Genome-Wide Analysis of Differentially Expressed Genes Relevant to Rhizome Formation in Lotus Root (Nelumbo nucifera Gaertn).
ABSTRACT: Lotus root is a popular wetland vegetable which produces edible rhizome. At the molecular level, the regulation of rhizome formation is very complex, which has not been sufficiently addressed in research. In this study, to identify differentially expressed genes (DEGs) in lotus root, four libraries (L1 library: stolon stage, L2 library: initial swelling stage, L3 library: middle swelling stage, L4: later swelling stage) were constructed from the rhizome development stages. High-throughput tag-sequencing technique was used which is based on Solexa Genome Analyzer Platform. Approximately 5.0 million tags were sequenced, and 4542104, 4474755, 4777919, and 4750348 clean tags including 151282, 137476, 215872, and 166005 distinct tags were obtained after removal of low quality tags from each library respectively. More than 43% distinct tags were unambiguous tags mapping to the reference genes, and 40% were unambiguous tag-mapped genes. From L1, L2, L3, and L4, total 20471, 18785, 23448, and 21778 genes were annotated, after mapping their functions in existing databases. Profiling of gene expression in L1/L2, L2/L3, and L3/L4 libraries were different among most of the selected 20 DEGs. Most of the DEGs in L1/L2 libraries were relevant to fiber development and stress response, while in L2/L3 and L3/L4 libraries, major of the DEGs were involved in metabolism of energy and storage. All up-regulated transcriptional factors in four libraries and 14 important rhizome formation-related genes in four libraries were also identified. In addition, the expression of 9 genes from identified DEGs was performed by qRT-PCR method. In a summary, this study provides a comprehensive understanding of gene expression during the rhizome formation in lotus root.
Project description:Radish (Raphanus sativus L.) is one of the most important vegetable crops worldwide. Taproot thickening represents a critical developmental period that determines yield and quality in radish life cycle. To isolate differentially expressed genes (DGEs) involved in radish taproot thickening process and explore the molecular mechanism underlying taproot development, three cDNA libraries from radish taproot collected at pre-cortex splitting stage (L1), cortex splitting stage (L2), and expanding stage (L3) were constructed and sequenced by RNA-Seq technology. More than seven million clean reads were obtained from the three libraries, from which 4,717,617 (L1, 65.35%), 4,809,588 (L2, 68.24%) and 4,973,745 (L3, 69.45%) reads were matched to the radish reference genes, respectively. A total of 85,939 transcripts were generated from three libraries, from which 10,450, 12,325, and 7392 differentially expressed transcripts (DETs) were detected in L1 vs. L2, L1 vs. L3, and L2 vs. L3 comparisons, respectively. Gene Ontology and pathway analysis showed that many DEGs, including EXPA9, Cyclin, CaM, Syntaxin, MADS-box, SAUR, and CalS were involved in cell events, cell wall modification, regulation of plant hormone levels, signal transduction and metabolisms, which may relate to taproot thickening. Furthermore, the integrated analysis of mRNA-miRNA revealed that 43 miRNAs and 92 genes formed 114 miRNA-target mRNA pairs were co-expressed, and three miRNA-target regulatory networks of taproot were constructed from different libraries. Finally, the expression patterns of 16 selected genes were confirmed using RT-qPCR analysis. A hypothetical model of genetic regulatory network associated with taproot thickening in radish was put forward. The taproot formation of radish is mainly attributed to cell differentiation, division and expansion, which are regulated and promoted by certain specific signal transduction pathways and metabolism processes. These results could provide new insights into the complex molecular mechanism underlying taproot thickening and facilitate genetic improvement of taproot in radish.
Project description:This study analyzes miRNA association with ALG-1 and ALG-2 in different stages during larval development of C. elegans Staged animals (L1, L2, L3, L4) - the alg-2 mutant expressing tagged-ALG-2, alg-1 mutant, and wild type controls - were lysed. ALG-1 IP or ALG-2 (GFP) IP was performed using tags from all four samples at all four timepoints. Small RNAs were released from antibodies and 5' end-labelled with AlexaFluor532. Labelled RNA was hybridized to a custom microRNA microarray platform to quantify miRNA content.
Project description:The role of NH and OH groups in the oxidative addition reactions of the complexes [PtMe2(?2-N,N'-L)], L = 2-C5H4NCH2NH-x-C6H4OH [3, x = 2, L = L1; 4, x = 3, L = L2; 5, x = 4, L = L3], has been investigated. Complex 3 is the most reactive. It reacts with CH2Cl2 to give a mixture of isomers of [PtMe2(CH2Cl)(?3-N,N',O-(L1-H)], 6, and decomposes in acetone to give [PtMe3(?3-N,N',O-(L1-H)], 7, both of which contain the fac tridentate deprotonated ligand. Complex 3 reacts with MeI to give complex 7, whereas 4 and 5 react to give [PtIMe3(?2-N,N'-L2))], 8, or [PtIMe3(?2-N,N'-L3)], 9, respectively. Each complex 3, 4, or 5 reacts with either dioxygen or hydrogen peroxide to give the corresponding complex [Pt(OH)2Me2(?2-N,N'-L)], 10, L = L1; 11, L = L2; 12, L = L3. The ligand L3 in complexes 9 and 12 is easily oxidized to the corresponding imine ligand 2-C5H4NCH=N-4-C6H4OH, L4, in forming the complexes [PtIMe3(?2-N,N'-L4)], 13, and [Pt(OH)2Me2(?2-N,N'-L4)], 14, respectively. The NH and OH groups play a significant role in supramolecular polymer or sheet structures of the complexes, formed through intermolecular hydrogen bonding, and these structures indicate how either intramolecular or intermolecular hydrogen bonding may assist some oxidative addition reactions.
Project description:Gout in the spine is very rare. The clinical symptoms of the spinal gout are various and lack of specificity. The authors report a case of spinal gout causing lumbar stenosis. We never find such wide-invasive spinal gouty lesion in the published studies.A 68-year-old male had low back pain radiating to bilateral lower limbs, accompanying with intermittent claudication that lasted for 3 months and aggravated 5 days ago.Spinal gout, lumbar stenosis.The patient underwent L2-L4 laminectomy, L2/3 L3/4 an d L4/5 discectomy and transforaminal lumbar interbody fusion with pedicle screw fixation.Dual-energy computed tomography detected extensive tophaceous deposits in L1/2 L2/3 L3/4 and L4/5 lumbar discs as well as the posterior column, especially L2-L3 and L4-L5 facet joints. During the surgery, we found a mass of chalky white material at the posterior column of L3 to L5 vertebral bodies, which also involved the intervertebral discs. Pathological examination confirmed the diagnosis of spinal gout.Although spinal gout is thought to be rare, the diagnosis should be considered if the patient had severe back pain and a history of gout. Dual-energy computed tomography is highly recommended for these patients.
Project description:BACKGROUND:The aim of this study was to investigate the correlation between radiographic measurement in lumbar spine and clinical information including symptoms or results of functional testing using a baseline data of longitudinal cohort study. METHODS:A total of 314 elderly subjects were recruited from 5 orthopedic clinics or affiliated facilities. Data for the present investigation were collected via an interviewer-administered questionnaire, which included questions on past medical history, drug history, pain area. And also results of functional testing and X-ray imaging of the lumbar spine were collected. Analysis was carried out to determine any correlation between results of X-ray imaging of the lumbar spine and other collected data, and sorted regarding Akaike Information Criterion (AIC). The correlations among these variables and odds ratio were also analyzed. RESULTS:T12/L1% disc height showed a minimum AIC value with buttock pain (- 4.57) and history of vertebral fracture (- 4.05). The L1/L2, L2/L3, and L3/L4% disc height had a minimal AIC value with knee pain (- 4.11, - 13.3, - 3.15, respectively), and odds ratio of knee pain were 3.5, 3.8, and 2.7, respectively. CONCLUSIONS:Correlation was recognized between the T12/L1% disc height and both buttock pain and previous vertebral fractures, and the L1/L2, L2/L3, and L3/L4% disc height showed a correlation with knee pain. Especially the L2/L3% disc height and knee pain had a strong correlation. It was suggested that these findings may provide additional basis to the concept that lumbar spinal lesion associates with knee pain clinically.
Project description:Despite the high burden of tuberculosis (TB) worldwide, specific factors influencing disease transmission remain elusive. Long term epidemiological studies and in vitro experimental models provide evidence of variable relative fitness of Mycobacterium tuberculosis (Mtb) strains but few such studies are available. Large sequence polymorphisms (LSP) are a robust molecular marker and are feasible as an epidemiological investigative tool. Few Mtb molecular epidemiological studies have been reported in Malawi owing to lack of laboratories with molecular tools. We characterized the genetic diversity of Mtb clinical isolates amongst TB patients in Blantyre, Malawi. We genotyped 64 Mtb clinical isolates using LSP-PCR, assigned specific lineages and confirmed 18 of the isolates using SMRT sequencing. The 64 isolates clustered into 4 lineages (L1-L4) with L4 predominating. There were 10/64 (16%) isolates belonging to L1, 6/64 (9%) belonging to L2, 2/64 (3%) belonging to L3 and 46/64 (72%) belonging to L4. Comparison with a previous study done in Karonga revealed concordance in L1 and L4 but discodance in L2 and L3. The phylogenetic tree constructed, comprised of 3/4 lineages present in Blantyre with 3/18 belonging to L1, 3/18 belonging to L2 and 12/18 belonging to L4. Four Mtb lineages were present in Blantyre with L4 predominating. Larger studies are needed to understand the molecular epidemiology of TB in Blantyre in light of increased bi-directional migration with South Africa.
Project description:The macronutrient potassium (K) is essential to plant growth and development. Crop yield potential is often affected by lack of soluble K. The molecular regulation mechanism of physiological and biochemical responses to K starvation in soybean roots and shoots is not fully understood. In the present study, two soybean varieties were subjected to low-K stress conditions: a low-K-tolerant variety (You06-71) and a low-K-sensitive variety (HengChun04-11). Eight libraries were generated for analysis: 2 genotypes ×2 tissues (roots and shoots) ×2 time periods [short term (0.5 to 12 h) and long term (3 to 12 d)]. RNA derived from the roots and shoots of these two varieties across two periods (short term and long term) were sequenced and the transcriptomes were compared using high-throughput tag-sequencing. To this end, a large number of clean tags (tags used for analysis after removal of dirty tags) corresponding to distinct tags (all types of clean tags) were identified in eight libraries (L1, You06-71-root short term; L2, HengChun04-11-root short term; L3, You06-71-shoot short term; L4, HengChun04-11-shoot short term; L5, You06-71-root long term; L6, HengChun04-11-root long term; L7, You06-71-shoot long term; L8, HengChun04-11-shoot long term). All clean tags were mapped to the available soybean (Glycine max) transcript database (http://www.soybase.org). Many genes showed substantial differences in expression across the libraries. In total, 5,440 transcripts involved in 118 KEGG pathways were either up- or down-regulated. Fifteen genes were randomly selected and their expression levels were confirmed using quantitative RT-PCR. Our results provide preliminary information on the molecular mechanism of potassium absorption and transport under low-K stress conditions in different soybean tissues.
Project description:To provide applied anatomical evidence of the preoperative assessment of oblique lumbar interbody fusion (OLIF), the anatomical parameters of the OLIF operative window were observed through computed tomography angiography (CTA). We selected imaging data from 60 adults (30 males, 30 females) who underwent abdominal CTA and T12-S1 vertebral computed tomography (CT) with three-dimensional reconstruction. The OLIF operative windows at the L1-2, L2-3, L3-4, L4-5 and L5-S1 levels were as follows: the vascular window, bare window, psoas major window, ideal operative window, and actual operative window. Each level's actual operative window was statistically analyzed based on an actual operative window of <1 cm and ?1 cm. The vascular window was largest at L4-5 (1.72 ± 0.58 cm). The bare window was largest at L5-S1 (1.59 ± 0.93 cm) and smallest at L3-4 (1.37 ± 0.51 cm). The psoas major window was largest at L3-4 (1.14 ± 0.35 cm) and smallest at L1-2 (0.41 ± 0.34 cm). The ideal operative window was largest at L4-5 (3.74 ± 0.36 cm) and smallest at L1-2 (3.23 ± 0.30 cm). The actual operative window was largest at L3-4, followed by L2-3, L4-5, L1-2, and L5-S1, which were 2.51 ± 0.56 cm, 2.28 ± 0.54 cm, 2.01 ± 0.74 cm, 1.80 ± 0.45 cm and 1.59 ± 0.93 cm, respectively (P = 0.000), and the percentages of the actual surgical window were 69%, 66%, 53%, 56% and 43%, respectively. The actual surgical window was <1 cm in 2 cases at L1-2 (3.3%), 4 cases at L4-5 (6.7%), and 17 cases at L5-S1 (28.3%) (11 males and 6 females). The regional anatomy of each level related to OLIF has its own peculiarities, and not all levels are suitable for OLIF. Before OLIF surgery, surgeons should analyze the imaging anatomy and select the appropriate surgical procedures.
Project description:To observe the regional anatomy of the lumbar artery (LA) associated with the extrapedicular approach applied during percutaneous vertebroplasty (PVP) and percutaneous kyphoplasty (PKP), we collected 78 samples of abdominal computed tomography angiography imaging data. We measured the nearest distance from the center of the vertebral body puncture point to the LA (distance VBPP-LA, DVBPP-LA). According to the DVBPP-LA, four zones, Zone I, Zone II, Zone III and Zone IV, were identified. LAs that passed through these zones were called Type I, Type II, Type III and Type IV LAs, respectively. A portion of the lumbar vertebrae had an intersegmental branch that originated from the upper segmental LA and extended longitudinally across the lateral wall of the pedicle; it was called Type V LA. Compared with the DVBPP-LA in L1, L2, L3 and L4, the overall difference and between-group differences were significant (P < 0.05). In L1, L2, L3, L4 and L5, there were 8, 4, 4, 0 and 1 Type I LAs, respectively. There were no Type V LAs in L1 and L2, but there were 2, 16 and 26 Type V LAs in L3, L4 and L5, respectively. In L1-L5, the numbers of Type I LA plus Type V LA were 8, 4, 6, 16 and 27, and the presence ratios were 5.1%, 2.6%, 5.6%, 10.3% and 17.3%, respectively. In L4 and L5, the male presence ratios of Type I LA plus Type V LA were 7.1% and 10.7%, respectively, and the female presence ratios were 13.9% and 25.0%, respectively. Thus, extrapedicular PVP (PKP) in lumbar vertebrae had a risk of LA injury and was not suggested for use in L4 and L5, especially in female patients.
Project description:The 3' untranslated region (3'UTR) constitutes a major site of post-transcriptional regulation of gene expression. Sequence elements in the 3'UTR interact with trans-acting regulators such as microRNAs that affect translation and stability. The overall aim is to use a 3'RACE cloning-sequencing stragety to identify the 3'UTRs of C. elegans transcripts and explore their heterogeneity in different developmental stages and tissues. Keywords: Transcriptome analysis For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE17781 pilot study [GSM443959..GSM443964]: N2 wildtype worms staged at embryo, L1, L2, L3, L4, and adult full experiment [GSM446651..GSM446661]: N2 wildtype worms staged at embryo, L1, L2, L3, L4, dauer, and adult. Illumina Genome Analyzer sequencing of isolated clones [GSM469439] 454 sequencing of RACE clones [GSM469976]