Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas.

BACKGROUND: In higher plants, inflorescence architecture is an important agronomic trait directly determining seed yield. However, little information is available on the regulatory mechanism of inflorescence development in perennial woody plants. Based on two inflorescence branching mutants, we investigated the transcriptome differences in inflorescence buds between two mutants and wild-type (WT) plants by RNA-Seq to identify the genes and regulatory networks controlling inflorescence architecture in Jatropha curcas L., a perennial woody plant belonging to Euphorbiaceae. RESULTS: Two inflorescence branching mutants were identified in germplasm collection of Jatropha. The duo xiao hua (dxh) mutant has a seven-order branch inflorescence, and the gynoecy (g) mutant has a three-order branch inflorescence, while WT Jatropha has predominantly four-order branch inflorescence, occasionally the three- or five-order branch inflorescences in fields. Using weighted gene correlation network analysis (WGCNA), we identified several hub genes involved in the cytokinin metabolic pathway from modules highly associated with inflorescence phenotypes. Among them, Jatropha ADENOSINE KINASE 2 (JcADK2), ADENINE PHOSPHORIBOSYL TRANSFERASE 1 (JcAPT1), CYTOKININ OXIDASE 3 (JcCKX3), ISOPENTENYLTRANSFERASE 5 (JcIPT5), LONELY GUY 3 (JcLOG3) and JcLOG5 may participate in cytokinin metabolic pathway in Jatropha. Consistently, exogenous application of cytokinin (6-benzyladenine, 6-BA) on inflorescence buds induced high-branch inflorescence phenotype in both low-branch inflorescence mutant (g) and WT plants. These results suggested that cytokinin is an important regulator in controlling inflorescence branching in Jatropha. In addition, comparative transcriptome analysis showed that Arabidopsis homologous genes Jatropha AGAMOUS-LIKE 6 (JcAGL6), JcAGL24, FRUITFUL (JcFUL), LEAFY (JcLFY), SEPALLATAs (JcSEPs), TERMINAL FLOWER 1 (JcTFL1), and WUSCHEL-RELATED HOMEOBOX 3 (JcWOX3), were differentially expressed in inflorescence buds between dxh and g mutants and WT plants, indicating that they may participate in inflorescence development in Jatropha. The expression of JcTFL1 was downregulated, while the expression of JcLFY and JcAP1 were upregulated in inflorescences in low-branch g mutant. CONCLUSIONS: Cytokinin is an important regulator in controlling inflorescence branching in Jatropha. The regulation of inflorescence architecture by the genes involved in floral development, including TFL1, LFY and AP1, may be conservative in Jatropha and Arabidopsis. Our results provide helpful information for elucidating the regulatory mechanism of inflorescence architecture in Jatropha.

Role of LAMA4 Gene in Regulating Extravillous Trophoblasts in Pathogenesis of Preeclampsia.

BACKGROUND Preeclampsia is a severe obstetric complication affecting the health of pregnant women. The aim of this study was to determine the effect of LAMA4 gene on extravillous trophoblasts (EVTs) in the pathogenesis of preeclampsia and its possible regulatory mechanism. MATERIAL AND METHODS HTR-8/SVneo cells were transfected with small-interfering ribonucleic acid (siRNA) targeting LAMA. The LAMA4 protein level was detected via Western blotting. Moreover, the influences of LAMA4 gene on the proliferation, migration and invasion of HTR-8/SVneo cells were detected via cell counting kit-8 (CCK-8) assay and Transwell assay. We also assessed the influences of LAMA4 gene on vascular endothelial growth factor (VEGF) and soluble fms-like tyrosine kinase-1 (sFlt-1) messenger RNA (mRNA) levels in HTR-8/SVneo cells as measured by reverse transcription-polymerase chain reaction (RT-PCR). RESULTS The cell lines with downregulation of LAMA4 gene were successfully established by transfection. Compared with those in the normal group, the proliferation, migration, and invasion of HTR-8/SVneo cells declined, the VEGF mRNA level was reduced, and the sFlt-1 mRNA level was increased in the silencing group. CONCLUSIONS Downregulation of the LAMA4 gene inhibits the proliferation, migration, and invasion of EVT to suppress the expression of vascular factors, leading to the occurrence or development of preeclampsia. Our data provide new insights into modulation of LAMA4 expression as a potential target for therapy against preeclampsia. Further research is needed on placenta sampling from pre-eclamptic pregnancies to validate the effect of LAMA4 expression compared to control pregnancies.

Analysis of the transcriptional responses in inflorescence buds of Jatropha curcas exposed to cytokinin treatment.

BACKGROUND: Jatropha curcas L. is a potential biofuel plant. Application of exogenous cytokinin (6-benzyladenine, BA) on its inflorescence buds can significantly increase the number of female flowers, thereby improving seed yield. To investigate which genes and signal pathways are involved in the response to cytokinin in J. curcas inflorescence buds, we monitored transcriptional activity in inflorescences at 0, 3, 12, 24, and 48 h after BA treatment using a microarray. RESULTS: We detected 5,555 differentially expressed transcripts over the course of the experiment, which could be grouped into 12 distinct temporal expression patterns. We also identified 31 and 131 transcripts in J. curcas whose homologs in model plants function in flowering and phytohormonal signaling pathways, respectively. According to the transcriptional analysis of genes involved in flower development, we hypothesized that BA treatment delays floral organ formation by inhibiting the transcription of the A, B and E classes of floral organ-identity genes, which would allow more time to generate more floral primordia in inflorescence meristems, thereby enhancing inflorescence branching and significantly increasing flower number per inflorescence. BA treatment might also play an important role in maintaining the flowering signals by activating the transcription of GIGANTEA (GI) and inactivating the transcription of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and TERMINAL FLOWER 1b (TFL1b). In addition, exogenous cytokinin treatment could regulate the expression of genes involved in the metabolism and signaling of other phytohormones, indicating that cytokinin and other phytohormones jointly regulate flower development in J. curcas inflorescence buds. CONCLUSIONS: Our study provides a framework to better understand the molecular mechanisms underlying changes in flowering traits in response to cytokinin treatment in J. curcas inflorescence buds. The results provide valuable information related to the mechanisms of cross-talk among multiple phytohormone signaling pathways in woody plants.

A deep-learning pipeline to diagnose pediatric intussusception and assess severity during ultrasound scanning: a multicenter retrospective-prospective study.

Ileocolic intussusception is one of the common acute abdomens in children and is first diagnosed urgently using ultrasound. Manual diagnosis requires extensive experience and skill, and identifying surgical indications in assessing the disease severity is more challenging. We aimed to develop a real-time lesion visualization deep-learning pipeline to solve this problem. This multicenter retrospective-prospective study used 14,085 images in 8736 consecutive patients (median age, eight months) with ileocolic intussusception who underwent ultrasound at six hospitals to train, validate, and test the deep-learning pipeline. Subsequently, the algorithm was validated in an internal image test set and an external video dataset. Furthermore, the performances of junior, intermediate, senior, and junior sonographers with AI-assistance were prospectively compared in 242 volunteers using the DeLong test. This tool recognized 1,086 images with three ileocolic intussusception signs with an average of the area under the receiver operating characteristic curve (average-AUC) of 0.972. It diagnosed 184 patients with no intussusception, nonsurgical intussusception, and surgical intussusception in 184 ultrasound videos with an average-AUC of 0.956. In the prospective pilot study using 242 volunteers, junior sonographers' performances were significantly improved with AI-assistance (average-AUC: 0.966 vs. 0.857, P < 0.001; median scanning-time: 9.46 min vs. 3.66 min, P < 0.001), which were comparable to those of senior sonographers (average-AUC: 0.966 vs. 0.973, P = 0.600). Thus, here, we report that the deep-learning pipeline that guides lesions in real-time and is interpretable during ultrasound scanning could assist sonographers in improving the accuracy and efficiency of diagnosing intussusception and identifying surgical indications.

Clinical implications of progranulin in gastric cancer and its regulation via a positive feedback loop involving AKT and ERK signaling pathways.

In previous years, progranulin (PGRN) has attracted increasing attention due to its oncogenic roles in several types of tumor. However, the clinical relevance of PGRN in gastric cancer remains to be elucidated. In the present study, 120 retrospective tissue samples were obtained from patients with primary gastric cancer, and the expression of PGRN was detected using immunohistochemistry. The results showed that 71 cases exhibited a high expression of PGRN, which was markedly higher than the 49 cases with a low expression of PGRN. Subsequent χ2 analysis confirmed for the first time, to the best of our knowledge, that a high level of PGRN was positively correlated with lymph node metastasis (P=0.048), lymphatic invasion (P=0.018) and advanced clinical stage (P=0.027). Survival analysis showed that PGRN was positively correlated with poorer overall survival (OS; P=0.0043) and progression­free survival (PFS; P=0.0022). Univariate and multivariate Cox regression analysis showed that PGRN and clinical stage had a significant effect on the OS and PFS of the patients with gastric cancer. In addition, cell experiments confirmed that extracellular PGRN promoted the intracellular expression of PGRN in a concentration­dependent manner in gastric cancer cells. The AKT and extracellular signal­regulated kinase signaling pathways were involved in the upregulation of intracellular PGRN induced by extracellular PGRN in MKN­45 and MGC­803 gastric cancer cells. Taken together, the results of the present study suggested that PGRN may be important in the progression and prognosis of gastric cancer, and that the expression of PGRN was regulated in a positive feedback loop. These findings enhance current knowledge regarding PGRN in tumors.

Identification and expression analysis of two small heat shock protein cDNAs from developing seeds of biodiesel feedstock plant Jatropha curcas.

Plant small heat shock proteins (sHSPs) are known to be important for environmental stress tolerance and involved in various developmental processes. In this study, two full-length cDNAs encoding sHSPs, designated JcHSP-1 and JcHSP-2, were identified and characterized from developing seeds of a promising biodiesel feedstock plant Jatropha curcas by expressed sequence tag (EST) sequencing of embryo cDNA libraries and rapid amplification of cDNA ends (RACE). JcHSP-1 and JcHSP-2 contained open-reading frames encoding sHSPs of 219 and 157 amino acids, with predicted molecular weights of 24.42kDa and 18.02kDa, respectively. Sequence alignment indicated that both JcHSP-1 and JcHSP-2 shared high similarity with other plant sHSPs. Real-time quantitative RT-PCR analysis showed that the transcriptional level of both JcHSP-1 and JcHSP-2 increased along with natural dehydration process during seed development. A sharp increase of JcHSP-2 transcripts occurred in response to water content dropping from 42% in mature seeds to 12% in dry seeds. Western blot analysis revealed that the accumulation profile of two cross-reacting proteins, whose molecular weight corresponding to the calculated size of JcHSP-1 and JcHSP-2, respectively, was well consistent with the mRNA expression pattern of JcHSP-1 and JcHSP-2 in jatropha seeds during maturation and natural dehydration. These results indicated that both JcHSPs might play an important role in cell protection and seed development during maturation of J. curcas seeds.

Analysis of expressed sequence tags from biodiesel plant Jatropha curcas embryos at different developmental stages.

Jatropha curcas is considered a potential biodiesel feedstock plant whose seeds contain up to 40% oil. However, little is currently known about the seed biology of Jatropha. Therefore, it would be valuable to understand the mechanisms of development and lipid metabolism in Jatropha seeds. In the present study, three cDNA libraries were constructed with mRNA from Jatropha embryos at different stages of seed development. A total of 9844 expressed sequence tags (ESTs) were produced from these libraries, from which 1070 contigs and 3595 singletons were obtained. One hundred and seven unigenes were found to be differentially expressed in the three cDNA libraries of Jatropha embryos, indicating that these genes may play key roles in seed development. We have identified 59 and 61 unigenes that might be involved in the development and lipid metabolism in Jatropha seeds, respectively. Some of these genes may also play important roles in embryogenesis, morphogenesis, defense response and adaptive mechanisms in plants.

Quantitative trait loci underlying domestication- and yield-related traits in an Oryza sativa x Oryza rufipogon advanced backcross population.

To understand the genetic characteristics of the traits related to differentiation between cultivated rice and its wild progenitor, genetic factors controlling domestication- and yield-related traits were identified using a BC3F2 population derived from an accession of common wild rice (donor, Oryza rufipogon Griff.) collected from Yuanjiang, Yunnan province, China, and an indica cultivar, Teqing (recipient, Oryza sativa L.). A genetic linkage map consisting of 125 simple sequence repeat (SSR) markers was constructed. Based on the phenotypes of the 383 BC3F2 families evaluated in two environments, two domestication-related morphological traits, panicle shape and growth habit, were found to be controlled by single Mendelian factors. This implies that the recessive mutations of single genes controlling some morphological traits could have been easily selected during early domestication. By single-point analysis and interval mapping, 59 putative quantitative trait loci (QTLs) that influence 11 quantitative traits were detected at two sites, and 37.5% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield-related traits in the Teqing background. Regions with significant QTLs for domestication- and yield-related traits were detected on chromosomes 1, 4, 5, 7, 8, and 12. Fine mapping and cloning of these domestication-related genes and QTLs will be useful in elucidating the origin and differentiation of Asian cultivated rice in the future.