Search

China is the largest rice-producing country, but the genomic landscape of rice diversity has not yet been clarified. In this study, we re-sequence 1070 rice varieties collected from China (400) and other regions in Asia (670). Among the six major rice groups (aus, indica-I, indica-II, aromatic, temperate japonica, and tropical japonica), almost all Chinese varieties belong to the indica-II or temperate japonica group. Most Chinese indica varieties belong to indica-II, which consists of two subgroups developed during different phases of rice breeding. The genomic segments underlying the differences between these subgroups span 36.32 Mb. The Chinese japonica rice varieties fall into the temperate japonica group, consisting of two subgroups based on their geographical distribution. The genomic segments underlying the differences between these subgroups span 27.69 Mb. These differentiated segments in the Chinese indica varieties span 45 genes with nonsynonymous mutations that are closely related to variations in plant height and grain width. Fifty-four genes with nonsynonymous mutations are associated with the differences in heading date between the two Chinese japonica subgroups. These findings provide new insights into rice diversity in China that will facilitate the molecular breeding.

The abounding variations hidden in wild rice (Oryza rufipogon) provided potential reservoirs of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. In this study, we constructed the telomere-to-telomere (T2T) genome assembly and annotation of wild rice Y476 with a total length of 421.1 Mb and 38,055 predicted protein-coding genes, which features evident improvements in the continuity and quality of sequence compared with the existing wild rice genomes. Of Y476 genome assembly, 128 Mb and 5,984 novel genes were not found in ‘Nipponbare’ reference, leading to 690 gene families expanded and 247 gene families contracted, including disease resistance and grain regulation gene family. Two sets of chromosome segments substitution lines (CSSLs) were constructed, using Y476 as the donor parent and cultivated rice as the recurrent parents, covering the whole genome of Y476, providing materials for introducing novel genes and identification of their function. Combining the T2T reference genome and CSSL population, 254 QTLs associated with agronomic traits, biotic and abiotic stresses were identified. A receptor-like kinase gene associated with rice blast resistance was identified, a 7.8-kb insertion was found in the intron of this gene which increased its expression level. Using CRISPR/Cas9 technology and transcriptomic data, we confirmed that this wild rice allele improves rice blast resistance via regulating OsMADS26 expression. Collectively, our findings provided not only a T2T gap-free reference genome but also a highly efficient platform for novel gene identification of O. rufipogon, and therefore, have important implications for wild rice utilization.

Severe acute pancreatitis (SAP), which is characterized by acute onset and high mortality, is complicated with systemic inflammatory response syndrome. This study investigated the molecular mechanism underlying SAP-induced intestinal mucosal barrier injury. SAP was established in rats by retrograde injection of sodium taurocholate (STC) into biliopancreatic duct. Transfection of miR-99a mimic was conducted 24 h before the SAP establishment. Histological properties of pancreatic and intestinal tissues were observed by hematoxylin-eosin staining. The serum levels of interleukin (IL)-1β, tumor necrosis factor (TNF)-α, procalcitonin (PCT), endotoxin (ET), and diamine oxidase (DAO) were measured by enzyme-linked immunosorbent assay. The expressions of miR-99a, NADPH oxidase (NOX)4, zonula occludens (ZO)-1, occludin, and claudin-1 in pancreatic and the intestinal tissue were determined by quantitative reverse transcription polymerase chain reaction or Western blot. STC injection damaged pancreatic and intestinal tissues of the rats. During the model construction, the serum levels of IL-1β, TNF-α, PCT, ET, and DAO were increased, whereas miR-99a expression in pancreatic and intestinal tissues of the rats was decreased. miR-99a mimic alleviated SAP-induced histological abnormality of pancreatic and intestinal tissues; moreover, it reversed the serum levels of IL-1β, TNF-α, PCT, ET, and DAO increased by SAP, decreased SAP-increased NOX4 expression and increased the expressions of ZO-1, occludin, and claudin-1 previously decreased by SAP in pancreatic and the intestinal tissues. Thus, overexpressed miR-99a could alleviate intestinal mucosal barrier injury in rats with SAP.

Objective MicroRNA (miR)-421 plays a key role in cancer progression. It has been reported that circulating miR-421may be a potential tumor marker for the diagnosis of several cancers. However, the role of miR-421 in plasma as a potential biomarker in the diagnosis of precancerous gastric lesions (Pre) and early-stage gastric cancer (GC) remains poorly understood. In this study, we investigated miR-421 in plasma as a novel potential biomarker for the detection of precancerous gastric lesions and early-stage (GC). Materials & Methods The miRNA content was determined by quantitative real-time polymerase chain reaction (qRT-PCR). MiR-421 content in all subjects was normalized by endogenous miRNA (miR-16). The diagnostic value of miR-421 for Pre and GC was assessed by comparing receiver operating characteristic (ROC) analysis with traditional tumor markers, including CEA, CA125, CA153, CA211 and CA50. The correlation between the expression of miR-421 and the pathological characteristics of Pre and GC was analyzed. Results Elevated expression of miR-421 in plasma can robustly distinguish the normal population from Pre and GC cases, especially in the early stages of gastric cancer cases (all p p p p Conclusions Overexpression of plasma miR-421 is a novel biomarker for the detection of precancerous lesions and early gastric cancer.

OsBAK1 gene belongs to a receptor like kinase gene family in rice and shares a highly conserved gene structure and sequence homology with Arabidopsis thaliana BAK1 gene. To investigate the role of OsBAK1 in rice immunity, the full-length cDNA of OsBAK1 was isolated by RT-PCR and the transgenic rice lines (over expression and RNA-interference lines) were generated using Agrobacterium-mediated transformation. The expression level of OsBAK1 was determined by q-PCR in overexpression and RNAi transgenic rice lines. Based on quantitative polymerase chain reaction (q-PCR) results, two overexpression lines and two RNAi lines were evaluated in bioassays for resistance to Xanthomonas oryzae pv. oryzae PXO99, the causal agent of rice bacterial blight disease. Pathogenicity bioassays showed overexpression OsBAK1 lines exhibited resistance to blight disease whereas OsBAK1 RNAi lines promoted susceptibility. Besides, OsBAK1 can complement the function of AtBAK1 in Arabidopsis bak1 protoplast, activating FRK1 expression, a marker gene in PTI signaling pathway, after treatment by flg22. Furthermore, the transcriptional level of OsBAK1 was induced significantly in rice by defense signaling molecules such as salicylic acid, jasmonic acid, and PXO99 inoculation. Our results illustrated OsBAK1 positively regulates plant defense against rice bacterium pathogen Xanthomonas oryzae pv. oryzae PXO99.

Childhood acute lymphoblastic leukemia (ALL) (age 0–14 years) is 20% more common in Latino Americans than non-Latino whites. We conduct a genome-wide association study in a large sample of 3263 Californian children with ALL (including 1949 of Latino heritage) and 3506 controls matched on month and year of birth, sex, and ethnicity, and an additional 12,471 controls from the Kaiser Resource for Genetic Epidemiology Research on Aging Cohort. Replication of the strongest genetic associations is performed in two independent datasets from the Children’s Oncology Group and the California Childhood Leukemia Study. Here we identify new risk loci on 17q12 near IKZF3/ZPBP2/GSDMB/ORMDL3, a locus encompassing a transcription factor important for lymphocyte development (IKZF3), and at an 8q24 region known for structural contacts with the MYC oncogene. These new risk loci may impact gene expression via local (four 17q12 genes) or long-range (8q24) interactions, affecting function of well-characterized hematopoietic and growth-regulation pathways., Childhood acute lymphoblastic leukemia is common in Latino Americans. Here, the authors conduct a genome-wide association study in a Californian cohort containing children of Latino heritage, and identify loci on 17q12 and 8q24 which may affect hematopoietic and growth-regulation pathways.

Cassava bacterial blight is the most destructive disease in cassava, causing a significant reduction in its production. The innate immunity response, which has a broad spectrum and a persistent effect, is the basal defence of plants in response to pathogens. Isolation and identification of innate immune-related genes in cassava will contribute to understanding the disease resistance mechanism. In Arabidopsis, the receptor-like cytoplasmic kinase (RLCK) AtBIK1 is known to be an important signal mediator in pathogen-associated molecular pattern-triggered immunity (PTI) response, forming a signal complex from various receptors including the flagellin receptor FLS2, the chitin receptor CERK1 and the receptor for bacterial EF-Tu EFR (Zhang et al. 2010). In the present study, we selected a candidate receptor-like cytoplasmic kinase gene, MeBIK1, from the cassava genome. MeBIK1 encodes a 409 amino acid polypeptide comprising a typical serine/threonine protein kinase domain, and is located on the cell membrane. MeBIK1 gene expression was significantly increased upon stimulation with flagellin (flg22) and peaked at 1 h. In vitro genetic complementation experiment showed that MeBIK1 complemented the reduced pathogen-associated molecular pattern-triggered immunity (PTI) response in Arabidopsis bik1 mutant. Arabidopsis MeBIK1 overexpression lines OX1 demonstrated a strong resistance to Xanthomonas axonopodis pv. manihotis HN01, whereas its sensitivity to Pseudomonas syringae pv. tomato DC3000 was enhanced. The peak level of reactive oxygen species (ROS) burst was reached in different Arabidopsis plants (bik1, OX1 and wild type) at 12 min after induction with flg22. However, the OX1 showed significantly higher ROS levels than the control and mutant, whereas the lowest level of ROS burst was found in the bik1 mutant. These results indicate that cassava MeBIK1 has a similar function as Arabidopsis AtBIK1 and improves disease resistance in transgenic Arabidopsis by regulating the PTI response.

Mitogen-activated protein kinases (MAPKs) play important roles in plant growth and development, plant abiotic stresses signalling pathway and plant–pathogen interactions. However, little is known about the roles of MAPKs in modulating plant growth and pathogen resistance. In this study, we found that OsMAPK12–1, an alternatively spliced form of BWMK1 in rice (Oryza sativa L.), was induced by various elicitors, such as jasmonic acid, salicylic acid, melatonin and bacterial pathogens. To further investigate the involvement of OsMAPK12–1 in plant growth and stress responses to bacterial pathogens, we constructed OsMAPK12–1 overexpression and knockdown (RNAi) transgenic rice lines. Interestingly, overexpressing OsMAP12–1 inhibited seed germination and seedling growth. Additionally, the OsMAP12-1-overexpression lines displayed enhanced disease resistance against Xanthomonas oryzae pv. oryzae PXO99 and Xanthomonas oryzae pv. oryzicola RS105, whereas the OsMAPK12-1-RNAi lines were more susceptible to these pathogens than wild type. These results suggest that OsMAPK12-1 plays a negative role in plant growth and positively modulates disease resistance against bacterial blight and streak in rice.

Oral infectious diseases are general terms for infectious diseases which occur in the oral cavity and maxillofacial region, which mainly include dental caries, dental pulp and periapical diseases, periodontal diseases, maxillofacial odontogenic and non-odontogenic infections, oral mucosal infections, and peri-implant inflammation.

Bacterium is dominant microflora population in human oral cavity, and the novel species and novel genus were discovered and named one after another. This article reviewed the major biological characteristics of 5 novel genus and 16 novel species isolated from the human oral cavity from 2009 to 2012.

Identification of genes involved in mangrove species' adaptation to salt stress can provide valuable information for developing salt-tolerant crops and understanding the molecular evolution of salt tolerance in halophiles. Ceriops tagal is a salt-tolerant mangrove tree growing in mudflats and marshes in tropical and subtropical areas, without any prior genome information. In this study, we assessed the biochemical and transcriptional responses of C. tagal to high salt treatment (500 mmol/L NaCl) by hydroponic experiments and RNA-seq. In C. tagal root tissues under salt stress, proline accumulated strongly from 3 to 12 h of treatment; meanwhile, malondialdehyde content progressively increased from 0 to 9 h, then dropped to lower than control levels by 24 h. These implied that C. tagal plants could survive salt stress through biochemical modification. Using the Illumina sequencing platform, approximately 27.39 million RNA-seq reads were obtained from three salt-treated and control (untreated) root samples. These reads were assembled into 47,111 transcripts with an average length of 514 bp and an N50 of 632 bp. Approximately 78% of the transcripts were annotated, and a total of 437 genes were putative transcription factors. Digital gene expression analysis was conducted by comparing transcripts from the untreated control to the three salt treated samples, and 7,330 differentially expressed transcripts were identified. Using k-means clustering, these transcripts were divided into six clusters that differed in their expression patterns across four treatment time points. The genes identified as being up- or downregulated are involved in salt stress responses, signal transduction, and DNA repair. Our study shows the main adaptive pathway of C. tagal in saline environments, under short-term and long-term treatments of salt stress. This provides vital clues as to which genes may be candidates for breeding salt-tolerant crops and clarifying molecular mechanisms of salt tolerance in C. tagal. The expression levels of 20 candidate genes measured by RNA-Seq were validated via qRT-PCR. Eighteen genes showed consistent expression patterns in RNA-Seq and qRT-PCR results, suggesting that the RNA-seq dataset was dependable for gene expression pattern analysis.

The predominant cultivable bacteria associated with juvenile periodontitis (JP) in China were studied for the first time. Subgingival plaque samples were taken on paper points from 23 diseased sites in 15 JP patients and from 7 healthy sites in 7 control subjects. Serially diluted plaque samples were plated on nonselective blood agar and on MGB agar, a selective medium for the isolation of Actinobacillus actinomycetemcomitans. Fifteen or more isolated colonies from each sample (in sequence without selection) were purified for identification. The results indicated that the microflora in healthy sulci of the 7 control subjects was significantly different from that in diseased sites of JP patients. The predominant species in healthy sulci were Streptococcus spp. and Capnocytophaga gingivalis. In JP patients, Eubacterium sp. was found in significantly higher frequency and proportion. Actinobacillus actinomycetemcomitans was not detected in any samples. It appears that this species is not associated with juvenile periodontitis in China.

To evaluate the experimental periodontitis in rats induced by ligature plus high sugar water with and without infection of periodontopathic bacteria.Forty SD rats (5 weeks of age) were randomly divided into a control group (N) and three experimental groups (P1, P2 and P3). All experimental groups were given silk ligatures around the cervix of the second maxillary molars and were provided with drinking water containing 10% glucose. Group P2 was inoculated with P. gingivalis, three times; group P3 was inoculated with P. gingivalis and F. nucleatum, three times. At weeks 0, 2 and 4, microbiological and histological examinations were made; alveolar bone loss was stereoscopically measured as the distance from the cement-enamel junction to the alveolar crest.Microbiological examination indicated that the bacteria inoculated in groups P2 and P3 were successfully colonized and both of P. gingivalis and F. nucleatum were predominant among the bacterial colonies of the examined sites. At week 2, histological examination showed gingival erosion and alveolar bone loss in all experimental groups and periodontal pockets in groups P2 and P3. The most serious lesions were observed in group P3. At week 4, the periodontal destruction in all experimental groups became more severe.Ligature, high sugar water combined with mixed infection of periodontopathic bacteria can successfully induce experimental periodontitis in rats.

To study the effect of Para-aminobenzonic acid (PABA) on cell-surface hydrophobicity of Actinomyces viscosus.Microbial adhesion to hydrocarbons (MATH) was used to measure the cell-surface hydrophobicity of Actinomyces viscosus which grew in modified Carlsson medium with different dilution of PABA.Following the increase of concentration of PABA, the value of cell-surface hydrophobicity of Actinomyces viscosus decreased, which were 0.38900 +/- 0.00026, 0.25462 +/- 0.00168, 0.16360 +/- 0.00026 respectively(P0.05).PABA could inhibit the adherence of Actinomyces viscosus by way of changing its cell-surface hydrophobicity.

To provide scientific evidence for underpinning the use of Radix Scutellariae in the treatment of pulp and periapical diseases.Using minute amount serial dilution test, this study assessed the minimal inhibitory concentration of Radix Scutellariae extreact against Porphyromanus Endodontics. The forms of Porphyromanus endodontics treated with Radix Scutellariae extract at different concentrations were observed by use of SEM.The MIC of Radix Scutellariae extract was determined to be 1 mg/ml. Radix Scutellariae changed the forms of Porphyromanus endodontics, making them become bigger, longer and crumbled.Radix Scutellariae could inhibit the growth of Porphyromanus Endodontics.

The purpose of this study was to evaluate the effects of squamous cell carcinoma on oral bacteria.This study investigated the microbial contents of the plaque on the surfaces of oral squamous cell carcinomas. Samples were obtained from the central surface of lesions, contiguous healthy mucosa and saliva of 42 patients with oral squamous carcinoma before and after operation.The median of bacterial colony forming units per milliliter (CFUs/ml) of saliva before operation was 8.10 x 10(8) CFUs/ml. The median of CFUs per square centimeter of the tumor surface was 5.21 x 10(5) CFUs/cm2 which was significantly higher than that of the healthy (the control) mucosa (1.77 x 10(4) CFUs/cm2, P = 0.0001). The CFUs per square centimeter of mucosa surface at the operative zone was 4.34 x 10(5) CFUs/cm2 which was also significantly higher than that of the healthy (control) mucosa(7.24 x 10(4) CFUs/cm2, P = 0.0001).Oral carcinoma can break the balance of oral microflora, which may be one of the reasons leading to the high susceptivity of these compromised patients to systemic infection.

This study was designed to find out the changes in microflora on the stress-bearing areas after insertion of removable partial dentures, and in turn to explore the difference between such changes caused by metal bases and acrylic resin bases respectively.Sixteen patients who were ready to accept removable partial dentures were selected and divided into two groups. Eight patients used metal bases while the other eight patients used acrylic resin bases. Then at the following three points: before dentures were inserted, one month after wearing and three months after wearing, the total cultivable flora were counted and the proportions of bacteria detected on the stress-bearing areas were calculated.No matter what type of bases was selected, the wearing of removable partial denture enhanced the accumulation of microflora on stress-bearing areas. The percentages of Candida albicans and Lactobacilli detected on stress-bearing areas also increased significantly (P0.05). When such changes were compared, the authors found that the increment of Candida albicans caused by acrylic resin bases was higher than that caused by metal bases (P0.05).The wearing of removable partial dentures forms new retention areas between the bases and the stress-bearing areas, as a result enhances the deposit of microbe and facilitate the growth of Candida albicans and Lactobacilli. Compared with increment of Candida albicans caused by metal bases, the increment relating to acrylic resin bases is more evident.

To compare the influence of 6 trace element agents containing fluoride versus 6 trace element agents not containing fluoride on the growth of mutants of S. mutans and detect the interaction between fluoride and trace elements.Six trace element agents containing fluoride [SnF2, ZnF2, SrF2, LaF2, (NH3)2MoF8, NaF] and 6 trace element agents not containing fluoride [SnCl2, SrCl2, LaCl2, ZnAc2, (NH3)2MoO4, NaCl] were selected. The continuous anaerobic cultivating technique and the absorbency of bacteria liquid and the count of bacteria were used to assess the effects of different agents on the growth of S. mutans.NaF, SnF2, SnCl2, ZnF2, ZnAc2, (NH3)2MoF8 and (NH3)2MoO4 were found to have strong inhibition effects on the growth of mutant of S. mutans(P0.01). SnF2 had more stronger inhibition effects than SnCl2; ZnF2 had more stronger inhibition effects than ZnAc2, no significant differences were seen between (NH3)2MoF8 and (NH3)2MoO4. SnF2 and ZnF2 had most potent inhibition effects(P0.01). No significant differences were observed between SrF2, SrCl2, LaCl2, LaF2, NaCl and the control groups(P0.05).The agents containing fluoride and trace elements, such as stannum and zinc had the effects of prohibiting the growth of mutant of S. mutans, As far as caries prevention is concerned, the agents containing both fluoride and trace elements are more effective than mono-fluoride, the potential mechanism may be the synergistic action between fluoride and trace elements.

Commercially pure titanium and titanium alloy as dental implants have show impressive clinical results. Despite the high success rates, some implants do fail. Compared to those studies on osseointegration of implants, the information pertaining to their failure is little. Further studies on the relationship between implant material and micro-organism are needed. The purpose of this investigation is to study the effect of two commonly used implant materials Titanium (TA2) and Ti-6AI-4V alloy (TC4) on the growth behaviour of three subgingival predominant bacteria Streptococcus sanguis (S. s), Porphyromanus gingivalis (P. g), Fusobacterium nucleatum (F. n) and their mixture.Under anaerobic condition, bacterial suspensions of S.s, P.g, F.n and their mixture were incubated together with the two implant materials respectively, setting the same bacterial suspensions as controls. After 2, 7 and 14 days, the bacterial growth amount was assayed by means of clone forming unit (CFU) method. The pH value of the bacterial suspension was determined by pH-Meter.The results showed that there was no difference in amount of bacterial growth or pH value between TA2 group and TC4 group (P0.05). There was also no statistically significant change as to the proportion of individual bacteria in bacterial mixture or the pH value of culture suspension.Under the condition of this investigation, the two studies implant materials have no examined influences on the growth of the subgingival bacteria and the pH value of their culture environment.

To study the effect of para-aminobenzoic acid (PABA) on the growth and metabolism of Porphyromonas gingivalis (P.g).After adding different concentrations of PABA into the medium, anaerobic technique was applied to culture P.g. The products' A value and action of TLP was assayed, and P.g grew in the medium was observed by a scanning electron microscope.PABA promoted the growth of P.g and action of TLP, which would reach the highest level when PABA was 1 mg/L, and would decrease with the increasing of concentration of PABA. When the concentration arrived at 100 mg/L, PABA had no effect on them. In the mean time, PABA had effect on the form and adherence of P.g. When the concentration was 1 mg/L and 100 mg/L, this effect was strong, but as the concentration was 10 mg/L, the effect disappeared.PABA influences the growth and metabolism of P.g, which indicate that Streptococcus sanguis has regulative effect on the microecology of subgingival plaque.

Background This study aimed to explore the active oxygen scavenging mechanism of Kandelia candel, in order to provide a theoretical basis for further analysis on the physiological mechanism of salt tolerance in mangrove plants. Different concentrations of NaCl solution (0, 150, 300 and 450 mmol/L) were used for salt stress treatments on Kandelia candel, physiological indicators in the root of Kandelia candel were measured in different processing time. Results With the increase of salt concentrations and processing time, the contents of total proteins in the root of Kandelia candel were reduced; the CAT activity, SOD activity, ASA content and MDA content all had decreased with the increase of salt concentrations and shown a trend from ascent to descent with the increase of processing time, the peak of ASA and MDA contents were observed at 6 h, that of SOD activity was observed at 9 h and that of CAT activity was at 12 h; POD activity had shown an overall upward trend with the increase of salt concentrations and processing time, which reached the maximum at 24 h; the variations of these physiological indicators were more significant in high concentrations of NaCl solution (450 mmol/L). Conclusions A certain salt concentration (Kandelia candel seedlings. At the early stage of high-salt stress, Kandelia candel can rapidly activate antioxidant defense system to resist the salt induced oxidative stress, thus reducing the damages of oxidative stress to plasma membrane, which might be an effective means for Kandelia candel to resist high salt stress.