2'-O-methylation at internal sites on mRNA promotes mRNA stability.

2'-O-methylation (Nm) is a prominent RNA modification well known in noncoding RNAs and more recently also found at many mRNA internal sites. However, their function and base-resolution stoichiometry remain underexplored. Here, we investigate the transcriptome-wide effect of internal site Nm on mRNA stability. Combining nanopore sequencing with our developed machine learning method, NanoNm, we identify thousands of Nm sites on mRNAs with a single-base resolution. We observe a positive effect of FBL-mediated Nm modification on mRNA stability and expression level. Elevated FBL expression in cancer cells is associated with increased expression levels for 2'-O-methylated mRNAs of cancer pathways, implying the role of FBL in post-transcriptional regulation. Lastly, we find that FBL-mediated 2'-O-methylation connects to widespread 3' UTR shortening, a mechanism that globally increases RNA stability. Collectively, we demonstrate that FBL-mediated Nm modifications at mRNA internal sites regulate gene expression by enhancing mRNA stability.

ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics.

Compared with conventional comparative genomics, the recent studies in pan-genomics have provided further insights into species genomic dynamics, taxonomy and identification, pathogenicity and environmental adaptation. To better understand genome characteristics of species of interest and to fully excavate key metabolic and resistant genes and their conservations and variations, here we present ProPan (https://ngdc.cncb.ac.cn/propan), a public database covering 23 archaeal species and 1,481 bacterial species (in a total of 51,882 strains) for comprehensively profiling prokaryotic pan-genome dynamics. By analyzing and integrating these massive datasets, ProPan offers three major aspects for the pan-genome dynamics of the species of interest: 1) the evaluations of various species' characteristics and composition in pan-genome dynamics; 2) the visualization of map association, the functional annotation and presence/absence variation for all contained species' gene clusters; 3) the typical characteristics of the environmental adaptation, including resistance genes prediction of 126 substances (biocide, antimicrobial drug and metal) and evaluation of 31 metabolic cycle processes. Besides, ProPan develops a very user-friendly interface, flexible retrieval and multi-level real-time statistical visualization. Taken together, ProPan will serve as a weighty resource for the studies of prokaryotic pan-genome dynamics, taxonomy and identification as well as environmental adaptation.

TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies.

Transcriptome-wide association studies (TWASs), as a practical and prevalent approach for detecting the associations between genetically regulated genes and traits, are now leading to a better understanding of the complex mechanisms of genetic variants in regulating various diseases and traits. Despite the ever-increasing TWAS outputs, there is still a lack of databases curating massive public TWAS information and knowledge. To fill this gap, here we present TWAS Atlas (https://ngdc.cncb.ac.cn/twas/), an integrated knowledgebase of TWAS findings manually curated from extensive literature. In the current implementation, TWAS Atlas collects 401,266 high-quality human gene-trait associations from 200 publications, covering 22,247 genes and 257 traits across 135 tissue types. In particular, an interactive knowledge graph of the collected gene-trait associations is constructed together with single nucleotide polymorphism (SNP)-gene associations to build up comprehensive regulatory networks at multi-omics levels. In addition, TWAS Atlas, as a user-friendly web interface, efficiently enables users to browse, search and download all association information, relevant research metadata and annotation information of interest. Taken together, TWAS Atlas is of great value for promoting the utility and availability of TWAS results in explaining the complex genetic basis as well as providing new insights for human health and disease research.

Knocking down a DNA demethylase gene affects potato plant defense against a specialist insect herbivore.

DNA demethylase (DML) is involved in plant development and responses to biotic and abiotic stresses; however, its role in plant-herbivore interaction remains elusive. Here, we found that herbivory by the potato tuber moth, Phthorimaea operculella, rapidly induced the genome-wide DNA methylation and accumulation of DML gene transcripts in potato plants. Herbivory induction of DML transcripts was suppressed in jasmonate-deficient plants, whereas exogenous application of methyl jasmonate (MeJA) improved DML transcripts, indicating that the induction of DML transcripts by herbivory is associated with jasmonate signaling. Moreover, P. operculella larvae grew heavier on DML gene (StDML2) knockdown plants than on wild-type plants, and the decreased biosynthesis of jasmonates in the former may be responsible for this difference, since the larvae feeding on these two genotypes supplemented with MeJA showed similar growth. In addition, P. operculella adult moths preferred to oviposit on StDML2 knockdown plants than on wild-type plants, which was associated with the reduced emission of ß-caryophyllene in the former. In addition, supplementing ß-caryophyllene to these two genotypes further disrupted moths' oviposit choice preference for them. Interestingly, in StDML2 knockdown plants, hypermethylation was found at the promoter regions for the key genes StAOS and StAOC in the jasmonate biosynthetic pathway, as well as for the key gene StTPS12 in ß-caryophyllene production. Our findings suggest that knocking down StDML2 can affect herbivore defense via jasmonate signaling and defense compound production in potato plants.

CancerSCEM: a database of single-cell expression map across various human cancers.

With the proliferating studies of human cancers by single-cell RNA sequencing technique (scRNA-seq), cellular heterogeneity, immune landscape and pathogenesis within diverse cancers have been uncovered successively. The exponential explosion of massive cancer scRNA-seq datasets in the past decade are calling for a burning demand to be integrated and processed for essential investigations in tumor microenvironment of various cancer types. To fill this gap, we developed a database of Cancer Single-cell Expression Map (CancerSCEM, https://ngdc.cncb.ac.cn/cancerscem), particularly focusing on a variety of human cancers. To date, CancerSCE version 1.0 consists of 208 cancer samples across 28 studies and 20 human cancer types. A series of uniformly and multiscale analyses for each sample were performed, including accurate cell type annotation, functional gene expressions, cell interaction network, survival analysis and etc. Plus, we visualized CancerSCEM as a user-friendly web interface for users to browse, search, online analyze and download all the metadata as well as analytical results. More importantly and unprecedentedly, the newly-constructed comprehensive online analyzing platform in CancerSCEM integrates seven analyze functions, where investigators can interactively perform cancer scRNA-seq analyses. In all, CancerSCEM paves an informative and practical way to facilitate human cancer studies, and also provides insights into clinical therapy assessments.

Retinoic Acid Upregulates METTL14 Expression and the m6A Modification Level to Inhibit the Proliferation of Embryonic Palate Mesenchymal Cells in Cleft Palate Mice.

Cleft palate only (CPO) is one of the most common craniofacial birth defects. Environmental factors can induce cleft palate by affecting epigenetic modifications such as DNA methylation, histone acetylation, and non-coding RNA. However, there are few reports focusing on the RNA modifications. In this study, all-trans retinoic acid (atRA) was used to simulate environmental factors to induce a C57BL/6J fetal mouse cleft palate model. Techniques such as dot blotting and immunofluorescence were used to find the changes in m6A modification when cleft palate occurs. RNA-seq and KEGG analysis were used to screen for significantly differentially expressed pathways downstream. Primary mouse embryonic palate mesenchymal (MEPM) cells were successfully isolated and used for in vitro experimental verification. We found that an increased m6A methylation level was correlated with suppressed cell proliferation in the palatine process mesenchyme of cleft palate mice. This change is due to the abnormally high expression of m6A methyltransferase METTL14. When using siRNAs and the m6A methyltransferase complex inhibitor SAH to interfere with the expression or function of METTL14, the teratogenic effect of atRA on primary cells was partially alleviated. In conclusion, METTL14 regulates palatal mesenchymal cell proliferation and cycle-related protein expression relies on m6A methylation modification, affecting the occurrence of cleft palate.

The RING-Type Domain-Containing Protein GNL44 Is Essential for Grain Size and Quality in Rice (Oryza sativa L.).

Grain size in rice (Oryza sativa L.) shapes yield and quality, but the underlying molecular mechanism is not fully understood. We functionally characterized GRAIN NUMBER AND LARGE GRAIN SIZE 44 (GNL44), encoding a RING-type protein that localizes to the cytoplasm. The gnl44 mutant has fewer but enlarged grains compared to the wild type. GNL44 is mainly expressed in panicles and developing grains. Grain chalkiness was higher in the gnl44 mutant than in the wild type, short-chain amylopectin content was lower, middle-chain amylopectin content was higher, and appearance quality was worse. The amylose content and gel consistency of gnl44 were lower, and protein content was higher compared to the wild type. Rapid Visco Analyzer results showed that the texture of cooked gnl44 rice changed, and that the taste value of gnl44 was lower, making the eating and cooking quality of gnl44 worse than that of the wild type. We used gnl44, qgl3, and gs3 monogenic and two-gene near-isogenic lines to study the effects of different combinations of genes affecting grain size on rice quality-related traits. Our results revealed additive effects for these three genes on grain quality. These findings enrich the genetic resources available for rice breeders.

Dirhodium C-H Functionalization of Hole-Transport Materials.

Hole-transport materials (HTMs) based on triarylamine derivatives play important roles in organic electronics applications including organic light-emitting diodes and perovskite solar cells. For some applications, triarylamine derivatives bearing appropriate binding groups have been used to functionalize surfaces, while others have been incorporated as side chains into polymers to manipulate the processibility of HTMs for device applications. However, only a few approaches have been used to incorporate a single surface-binding group or polymerizable group into triarylamine materials. Here, we report that Rh-carbenoid chemistry can be used to insert carboxylic esters and norbornene functional groups into sp2 C-H bonds of a simple triarylamine and a 4,4'-bis(diarylamino)biphenyl, respectively. The norbenene-functionalized monomer was polymerized by ring-opening metathesis; the electrochemical, optical, and charge-transport properties of these materials were similar to those of related materials synthesized by conventional means. This method potentially offers straightforward access to a diverse range of HTMs with different functional groups.

Surface doping of rubrene single crystals by molecular electron donors and acceptors.

The surface molecular doping of organic semiconductors can play an important role in the development of organic electronic or optoelectronic devices. Single-crystal rubrene remains a leading molecular candidate for applications in electronics due to its high hole mobility. In parallel, intensive research into the fabrication of flexible organic electronics requires the careful design of functional interfaces to enable optimal device characteristics. To this end, the present work seeks to understand the effect of surface molecular doping on the electronic band structure of rubrene single crystals. Our angle-resolved photoemission measurements reveal that the Fermi level moves in the band gap of rubrene depending on the direction of surface electron-transfer reactions with the molecular dopants, yet the valence band dispersion remains essentially unperturbed. This indicates that surface electron-transfer doping of a molecular single crystal can effectively modify the near-surface charge density, while retaining good charge-carrier mobility.

Astaxanthin alleviates PM2.5-induced cardiomyocyte injury via inhibiting ferroptosis.

BACKGROUND: Long-term exposure of humans to air pollution is associated with an increasing risk of cardiovascular diseases (CVDs). Astaxanthin (AST), a naturally occurring red carotenoid pigment, was proved to have multiple health benefits. However, whether or not AST also exerts a protective effect on fine particulate matter (PM2.5)-induced cardiomyocyte damage and its underlying mechanisms remain unclear. METHODS: In vitro experiments, the H9C2 cells were subjected to pretreatment with varying concentrations of AST, and then cardiomyocyte injury model induced by PM2.5 was established. The cell viability and the ferroptosis-related proteins expression were measured in different groups. In vivo experiments, the rats were pretreated with different concentrations of AST for 21 days. Subsequently, a rat model of myocardial PM2.5 injury was established by intratracheal instillation every other day for 1 week. The effects of AST on myocardial tissue injury caused by PM2.5 indicating by histological, serum, and protein analyses were examined. RESULTS: AST significantly ameliorated PM2.5-induced myocardial tissue injury, inflammatory cell infiltration, the release of inflammatory factors, and cardiomyocyte H9C2 cell damage. Mechanistically, AST pretreatment increased the expression of SLC7A11, GPX4 and down-regulated the expression of TfR1, FTL and FTH1 in vitro and in vivo. CONCLUSIONS: Our study suggest that ferroptosis plays a significant role in the pathogenesis of cardiomyocyte injury induced by PM2.5. AST may serve as a potential therapeutic agent for mitigating cardiomyocyte injury caused by PM2.5 through the inhibition of ferroptosis.

Value of T6SS Core Gene hcp in Acinetobacter baumannii Respiratory Tract Infection.

Hospital-acquired pneumonia caused by Acinetobacter baumannii is a major healthcare burden. Type VI Secretion System (T6SS) contributes to both virulence and drug resistance in this bacteria. This study aims to investigate the diagnostic value of hemolysin co-regulated protein (Hcp) gene in A. baumannii pneumonia and further explore the effect of hcp on clinical, pathogenicity and drug resistance. 53 clinical A. baumannii strains from patients' respiratory tract at a teaching hospital were included in this study. Real-time quantitative polymerase chain reaction (qRT-PCR) was carried out to examine the expression of hcp. Recombinant Hcp expression plasmids (pET-28a(+)-hcp) were constructed and his-tagged Hcp were purified to stimulate Tohoku Hospital Pediatrics-1 (THP-1) macrophages. Nuclear Factor Kappa B p65 (NF-κBp65) and Interleukin 8 (IL-8) were detected by qRT-PCR. Antimicrobial susceptibility testing (AST) were examined by an automated instrument system. Hcp gene had 92.6% sensitivity and 75% specificity for distinguishing invasive or colonizing A. baumannii from the respiratory tract. His-tagged Hcp induced NF-κBp65 and IL-8 at gene level in THP-1 macrophages. Additional, high hcp expression isolates showed higher rate of antimicrobial agent exposure (< 30 days) of carbapenems, antibiotic combination therapy and multiple or extensive drug-resistant (MDR/XDR) and exhibited higher resistance rate to clinical commonly-used antimicrobial agents. Hcp gene could serve as a novel diagnostic biomarker to distinguish A. baumannii respiratory tract infection from colonization and participate in eliciting inflammatory responses in vitro. T6SS/hcp may play a role in the development of carbapenem-resistant A. baumannii (CRAB), multiple or extensive drug-resistant A. baumannii (MDRAB/XDRAB). Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-023-01083-8.

Construction of a single nucleotide polymorphism linkage map and identification of quantitative trait loci controlling heat tolerance in cowpea, Vigna unguiculata (L.) Walp.

Plant tolerance to heat or high temperature is crucial to crop production, especially in the situation of elevated temperature resulting from global climate change. Cowpea, Vigna unguiculata (L.) Walp., is an internationally important legume food crop and an excellent pool of genes for numerous traits resilient to environmental extremes, particularly heat and drought. Here, we report a single nucleotide polymorphism (SNP) genetic map for cowpea and identification of the loci controlling the heat tolerance in the species. The SNP map consists of 531 bins containing 4,154 SNPs grouped into 11 linkage groups, and collectively spans 1,084.7 cM, thus having a density of one SNP in 0.26 cM or 149 kb. The 11 linkage groups of the map were aligned to the 11 cowpea chromosomes. Quantitative trait locus (QTL) mapping identified nine QTLs responsible for the cowpea heat tolerance on seven of the 11 chromosomes, with each QTL explaining 6.5-21.8% of heat tolerance phenotypic variation. Moreover, we aligned these nine QTLs to the cowpea genome. Each of the QTLs was positioned in a genomic region ranging from 209,000 bp to 12,590,450 bp, and the QTL with the largest effect (21.8%) on heat tolerance, qHT4-1, was located within an interval of only 234,195 bp. These results provide SNP markers useful for marker-assisted selection for heat tolerance and lay a foundation for cloning, characterization, and applications of the genes controlling the cowpea heat tolerance for heat tolerance genetic improvement in cowpea and related crops.

Heat stress affects potato's volatile emissions that mediate agronomically important trophic interactions.

Potato, a cool-weather crop, emits volatile organic compounds (VOCs) which attract the specialist herbivore, Phthorimaea operculella, but also this herbivore's parasitic wasp, Trichogramma chilonis, an important biocontrol agent. What happens to this trophic system when heat stress challenges this agro-ecosystem? We studied how high temperature (HT) pre-treatments influence potato's VOC emissions and their subsequent effects on the preferences of insects, as evaluated in oviposition assays and Y-tube olfactometers. HT pre-stressed plants were less attractive to P. operculella adult moths, which were repelled by HT VOCs, but increased the recruitment of the parasitoid, T. chilonis, which were attracted. VOC emissions, including the most abundant constituent, ß-caryophyllene, were enhanced by HT treatments; some constituents elicited stronger behavioural responses than others. Transcripts of many genes in the biosynthetic pathways of these VOCs were significantly enhanced by HT treatment, suggesting increases in de novo biosynthesis. HT increased the plant's stomatal apertures, and exogenous applications of the hormone, ABA, known to suppress stomatal apertures, reduced leaf volatile emissions and affected the HT-altered plant attractions to both insects. From these results, we infer that HT stress affects this plant-insect interaction through its influence on VOC emissions, potentially decreasing herbivore ovipositions while increasing ovipositions of the parasitoid.

Can Common Pool Resource Theory Catalyze Stakeholder-Driven Solutions to the Freshwater Salinization Syndrome?

Freshwater salinity is rising across many regions of the United States as well as globally, a phenomenon called the freshwater salinization syndrome (FSS). The FSS mobilizes organic carbon, nutrients, heavy metals, and other contaminants sequestered in soils and freshwater sediments, alters the structures and functions of soils, streams, and riparian ecosystems, threatens drinking water supplies, and undermines progress toward many of the United Nations Sustainable Development Goals. There is an urgent need to leverage the current understanding of salinization's causes and consequences─in partnership with engineers, social scientists, policymakers, and other stakeholders─into locally tailored approaches for balancing our nation's salt budget. In this feature, we propose that the FSS can be understood as a common pool resource problem and explore Nobel Laureate Elinor Ostrom's social-ecological systems framework as an approach for identifying the conditions under which local actors may work collectively to manage the FSS in the absence of top-down regulatory controls. We adopt as a case study rising sodium concentrations in the Occoquan Reservoir, a critical water supply for up to one million residents in Northern Virginia (USA), to illustrate emerging impacts, underlying causes, possible solutions, and critical research needs.

Delayed Luminescence in 2-Methyl-5-(penta(9-carbazolyl)phenyl)-1,3,4-oxadiazole Derivatives.

2,5-Diphenyl-1,3,4-oxadiazole has been widely used as an acceptor portion of donor-acceptor fluorophores that exhibit thermally activated delayed fluorescence (TADF), but analogous 2-alkyl-5-phenyl-1,3,4-oxadiazoles have been much less widely investigated. Here the properties of carbazole-substituted 2-methyl-5-phenyl-1,3,4-oxadiazoles are compared to those of their 2,5-diphenyl analogues. The fluorescence of each of the former compounds is blue-shifted by ca. 50-100 meV relative to that in the latter, while similar estimated values of the singlet-triplet energy separation (ΔEST) are maintained. In particular, 2-methyl-5-(penta(9-carbazolyl)phenyl)-1,3,4-oxadiazole and 2-methyl-5-(penta(3,6-di-tert-butyl-9-carbazolyl)phenyl)-1,3,4-oxadiazole exhibit solution fluorescence maxima of 466 and 485 nm and estimated ΔEST values of 0.12 and 0.03 eV, respectively. In both cases the reverse intersystem crossing (RISC) rates inferred from their solution fluorescence behavior are over twice those of the corresponding 2-phenyl derivatives. Organic light-emitting diodes (OLEDs) in which the 2-methyl derivatives are used as emitters yield external quantum efficiency (EQE) values of up to 23%. OLEDs with 2-methyl-5-(penta(9-carbazolyl)phenyl)-1,3,4-oxadiazole and 2-methyl-5-(penta(3,6-di-tert-butyl-9-carbazolyl)phenyl)-1,3,4-oxadiazole emitters show reduced efficiency rolloff at high current densities relative to their 2-phenyl counterparts, the latter exhibiting an EQE of 16% at 1000 cd m-2.

FOSL1 promotes metastasis of head and neck squamous cell carcinoma through super-enhancer-driven transcription program.

Previously, we discovered that FOSL1 facilitates the metastasis of head and neck squamous cell carcinoma (HNSCC) cancer stem cells in a spontaneous mouse model. However, the molecular mechanisms remained unclear. Here, we demonstrated that FOSL1 serves as the dominant activating protein 1 (AP1) family member and is significantly upregulated in HNSCC tumor tissues and correlated with metastasis of HNSCC. Mechanistically, FOSL1 exerts its function in promoting tumorigenicity and metastasis predominantly via selective association with Mediators to establish super-enhancers (SEs) at a cohort of cancer stemness and pro-metastatic genes, such as SNAI2 and FOSL1 itself. Depletion of FOSL1 led to disruption of SEs and expression inhibition of these key oncogenes, which resulted in the suppression of tumor initiation and metastasis. We also revealed that the abundance of FOSL1 is positively associated with the abundance of SNAI2 in HNSCC and the high expression levels of FOSL1 and SNAI2 are associated with short overall disease-free survival. Finally, the administration of the FOSL1 inhibitor SR11302 significantly suppressed tumor growth and lymph node metastasis of HNSCC in a patient-derived xenograft model. These findings indicate that FOSL1 is a master regulator that promotes the metastasis of HNSCC through a SE-driven transcription program that may represent an attractive target for therapeutic interventions.

PADS Arsenal: a database of prokaryotic defense systems related genes.

Defense systems are vital weapons for prokaryotes to resist heterologous DNA and survive from the constant invasion of viruses, and they are widely used in biochemistry investigation and antimicrobial drug research. So far, numerous types of defense systems have been discovered, but there is no comprehensive defense systems database to organize prokaryotic defense gene datasets. To fill this gap, we unveil the prokaryotic antiviral defense system (PADS) Arsenal (https://bigd.big.ac.cn/padsarsenal), a public database dedicated to gathering, storing, analyzing and visualizing prokaryotic defense gene datasets. The initial version of PADS Arsenal integrates 18 distinctive categories of defense system with the annotation of 6 600 264 genes retrieved from 63,701 genomes across 33 390 species of archaea and bacteria. PADS Arsenal provides various ways to retrieve defense systems related genes information and visualize them with multifarious function modes. Moreover, an online analysis pipeline is integrated into PADS Arsenal to facilitate annotation and evolutionary analysis of defense genes. PADS Arsenal can also visualize the dynamic variation information of defense genes from pan-genome analysis. Overall, PADS Arsenal is a state-of-the-art open comprehensive resource to accelerate the research of prokaryotic defense systems.

[Compound Chamomile and Lidocaine Hydrochloride Gel applied at different time-windows for premature ejaculation: A prospective single-center randomized controlled study].

OBJECTIVE: To investigate the efficacy and safety of Compound Chamomile and Lidocaine Hydrochloride Gel (CCLH) (Kamistad) applied at different time-windows on premature ejaculation (PE). METHODS: This prospective study included 72 PE patients treated by application of CCLH to the glans and penile body in our hospital from February to October 2021. According to the time of drug administration before insertion into the vagina, we randomly divided the patients into a 5-minute group (n = 39) and a 15-minute group (n = 33). Before and after 1 and 2 weeks of treatment, we compared the intravaginal ejaculation latency time (IELT), PE diagnostic tool (PEDT) score, quality of life, and adverse reactions between the two groups of patients. RESULTS: Totally 62 of the patients completed the follow-up, 35 in the 5-minute group and 27 in the 15-minute group, and all showed significant improvement in IELT (P < 0.01) and PEDT score (P < 0.05) after treatment compared with the baseline. No allergic reactions, such as redness and swelling, developed at the application site in any of the patients, and no adverse significant effect was observed on the erectile hardness in 61 of the cases. Six cases showed increased erectile hardness instead. Fifty-seven of the patients experienced no obvious penile numbness or reduced sexual satisfaction, and all could complete their sexual activities. CONCLUSION: Compound Chamomile and Lidocaine Hydrochloride Gel applied at different time-windows is effective on PE, with a 5-minute rapid onset of action before intercourse, and no obvious adverse effects.

QTL mapping for starch paste viscosity of rice (Oryza sativa L.) using chromosome segment substitution lines derived from two sequenced cultivars with the same Wx allele.

BACKGROUND: The eating and cooking qualities (ECQs) of rice (Oryza sativa L.) are key characteristics affecting variety adoption and market value. Starch viscosity profiles tested by a rapid visco analyzer (RVA) offer a direct measure of ECQs and represent the changes in viscosity associated with starch gelatinization. RVA profiles of rice are controlled by a complex genetic system and are also affected by the environment. Although Waxy (Wx) is the major gene controlling amylose content (AC) and ECQs, there are still other unknown genetic factors that affect ECQs. RESULTS: Quantitative trait loci (QTLs) for starch paste viscosity in rice were analyzed using chromosome segment substitution lines (CSSLs) developed from the two cultivars 9311 and Nipponbare, which have same Wx-b allele. Thus, the effect of the major locus Wx was eliminated and the other locus associated with the RVA profile could be identified. QTLs for seven parameters of the starch RVA profile were tested over four years in Nanjing, China. A total of 310 QTLs were identified (from 1 to 55 QTLs per trait) and 136 QTLs were identified in more than one year. Among them, 6 QTLs were stalely detected in four years and 26 QTLs were detected in at least three years including 13 pleiotropic loci, controlling 2 to 6 RVA properties simultaneously. These stable QTL hotspots were co-located with several known starch synthesis-related genes (SSRGs). Sequence alignments showed that nucleotide and amino acid sequences of most SSRGs were different between the two parents. Finally, we detected stable QTLs associated with multiple starch viscosity traits near Wx itself, supporting the notion that additional QTLs near Wx control multiple characteristic values of starch viscosity. CONCLUSIONS: By eliminating the contribution from the major locus Wx, multiple QTLs associated with the RVA profile of rice were identified, several of which were stably detected over four years. The complexity of the genetic basis of rice starch viscosity traits might be due to their pleiotropic effects and the multiple QTL hot spots. Minor QTLs controlling starch viscosity traits were identified by using the chromosome segment substitution strategy. Allele polymorphism might be the reason that QTLs controlling RVA profile characteristics were detected in some known SSRG regions.

Silencing SHMT2 inhibits the progression of tongue squamous cell carcinoma through cell cycle regulation.

BACKGROUND: Serine hydroxymethyltransferase 2 (SHMT2) is a vital metabolic enzyme in one carbon metabolism catalyzing the conversion of serine to glycine, which has been reported to play a crucial role in the progression of tumors. However, its function in tongue squamous cell carcinoma (TSCC) remains unclear. METHODS: SHMT2 expression was analyzed using samples in online databases, and was assessed through immunohistochemistry staining of collected clinical specimens. The correlation between SHMT2 expression and the cell cycle was predicted through bioinformatic analysis, including weighted gene co-expression network analysis (WGCNA) and gene set enrichment analysis (GSEA). After transfection with siRNA, CCK8 assay, Edu staining, flow cytometry, trans-well assay, and wound healing experiments were performed to verify the functional role of SHMT2 in vitro. A stable cell line with SHMT2 silencing was established to detect the oncogenic function of SHMT2 in vivo. RESULTS: The expression of SHMT2 was up-regulated in TSCC tissues and cell lines compared with normal groups, and highly expressed SHMT2 significantly indicated a poorer clinical outcome for TSCC patients. Bioinformatic analysis found that high expression of SHMT2 was closely related with biologic process including cell cycle and cell cycle G1/S transition. Down regulating of SHMT2 significantly suppressed the proliferation, invasive and migrative ability of TSCC cells, and induced the prolongation of the G1 phase of the cell cycle in vitro. Furthermore, western blot showed that cell cycle-related regulators such as cyclin-dependent kinase 4 (CDK4) and cyclinD1 expression levels were decreased, while the expression levels of the cyclin-dependent kinase inhibitors p21Cip1 and p27Kip1 were increased after SHMT2 knockdown. Silencing SHMT2 in the HN6 cell line using short hairpin RNA also impeded tumor growth in vivo. CONCLUSIONS: Overexpression of SHMT2 in TSCC indicated low survival rates, and was associated with aggressive behaviors of TSCC. It was also found to be involved in cell cycle regulation of TSCC cells. SHMT2 may serve as a novel prognostic indicator of TSCC.