Simultaneous sequencing of 102 Y-STRs on Ion Torrent ™ GeneStudio ™ S5 System.

The Precision ID NGS System from Thermo Fisher Scientific is a mainstream next-generation sequencing (NGS) platform used in forensic laboratories to detect almost all commonly used forensic markers, except for Y-chromosomal short tandem repeats (Y-STRs). This study aimed to: 1) develop a Y-STR panel compatible with the automatic workflow of the NGS system using Ion AmpliSeq Technology, 2) evaluate the panel performance following the SWGDAM guidelines, and 3) explore the possibility of using a combination workflow to detect autosomal STRs and Y-STRs (AY-STR NGS workflow). The GrandFiler Y-STR Panel was successfully designed using the 'separating' and 'merging' strategies, including 102 Y-STRs and Amelogenin with an average amplicon length of 133 bp. It is a mega Y-STR multiplex system in which up to 16 samples can be sequenced simultaneously on an Ion 530 ™ Chip. Developmental validation studies of the performance of the NGS platform, species specificity, reproducibility, concordance, sensitivity, degraded samples, case-type samples, and mixtures were conducted to unequivocally determine whether the GrandFiler Y-STR Panel is suitable for real scenarios. The newly developed Y-STR panel showed compelling run metrics and NGS performance, including 92.47% bases with ≥ Q20, 91.80% effective reads, 2106 × depth of coverage (DoC), and 97.09% inter-locus balance. Additionally, it showed high specificity for human males and 99.40% methodological and bioinformatical concordance, generated complete profiles at ≥ 0.1 ng input DNA, and recovered more genetic information from severely degraded and diverse case samples. Although the outcome when used on mixtures was not as expected, more genetic information was obtained compared to that from capillary electrophoresis (CE) methods. The AY-STR NGS workflow was established by combining the GrandFiler Y-STR Panel with the Precision ID GlobalFiler ™ NGS STR Panel v2 at a 2:1 concentration ratio. The combination workflow on NGS performance, reproducibility, concordance, and sensitivity was as stable as the single Y-STR NGS workflow, providing more options for forensic scientists when dealing with different case scenarios. Overall, the GrandFiler Y-STR Panel was confirmed as the first to effectively detect a large number of Y-STR markers on the Precision ID NGS System, which is compatible with 51 Y-STRs in commercial CE kits and 51 Y-STRs in commercial NGS kits and the STRBase. The panel is as robust, reliable, and sensitive as current CE/NGS kits, and is suitable for solving real cases, especially for severely degraded samples (degradation index > 10).

Performance and characterization of 94 identity-informative SNPs in Northern Han Chinese using ForenSeq ™ DNA signature prep kit.

Target and flanking region (FR) variation at 94 identity-informative SNPs (iSNPs) are investigated in 635 Northern Han Chinese using the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. The dataset presents the following performance characteristics (average values): ≥60% bases with a quality score of 20 or higher (%≥ Q20); >700 × of depth of coverage (DoC) from both Sample Details Reports and Flanking Region Reports; >80% of effective reads; ≥60% of allele coverage ratio (ACR); and ≥70% of inter-locus balance, while some stable low-performance characteristics are also observed: low DoC at rs1736442, rs1031825, rs7041158, rs338882, rs2920816, rs1493232, rs719366, and rs2342747; high noise at rs891700; and imbalanced ACR at rs6955448 and rs338882. The average amplicon length is 69 bp, suitable for detecting degraded samples. Bioinformatic concordance achieves 99.99% between the ForenSeq Universal Analysis Software (UAS) and the Integrative Genomic Viewer (IGV) inspection. Discordance results from flanking region deletions of rs10776839, rs8078417, rs2831700, and rs1454361. Due to FR variants within amplicons detected by massively parallel sequencing (MPS), the increases in the number of unique alleles, effective alleles (Ae), and observed heterozygosity (Hobs) are 46.81%, 4.51%, and 3.29%, respectively. Twelve FR variants are first reported to dbSNP, such as rs1252699848, rs1665500714, rs1771121532, rs2097285015, rs1851671415, rs2045669877, rs2046758811, rs2044248635, rs1251308240, rs1968822112, rs1981638299, and rs1341756746. All 94 iSNPs from target and amplicon data are in Hardy-Weinberg equilibrium (HWE) and independent within autosomes. As expected, forensic parameters from the amplicon data increase significantly on the combined power of discrimination (CPD = 1 - 3.9876 × 10-38) and the combined power of exclusion (CPE = 1 - 6.6690 × 10-8). Additionally, the power of the system effectiveness (CPD = 1 - 6.7054 × 10-72 and CPE = 1 - 4.4719 × 10-20) with sequence-based 27 autosomal STRs and 94 iSNP amplicons in combination is substantially improved compared to one type of marker alone. In conclusion, we have established a traditional length-based and current sequence-based reference database with 58 STRs and 94 iSNPs in the Northern Han Chinese population. We hope these data can serve as a solid reference and foundation for forensic practice.

LOXL1-AS1 inhibits JAK2 ubiquitination and promotes cholangiocarcinoma progression through JAK2/STAT3 signaling.

This study thoroughly investigated the role of the long non-coding RNA LOXL1-AS1 in the pathogenesis of cholangiocarcinoma (CCA). Through bioinformatics analysis and tissue samples validation, the study found that LOXL1-AS1 was significantly elevated in CCA, with its high expression closely tied to clinical pathological features and prognosis. In vitro and in vivo experiments revealed that LOXL1-AS1 was crucial in regulating CCA cell apoptosis, proliferation, migration, and invasion. Further investigations using FISH, subcellular localization experiments, RNA pull down, and RIP uncovered that LOXL1-AS1 primarily resided in the cytoplasm and influenced CCA progression by modulating the JAK2/STAT3 signaling pathway. Notably, LOXL1-AS1 might regulate the activity of JAK2 through modulating its ubiquitination and degradation. YY1 had also been found to act as an upstream transcription factor of LOXL1-AS1 to impact CCA cell malignancy. These findings shed light on the pivotal role of LOXL1-AS1 in CCA and offered potential directions for novel therapeutic strategies, providing a fresh perspective on tumor pathogenesis.

NNMT/1-MNA Promote Cell-Cycle Progression of Breast Cancer by Targeting UBC12/Cullin-1-Mediated Degradation of P27 Proteins.

Cell cycle dysregulation is a defining feature of breast cancer. Here, 1-methyl-nicotinamide (1-MNA), metabolite of nicotinamide N-methyltransferase(NNMT) is identified, as a novel driver of cell-cycle progression in breast cancer. NNMT, highly expressed in breast cancer tissues, positively correlates with tumor grade, TNM stage, Ki-67 index, and tumor size. Ablation of NNMT expression dramatically suppresses cell proliferation and causes cell-cycle arrest in G0/G1 phase. This phenomenon predominantly stems from the targeted action of 1-MNA, resulting in a specific down-regulation of p27 protein expression. Mechanistically, 1-MNA expedites the degradation of p27 proteins by enhancing cullin-1 neddylation, crucial for the activation of Cullin-1-RING E3 ubiquitin ligase(CRL1)-an E3 ubiquitin ligase targeting p27 proteins.  NNMT/1-MNA specifically up-regulates the expression of UBC12, an E2 NEDD8-conjugating enzyme required for cullin-1 neddylation. 1-MNA showes high binding affinity to UBC12, extending the half-life of UBC12 proteins via preventing their localization to lysosome for degradation. Therefore, 1-MNA is a bioactive metabolite that promotes breast cancer progression by reinforcing neddylation pathway-mediated p27 degradation. The study unveils the link between NNMT enzymatic activity with cell-cycle progression, indicating that 1-MNA may be involved in the remodeling of tumor microenvironment.

Metabolic-suppressed cancer-associated fibroblasts limit the immune environment and survival in colorectal cancer with liver metastasis.

Background: Colorectal cancer liver metastasis is a major risk factor of poor outcomes, necessitating proactive interventions and treatments. Cancer-associated fibroblasts (CAFs) play essential roles in metastasis, with a focus on metabolic reprogramming. However, knowledge about associations between Cancer-associated fibroblasts metabolic phenotypes and immune cell is limited. This study uses single-cell and bulk transcriptomics data to decode roles of metabolism-related subtype of Cancer-associated fibroblasts and immune cells in liver metastasis, developing a CAF-related prognostic model for colorectal cancer liver metastases. Methods: In this study, Cancer-associated fibroblasts metabolism-related phenotypes were screened using comprehensive datasets from The Cancer Genome Atlas and gene expression omnibus (GEO). Cox regression and Lasso regression were applied to identify prognostic genes related to Cancer-associated fibroblasts, and a model was constructed based on the Cancer-associated fibroblasts subtype gene score. Subsequently, functional, immunological, and clinical analyses were performed. Results: The study demonstrated the metabotropic heterogeneity of Cancer-associated fibroblasts cells. Cancer-associated fibroblasts cells with varying metabolic states were found to exhibit significant differences in communications with different immune cells. Prognostic features based on Cancer-associated fibroblasts signature scores were found to be useful in determining the prognostic status of colorectal cancer patients with liver metastases. High immune activity and an enrichment of tumor-related pathways were observed in samples with high Cancer-associated fibroblasts signature scores. Furthermore, Cancer-associated fibroblasts signature score could be practical in guiding the selection of chemotherapeutic agents with higher sensitivity. Conclusion: Our study identified a prognostic signature linked to metabotropic subtype of Cancer-associated fibroblasts. This signature has promising clinical implications in precision therapy for colorectal cancer liver metastases.

Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father-son pairs.

A total of 2 548 unrelated healthy father-son pairs from a Northern Han Chinese population were genotyped at 41 Y chromosomal short tandem repeat (Y-STRs) including DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS522, DYS549, DYS533, DYS557, DYS570, DYS576, DYS593, DYS596, DYS627, DYS635, DYS643, DYS645, Y-GATA-H4, DYF387S1a/b, DYF404S1a/b, DYS385a/b, and DYS527a/b. In 2 548 father samples, 2 387 unique haplotypes were detected with the haplotype diversity and discrimination capacity values of 0.999 956 608 and 0.96 741 007. The average gene diversity (GD) value was 0.6934 with a range from 0.1051 at DYS645 to 0.9657 at DYS385a/b. When comparing alleles at 24 overlapped Y-STRs between the ForenSeq™ deoxyribonucleic acid (DNA) Signature Prep Kit on the MiSeq FGx® Forensic Genomics System and the Goldeneye® DNA ID Y Plus Kit on the Applied Biosystems™ 3730 DNA Analyzer from 308 father samples in mutational pairs, 258 alleles were detected by massively parallel sequencing (MPS) typing including 156 length-based alleles that could be obtained by capillary electrophoresis (CE) typing, 95 repeat region (RR) variant alleles and seven flanking region variant alleles. Hereof, we found 16 novel RR variant alleles and firstly identified two SNPs (rs2016239814 at DYS19 and rs2089968964 at DYS448) and one 4-bp deletion (rs2053269960 at DYS439) that had been validated by the Database of Short Genetic Variation. Sanger sequencing or MPS was employed to confirm 356 mutations from 104 468 allele transfers generated from CE, where 96.63% resulted in one-step mutations, 2.25% in two-step, and 1.12% in multi-step, and the overall ratio of repeat gains versus losses was balanced (173 gains vs. 183 losses). In 308 father-son pairs, 268 pairs occurred mutations at a single locus, 33 pairs at two loci, six pairs at three loci, and one pair at four loci. The average Y-STR mutation rate at 41 Y-STRs was ⁓3.4 × 10-3 (95% confidence intervals: 3.1 × 10-3-3.8 × 10-3). The mutation rates at DYS576 and DYS627 were higher than 1 × 10-2 in Northern Han Chinese, whilst the mutation rates at DYF387S1a/b, DYF404S1a/b, DYS449, DYS518, and DYS570 were lower than initially defined. In this study, the classical molecular factors (the longer STR region, the more complex motif and the order father) were confirmed to drive Y-STR mutation rates increased, but the length of repeat unit did not conform to the convention. Lastly, the interactive graphical and installable StatsY was developed to facilitate forensic scientists to automatically calculate allele and haplotype frequencies, forensic parameters, and mutation rates at Y-STRs. Key points: 308 of 2 548 father-son pairs from Northern Han Chinese occurred at least one mutation(s) across 41 Y-STRs.Sanger sequencing or MPS was employed to confirm those mutations generated from CE.The longer STR region, the more complex motif and the order father drove Y-STR mutation rates increased.StatsY was developed to calculate allele and haplotype frequencies, forensic parameters and mutation rates at Y-STRs.

Circular RNA nuclear receptor interacting protein 1 promoted biliary tract cancer epithelial-mesenchymal transition and stemness by regulating the miR-515-5p/AKT2 axis and PI3K/AKT/mTOR signaling pathway.

Biliary tract cancer (BTC) is a devastating malignancy that is notoriously difficult to diagnose and is associated with high mortality. Circular RNA (circRNA) is a class of endogenous non-coding RNA which has been regarded as the key regulator of tumor initiation and progression, including BTC. Circular RNA nuclear receptor interacting protein 1 (circ_NRIP1), as a circular RNA, is abnormally expressed in many human tumors and exhibits diverse functions in cancer progression. However, its biological significance in BTC has not been thoroughly investigated. In this research, we elucidated that circ_NRIP1 was notably overexpressed in both BTC tissues and cells. We further established a correlation between circ_NRIP1 expression and clinicopathological features in BTC patients, highlighting its clinical relevance. Through functional assays, we observed that knockdown of circ_NRIP1 significantly inhibited tumor cell proliferation, invasion, stemness maintenance, and epithelial-mesenchymal transition, indicating its active involvement in promoting BTC progression. Additionally, it attenuated growth of xenograft and metastasis models. Mechanically, we revealed that circ_NRIP1 served as the competing endogenous RNA to sequester miR-515-5p through complementary base pairing mechanism, thereby upregulated AKT2 expression and indirectly activated PI3K/AKT/mTOR signaling pathway. Generally, targeting the circ_NRIP1/miR-515-5p/AKT2 axis and aberrant activation of the PI3K/AKT/mTOR pathway may hold promising therapeutic strategies for BTC. Our research contributes to a better understanding of the underlying biological basis of BTC and paves the way for the development of innovative treatment approaches.

High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System.

Sequence polymorphisms were characterized at 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), and 24 Y chromosomal STRs (Y-STRs) in 635 Northern Han Chinese with the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Since repeat region (RR) and flanking region (FR) variation can be detected by massively parallel sequencing (MPS), the increase in the number of unique alleles and the average of gene diversity was 78.18% and 3.51% between sequence and length, respectively. A total of 74 novel RR variants were identified at 33 STRs compared with STRSeq and previous studies, and 13 FR variants (rs1770275883, rs2053373277, rs2082557941, rs1925525766, rs1926380862, rs1569322793, rs2051848492, rs2051848696, rs2016239814, rs2053269960, rs2044518192, rs2044536444, and rs2089968964) were first submitted to dbSNP. Also, 99.94% of alleles were concordant between the ForenSeq DNA Signature Prep Kit and commercial CE kits. Discordance resulted from the low performance at D22S1045 and occasionally at DYS392, flanking region deletions at D7S820 and DXS10074, and the strict alignment algorithm at DXS7132. Null alleles at DYS505 and DYS448 and multialleles at DYS387S1a/b, DYS385a/b, DYS448, DYS505, DXS7132, and HPRTB were validated with other MPS and CE kits. Thus, a high-resolution sequence-based (SB) and length-based (LB) allele frequencies dataset from Northern Han Chinese has been established already. As expected, forensic parameters increased significantly on combined power of discrimination (PD) and combined power of exclusion (PE) at A-STRs, mildly on combined PD and combined mean exclusion chance (MEC) at X-STRs, and barely on discrimination capacity (DC) at Y-STRs. Additionally, MiSeq FGx quality metrics and MPS performance were evaluated in this study, which presented the high-quality of the dataset at 20 consecutive runs, such as ≥ 60% bases with a quality score of 20 or higher (%≥ Q20), > 60% of effective reads, > 2000 × of depth of coverage (DoC), ≥ 60% of allele coverage ratio (ACR) or heterozygote balance, ≥ 70% of inter-locus balance, and ≤ 0.4 of the absolute value of observed minus expected heterozygosity (|Hexp - Hobs|). In conclusion, MiSeq FGx can help us generate a high-resolution and high-quality dataset for human identification and population genetic studies.

A Noninvasive Sweat Glucose Biosensor Based on Glucose Oxidase/Multiwalled Carbon Nanotubes/Ferrocene-Polyaniline Film/Cu Electrodes.

Diabetes remains a great threat to human beings' health and its world prevalence is projected to reach 9.9% by 2045. At present, the detection methods used are often invasive, cumbersome and time-consuming, thus increasing the burden on patients. In this paper, we propose a novel noninvasive and low-cost biosensor capable of detecting glucose in human sweat using enzyme-based electrodes for point-of-care uses. Specifically, an electrochemical method is applied for detection and the electrodes are covered with multilayered films including ferrocene-polyaniline (F-P), multi-walled carbon nanotubes (MWCNTs) and glucose oxidase (GOx) on Cu substrates (GOx/MWCNTs/F-P/Cu). The coated layers enhance the immobilization of GOx, increase the conductivity of the anode and improve the electrochemical properties of the electrode. Compared with the Cu electrode and the F-P/Cu electrode, a maximum peak current is obtained when the MWCNTs/F-P/Cu electrode is applied. We also study its current response by cyclic voltammetry (CV) at different concentrations (0-2.0 mM) of glucose solution. The best current response is obtained at 0.25 V using chronoamperometry. The effective working lifetime of an electrode is up to 8 days. Finally, to demonstrate the capability of the electrode, a portable, miniaturized and integrated detection device based on the GOx/MWCNTs/F-P/Cu electrode is developed. The results exhibit a short response time of 5 s and a correlation coefficient R2 of 0.9847 between the response current of sweat with blood glucose concentration. The LOD is of 0.081 mM and the reproducibility achieved in terms of RSD is 3.55%. The sweat glucose sensor is noninvasive and point-of-care, which shows great development potential in the health examination and monitoring field.

Circular RNAs regulate parental gene expression: A new direction for molecular oncology research.

CircRNAs have been the focus of research in recent years. They are differentially expressed in various human tumors and can regulate oncogenes and tumor suppressor genes expression through various mechanisms. The diversity, stability, evolutionary conservatism and cell- or tissue-specific expression patterns of circRNAs also endow them with important regulatory roles in promoting or inhibiting tumor cells malignant biological behaviors progression. More interestingly, emerging studies also found that circRNAs can regulate not only other genes expression, but also their parental gene expression and thus influence tumors development. Apart from some conventional features, circRNAs have a certain specificity in the regulation of parental gene expression, with a higher proportion affecting parental gene transcription and easier translation into protein to regulate parental gene expression. CircRNAs are generally thought to be unable to produce proteins and therefore the protein-coding ability exhibited by circRNAs in regulating parental gene expression is unique and indicates that the regulatory effects of parental gene expression by circRNAs are not only a competitive binding relationship, but also a more complex molecular relationship between circRNAs and parental gene, which deserves further study. This review summarizes the molecular mechanisms of circRNAs regulating parental gene expression and their biological roles in tumorigenesis and development, aiming to provide new ideas for the clinical application of circRNAs in tumor-targeted therapy.

Ion Torrent ™ Genexus ™ Integrated Sequencer and ForeNGS Analysis Software-An automatic NGS-STR workflow from DNA to profile for forensic science.

The Ion Torrent ™ Genexus ™ Sequencer (Genexus) is a highly integrated instrument that can automate library construction, templating, and sequencing in a single-instrument run. By programing the ForeNGS Analysis Software (FNAS), we bridged the gap between sequencing and genotyping without manual intervention. FNAS can automatically transfer sequencing output files from Genexus, analyze the repeat and flanking regions aligned to the GRCh38 assembly, name the alleles according to the ISFG guidelines, and generate user-friendly interactive profiles. Genexus and FNAS can accomplish the fully automatic DNA-to-Profile workflow in forensics. Based on our experiences, the optimal assay parameters on Genexus were validated as follows: 24 cycles of target amplification for library construction; 40 µL of library and 400 bp of template size for templating; 852 flows of dNTPs by order of Ion samba HID2 for sequencing; and 750,000 reads per sample at minimum for 16 samples multiplexed on a lane. By developmental validations of the Precision ID Globalfiler ™ NGS STR Panel v2, Genexus presented competitive performance at the optimal assay parameters qualified to detect commonly used forensic STR markers. It could produce repeatable and reproducible results, and human profiles could be easily separated from nonhuman profiles. Additionally, Genexus was sensitive enough to detect samples with 100 pg of input DNA, and it was suitable for various types of case samples, especially for low copy number samples and degraded samples. Moreover, minor contributors could be detected between the 4:1 and 1:4 mixtures with an analysis threshold of 50 × . The Genexus workflow is a robust and labor-effective solution enabling forensic scientists to obtain NGS-STR profiles within a single day and with only the need to prepare DNA extracts, then set up Genexus, and finally interpret profiles on FNAS.

Flexible Two-Dimensional Vanadium Carbide MXene-Based Membranes with Ultra-Rapid Molecular Enrichment for Surface-Enhanced Raman Scattering.

Two-dimensional (2D) MXene materials have attracted broad interest in surface-enhanced Raman scattering (SERS) applications by virtue of their abundant surface terminations and excellent photoelectric properties. Herein, we propose to design highly sensitive MXene-based SERS membranes by integrating a 2D downsizing strategy with molecular enrichment approaches. Two types of 2D vanadium carbide (V4C3 and V2C) MXenes are demonstrated for ultrasensitive SERS sensing, and corresponding SERS mechanisms including the effect of 2D vanadium carbide thickness on their electron density states and interfacial photoinduced charge transfer resonance were discussed. A 2D downsizing strategy authorizes nonplasmonic SERS detection with a sensitivity of 1 × 10-7 M. Moreover, the performance can be further upgraded by vacuum-assisted filtration, which enables an ultrarapid molecular enrichment (within 2 min), ultrahigh molecular removal rate (over 95%), and improved sensitivity (5 × 10-9 M). This work may shed light on the MXene-based materials as an innovative platform for nonplasmonic SERS detection.

Upregulation of circ_0059961 suppresses cholangiocarcinoma development by modulating miR-629-5p/SFRP2 axis.

BACKGROUND: Cholangiocarcinoma (CCA) is a dangerous malignancy with a poor prognosis due to inefficient chemotherapy and surgery, and its pathophysiology could be linked to circular RNA (circRNAs) dysregulation. As a result, we wanted to see what role circ_0059961 plays in CCA. METHODS: The quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression of circ_0059961, miR-629-5p, and secreted frizzled related protein 2 (SFRP2). Cell counting kit-8 (CCK-8) and 5-Ethynyl-2'-deoxyuridine (Edu) assay were used to determine the role of circ_0059961 in proliferation. The MMP (Δψm) assay was used to assess cell apoptosis. Transwell assay was used to detect cell migration and invasion. The SFRP2 protein and epithelia-mesenchymal transition (EMT) process related proteins expression were measured using Western blot. The putative relationship between miR-629-5p and circ_0059961 or SFRP2 was validated by dual-luciferase reporter assay. The circ_0059961 roles in cholangiocarcinoma were also investigated by tumor xenograft assay. RESULTS: Circ_0059961 expression was decreased in CCA tissues and carcinoma cells. Overexpressed circ_0059961 reduced tumor cell proliferation, migration, and invasion while inducing apoptosis. Circ_0059961 was proven to be a target of miR-629-5p, while miR-629-5p was confirmed to be a target of SFRP2. Circ_0059961 targeted miR-629-5p to modulate SFRP2 expression. Upregulation of miR-629-5p reversed the tumor-suppressive effects of circ_0059961 overexpression in rescue trials. Furthermore, SFRP2 overexpression restored miR-629-5p enrichment-promoted cell proliferation, migration, and invasion. Upregulated circ_0059961 reduced solid tumor growth in vivo. CONCLUSION: Upregulation of circ_0059961 augmented SFRP2 expression by targeting miR-629-5p, which blocked cholangiocarcinoma tumor cell proliferation, migration, and invasion.

Case study of the in-situ restoration of black-odorous water by combined process of forced aeration and biological contact oxidation.

Black and odorous water bodies are an extreme phenomenon that impair ecological integrity, adversely affect the lives of residents and the town's image, and cause unpleasant sensory experiences. Herein, we consider a black and smelly river in Heshan City, Guangdong Province, as a case study. The proposed comprehensive governance process combines the use of pollution control and interception, sediment remediation, aeration oxygenation, a high-efficiency biological contact oxidation/denitrification pond, and ecosystem construction. The project operation results showed that the combined process can effectively improve water quality. The water quality of the river improved to the Class V standard. All indicators met the requirements of the 'China Surface Water Environmental Quality Standard' (GB3838-2002). River water quality indicators, monitored for four months, revealed that water transparency and dissolved oxygen increased by 5.9 times and 24.5 times, respectively. Dichromate index (CODcr), total phosphorus (TP), and ammonia nitrogen (NH3-N) were reduced by 5.8, 4.17, and 5.17 times when compared to the values observed before treatment. The black-odor and eutrophication of the river were successfully eliminated, and the water quality improved significantly. In general, the combined process exhibits a high technical feasibility for implementation, providing a specific reference value for the treatment of black and odorous water bodies in urban settings.

PSMA3-AS1 induced by transcription factor PAX5 promotes cholangiocarcinoma proliferation, migration and invasion by sponging miR-376a-3p to up-regulate LAMC1.

Long noncoding RNAs (lncRNAs) have been reported to exhibit a crucial regulatory role in tumor progression, including cholangiocarcinoma (CCA). As a promising lncRNA, proteasome 20S subunit alpha 3 antisense RNA 1 (PSMA3-AS1) is involved in development of various tumors. However, the role and function of PSMA3-AS1 in CCA remain unclear. The aim of this study is to examine the expression, function, mechanism, and clinical significance of PSMA3-AS1 in CCA development. By TCGA database analysis, we found that PSMA3-AS1 was overexpressed in CCA. Consistent with the TCGA analysis, PSMA3-AS1 was significantly overexpressed in CCA tissues and cells by RT-qPCR. Upregulated PSMA3-AS1 was related to lymph node invasion, advanced TNM stage and poor survival, and was an independent risk factor of prognosis for CCA patients. Functionally, CCK-8, EdU and colony formation assays confirmed that upregulated PSMA3-AS1 promoted CCA cell proliferation, whereas downregulated PSMA3-AS1 inhibited proliferation. This result was further confirmed by subcutaneous tumor formation in nude mice. Wound healing and transwell assays confirmed that increased PSMA3-AS1 promoted CCA cell migration and invasion, whereas decreased PSMA3-AS1 inhibited these biological phenotypes. In addition, PSMA3-AS1 promoted the EMT process of CCA by downregulating E-cadherin and upregulating N-cadherin and vimentin. Mechanistically, transcription factor PAX5 bound to the promoter region of PSMA3-AS1 and promoted its transcription. Simultaneously, PSMA3-AS1 primarily localized in the cytoplasm could competitively bind miR-376a-3p to upregulate LAMC1, thereby accelerating CCA progression. This study uncovers that PSMA3-AS1 functions as a cancer-promoting gene in CCA, and PAX5/PSMA3-AS1/miR-376a-3p/LAMC1 axis plays a vital role in CCA development.

Effects of fallow tillage on winter wheat yield and predictions under different precipitation types.

In northern China, precipitation that is primarily concentrated during the fallow period is insufficient for the growth stage, creates a moisture shortage, and leads to low, unstable yields. Yield prediction in the early growth stages significantly informs field management decisions for winter wheat (Triticum aestivum L.). A 10-year field experiment carried out in the Loess Plateau area tested how three tillage practices (deep ploughing (DP), subsoiling (SS), and no tillage (NT)) influenced cultivation and yield across different fallow periods. The experiment used the random forest (RF) algorithm to construct a prediction model of yields and yield components. Our results revealed that tillage during the fallow period was more effective than NT in improving yield in dryland wheat. Under drought condition, DP during the fallow period achieved a higher yield than SS, especially in drought years; DP was 16% higher than SS. RF was deemed fit for yield prediction across different precipitation years. An RF model was developed using meteorological factors for fixed variables and soil water storage after tillage during a fallow period for a control variable. Small error values existed in the prediction yield, spike number, and grains number per spike. Additionally, the relative error of crop yield under fallow tillage (5.24%) was smaller than that of NT (6.49%). The prediction error of relative meteorological yield was minimum and optimal, indicating that the model is suitable to explain the influence of meteorological factors on yield.

Effects of phosphorus fertilizer on root characteristics, uptake and utilization of phosphorus and yield of dryland wheat with contrasting yearly rainfall pattern.

To understand the growth responses of dryland wheat to different application rates of phosphorus fertilizer in different rainfall years, we examined root characteristics, spike number, yield and phosphate utilization. Results would help improve phosphate fertilizer use in dryland wheat production. We carried out a field experiment at the research station of Shanxi Agricultural University from 2012 to 2016. We examined the effects of four application rates of phosphorus (0, 75, 150 and 225 kg·hm-2 on root growth, phosphate utilization and yield formation of dryland wheat in different years with contrasting rainfall pattern. Compared with the treatment without phosphorus fertilization, phosphate application increased root surface area at all growth stages and root weight density in the 0-80 cm soil layer at jointing, anthesis, and maturity stages. Phosphate application significantly increased soil water consumption from jointing to anthesis, and total soil water consumption in the growing season. Phosphate application enhanced the amount of pre-anthesis phosphate translocation and phosphate accumulation of grain. Spike number, yield and water use efficiency were increased with 75, 150 and 225 kg P·hm-2 by 9.2% to 22.5%, 11.8% to 30.0%, and 2.1% to 12.1%, respectively. In the dry years, the application rates of 150 and 225 kg P·hm-2 in comparison to 75 kg P·hm-2 significantly increased root weight density and root surface area at all stages, soil water consumption from sowing to jointing and from jointing to anthesis, and total water consumption in the growing season. In comparison to the rate of 75 kg P·hm-2, 150 and 225 kg P·hm-2 increased soil water consumption from sowing to jointing by 7.3-8.7 mm, soil water consumption from jointing to anthesis by 15.6-18.1 mm, and total water consumption by 15.6-18.1 mm. Significant increase in the pre-anthesis phosphate translocation and phosphate accumulation in grain was higher under 150 and 225 kg P·hm-2 than that under 75 kg P·hm-2 in dry years. Furthermore, the two rates (150 and 225 kg P·hm-2) in dry years increased spike number by 9.3%-10.7% and yield by 11.9%-14.6%. The application rate of 150 kg P·hm-2 significantly improved phosphorus use efficiency by 20%-82% in comparison to other rates. In normal years, the rates of 150 and 225 kg P·hm-2 increased root surface area, root weight density at both anthesis and maturity compared with 75 kg P·hm-2. Soil water consumption from anthesis to maturity and total soil water consumption in the growing season were also increased by 1.2-15.0 and 3.8-23.1 mm, respectively. In addition, phosphorus accumulation in post-anthesis and phosphate accumulation in grain were increased in both 150 and 225 kg P·hm-2, which increased spike number by 1.4%-9.6% and yield by 3.5%-10.4%. The effects of phosphate application at the rate of 150 kg P·hm-2 were significantly different from 75 and 225 kg P·hm-2. In conclusion, phosphorus fertilizer application enhanced uptake of water and phosphate in dryland wheat at early and middle growth stages in dry years and at the late growth stage in normal years. Phosphorus application increased wheat yield mainly due to the increases of spike number. The application of 150 kg P·hm-2 is the best choice for high water and phosphorus fertilizer use efficiency and high yield in both dry and normal years.

Genomic adaptations to cereal-based diets contribute to mitigate metabolic risk in some human populations of East Asian ancestry.

Adoption of diets based on some cereals, especially on rice, signified an iconic change in nutritional habits for many Asian populations and a relevant challenge for their capability to maintain glucose homeostasis. Indeed, rice shows the highest carbohydrates content and glycemic index among the domesticated cereals and its usual ingestion represents a potential risk factor for developing insulin resistance and related metabolic diseases. Nevertheless, type 2 diabetes and obesity epidemiological patterns differ among Asian populations that rely on rice as a staple food, with higher diabetes prevalence and increased levels of central adiposity observed in people of South Asian ancestry rather than in East Asians. This may be at least partly due to the fact that populations from East Asian regions where wild rice or other cereals such as millet have been already consumed before their cultivation and/or were early domesticated have relied on these nutritional resources for a period long enough to have possibly evolved biological adaptations that counteract their detrimental side effects. To test such a hypothesis, we compared adaptive evolution of these populations with that of control groups from regions where the adoption of cereal-based diets occurred many thousand years later and which were identified from a genome-wide dataset including 2,379 individuals from 124 East Asian and South Asian populations. This revealed selective sweeps and polygenic adaptive mechanisms affecting functional pathways involved in fatty acids metabolism, cholesterol/triglycerides biosynthesis from carbohydrates, regulation of glucose homeostasis, and production of retinoic acid in Chinese Han and Tujia ethnic groups, as well as in people of Korean and Japanese ancestry. Accordingly, long-standing rice- and/or millet-based diets have possibly contributed to trigger the evolution of such biological adaptations, which might represent one of the factors that play a role in mitigating the metabolic risk of these East Asian populations.

An Update on the Roles of circRNA-ZFR in Human Malignant Tumors.

CircRNAs (circular RNAs) are single-stranded RNAs that form covalently closed loops and function as important regulatory elements of the genome through multiple mechanisms. Increasing evidence had indicated that circRNAs, which might serve as either oncogenes or tumor suppressors, played vital roles in the pathophysiology of human diseases, especially in tumorigenesis and progression. CircRNA-ZFR (circular RNA zinc finger RNA binding protein) is a circular RNA that had attracted much attention in recent years. It has been found that circRNA-ZFR was abnormally expressed in a variety of malignant tumors, and its dysregulated expression was closely related to tumor stage, cancer metastasis and patients' prognosis. Recent studies had shown that aberrantly expressed circRNA-ZFR could regulate the malignant biological behaviors of tumors through various mechanisms; further exploration of circRNA-ZFR expression in tumors and its regulation on malignant biological behaviors such as tumor proliferation, invasion and drug resistance will provide new ideas for clinical tumors diagnosis and treatment.

Low-density lipoprotein cholesterol and all-cause mortality: findings from the China health and retirement longitudinal study.

OBJECTIVES: To investigate the relationship between low-density lipoprotein cholesterol (LDL-C) and all-cause mortality among middle-aged and elderly Chinese population. DESIGN: Prospective cohort study. SETTING: This study used data from the China Health and Retirement Longitudinal Study. PARTICIPANTS: Middle-aged and elderly participants with complete data were enrolled for a 4-year follow-up of total mortality and plasma levels of LDL-C, including 4981 male respondents and 5529 female respondents. RESULTS: During a 4-year follow-up, there were 305 and 219 deaths in men and women, respectively. Compared with the first quintile (Q1) of LDL-C, the adjusted HRs (95% CIs) were 0.818 (0.531 to 1.260) for Q2, 0.782 (0.507 to 1.208) for Q3, 0.605 (0.381 to 0.962) for Q4 and 0.803 (0.506 to 1.274) for Q5 in men. The results from restricted cubic spine (RCS) showed that when the 20th percentile of LDL-C levels (84 mg/dL) was used as the reference, a lower LDL-C concentration (<84 mg/dL) was associated with a higher 4-year all-cause mortality risk. By contrast, both quintile analysis and RCS analysis did not show a statistically significant association in women. CONCLUSIONS: Compared with moderately elevated LDL-C (eg, 117-137 mg/dL), a lower plasma level of LDL-C (eg, ≤84 mg/dL) was associated with an increased risk of 4-year all-cause mortality in middle-aged and elderly Chinese men. The results suggest the potential harmful effect of a quite low level of LDL-C on total mortality.