastases (N = 21) and non-distal metastases (N = 324). LASSO regression models were used to screen for relevant parameters and to compare basic clinical information between the two groups of patients. Risk factors for distal metastasis were identified based on the results of univariate and multivariate logistic regression analyses. The nomogram was established based on the results of multivariate logistic regression, and we drawn the corresponding correlation heat map. The predictive accuracy of the nomogram was evaluated by receiver operating characteristic (ROC) curves and calibration plots. The utility of the model in clinical applications was illustrated by applying decision curve analysis (DCA), and overall survival(OS) analysis was performed using the method of Kaplan-meier. RESULTS: This study identified 4 independent risk factors for distal metastasis of CCA, including CA199, cholesterol, hypertension and margin invasion, and developed the nomogram based on this. The result of validation showed that the model had significant accuracy for diagnosis with the area under ROC (AUC) of 0.882 (95% CI: 0.843-0.914). Calibration plots and DCA showed that the model had high clinical utility. CONCLUSIONS: This study established and validated a model of nomogram for predicting distal metastasis in patients with CCA. Based on this, it could guide clinicians to make better decisions and provide more accurate prognosis and treatment for patients with CCA.

Interpretable machine learning-based clinical prediction model for predicting lymph node metastasis in patients with intrahepatic cholangiocarcinoma.

OBJECTIVE: Prediction of lymph node metastasis (LNM) for intrahepatic cholangiocarcinoma (ICC) is critical for the treatment regimen and prognosis. We aim to develop and validate machine learning (ML)-based predictive models for LNM in patients with ICC. METHODS: A total of 345 patients with clinicopathological characteristics confirmed ICC from Jan 2007 to Jan 2019 were enrolled. The predictors of LNM were identified by the least absolute shrinkage and selection operator (LASSO) and logistic analysis. The selected variables were used for developing prediction models for LNM by six ML algorithms, including Logistic regression (LR), Gradient boosting machine (GBM), Extreme gradient boosting (XGB), Random Forest (RF), Decision tree (DT), Multilayer perceptron (MLP). We applied 10-fold cross validation as internal validation and calculated the average of the areas under the receiver operating characteristic (ROC) curve to measure the performance of all models. A feature selection approach was applied to identify importance of predictors in each model. The heat map was used to investigate the correlation of features. Finally, we established a web calculator using the best-performing model. RESULTS: In multivariate logistic regression analysis, factors including alcoholic liver disease (ALD), smoking, boundary, diameter, and white blood cell (WBC) were identified as independent predictors for LNM in patients with ICC. In internal validation, the average values of AUC of six models ranged from 0.820 to 0.908. The XGB model was identified as the best model, the average AUC was 0.908. Finally, we established a web calculator by XGB model, which was useful for clinicians to calculate the likelihood of LNM. CONCLUSION: The proposed ML-based predicted models had a good performance to predict LNM of patients with ICC. XGB performed best. A web calculator based on the ML algorithm showed promise in assisting clinicians to predict LNM and developed individualized medical plans.

Identification of the synonymous variant c.3141G > A in TNRC6B gene that altered RNA splicing by minigene assay.

BACKGROUND: Global developmental delay with speech and behavioral abnormalities (OMIM: 619243) is an autosomal dominant disease caused by variants in TNRC6B gene. METHOD: We reviewed and summarized clinical manifestations and genotypes in patients previously reported with TNRC6B gene variants. We used several prediction tools to predict pathogenicity and performed minigene assays to verify the function of the synonymous variant affecting RNA splicing. RESULT: The patient presented with convulsive seizures and developmental delay. WES combined with functional studies diagnosed a child with a synonymous variant in TNRC6B gene. Through minigene assay and Sanger sequencing, we demonstrated that c.3141G > A variant induced exon 7 skipping and the synonymous variant was pathogenic. CONCLUSION: Synonymous variants do not change the amino acids encoded by the codon, so we usually consider synonymous variants to be benign and ignore their pathogenicity. Minigene assay is a valuable tool to identify the effect of variation on RNA splicing and identify synonymous variants' benign or pathogenic. We showed that the synonymous variant was pathogenic by minigene assay. WES combined with minigene assay establishes a robust basis for genetic counseling and diagnosing diseases.

In-depth Profiling and Quantification of the Lysine Acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer.

Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide with limited therapeutic options. Comprehensive investigation of protein posttranslational modifications in HCC is still limited. Lysine acetylation is one of the most common types of posttranslational modification involved in many cellular processes and plays crucial roles in the regulation of cancer. In this study, we analyzed the proteome and K-acetylome in eight pairs of HCC tumors and normal adjacent tissues using a timsTOF Pro instrument. As a result, we identified 9219 K-acetylation sites in 2625 proteins, of which 1003 sites exhibited differential acetylation levels between tumors and normal adjacent tissues. Interestingly, many novel tumor-specific K-acetylation sites were characterized, for example, filamin A (K865), filamin B (K697), and cofilin (K19), suggesting altered activities of these cytoskeleton-modulating molecules, which may contribute to tumor metastasis. In addition, we observed an overall suppression of protein K-acetylation in HCC tumors, especially for enzymes from various metabolic pathways, for example, glycolysis, tricarboxylic acid cycle, and fatty acid metabolism. Moreover, the expression of deacetylase sirtuin 2 (SIRT2) was upregulated in HCC tumors, and its role of deacetylation in HCC cells was further explored by examining the impact of SIRT2 overexpression on the proteome and K-acetylome in Huh7 HCC cells. SIRT2 overexpression reduced K-acetylation of proteins involved in a wide range of cellular processes, including energy metabolism. Furthermore, cellular assays showed that overexpression of SIRT2 in HCC cells inhibited both glycolysis and oxidative phosphorylation. Taken together, our findings provide valuable information to better understand the roles of K-acetylation in HCC and to treat this disease by correcting the aberrant acetylation patterns.

Effective Prediction of Drug Transport in a Partially Liquefied Vitreous Humor: Physics-informed Neural Network Modeling for Irregular Liquefaction Geometry.

As the medium for intravitreal drug delivery, the vitreous body can significantly influence drug delivery because of various possible liquefaction geometries. This work innovatively proposes a varying-porosity approach that is capable of solving the pressure and velocity fields in the heterogeneous vitreous with randomly-shaped liquefaction geometry, validated with a finite difference model. Doing so enables patient-specific treatment for intravitreal drug delivery and can significantly improve treatment efficacy. A physics-informed neural network (PINN) model is also established for the simulation, and three cases are used for validation. Despite limited information, the PINN model, together with the varying-porosity approach, captured fluid and drug transport in the partially liquefied vitreous. This opens the possibility for optimizing intravitreal drug delivery based on ultrasonography in clinical practice.

Gut mycobiome as a potential non-invasive tool in early detection of lung adenocarcinoma: a cross-sectional study.

BACKGROUND: The gut mycobiome of patients with lung adenocarcinoma (LUAD) remains unexplored. This study aimed to characterize the gut mycobiome in patients with LUAD and evaluate the potential of gut fungi as non-invasive biomarkers for early diagnosis. METHODS: In total, 299 fecal samples from Beijing, Suzhou, and Hainan were collected prospectively. Using internal transcribed spacer 2 sequencing, we profiled the gut mycobiome. Five supervised machine learning algorithms were trained on fungal signatures to build an optimized prediction model for LUAD in a discovery cohort comprising 105 patients with LUAD and 61 healthy controls (HCs) from Beijing. Validation cohorts from Beijing, Suzhou, and Hainan comprising 44, 17, and 15 patients with LUAD and 26, 19, and 12 HCs, respectively, were used to evaluate efficacy. RESULTS: Fungal biodiversity and richness increased in patients with LUAD. At the phylum level, the abundance of Ascomycota decreased, while that of Basidiomycota increased in patients with LUAD. Candida and Saccharomyces were the dominant genera, with a reduction in Candida and an increase in Saccharomyces, Aspergillus, and Apiotrichum in patients with LUAD. Nineteen operational taxonomic unit markers were selected, and excellent performance in predicting LUAD was achieved (area under the curve (AUC) = 0.9350) using a random forest model with outcomes superior to those of four other algorithms. The AUCs of the Beijing, Suzhou, and Hainan validation cohorts were 0.9538, 0.9628, and 0.8833, respectively. CONCLUSIONS: For the first time, the gut fungal profiles of patients with LUAD were shown to represent potential non-invasive biomarkers for early-stage diagnosis.

C-H Bond Activation Relay (CHAR) of Proline Ester Derivatives Promoted by In Situ Triarylamine Radical Cation: Selective Synthesis of 4-Bromopyrrole Derivatives.

Using the in situ generated triarylamine radical cation as an initiator, the sp3 C-H bond of proline esters was smoothly oxidized and brominated through C-H activation relay (CHAR), giving a series of 4-bromopyrroles in good yields with high regioselectivity. The mechanistic study revealed that the oxidation of the active C-H bond initiated the followed 1,5-HAT and bromination, which provides a new method to realize the functionalization of the remote C-H bond.

Halogen Bond (XB) Promoted α-Tribromomethylation of N-Aryltetrahydroisoquinolines and Further Cyclization to 5,6-Dihydroindolo[2,1-a]isoquinolines.

Using CBr4 as a halogen bond donor and the source of tribromomethyl group, a halogen bond promoted tribromomethylation of N-aryltetrahydroisoquinolines was achieved. This reaction was also extended to the construction of the dibenzopyrrocoline alkaloid skeleton through a one-pot process. The mechanistic study confirmed the existence of the halogen bond.

Plasma Reference Ranges for Brain Injury Biomarkers (NfL, NfH, MCP-1, and MMP-9) in Healthy Chinese.

BACKGROUND: Brain injury triggers neuroaxonal injury and neural death, that leads to the development of secondary sequelae. Throughout this process, brain injury factors released into circulation via the injured neurovascular unit are important prognostic parameters. Plasma NfL, NfH, MCP-1, and MMP-9 have been identified as potential indicators in this regard. METHODS: Using a microfluidic ELISA platform, we measured plasma from 273 healthy subjects that underwent quantifications of NfL, NfH, MCP-1, and MMP-9 levels. We investigated the possible associations between biomarkers and basic demographics. RESULTS: The median concentration of plasma NfL was 10.40 (IQR = 6.73 - 16.60) pg/mL, NfH was 70.70 (IQR = 39.75 - 125.50) pg/mL, MCP-1 was 191.0 (IQR = 162.0 - 237.5) pg/mL, and MMP-9 was 169,255 (IQR = 107,657 - 231,276) pg/mL. Among all four biomarkers, plasma NfL and NfH levels were positively correlated with age (r = 0.557, p < 0.001, r = 0.364, p = 0.003). NfL was also correlated with NfH (r = 0.391, p = 0.002). CONCLUSIONS: These data provide a basis for the potential application of a brain-injury biomarker panel in routine clinical practice. It lays a significant foundation in supporting circulating CNS-biomarkers as noninvasive biomarkers for neurological disorders.

Fe-Ni/MWCNTs Nano-Composites for Hexavalent Chromium Reduction in Aqueous Environment.

A novel Cr (VI) removal material was designed and produced comprising multi-walled carbon nanotubes (MWCNTs) as a support with a high specific surface area and the loaded Fe-Ni bimetallic particles as catalytic reducing agents. Such a design permits the composite particle to perform the adsorption, reduction, and immobilisation of Cr (VI) quickly and efficiently. Due to MWCNTs' physical adsorption, Cr (VI) in solution aggregates in the vicinity of the composite, and Fe rapidly reduces Cr (VI) to Cr (III) catalysed by Ni. The results demonstrated that the Fe-Ni/MWCNTs exhibits an adsorption capacity of 207 mg/g at pH = 6.4 for Cr (VI) and 256 mg/g at pH 4.8, which is about twice those reported for other materials under similar conditions. The formed Cr (III) is solidified to the surface by MWCNTs and remains stable for several months without secondary contamination. The reusability of the composites was proven by retaining at least 90% of the adsorption capacity for five instances of reutilization. Considering the facile synthesis process, low cost of raw material, and reusability of the formed Fe-Ni/MWCNTs, this work shows great potential for industrialisation.

Tris(4-bromophenyl)aminium Hexachloroantimonate as a "Waste-Utilized"-Type Initiator-Promoted C-H Chlorination via C-H Activation Relay: Synthesis of Chlorinated Pyrroles.

Using tris(4-bromophenyl)aminium hexachloroantimonate as a "waste-utilized"-type initiator, the aerobic oxidation of the sp3 C-H bond of proline esters was realized via C-H activation relay, giving a series of halogenated pyrroles in high yields. The mechanistic study revealed that the counterion, SbCl6-, was involved in the radical chlorination process, which provides a new way to understand the role of the counterions.

Thyroid cancer and Its Associations with Dietary Quality in A 1:1 matched Case-Control Study.

Thyroid cancer (TC) incidence has increased greatly during the past decades with a few established risk factors, while no study is available that has assessed the association of the Chinese Health Dietary Index (CHDI) with TC. We conducted a 1:1 matched case-control study in two hospitals in Shanghai, China. Diet quality scores were calculated according to CHDI using a validated and reliable food-frequency questionnaire. Conditional logistic regression analysis and Restricted cubic spline (RCS) analysis was used to reveal potential associations between CHDI score and thyroid cancer risk. A total of 414 pairs of historically confirmed TC patients and healthy controls were recruited from November 2012 to December 2015. The total score of cases and controls were 67.5 and 72.8, respectively (p < 0.001). The median score of total vegetables, fruit, diary, dark green and orange vegetables, fish, shellfish and mollusk, soybean, and whole grains, dry bean and tuber in cases was significantly lower than those in controls. Compared to the reference group (≤60 points), the average (60∼80 points) and high (≥80 points) levels of the CHDI score were associated with a reduced risk of TC (OR: 0.40, 95% Cl: 0.26∼0.63 for 60∼80 points; OR: 0.22, 95% Cl: 0.12∼0.38 for ≥80 points). In age-stratified analyses, the favorable association remained significant among participants who younger than 50 years old. Our data suggested that high diet quality as determined by CHDI was associated with lower risk of TC.