Genome-wide analysis of tobacco NtTOM1/TOM3 gene family and identification of NtTOM1a/ NtTOM3a response to tobacco mosaic virus.

BACKGROUND: TOBAMOVIRUS MULTIPLICATION 1 (TOM1) and its homolog TOBAMOVIRUS MULTIPLICATION 3 (TOM3) play a prominent role in the multiplication of tobacco mosaic virus (TMV) in higher plants. Although homologs of NtTOM1/TOM3 genes have been identified in several plant species, little is known about the characteristics and functions of NtTOM1/TOM3 at the genome-wide level in tobacco (Nicotiana tabacum L.). RESULTS: In this study, we performed genome-wide identification and expression pattern analysis of the tobacco NtTOM1/TOM3 gene family. Twelve NtTOM1/TOM3 genes were identified and classified into four groups based on phylogenetic analysis. Sequence and conserved domain analyses showed that all these genes contained a specific DUF1084 domain. Expression pattern analysis showed that NtTOM1a, NtTOM1b, NtTOM1d, NtTOM3a, NtTOM3b, and NtTOM3d were induced by TMV at 1-, 3-, and 9 dpi, whereas the expression of other genes was not responsive to TMV at the early infection stage. TMV virion accumulation showed no obvious difference in either nttom1a or nttom3a mutants compared with the wild type. However, the virus propagation was significantly, but not completely, inhibited in the nttom1atom3a double mutant, indicating that other gene family members may function redundantly, such as NtTOM1b and NtTOM1d. In addition, overexpression of NtTOM1a or NtTOM3a also inhibited the TMV replication to some extent. CONCLUSIONS: The present study performed genome-wide analysis of the NtTOM1/TOM3 gene family in tobacco, and identified NtTOM1a and NtTOM3a as important genes involved in TMV multiplication based on functional analysis. These results provide a theoretical basis for further improving TMV resistance in tobacco.

Fine mapping and identification of two NtTOM2A homeologs responsible for tobacco mosaic virus replication in tobacco (Nicotiana tabacum L.).

BACKGROUND: Tobacco mosaic virus (TMV) is a widely distributed viral disease that threatens many vegetables and horticultural species. Using the resistance gene N which induces a hypersensitivity reaction, is a common strategy for controlling this disease in tobacco (Nicotiana tabacum L.). However, N gene-mediated resistance has its limitations, consequently, identifying resistance genes from resistant germplasms and developing resistant cultivars is an ideal strategy for controlling the damage caused by TMV. RESULTS: Here, we identified highly TMV-resistant tobacco germplasm, JT88, with markedly reduced viral accumulation following TMV infection. We mapped and cloned two tobamovirus multiplication protein 2A (TOM2A) homeologs responsible for TMV replication using an F2 population derived from a cross between the TMV-susceptible cultivar K326 and the TMV-resistant cultivar JT88. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated loss-of-function mutations of two NtTOM2A homeologs almost completely suppressed TMV replication; however, the single gene mutants showed symptoms similar to those of the wild type. Moreover, NtTOM2A natural mutations were rarely detected in 577 tobacco germplasms, and CRISPR/Cas9-mediated variation of NtTOM2A led to shortened plant height, these results indicating that the natural variations in NtTOM2A were rarely applied in tobacco breeding and the NtTOM2A maybe has an impact on growth and development. CONCLUSIONS: The two NtTOM2A homeologs are functionally redundant and negatively regulate TMV resistance. These results deepen our understanding of the molecular mechanisms underlying TMV resistance in tobacco and provide important information for the potential application of NtTOM2A in TMV resistance breeding.

Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement.

Maize is an important crop worldwide, as well as a valuable model with vast genetic diversity. Accurate genome and annotation information for a wide range of inbred lines would provide valuable resources for crop improvement and pan-genome characterization. In this study, we generated a high-quality de novo genome assembly (contig N50 of 15.43 Mb) of the Chinese elite inbred line RP125 using Nanopore long-read sequencing and Hi-C scaffolding, which yield highly contiguous, chromosome-length scaffolds. Global comparison of the RP125 genome with those of B73, W22, and Mo17 revealed a large number of structural variations. To create new germplasm for maize research and crop improvement, we carried out an EMS mutagenesis screen on RP125. In total, we obtained 5818 independent M2 families, with 946 mutants showing heritable phenotypes. Taking advantage of the high-quality RP125 genome, we successfully cloned 10 mutants from the EMS library, including the novel kernel mutant qk1 (quekou: "missing a small part" in Chinese), which exhibited partial loss of endosperm and a starch accumulation defect. QK1 encodes a predicted metal tolerance protein, which is specifically required for Fe transport. Increased accumulation of Fe and reactive oxygen species as well as ferroptosis-like cell death were detected in qk1 endosperm. Our study provides the community with a high-quality genome sequence and a large collection of mutant germplasm.

iTRAQ-based analysis of sperm proteome from normozoospermic men achieving the rescue-ICSI pregnancy after the IVF failure.

BACKGROUND: In the assisted reproduction, the infertile molecules of spermatozoa from normozoospermic men who underwent the unexplained failure of in vitro fertilization (IVF) due to the lack of sperm binding to the normal zona pellucida, and then achieved pregnancy with the rescue intracytoplasmic sperm injection (R-ICSI) remain unclear. More works are still necessary to explore this male infertile mechanism. METHODS: Normozoospermicmen with the IVF pregnancy and normozoospermic men with the R-ICSI pregnancy after the conventional IVF failure were collected. iTRAQ-based proteomic approach were performed to reveal the new infertile causes between the IVF pregnancy men and the R-ICSI pregnancy men. To validate the confidence of proteome data, the individual samples were analyzed by western blot and immunofluorescence. Further, the spontaneous acrosome reactions were measured to evaluate the sperm quality. RESULTS: Compared with IVF pregnancy group, 56 sperm proteins were differentially expressed in the R-ICSI pregnancy group. Bioinformatic analyses (PANTHER, DAVID, PubMed and STRING) indicated these altered sperm proteins were involved in various molecular functions: reproduction, chromosome organization, and sperm-oocyte interaction. Moreover, the confidence of proteome data was confirmed by western blot and immunofluorescence using the individual samples, which were consistent with our proteomic data. Additionally, an increased rate of the spontaneous acrosome reaction rate was found in the R-ICSI pregnancy group. CONCLUSIONS: The sealtered sperm proteins and the increased spontaneous acrosome reaction rate might account for this unexplained male infertility in the R-ICSI pregnancy patients. The present proteomic results will throw light on the better understanding of the unexplained infertile mechanisms underlying these normozoospermic man who achieved R-ICSI pregnancy after IVF failure.

In-depth quantitative proteome analysis of seminal plasma from men with oligoasthenozoospermia and normozoospermia.

RESEARCH QUESTION: Can seminal plasma markers for oligoasthenozoospermia be identified by comparison of the human seminal plasma proteome in men with oligoasthenozoospermia and normozoospermia? DESIGN: An in-depth quantitative proteome analysis was conducted using a high-throughput method named isobaric tag for relative and absolute quantification. A total of 734 seminal plasma proteins were quantified by mass spectrometry. RESULTS: Compared with the seminal plasma from men with normozoospermia, 22 upregulated proteins and 20 downregulated proteins were identified in the oligoasthenozoospermic seminal plasma. These differential seminal plasma proteins were involved in various physiological processes, including metabolism, transport, antioxidation and immune response. The confidence of some proteome data was further verified by western blot of (prostate-specific antigen [KLK3], lactotransferrin [LTF], alpha-1-antitrypsin [SERPINA1] and glyceraldehyde-3-phosphate dehydrogenase [GAPDH]). Additionally, 38% of the seminal plasma proteins identified in this study have not been reported in previously published studies on seminal plasma proteome, and 53% of our seminal plasma proteins were shared with published studies on human plasma proteome. CONCLUSIONS: Our seminal plasma proteome research provides new complementary high-confidence data, and also enhances understanding of the pathogenic mechanisms in oligoasthenozoospermia.

Analysis of the mechanism of resistance to enzymatic hydrolysis of RS-5 resistant starch.

RS-5 refers to the resistant starch formed by complexation of starch molecules with other molecules. In this study, the molecular mechanism of RS-5 was analysed. First, it was found, when α-amylase acted on the starch-lipid complexes, the glucose residues involved in complexation cannot be hydrolyzed by α-amylase, while the glucose residues not directly involved in complexation can be hydrolyzed. Second, lipid molecules are not necessary for the formation of RS-5 and can be replaced with small peptides or decanal molecules. Considering the multiple health hazards that may result from excessive lipid intake, small peptides composed of essential amino acids may be more desirable materials for RS-5 preparation. Third, starch-lipid complexes had strong interactions with α-amylase, which provides evidence in support of the sliding continuum hydrolysis hypothesis of α-amylase. These results revealed the mechanism of RS-5 at the molecular level, which provides a reference for the production and research of RS-5.

Dehydroevodiamine inhibits PEDV through regulateing ERK1/2 MAPK pathway in Vero cells.

Porcine epidemic diarrhea virus (PEDV) results in severe economic losses to the swine industry due to its widespread prevalence and high mortality. Currently, there is no effective treatment against PEDV. New antiviral therapies are urgently needed to control this highly contagious pathogen. In this research, the anti-PEDV activity and mechanism of Dehydroevodiamine (DHED) were investigated in vitro. Our results showed that DHED exerted satisfactory anti-PEDV activity by ameliorating cytopathic effects (CPEs), reducing virus titer, and inhibiting PEDV N protein expression and gene transcription dose-dependently. The antiviral mechanism of DHED is related to its inhibition of the entry, replication, and assembly stages of PEDV life cycle. In addition, DHED can regulate the MAPK signaling pathway, and suppress phosphorylated ERK1/2 activation, thus exerting antiviral effects. In conclusion, our research confirmed the anti-PEDV activity and mechanism of DHED, preliminarily providing a new strategy for anti-PEDV drug development.

In vivo study revealed pro-tumorigenic effect of CMTM3 in hepatocellular carcinoma involving the regulation of peroxisome proliferator-activated receptor gamma (PPARγ).

PURPOSE: To clarify the ambiguity of the function of CMTM3 in the development of hepatocellular carcinoma (HCC) and explore its molecular mechanism. METHODS: The Cmtm3-KO C57BL/6 mouse strain was established using CRISPR-Cas9. Acute liver damage and HCC models were induced by peritoneal injection of 100 or 25 mg/kg.BW N-Nitrosodiethylamine (DEN) to male mice. Liver function and histology were evaluated by blood serum levels of AST and ALT, and HE staining. Gene and protein expression in liver tissues was investigated by RNA-seq, RT-qPCR, Western blotting, immunohistochemistry, and immunofluorescence. Protein-protein interactions were studied by STRING and topological measures. The mRNA expression of CMTM3 and PPARs and patient survival were analyzed using the UALCAN database. RESULTS: Global knockout of Cmtm3 in KO mice was successfully confirmed. Cmtm3 knockout alleviated DEN-induced acute damage to liver histological integrity and liver function, reduced DNA damage and apoptosis, and also caused a significantly reduced number (WT: 8.7 ± 5.5 vs. KO: 2.7 ± 3.1, P = 0.0394) and total size of tumors (WT: 130.9 ± 181.8 mm2 vs. KO: 9.3 ± 11.5 mm2, P = 0.026) in the liver. Mechanistically, Cmtm3 knockout resulted in reduced expression and inactivation of Pparγ and its downstream lipid metabolism genes (e.g. Adipoq) upon DEN intoxication. CMTM3 and PPARγ were both overexpressed in HCC, and higher levels of both genes were associated with worse overall survival of HCC patients. CONCLUSION: This study clarified the pro-tumorigenesis role of CMTM3 in HCC in vivo, possibly through the upregulation of PPARγ and activation of the PPAR pathway.

Synthesis of biochar@α-Fe2O3@Shewanella loihica complex for remediation of soil contaminated by hexavalent chromium: Optimization of conditions and mechanism.

The reduction of hexavalent chromium combined with the process of dissimilatory iron reduction is an important strategy for microbial remediation of chromium-contaminated soil. However, its applicability is limited by the slow speed of bacterial bioreduction and the toxic effect of heavy metals on bacteria. Here, biochar (BC) was used as a substrate and was loaded with iron oxide in the form of hematite and Shewanella loihica to synthesize a BC@α-Fe2O3@S. loihica complex and thus achieve combined microbial-chemical remediation. After optimization by a Box-Behnken design, the optimal dosages of the complex, humic acid (as an electron shuttle), and sodium lactate (as an electron donor) were found to be 1.38 mL/g, 33.94 mg/g, and 12.95%, respectively. The Cr(VI) reduction rate in soil contaminated with 1000 mg/kg Cr(VI) reached 98.26%, and remediation could be achieved within 7 days. Characterization of the BC@α-Fe2O3@S. loihica complex before and after it was used for remediation by energy-dispersive X-ray spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and Fourier transform infrared spectroscopy proved that the oxygen-containing functional groups and aromatic compounds on the surface of the BC participated in the adsorption and reduction of Cr(VI) and that the loaded hematite particles were fully utilized by microorganisms. Therefore, the BC@α-Fe2O3@S. loihica complex has great potential for the remediation of Cr(VI)-contaminated soil.

Isolation and pathogenic characterization of duck adenovirus 3 mutant circulating in China.

Duck adenoviruses (DAdVs) include serotype 1 (DAdV-1) in the genus Atadenovirus and serotypes 2-4 (DAdV-2, 3, and 4) in the genus Aviadenovirus. DAdV-3 was initially isolated from Chinese Muscovy ducks in 2014, whereby the infected ducks exhibited yellowing and hemorrhaging in the liver, along with slight pericardial effusion, swelling, and hemorrhaging in the kidneys. In recent years, duck adenovirus infections have appeared in Muscovy duck farms in Fujian, Zhejiang, Anhui, Guangdong, and other places in China. They have an incidence rate of 40 to 55% and a mortality rate of 35 to 43%, resulting in great losses to the duck breeding industry. In this study, 7 DAdV-3 strains, designated as TZ193, FJPT20161124, GX20170519, FJZZ, GDMM, AHAQ, and GDHS were isolated from Muscovy ducks in different provinces of China during 2016-2019, and their complete genomics were sequenced. Their genomes all exhibited significant deletions in ORF67, which also had G to A transitions at the 41st and 977th nt positions, resulting in a stop codon. The pathogenicity of TZ193, a novel isolate of DAdV-3, was investigated in Muscovy ducks. TZ193 caused characteristic lesions of swelling as well as hemorrhagic liver and kidney in the infected ducklings. Moreover, the mortality rate of TZ193 in 5-day-old domestic ducks was 100%. Our data provide concrete evidence for the identification of the DAdV-3 novel variant mutant in China, which effects increased mortality in ducks. This highlights the necessity for monitoring the specific molecular epidemiology of novel DAdV-3 mutants and the development of new vaccines in the future.

MicroRNA-539 inhibits the progression of Wilms' Tumor through downregulation of JAG1 and Notch1/3.

BACKGROUND: Previous studies demonstrated that miR-539 play an important role in the carcinogenesis of some cancers. The aim of the present study was to determine the role of miR-539 in the pathogenesis of Wilms' Tumor (WT). METHODS: The expression level of miR-539 was measured by qRT-PCR in 42 WT tissues and SK-NEP-1 cell line. Protein expression of genes (E-cadherin, N-cadherin, Vimentin, Notch 1, Notch 3 and JAG1) was assessed by Western blot. The function of miR-539 was investigated in SK-NEP-1 cells by MTT and Transwell assays. The relationship between miR-539 and JAG1 was verified by a dual luciferase assay in SK-NEP-1 cells. RESULTS: The expression level of miR-539 was significantly decreased in WT tissues. Downregulation of miR-539 was closely related to NWTS-5 stage, lymph node metastasis and histological type of WT patients. Furthermore, low miR-539 expression was associated with a shorter overall survival rate in WT patients. In vitro, overexpression of miR-539 suppressed proliferation, migration and invasion of SK-NEP-1 cells. In addition, JAG1 was a direct target of miR-539. MiR-539 inhibited the development of WT by inhibiting JAG1-Notch1/3 expressing and blocking EMT. CONCLUSION: MiR-539 inhibited the progression of WT through downregulation of JAG1 and Notch1/3.

Supplementation of cryopreservation medium with TAT-Peroxiredoxin 2 fusion protein improves human sperm quality and function.

OBJECTIVE: To investigate the potential effects of TAT-PRDX2 protein supplementation to the cryopreservation medium on post-thaw sperm quality and function. DESIGN: In vitro prospective study. SETTING: Medical university hospital. PATIENT(S): Fifty normozoospermic, 50 asthenozoospermic, and 50 oligoasthenozoospermic men undergoing semen analysis for couple infertility. INTERVENTION(S): Each semen sample was divided into three aliquots: fresh, cryopreserved control (without additive), and cryopreserved with TAT-PRDX2 protein. MAIN OUTCOME MEASURE(S): Sperm motility, viability, mitochondrial potential, and DNA damage as well as reactive oxygen species (ROS) levels and lipid peroxidation were analyzed. Acrosome reaction and zona-free hamster oocyte penetration tests were performed to assess the fertilization ability of cryopreserved spermatozoa. RESULT(S): In normozoospermic and asthenozoospermic groups, the addition of 150 µg/mL TAT-PRDX2 significantly reduced intracellular ROS and malondialdehyde levels and enhanced post-thaw sperm motility and viability when compared with the cryopreserved control of the respective groups but did not produce any significant protective effect in the oligoasthenozoospermic group. Mitochondrial potential was significantly increased, whereas DNA fragmentation was significantly decreased, after TAT-PRDX2 supplementation only in the asthenozoospermic group when compared with the cryopreserved control. Although the penetration rate and the penetration index were not markedly improved, TAT-PRDX2 supplementation obviously reduced spontaneous acrosome reaction and increased calcium ionophore-induced acrosome reaction in the normozoospermic and asthenozoospermic groups. CONCLUSION(S): TAT-PRDX2 protein effectively exerted cryoprotective effects on spermatozoa by reducing intracellular ROS level and thereby improved post-thaw sperm quality and function, especially for asthenozoospermic samples. TAT-PRDX2 protein is a promising additive for developing a new and highly efficient semen cryoprotectant.

Expression and clinical significance of SATB1 and TLR4 in breast cancer.

This study investigated the expression of special AT-rich sequence-binding protein 1 (SATB1) and toll-like receptor 4 (TLR4) protein in breast cancer and its clinical significance. We collected breast cancer tissues from 120 patients and adjacent non-cancerous tissue from 53 patients. SATB1 was expressed in 89 cases of breast cancer (74.17%) and in 7 cases of adjacent non-cancerous tissue (13.21%). TLR4 was expressed in 70 cases of breast cancer tissues (58.33%) and in 48 cases of adjacent non-cancerous tissue (90.57%). The differences of SATB and TLR4 in breast cancer and adjacent non-cancerous tissue were statistically significant. We found a negative correlation between the expression of SATB1 and TLR4 (r=-0.624, P<0.05). The expression of SATB1 and TLR4 were not significantly correlated with age, menopause, and PR and HER-2 protein expression, but were significantly correlated with tumor size, local lymphatic metastasis, histopathological grade, tumor stage, and ER protein expression (P<0.05). Overall, SATB1 and TLR4 proteins are involved in the development of breast cancer, a finding of great significance to identify therapeutic targets and prognosis markers for breast cancer.

Screening and functional analysis of a differential protein profile of human breast cancer.

To improve the understanding of the enriched functions of proteins and to identify potential biomarkers in human breast cancer, the present study constructed a differentially expressed protein profile by screening immunohistochemistry maps of human breast cancer proteins. A total of 1,688 proteins were found to be differentially expressed in human breast cancer, including 773 upregulated and 915 downregulated proteins. Of these proteins, secreted and membrane proteins were screened and clustered, and more enriched biological functions and pathways were presented in the upregulated protein profiles. Furthermore, altered serum levels of peroxiredoxin (PRDX)2, PRDX6, cathepsin (CTS)B and CTSD were detected by ELISA assay. The present study provides a novel global mapping of potential breast cancer biomarkers that could be used as background to identify the altered pathways in human breast cancer, as well as potential cancer targets.

Functional analysis of human cancer-associated genes and their association with the testes and epididymis.

Human cancer-associated UniGene sets (NCBI GeneBank) provide a platform for identifying differentially-expressed genes in human cancers. The present study identified and characterized a set of human cancer-associated genes using the Digital Differential Display (DDD) and functional analysis tools. A total of 1,904 genes were differentially expressed in 15 cancer types, including genes that had been previously shown to be specific in certain human cancers. A total of 274 genes were uniquely expressed in certain cancer types, including 37 genes that were highly expressed in the human testes and epididymis. These genes mainly functioned as ribosomal proteins, enzymes, receptors, secretory proteins and cell adhesion molecules. The most common domains that were encoded by the cancer-associated genes were those of cytochrome P450 CYP2D6, serpin and apolipoprotein A-I. A further gene ontology (GO) enrichment analysis revealed seven major functional clusters, which corresponded to the enriched pathways involved in cancer. The present study provides a source of cancer-associated genes and their functions. The results provide new insights into cancer biology and the involvement of highly-expressed epididymal genes in cancer biomarkers.

A specific induction of interleukin-10 by the Map41 recombinant PPE antigen of Mycobacterium avium subsp. paratuberculosis.

Interleukin-10 (IL-10) is not only an essential immunoregulator in host immunity, but also it accounts for the intracellular survival of mycobacteria because of its inhibitory activity against anti-mycobacterial functions of macrophage. It has been also indicated that blood cells from calves infected with Mycobacterium avium subsp. paratuberculosis (Map) produce a large amount of IL-10 after stimulation with Map antigen, and it leads to suppression of Interferon-gamma (IFN-gamma) production in T-cells. This characteristic expression of IL-10 in Map-infected cattle seems to be playing important roles in the pathogenesis of Johne's disease caused by Map, and could be an important diagnostic indicator. The aim of this study was to investigate the diagnostic significance of IL-10 production from blood cells stimulated by a PPE (Proline-Proline-Glutamic acid) protein family of Map. The recombinant PPE protein, Map41, which has been reported as one of the IFN-gamma inducing antigens of Map, also strongly induced IL-10 from macrophages obtained from infected calves. The elicited IL-10 production in response to Map41 from experimentally infected calves was as early as 2 weeks after the inoculation of Map, and the IL-10 production was detected earlier than that of IFN-gamma. The blood cells from calves immunized with Map produced higher amounts of IL-10 against Map41 stimulation than those of calves immunized with various Mycobacterium species. Furthermore, this IL-10 induction also showed high specificity to Map in guinea pigs experimentally infected with various Mycobacterium species. These observations suggest that IL-10 assay is a useful diagnostic method in the early stage of Johne's disease.

Human embryos derived by somatic cell nuclear transfer using an alternative enucleation approach.

Somatic cell nuclear transfer (SCNT) was used to generate patient-specific embryonic stem cells (ESCs) from blastocysts cloned by nuclear transfer (ntESCs). In this study, a total of 135 oocytes were obtained from 12 healthy donors (30-35 years). Human oocytes, obtained within 2 h following transvaginal aspiration, were enucleated using a Spindle Imaging System to position the spindle and chromosomes that lay on the metaphase plate, and a Zona Infrared Laser Optical System was used to open a single hole in the zona pellucida at the ~ 2 o'clock position. Human fibroblasts and lymphocytes were used to construct SCNT embryos. Nearly half (26 of 58) of the oocytes were fused after electrofusion and embryo development rates were 96.2% (two-cell, 25 of 26), 92.3% (four-cell, 24 of 26), 61.5% (eight-cell, 16 of 26), 34.6% (16-cell, 9 of 26), 26.9% (morula, 7 of 26), and 19.2% (blastocyst, 5 of 26), respectively, following incubation in improved G-series sequential medium. One cloned blastocyst was used for STR-DNA identification and genetic polymorphism analysis of mtDNA, and STR-DNA analysis of all cloned blastocysts indicated they were derived from SCNT. Quantitative analysis showed that mtDNA of cloned embryos reflected the change tendency of those observed in human IVF embryos. Our research provides an alternative enucleation approach for producing human SCNT-derived blastocysts, and may aid in providing a new method for human therapeutic cloning.