Genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in quinoa (Chenopodium quinoa) under abiotic stress.

The MYB transcription factor (TF) are among the largest gene families of plants being responsible for several biological processes. The R2R3-MYB gene family are integral player regulating plant primary and secondary metabolism, growth and development, and responses to hormones and stresses. The phylogenetic analysis combined with gene structure analysis and motif determination resulted in division of R2R3-MYB gene family into 27 subgroups. Evidence generated from synteny analyses indicated that CqR2R3-MYBs gene family is featured by tandem and segmental duplication events. On the basis of RNA-Seq data, the expression patterns of different tissues under salt treatment were investigated resulting CqR2R3-MYB genes high expression both in roots and stem of quinoa (Chenopodium quinoa ) plants. More than half of CqR2R3-MYB genes showed expression under salt stress. Based on this result, CqR2R3-MYB s may regulate quinoa plant growth development and resistance to abiotic stresses. These findings provided comprehensive insights on role of CqR2R3-MYBs gene family members in quinoa and candidate MYB gene family members can be further studies on their role for abiotic stress tolerance in crop plants.

Discussion on Static Resistance of Granite under Penetration.

A total of 9 tests were carried out with 30 mm and 78 mm caliber scaled projectiles penetrating into granite targets. The penetration depth, crater diameter, and mass loss rate were examined and discussed. The results indicate that the dimensionless penetration depth of large-caliber projectiles is 20% greater than small-caliber projectiles. Based on the description of static resistance Ra in the Forrestal semi-empirical formula, the size effect of dimensionless penetration depth can be attributed to the size effect of static resistance Ra, and it can be seen that the penetration static resistance of projectile A is 40% higher than that of projectile B. Numerical simulations of projectile penetration into granite targets were conducted using the finite element program ANSYS/LS-DYNA. In terms of penetration depth and crater damage, the numerical simulation results agree well with the test data. This suggests that the selection of parameters was reasonable. The influence of compressive strength, projectile striking velocity, mass, diameter, and caliber-radius-head (CRH) ratio on the static resistance Ra were studied by RHT model parameterization. Based on the numerical results from the parametric study, an empirical formula was derived to predict the static resistance Ra.

Experiment Study on the Influence of Density and Confining Pressure on Triaxial Shear Properties of Calcareous Sand.

Calcareous sand is one of the main building materials in the construction of islands and reefs, and its shear property is very important for predicting their strength and deformation. However, the correlation research on the shear properties of calcareous sand is limited. In this paper, a series of the triaxial consolidation drainage shear tests of calcareous sand with relative densities (Dr) of 70% and 90% under confining pressures of 100, 200, 400 and 800 kPa were carried out by a triaxial testing apparatus, and the effects of relative density and confining pressure on the deformation and strength characteristics of calcareous sand were analyzed. The results show that the stress-strain curves of calcareous sand show a strain softening characteristic, and both peak deviatoric stress and failure strain increase with confining pressure, but the increase in failure strain is restrained when the confining pressure is larger than 400 kPa. The initial shear modulus of calcareous sand is positively correlated with confining pressure. Additionally, the molar circular envelope of calcareous sand is linear in the range of 100~400 kPa, but it deviates from linear when confining pressure exceeds 400 kPa. The critical state line (CSL) of calcareous sand is nonlinear, with almost the same exponent for calcareous sand with different relative densities. The research results have important reference value for the foundation construction of islands and reefs.

Progress on genomics and locus of important agronomic traits in Chenopodium quinoa.

Quinoa (Chenopodium quinoa, Willd.) as a new health food in the 20th century, its comprehensive nutritional composition, stress resistance and other characteristics have been paid much of attention, and enjoys the reputation of "nutritional gold", "vegetarian king" and "food in the future" in the world. In recent years, with the rapid development of genomics and high-throughput sequencing technology, the high-quality whole genome sequence of quinoa has been completed, and the omics analysis and functional research of a series of key genes have been gradually carried out. In this review, we summarize the research progress in quinoa genomics, gene family analysis of important transcription factors, genetic map construction, QTL mapping of important traits, and genes for important agronomic and yield traits. Moreover, according to the current status of quinoa breeding, this paper also put forward five key problems in quinoa breeding, and pointed out four important directions of genetic improvement and breeding of quinoa in the future, so as to provide reference for the realization of directional genetic improvement of quinoa in the future.

[Advances in liquid chromatography-mass spectrometry analysis of several important secondary metabolites in plant metabolomics].

Metabolomics, which mainly studies the metabolite components of organisms, tissues, cells and their dynamic changes, is an emerging omics technology following genomics and proteomics. Metabolites are the final products of cellular regulation, and the concentration of metabolites is considered to be the ultimate response of a biological system to genetic or environmental changes. Secondary metabolites with chemical diversity are widely present in living organisms, thus accurate quantification of secondary metabolites through appropriate analytical platforms is an important task of metabolomics. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is the most commonly used method for the detection of metabolites, providing a basis for the wide application of plant secondary metabolites. This review summarizes the advances of using LC-MS/MS techniques for the detection of phytohormone, folic acid, flavonoids and other secondary metabolites.

Blockade of TIM-3 and PD-1 enhances the antitumor effects of MAGE-A11 antigen-specific cytotoxic T lymphocytes.

Cancer immunotherapy is an attractive approach for antigen-specific T cell-mediated antitumor therapy, especially for the induction of cytotoxic T lymphocytes (CTLs). An human leukocyte antigen (HLA)-A2-restricted melanoma-associated antigen-A11 (MAGE-A11) peptide was developed that exhibited a potent capacity to induce cytotoxicity towards MAGE-A11-positive breast cancer cells by activating CTLs. However, this antitumor immune response can be suppressed by inhibitory pathways. Programmed death-1 (PD-1) and T cell immunoglobulin domain and mucin domain 3 (TIM-3) pathways are two important pathways involved in the tumor-mediated immune suppression. The present study aimed to augment the efficacy of MAGE-A11 antigen-specific CTLs via blocking PD-1 and TIM-3. The results showed that the expression levels of PD-1 and TIM-3 were unregulated during T cell induction, expansion and target cell killing. Blockade of PD-1 and TIM-3 modulated T cell proliferation, transformation and survival. In addition, treatment of cells with antibodies against PD-1 and TIM-3 enhanced the cytotoxicity of MAGE-A11 antigen-specific CTLs against breast cancer cells. The aforementioned findings suggested that MAGE-A11 antigen-specific CTLs accompanied by PD-1 and TIM-3 blockade could be considered as a potential therapy approach for breast cancer.

Epidemiology, Environmental Risks, Virulence, and Resistance Determinants of Klebsiella pneumoniae From Dairy Cows in Hubei, China.

Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen, which causes serious infections in humans and animals. To investigate the antimicrobial resistance pattern and virulence profile of K. pneumoniae, a total of 887 samples were collected from both the healthy and mastitis cows and the bedding, feed, feces, air, drinking water, spraying water, washing water, and milk cup swabs from five dairy farms in Hubei, China, during 2019 and 2020. K. pneumoniae was isolated and identified using PCR of the khe and 16S rDNA sequencing. A genotypic characterization was performed for K. pneumoniae isolates using wzi typing and multilocus sequence typing (MLST). Antimicrobial resistances were confirmed using broth microdilution against 17 antimicrobial agents and resistance and virulence genes were determined by PCR. The prevalence of K. pneumoniae was 26.94% (239/887) distributed in 101 wzi allele types (199/239, 83.26%) and 100 sequence types (STs) (209/239, 87.45%), including 5 new wzi allele type and 25 new STs. Phylogenetic analysis showed that K. pneumoniae isolated from milk, nipple swab, feed, and feces is classified in the same clone complex. By comparing with the PubMLST database, at least 67 STs have the risk of spreading in different species and regions. Interestingly, 60 STs have been isolated from humans. The isolates were highly sensitive to meropenem and colistin, but resistant to ampicillin (100%), sulfisoxazole (94.56%), cephalothin (47.28%), streptomycin (30.13%), and so on. Noteworthy, multidrug-resistant (MDR) rate was found to be 43.93% in this study. By PCR, 30 of 68 antimicrobial resistance (AMR) genes were identified; the prevalence rate of blaTEM, blaSHV, strA, strB, aadA1, and aac(6')-Ib-cr was more than 50%. Eleven CTX-M-producing K. pneumoniae were found. The detection rate of fimH, mrkD, uge, wabG, entB, iutA, iroN, and ureA was over 85%. This study reinforces the epidemiological importance of K. pneumoniae in food-producing animals in Hubei. The emergence and spread of environmental MDR K. pneumoniae may pose a potential threat to food safety and public health.

Correlation between promoter methylation of the LDH-C4 gene and DNMT expression in breast cancer and their prognostic significance.

DNA methylation plays an important role in tumorigenesis and development. The potential of aberrant DNA methylation to act as a biomarker for tumor diagnosis and prognostic evaluation is currently being explored. Lactate dehydrogenase C4 (LDH-C4) is a member of the cancer/testis antigen family that is expressed in a broad range of human tumor types, with particularly high expression patterns observed in lung cancer, melanoma and breast cancer. However, whether the methylation of the promoter region of LDH-C4 can be used as a tumor marker and its association with prognosis remain poorly understood. The present study aimed to determine the potential of the methylation status of LDH-C4 and DNA methyltransferase (DNMT) expression to be biological markers for the prognostic evaluation of breast cancer. Methylation-specific PCR was conducted to evaluate alterations in the methylation levels of LDH-C4. Immunohistochemical analysis was performed to assess the expression levels of DNMTs in breast cancer tissues. The association between the methylation status of LDH-C4 or the expression of DNMTs, and clinical pathological parameters was also evaluated. The results of the present study revealed that the demethylation rate of LDH-C4 in breast cancer tissues was significantly increased compared with that of adjacent tissues, and associations were identified between the demethylation of LDH-C4 and the histological grade, estrogen receptor, progesterone receptor and HER-2 status, and lymph node metastasis. The level of LDH-C4 demethylation was negatively correlated with the expression of DNMTs. Demethylation of the LDH-C4 promoter and DNMT expression predicted an unfavorable prognosis of patients with breast cancer. In addition, demethylation of the LDH-C4 promoter, high expression of DNMT3a and DNMT3b, histological grade and lymph node metastasis were all discovered to be independent prognostic factors in patients with breast cancer. In conclusion, results of the present study indicated that the demethylation of LDH-C4 and DNMT expression levels may be closely associated with the occurrence and development of breast cancer, in addition to lymph node metastasis. Thus, both may be used to assist the clinical evaluation of prognosis.

Transcriptome Analysis Reveals the Molecular Mechanism of GABA Accumulation during Quinoa (Chenopodium quinoa Willd.) Germination.

Quinoa (Chenopodium quinoa Willd.) with a history of 5000 years as food is extremely rich in nutrients and bioactive compounds, including γ-aminobutyric acid (GABA), a natural four-carbon non-protein amino acid with great benefits to human health. In quinoa, GABA generally increases with the germination time, but the underlying molecular mechanism is unclear. Here, we found that the GABA content in quinoa varied significantly among 25 varieties using an automatic amino acid analyzer. Next, six varieties (three low-GABA and three high-GABA varieties) were used for further analyses. The content of GABA in six varieties all showed an increasing trend after germination. In addition, Pearson's correlation analysis showed that the changes in GABA content were closely related to the transcript level or enzyme activity of three key enzymes including glutamate decarboxylase (GAD), GABA transaminase (GABA-T), and succinate-semialdehyde dehydrogenase (SSADH) in the GABA shunt, especially GAD. Based on RNA-sequencing analysis, eight GAD genes, two GABA-T genes, one SSADH gene, nine polyamine oxidase (PAO) genes, five diamine oxidase (DAO) genes, four 4-aminobutyraldehyde dehydrogenase (BADH) genes, and three thermospermine synthase ACAULIS5 (ACL5) genes were identified. Among these, CqGAD8 and CqGABA-T2 may make a greater contribution to GABA accumulation during quinoa germination.

Expression of LINC01606 in multiple myeloma and its effect on cell invasion and migration.

Given the increasing incidence of multiple myeloma (MM) in recent years, a full understanding of its pathogenesis to find effective molecular markers carries huge implications for future clinical diagnosis and treatment of MM. As the research advances, accumulating studies have pointed out that long non-coding RNAs (LncRNAs) may be the key to the future diagnosis and treatment of neoplastic diseases. OBJECTIVE: This study investigated the clinical implications of LncRNA LINC01606 in MM and its effects on the biological behavior of MM cells. METHODS: In this prospective study, 72 patients with MM (group A) admitted between July 2014 and July 2016 and 68 healthy subjects (group B) who concurrently underwent physical examination in our hospital were included. The expression of LINC01606 in peripheral blood of patients in the two groups was detected to analyze its diagnostic and prognostic value in MM. In addition, MM cells were purchased and transfected with plasmids for mimics, inhibitors and negative control of LINC01606 and miR-579-3p respectively to detect the changes in cell proliferation, invasion and migration. RESULTS: The expression of LINC01606 in group A was higher than that in group B (P<0.050). The sensitivity and specificity of peripheral blood LINC01606 in predicting MM were 85.29% and 72.39%, respectively (P<0.001). Prognostic follow-up analysis revealed higher LINC01606 levels in the dead than those in the survival. The predictive sensitivity of LINC01606 for the 3-year mortality of MM patients was 63.16%, and the specificity was 86.00% (P<0.001). Higher expression of LINC01606 indicated increased risk of 3-year mortality in patients with MM (P<0.001). Compared with LINC01606 overexpression and miR-579-3p inhibition, the proliferation, invasion and migration of cells decreased more significantly by LINC01606 inhibition and miR-579-3p overexpression (P<0.050). Dual luciferase reporter (DLR) assay confirmed the targeting relationship between LINC01606 and miR-579-3p. There was no significant difference in the activity of MM cells co-transfected with LINC01606-inhibitor and miR-579-3p-inhibitor plasmids compared with the blank group (P>0.050). CONCLUSIONS: LINC01606, with a high expression profile in MM, promotes the proliferation, migration and invasion of MM cells through targeted inhibition of miR-579-3p, which may be the key to future diagnosis and treatment of MM.

Structure, preparation, modification, and bioactivities of ß-glucan and mannan from yeast cell wall: A review.

In order to solve the antibiotic resistance, the research on antibiotic substitutes has received an extensive attention. Many studies have shown that ß-glucan and mannan from yeast cell wall have the potential to replace antibiotics for the prevention and treatment of animal diseases, thereby reducing the development and spread of antibiotic-resistant bacterial pathogens. ß-Glucan and mannan had a variety of biological functions, including improving the intestinal environment, stimulating innate and acquired immunity, adsorbing mycotoxins, enhancing antioxidant capacity, and so on. The biological activities of ß-glucan and mannan can be improved by chemically modifying its primary structure or reducing molecular weight. In this paper, the structure, preparation, modification, and biological activities of ß-glucan and mannan were reviewed, which provided future perspectives of ß-glucan and mannan.

A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value.

Chenopodium quinoa is a halophytic pseudocereal crop that is being cultivated in an ever-growing number of countries. Because quinoa is highly resistant to multiple abiotic stresses and its seed has a better nutritional value than any other major cereals, it is regarded as a future crop to ensure global food security. We generated a high-quality genome draft using an inbred line of the quinoa cultivar Real. The quinoa genome experienced one recent genome duplication about 4.3 million years ago, likely reflecting the genome fusion of two Chenopodium parents, in addition to the γ paleohexaploidization reported for most eudicots. The genome is highly repetitive (64.5% repeat content) and contains 54 438 protein-coding genes and 192 microRNA genes, with more than 99.3% having orthologous genes from glycophylic species. Stress tolerance in quinoa is associated with the expansion of genes involved in ion and nutrient transport, ABA homeostasis and signaling, and enhanced basal-level ABA responses. Epidermal salt bladder cells exhibit similar characteristics as trichomes, with a significantly higher expression of genes related to energy import and ABA biosynthesis compared with the leaf lamina. The quinoa genome sequence provides insights into its exceptional nutritional value and the evolution of halophytes, enabling the identification of genes involved in salinity tolerance, and providing the basis for molecular breeding in quinoa.

The complete mitochondrial genome of Tetrancistrum nebulosi (Monogenea: Ancyrocephalidae).

The first complete mitochondrial (mt) genome of Ancyrocephalidae is reported herein. The mt genome of Tetrancistrum nebulosi was 13,392 bp in length containing 12 protein-coding genes (lacking atp8), 22 tRNA genes and 2 rRNA genes. The longest non-coding region was located between nad5 and trnG, and the A + T content was 72.4%. All tRNAs had the typical clover-leaf secondary structure except for trnS1((AGN)), trnR, trnF and trnQ. The rrnL and rrnS subunits were separated by trnC, as documented in the monopisthocotylean groups (Benedenia and Gyrodactylus species), while they were adjacent to each other in the polyopisthocotylean species (Microcotyle sebastis, Polylabris halichoeres and Pseudochauhanea macrorchis).

Complete mitochondrial genome of the sandfish Holothuria scabra (Holothuroidea, Holothuriidae).

The complete mitochondrial genome (mitogenome) sequence of Holothuria scabra, an economically and ecologically important tropical sea cucumber, was first sequenced and annotated. The mitochondrial DNA is 15,779 bp in length and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a 456 bp putative control region, of which gene order is identical to the echinoderm ground pattern. Comparative analyses between H. scabra and other holothurians revealed three new findings: (1) the mitogenome of H. scabra is highly compact having five regions with overlapping genes and least intergenic nucleotides among the sequenced holothurians, only accounting for 3.58% of its mitogenome; (2) the genus Holothuria mitogenomes show a pattern of high interspecies divergence at the 13 PCGs, and the genetic p-distance reaches 25.68% between H. scabra and H. forskali; (3) the incomplete stop codon T of cox2 shared with H. forskali may be a common feature in the genus Holothuria.

Complete mitochondrial genome of the Olympia oyster Ostrea lurida (Bivalvia, Ostreidae).

The complete mitochondrial (mt) genome of the Olympia oyster Ostrea lurida (16,344 bp), an economically important bivalve, was newly sequenced and annotated. Ostrea lurida is the largest reported Ostrea oyster mt genomes to date and has a comparatively highest overall A + T content (65%) among the available genomes of marine oysters. High levels of variability of nad2 and nad6 genes and that of major non-coding region (MNR) indicate their potential value as useful molecular markers for population and conservation genetic studies in the future. Phylogenetic analyses based on concatenated nucleotide sequences from all 13 PCGs and 2 rRNA genes show that the European flat oyster Ostrea edulis is sister to the Asian slipper oyster Ostrea denselamellosa, while O. lurida is put at the most basal position of the clade, and indicate that Ostrea are closer to Saccostrea than Crassostrea, although gene arrangement shows a closer relationship between Ostrea and Crassostrea. The observations of the evolutionary pattern of start codon usage among the three congeneric oysters indicate that variation in start codon usage is species-correlated rather than gene-correlated, and to some extent, bears useful phylogenetic information.

The mitochondrial genome of the scallop Mimachlamys senatoria (Bivalvia, Pectinidae).

The mitochondrial (mt) genome of the scallop Mimachlamys senatoria (17,383 bp), an economically and ecologically important bivalve, was newly sequenced and annotated. Comparative analyses between M. senatoria and its congeneric sister species M. nobilis revealed three new findings: (1) M. senatoria is more prone to use G-rich start/stop codon, and variation in start/stop codon usage is species-correlated rather than gene-correlated, and in some extent, bears useful phylogenetic information; (2) The A + T content is unexpectedly low (54.1%) in MNR and that is unexpectedly high (65.4%) in atp8 in both congeneric scallops, which may represent a novel evolutionary pattern of mt genomic nucleotide composition; and (3) The tRNA gene cluster "NGV" locating upstream of the nad1 in M. senatoria is replaced by "NTGV" in M. nobilis, and a parsimonious explanation for the existence of trnT in M. nobilis is that this gene was derived from a recently duplicated trnG gene via an alloacceptor tRNA gene recruitment process.

The complete mitochondrial genome of Neobenedenia melleni (Platyhelminthes: Monogenea): mitochondrial gene content, arrangement and composition compared with two Benedenia species.

The complete mitochondrial (mt) genome sequences of Neobenedenia melleni were determined and compared with those of Benedenia seriolae and B. hoshinai. This circular genome comprises 13,270 bp and includes all 36 typical mt genes found in flatworms. Total AT content of N. melleni is 75.9 %. ATG is the most common start codon, while nad4L is initiated by GTG. All protein-coding genes are predicted to terminate with TAG and TAA. N. melleni has the trnR with a TCG anticodon, which is the same to B. seriolae but different from B. hoshinai (ACG). The mt gene arrangement of N. melleni is similar to that of B. seriolae and B. hoshinai with the exception of three translocations (trnF, trnT and trnG). The overlapped region between nad4L and nad4 was found in the N. melleni mt genome, which was also reported for the published Gyrodactylus species, but it was not found in those of B. seriolae and B. hoshinai, which are non-coding regions instead. The present study provides useful molecular characters for species or strain identification and systematic studies of this parasite.

Evolution of the tRNA gene family in mitochondrial genomes of five Meretrix clams (Bivalvia, Veneridae).

In contrast to the extreme conservation of nuclear-encoded tRNAs, organization of the mitochondrial (mt) tRNA gene family in invertebrates is highly dynamic and rapidly evolving. While gene duplication and loss, gene isomerism, recruitment, and rearrangements have occurred sporadically in several invertebrate lineages, little is known regarding the pattern of their evolution. Comparisons of invertebrate mt genomes at a generic level can be extremely helpful in investigating evolutionary patterns of variation, as intermediate stages of the process may be identified. Variation of mitochondrial tRNA organization among Meretrix clams provides good materials to investigate mt tRNA evolution. We characterized the complete mt genome of the lyrate Asiatic hard clam Meretrix lyrata, re-annotated tRNAs of four previously sequenced Meretrix clams, and undertook an intensive comparison of tRNA gene families in these clams. Our results 1) provide evidence that the commonly observed duplication of trnM may have occurred independently in different bivalve lineages and, based on the higher degree of trnM gene similarity, may have occurred more recently than expected; 2) suggest that "horizontal" evolution may have played an important role in tRNA gene family evolution based on frequent gene duplications and gene recruitment events; and 3) reveal the first case of isoacceptor "vertical" tRNA gene recruitment (VTGR) and present the first clear evidence that VTGR allows rapid evolution of tRNAs. We identify the trnS(-UCR) gene in Meretrix clams, previously considered missing in this lineage, and speculate that trnS(-UCR) lacking the D-arm in both M. lyrata and Meretrix lamarckii may represent the ancestral status. Phylogenetic analysis based on 13 concatenate protein-coding genes provided opportunities to detect rapidly evolved tRNA genes via VTGR and gene isomerism processes. This study suggests that evolution of the mt tRNA gene family in bivalves is more complex than previously thought and that comparison of several congeneric species is a useful strategy in investigating evolutionary patterns and dynamics of mt tRNA genes.

Genetic diversity and substantial population differentiation in Crassostrea hongkongensis revealed by mitochondrial DNA.

The Hong Kong oyster, Crassostrea hongkongensis, is an important fisheries resource that is cultivated in the coastal waters of the South China Sea. Despite significant advances in understanding biological and taxonomic aspects of this species, no detailed study of its population genetic diversity in regions of extensive cultivation are available. Direct sequencing of the mtDNA cox1 gene region was used to investigate genetic variation within and between eleven C. hongkongensis populations collected from typical habitats. Sixty-two haplotypes were identified; only haplotype 2 (21.74% of total haplotypes) was shared among all the eleven populations, and most of the observed haplotypes were restricted to individual populations. Both AMOVA and FST analyses revealed significant population structure, and the isolation by distance (IBD) was confirmed. The highest local differentiation was observed between the sample pools from Guangxi versus Guangdong and Fujian, which are separated by a geographic barrier, the Leizhou Peninsula. Current knowledge from seed management suggests that seed transfer from Guangxi province has likely reduced the divergence that somewhat naturally exists between these pools. The findings from the present study could be useful for genetic management and may serve as a baseline by which to monitor future changes in genetic diversity, either due to natural or anthropogenic impacts.