An improved method for RNA isolation and cDNA library construction from immature seeds of Jatropha curcas L

<p>Abstract</p> <p>Background</p> <p>RNA quality and quantity is sometimes unsuitable for cDNA library construction, from plant seeds rich in oil, polysaccharides and other secondary metabolites. Seeds of jatropha (<it>Jatropha curcas </it>L.) are rich in fatty acids/lipids, storage proteins, polysaccharides, and a number of other secondary metabolites that could either bind and/or co-precipitate with RNA, making it unsuitable for downstream applications. Existing RNA isolation methods and commercial kits often fail to deliver high-quality total RNA from immature jatropha seeds for poly(A)⁺RNA purification and cDNA synthesis.</p> <p>Findings</p> <p>A protocol has been developed for isolating good quality total RNA from immature jatropha seeds, whereby a combination of the CTAB based RNA extraction method and a silica column of a commercial plant RNA extraction kit is used. The extraction time was reduced from two days to about 3 hours and the RNA was suitable for poly(A)⁺RNA purification, cDNA synthesis, cDNA library construction, RT-PCR, and Northern hybridization. Based on sequence information from selected clones and amplified PCR product, the cDNA library seems to be a good source of full-length jatropha genes. The method was equally effective for isolating RNA from mustard and rice seeds.</p> <p>Conclusions</p> <p>This is a simple CTAB + silica column method to extract high quality RNA from oil rich immature jatropha seeds that is suitable for several downstream applications. This method takes less time for RNA extraction and is equally effective for other tissues where the quality and quantity of RNA is highly interfered by the presence of fatty acids, polysaccharides and polyphenols.</p

Expression of fatty acid and lipid biosynthetic genes in developing endosperm of Jatropha curcas

BACKGROUND: Temporal and spatial expression of fatty acid and lipid biosynthetic genes are associated with the accumulation of storage lipids in the seeds of oil plants. In jatropha (Jatropha curcas L.), a potential biofuel plant, the storage lipids are mainly synthesized and accumulated in the endosperm of seeds. Although the fatty acid and lipid biosynthetic genes in jatropha have been identified, the expression of these genes at different developing stages of endosperm has not been systemically investigated. RESULTS: Transmission electron microscopy study revealed that the oil body formation in developing endosperm of jatropha seeds initially appeared at 28 days after fertilization (DAF), was actively developed at 42 DAF and reached to the maximum number and size at 56 DAF. Sixty-eight genes that encode enzymes, proteins or their subunits involved in fatty acid and lipid biosynthesis were identified from a normalized cDNA library of jatropha developing endosperm. Gene expression with quantitative reverse-transcription polymerase chain reaction analysis demonstrated that the 68 genes could be collectively grouped into five categories based on the patterns of relative expression of the genes during endosperm development. Category I has 47 genes and they displayed a bell-shaped expression pattern with the peak expression at 28 or 42 DAF, but low expression at 14 and 56 DAF. Category II contains 8 genes and expression of the 8 genes was constantly increased from 14 to 56 DAF. Category III comprises of 2 genes and both genes were constitutively expressed throughout endosperm development. Category IV has 9 genes and they showed a high expression at 14 and 28 DAF, but a decreased expression from 42 to 56 DAF. Category V consists of 2 genes and both genes showed a medium expression at 14 DAF, the lowest expression at 28 or 42 DAF, and the highest expression at 56 DAF. In addition, genes encoding enzymes or proteins with similar function were differentially expressed during endosperm development. CONCLUSION: The formation of oil bodies in jatropha endosperm is developmentally regulated. The expression of the majority of fatty acid and lipid biosynthetic genes is highly consistent with the development of oil bodies and endosperm in jatropha seeds, while the genes encoding enzymes with similar function may be differentially expressed during endosperm development. These results not only provide the initial information on spatial and temporal expression of fatty acid and lipid biosynthetic genes in jatropha developing endosperm, but are also valuable to identify the rate-limiting genes for storage lipid biosynthesis and accumulation during seed development

Li2O-Reinforced Solid Electrolyte Interphase on Three-Dimensional Sponges for Dendrite-Free Lithium Deposition

Lithium (Li) metal, with ultra-high theoretical capacity and low electrochemical potential, is the ultimate anode for next-generation Li metal batteries. However, the undesirable Li dendrite growth usually results in severe safety hazards and low Coulombic efficiency. In this work, we design a three-dimensional CuO@Cu submicron wire sponge current collector with high mechanical strength SEI layer dominated by Li2O during electrochemical reaction process. The 3D CuO@Cu current collector realizes an enhanced CE of above 91% for an ultrahigh current of 10 mA cm−2 after 100 cycles, and yields decent cycle stability at 5 C for the full cell. The exceptional performances of CuO@Cu submicron wire sponge current collector hold promise for further development of the next-generation metal-based batteries

Tenofovir alafenamide versus entecavir for treating hepatitis B virus-related acute-on-chronic liver failure: real-world study

Background and aimsReal-world data regarding hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) patients receiving tenofovir alafenamide (TAF) as an antiviral drug are limited. Hence, we evaluated the efficacy and kidney safety of TAF among this population.MethodsA total of 272 HBV-related ACLF patients hospitalized at Xiangya Hospital of Central South University were enrolled in this retrospective research. All patients received antiviral therapy with TAF (n = 100) or ETV (n = 172) and comprehensive medical treatments.ResultsThrough 1:1 propensity score matching, 100 patients were finally included in each group. At week 48, the survival rates without transplantation of the TAF group and ETV group were 76.00 and 58.00%, separately (P = 0.007). After 4 weeks of treatment, the TAF treatment group exhibited a significantly decline in HBV DNA viral load (P = 0.029). The mean estimated glomerular filtration rate was apparently improved in the TAF group compared with the ETV group (TAF 5.98 ± 14.46 vs. ETV 1.18 ± 18.07 ml/min/1.73 m2) (P &lt; 0.05). There were 6 patients in TAF group and 21 patients in ETV group with chronic kidney disease (CKD) stage progression ≥ 1. By contrast, the ETV treatment group has a greater risk of renal function progression in CKD 1 stage patients (P &lt; 0.05).ConclusionThis real-world clinical study showed that TAF is more effective than ETV in reducing viral load and improving survival rate in HBV-ACLF patients and the risk of renal function decline is lower.Clinical trial registrationhttps://ClinicalTrials.gov, identifier NCT05453448

Automated Grading of Radiographic Knee Osteoarthritis Severity Combined with Joint Space Narrowing

The assessment of knee osteoarthritis (KOA) severity on knee X-rays is a central criteria for the use of total knee arthroplasty. However, this assessment suffers from imprecise standards and a remarkably high inter-reader variability. An algorithmic, automated assessment of KOA severity could improve overall outcomes of knee replacement procedures by increasing the appropriateness of its use. We propose a novel deep learning-based five-step algorithm to automatically grade KOA from posterior-anterior (PA) views of radiographs: (1) image preprocessing (2) localization of knees joints in the image using the YOLO v3-Tiny model, (3) initial assessment of the severity of osteoarthritis using a convolutional neural network-based classifier, (4) segmentation of the joints and calculation of the joint space narrowing (JSN), and (5), a combination of the JSN and the initial assessment to determine a final Kellgren-Lawrence (KL) score. Furthermore, by displaying the segmentation masks used to make the assessment, our algorithm demonstrates a higher degree of transparency compared to typical "black box" deep learning classifiers. We perform a comprehensive evaluation using two public datasets and one dataset from our institution, and show that our algorithm reaches state-of-the art performance. Moreover, we also collected ratings from multiple radiologists at our institution and showed that our algorithm performs at the radiologist level. The software has been made publicly available at https://github.com/MaciejMazurowski/osteoarthritis-classification

A First Generation Microsatellite- and SNP-Based Linkage Map of Jatropha

Jatropha curcas is a potential plant species for biodiesel production. However, its seed yield is too low for profitable production of biodiesel. To improve the productivity, genetic improvement through breeding is essential. A linkage map is an important component in molecular breeding. We established a first-generation linkage map using a mapping panel containing two backcross populations with 93 progeny. We mapped 506 markers (216 microsatellites and 290 SNPs from ESTs) onto 11 linkage groups. The total length of the map was 1440.9 cM with an average marker space of 2.8 cM. Blasting of 222 Jatropha ESTs containing polymorphic SSR or SNP markers against EST-databases revealed that 91.0%, 86.5% and 79.2% of Jatropha ESTs were homologous to counterparts in castor bean, poplar and Arabidopsis respectively. Mapping 192 orthologous markers to the assembled whole genome sequence of Arabidopsis thaliana identified 38 syntenic blocks and revealed that small linkage blocks were well conserved, but often shuffled. The first generation linkage map and the data of comparative mapping could lay a solid foundation for QTL mapping of agronomic traits, marker-assisted breeding and cloning genes responsible for phenotypic variation

Contrastive Cross-Modal Knowledge Sharing Pre-training for Vision-Language Representation Learning and Retrieval

Recently, the cross-modal pre-training task has been a hotspot because of its wide application in various down-streaming researches including retrieval, captioning, question answering and so on. However, exiting methods adopt a one-stream pre-training model to explore the united vision-language representation for conducting cross-modal retrieval, which easily suffer from the calculation explosion. Moreover, although the conventional double-stream structures are quite efficient, they still lack the vital cross-modal interactions, resulting in low performances. Motivated by these challenges, we put forward a Contrastive Cross-Modal Knowledge Sharing Pre-training (COOKIE) to grasp the joint text-image representations. Structurally, COOKIE adopts the traditional double-stream structure because of the acceptable time consumption. To overcome the inherent defects of double-stream structure as mentioned above, we elaborately design two effective modules. Concretely, the first module is a weight-sharing transformer that builds on the head of the visual and textual encoders, aiming to semantically align text and image. This design enables visual and textual paths focus on the same semantics. The other one is three specially designed contrastive learning, aiming to share knowledge between different models. The shared cross-modal knowledge develops the study of unimodal representation greatly, promoting the single-modal retrieval tasks. Extensive experimental results on multi-modal matching researches that includes cross-modal retrieval, text matching, and image retrieval reveal the superiors in calculation efficiency and statistical indicators of our pre-training model

Oral Resveratrol Prevents Osteoarthritis Progression in C57BL/6J Mice Fed a High-Fat Diet

The effects of resveratrol on osteoarthritis (OA) pathogenesis have been demonstrated in vitro and in animal models employing intra-articular injections. However, the potential for oral resveratrol supplements to mediate protective effects on OA have not been examined. Therefore, the aim of the present study was to investigate the potential anti-OA effects of oral resveratrol on mice fed a high-fat diet (HFD). C57BL/6J male mice were fed either a standard diet or a HFD, and a subset of the latter also received varying doses of resveratrol. Twelve weeks later, all of the animals were sacrificed and knee joints were evaluated with histological, immunohistochemical, and TUNEL analyses. Mice that received a HFD had significantly greater body weights than the control mice and also exhibited features consistent with knee OA. The mice that received a HFD in combination with low, intermediate, or high doses of resveratrol were only slightly heavier than the control mice at the end of 12 weeks. Quantitative histological assessments indicated that resveratrol treatment partly recovered joint structure in the mice that received a HFD, while high doses of resveratrol prevented the degradation of type II collagen into C-telopeptide of type II collagen (CTX-II) and retained type II collagen expression in cartilage. Furthermore, TUNEL analyses revealed a reduction in chondrocyte apoptosis in the resveratrol-treated mice compared with the HFD mice. Thus, oral resveratrol appears to exert anti-OA effects in a mouse model of HFD-induced OA, thereby highlighting the potential preventive and therapeutic value of administering resveratrol for obesity-associated OA

Crosskingdom growth benefits of fungus-derived phytohormones in Choy Sum

10.1101/2020.02.04.93377

Protective Effect of Resveratrol against IL-1β-Induced Inflammatory Response on Human Osteoarthritic Chondrocytes Partly via the TLR4/MyD88/NF-κB Signaling Pathway: An “in Vitro Study”

Resveratrol is a natural polyphenolic compound that prevents inflammation in chondrocytes and animal models of osteoarthritis (OA) via yet to be defined mechanisms. The purpose of this study was to determine whether the protective effect of resveratrol on IL-1β-induced human articular chondrocytes was associated with the TLR4/MyD88/NF-кB signaling pathway by incubating human articular chondrocytes (harvested from osteoarthritis patients) with IL-1β before treatment with resveratrol. Cell viability was evaluated using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay and TNFα levels in culture supernatants were measured by ELISA(Enzymelinked immunosorbent assay). The levels of TLR4 and its downstream signaling targets (MyD88 and TRAF6) and IL-1β were assessed by measuring the levels of mRNA and protein expression by real-time RT-PCR and western blot analysis, respectively, in addition to assessing NF-кB activation. In addition, TLR4 siRNA was used to block TLR4 expression in chondrocytes further demonstrating that resveratrol prevented IL-1β-mediated inflammation by TLR4 inhibition. We found that resveratrol prevented IL-1β-induced reduction in cell viability. Stimulation of chondrocytes with IL-1β caused a significant up-regulation of TLR4 and its downstream targets MyD88 and TRAF6 resulting in NF-кB activation associated with the synthesis of IL-1β and TNFα. These IL-1β-induced inflammatory responses were all effectively reversed by resveratrol. Furthermore, activation of NF-кB in chondrocytes treated with TLR4 siRNA was significantly attenuated, but not abolished, and exposure to resveratrol further reduced NF-кB translocation. These data suggested that resveratrol prevented IL-1β-induced inflammation in human articular chondrocytes at least in part by inhibiting the TLR4/MyD88/NF-кB signaling pathway suggesting that resveratrol has the potential to be used as a nutritional supplement to counteract OA symptoms