The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes. They are known to play important roles in the specification of tissue types in animals. On the other hand, few plant bHLH proteins have been studied functionally. Recent completion of whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) allows genome-wide analysis and comparison of the bHLH family in flowering plants. We have identified 167 bHLH genes in the rice genome, and their phylogenetic analysis indicates that they form well-supported clades, which are defined as subfamilies. In addition, sequence analysis of potential DNA-binding activity, the sequence motifs outside the bHLH domain, and the conservation of intron/exon structural patterns further support the evolutionary relationships among these proteins. The genome distribution of rice bHLH genes strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of the bHLH gene family, consistent with the birth-and-death theory of gene family evolution. Bioinformatics analysis suggests that rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs. In addition, similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.

Chilling injury is one of the most important limiting factors affecting rice production in temperate and high-elevation areas. In this study, 146 microsatellite markers were employed to identify quantitative trait loci (QTL) conferring cold tolerance at seedling stage (CTS) .The mapping population consisted of 193 doubled haploid (DH) lines, which derived from a cross between a cold-tolerant japonica variety (AAV002863) and a cold-sensitive indica cultivar (Zhenshan97B). Tolerance to cold was assessed by the survival percentage of seedlings after cold treatment. In a climate chamber, after treatment at 68C/108C for 7 d, the measurement was taken on the sixth day of the recovery stage at room temperature. The phenotypic distribution of the DH population approximately fitted normality with skewness and kurtosis less than 0.3, and the difference among the three repetitions was not significant. Five main effect QTLs were identified with LOD > 4.0 on chromosomes 1, 2, 8 using a composite interval mapping approach. The accumulated contribution of the five QTLs was 62.28%, and a major QTL (LOD = 15.09) was identified on chromosome 2 flanked by RM561 and RM341, which explained 27.42% of the total phenotypic variation. Four significant epistatic interactions were also detected with a total contribution of 20.14%.

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The majority of 170 rice accessions used in this study were diverse landraces or varieties from a putative mini-core collection of Chinese germplasm along with some widely used parental lines in genetic analysis or breeding (a few from abroad). The population was genotyped using 84 SSR or InDel markers on chromosome 7 and 48 markers on other chromosomes. The phenotyping of heading date, plant height and panicle length were carried out in different locations for 2 years. Based on morphological characterization, distance-based clustering and model-based estimation of marker data, the population showed a predominant structure with two subpopulations in correspondence with indica and japonica subspecies. The estimation of linkage disequilibrium in 2 Mb windows varied along chromosome 7 and showed parallel changes with inter-subspecies differentiation of marker loci (Fst). Based on the mixed linear model considering population structure and family relatedness [i.e. the (Q + K) model], one to three associated markers (P < or = 0.0001) per trait per experiment were scanned out on rice chromosome 7. Most significant loci were repeated for the data from both field experiments while two loci were associated with two or three traits. Marker-based allelic effects were shown in a couple of associated markers as examples. The application of association results in breeding program was also discussed.

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Our transcriptome analysis revealed in bladder cancer (BCa) tissues a significant induction of lysosomal-associated multispanning membrane protein 5 (LAPTM5), a lysosomal membrane protein preferentially expressing in immune cells and hematopoietic cells. Transportation of LAPTM5 from Golgi to lysosome could be inhibited by deficiency of Nedd4, a key member of E3 ubiquitin ligase family overexpressing in invasive BCa and promoting its progression. Therefore, we hypothesize that LAPTM5 may be closely correlated with BCa tumorigenesis. In human BCa tissues, we observed that LAPTM5 was significantly induced at both mRNA and protein levels, which is consistent with our microarray result. Furthermore, we established a BCa cell model with downregulated LAPTM5, revealing a significantly delayed growth rate in the BCa cells with knockdown of LAPTM5. Moreover, cell cycle arrest at G0/G1 phase was triggered by decreased LAPTM5 as well, which could lead to delayed BCa cell growth. In contrast, no significant alteration of apoptosis in the BCa cells with downregulated LAPTM5 was noticed. Analysis of the changes of migration and invasion, showed significant reduced LAPTM5 suppressed cell metastasis. Furthermore, proteins involved in epithelial-mesenchymal transition (EMT) were strongly altered, which plays a central role in metastasis. In addition, phosphorylated ERK1/2 and p38, key members of mitogen-activated protein kinase (MAPK) family regulating BCa tumorigenesis, were strongly decreased. Taken together, our results suggested that decreased LAPTM5 inhibited proliferation and viability, as well as induced G0/G1 cell cycle arrest possibly via deactivation of ERK1/2 and p38 in BCa cells.

Stomata are highly specialized epidermal structures that control transpiration and gas exchange between plants and the environment. Signal networks underlying stomatal development have been previously uncovered but much less is known about how signals involved in stomatal development are transmitted to RNA polymerase II (Pol II or RPB), which plays a central role in the transcription of mRNA coding genes. Here, we identify a partial loss-of-function mutation of the third largest subunit of nuclear DNA-dependent Pol II (NRPB3) that exhibits an increased number of stomatal lineage cells and paired stomata. Phenotypic and genetic analyses indicated that NRPB3 is not only required for correct stomatal patterning, but is also essential for stomatal differentiation. Protein-protein interaction assays showed that NRPB3 directly interacts with two basic helix-loop-helix (bHLH) transcription factors, FAMA and INDUCER OF CBF EXPRESSION1 (ICE1), indicating that NRPB3 serves as an acceptor for signals from transcription factors involved in stomatal development. Our findings highlight the surprisingly conserved activating mechanisms mediated by the third largest subunit of Pol II in eukaryotes.

BackgroundRecently, pretreatment monocyte counts and the lymphocyte/monocyte ratio (LMR) have been proven to be significantly associated with the clinical outcomes of several types of cancer. In this study, we analyzed the prognostic significance of the LMR in stage Ib1–IIa cervical cancer patients who underwent a radical operation.MethodsA total of 485 patients with stage Ib1–IIa cervical cancer were included in this retrospective study. We evaluated the prognostic values of the absolute lymphocyte count, absolute monocyte count, and LMR by applying receiver operating characteristic curves. Kaplan–Meier curves and multivariate Cox proportional analyses were used to determine the recurrence-free survival (RFS) and overall survival (OS).ResultsThe area under the curve was 0.640 for the RFS and 0.647 for the OS using the LMR. In the univariate analysis, an elevated preoperative LMR was significantly associated with an increased RFS (hazard ratio [HR], 0.373; 95% confidence interval [CI]: 0.247–0.563; P<0.001), and this result remained significant in the multivariate analysis (HR, 0.439; 95% CI: 0.279–0.693; P<0.001). In the univariate analysis, an elevated LMR was also significantly associated with an increased OS (HR, 0.381; 95% CI: 0.233–0.622; P<0.001), and the significance persisted in the multivariate analysis (HR, 0.417; 95% CI: 0.244–0.714; P=0.001).ConclusionA decreased pretreatment LMR is associated with a poor prognosis in stage Ib1–IIa cervical cancer patients who undergo a radical operation. A prospective study is warranted for further validation of our findings.