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#33631798   // To Up

Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton.

Long noncoding RNAs (lncRNAs) are crucial factors during plant development and environmental responses. To build an accurate atlas of lncRNAs in the diploid cotton Gossypium arboreum, we combined Isoform-sequencing, strand-specific RNA-seq (ssRNA-seq), and cap analysis gene expression (CAGE-seq) with PolyA-seq and compiled a pipeline named plant full-length lncRNA to integrate multi-strategy RNA-seq data. In total, 9,240 lncRNAs from 21 tissue samples were identified. 4,405 and 4,805 lncRNA transcripts were supported by CAGE-seq and PolyA-seq, respectively, among which 6.7% and 7.2% had multiple transcription start sites (TSSs) and transcription termination sites (TTSs). We revealed that alternative usage of TSS and TTS of lncRNAs occurs pervasively during plant growth. Besides, we uncovered that many lncRNAs act in cis to regulate adjacent protein-coding genes (PCGs). It was especially interesting to observe 64 cases wherein the lncRNAs were involved in the TSS alternative usage of PCGs. We identified lncRNAs that are coexpressed with ovule- and fiber development-associated PCGs, or linked to GWAS single-nucleotide polymorphisms. We mapped the genome-wide binding sites of two lncRNAs with chromatin isolation by RNA purification sequencing. We also validated the transcriptional regulatory role of lnc-Ga13g0352 via virus-induced gene suppression assay, indicating that this lncRNA might act as a dual-functional regulator that either activates or inhibits the transcription of target genes.
Xiaomin Zheng, Yanjun Chen, Yifan Zhou, Keke Shi, Xiao Hu, Danyang Li, Hanzhe Ye, Yu Zhou, Kun Wang

1562 related Products with: Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton.

250ul100 µg1 mg100 ug200ul2 Pieces/Box300 units100 µg1 mg25ug100ug/vial5 x 50 ug

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#33631555   2021/02/22 To Up

A comparison of alternative mRNA splicing in the CD4 and CD8 T cell lineages.

T cells can be subdivided into a number of different subsets that are defined by their distinct functions. While the specialization of different T cell subsets is partly achieved by the expression of specific genes, the overall transcriptional profiles of all T cells appear very similar. Alternative mRNA splicing is a mechanism that facilitates greater transcript/protein diversity from a limited number of genes, which may contribute to the functional specialization of distinct T cell subsets. In this study we employ a combination of short-read and long-read sequencing technologies to compare alternative mRNA splicing between the CD4 and CD8 T cell lineages. While long-read technology was effective at assembling full-length alternatively spliced transcripts, the low sequencing depth did not facilitate accurate quantitation. On the other hand, short-read technology was ineffective at assembling full-length transcripts but was highly accurate for quantifying expression. We show that integrating long-read and short-read data together achieves a more complete view of transcriptomic diversity. We found that while the overall usage of transcript isoforms was very similar between the CD4 and CD8 lineages, there were numerous alternative spliced mRNA isoforms that were preferentially used by one lineage over the other. These alternative spliced isoforms included ones with different exon usage, exon exclusion or intron inclusion, all of which are expected to significantly alter the protein sequence.
Xin Liu, Matthew V Andrews, Jarrod P Skinner, Timothy M Johanson, Mark M W Chong

2603 related Products with: A comparison of alternative mRNA splicing in the CD4 and CD8 T cell lineages.

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#33631433   2021/02/22 To Up

Mining Unknown Porcine Protein Isoforms by Tissue-Based Map of Proteome Enhances the Pig Genome Annotation.

A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model. We developed the tissue-based proteome map using 34 major normal pig tissues. A total of 5841 unknown protein isoforms were identified and systematically characterized, including 2225 novel protein isoforms, 669 protein isoforms from 460 genes symbolized beginning with LOC, and 2947 protein isoforms without clear NCBI annotation in current pig reference genome. These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues, further improving the genome annotation of the corresponding protein-coding genes. Combining the well-annotated genes that have parallel expression pattern and subcellular witness, we predicted the tissue-related subcellular components and potential function for these unknown proteins. Finally, we mined 3081 orthologous genes for 52.75% of unknown protein isoforms across multiple species, referring to 68 KEGG pathways as well as 23 disease signaling pathways. These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology, as well as biomedical model application to human medicine.
Pengju Zhao, Xianrui Zheng, Ying Yu, Zhuocheng Hou, Chenguang Diao, Haifei Wang, Huimin Kang, Chao Ning, Junhui Li, Wen Feng, Wen Wang, George E Liu, Bugao Li, Jacqueline Smith, Yangzom Chamba, Jian-Feng Liu

2859 related Products with: Mining Unknown Porcine Protein Isoforms by Tissue-Based Map of Proteome Enhances the Pig Genome Annotation.

1 Set1 Set1 Set1 Set101 Set1 Set51001 Set

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#33629930   2021/02/25 To Up

Regulation of miR-186-YY1 axis by the p53 translational isoform ∆40p53: implications in cell proliferation.

We have earlier shown that p53-FL and its translational isoform ∆40p53 are differentially regulated. In this study, we have investigated the cellular effect of ∆40p53 regulation on downstream gene expression, specifically miRNAs. Interestingly, ∆40p53 showed antagonistic regulation of miR-186-5p as compared to either p53 alone or a combination of both the isoforms. We have elucidated the miR-186-5p mediated effect of ∆40p53 in cell proliferation. Upon expression of ∆40p53, we observed a significant decrease in YY1 levels, an established target of miR-186-5p, which is involved in cell proliferation. Further assays with anti-miR-186 established the interdependence of ∆40p53- miR-186-5p-YY1- cell proliferation. The results unravel a new dimension toward the understanding of ∆40p53 functions, which seems to regulate cellular fate independent of p53FL.
Aanchal Katoch, Sachin Kumar Tripathi, Apala Pal, Saumitra Das

2275 related Products with: Regulation of miR-186-YY1 axis by the p53 translational isoform ∆40p53: implications in cell proliferation.

50 ug2 Pieces/Box100 ml.96 wells25 ml.5 x 50 ug1x10e7 cells24 tests100ug Lyophilized100ug

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#33629774   2021/02/25 To Up

Alternative splicing: An important regulatory mechanism in colorectal carcinoma.

Alternative splicing (AS) is a process that produces various mRNA splicing isoforms via different splicing patterns of mRNA precursors (pre-mRNAs). AS is the primary mechanism for increasing the types and quantities of proteins to improve biodiversity and influence multiple biological processes, including chromatin modification, signal transduction, and protein expression. It has been reported that AS is involved in the tumorigenesis and development of colorectal carcinoma (CRC). In this review, we delineate the concept, types, regulatory processes, and technical advances of AS and focus on the role of AS in CRC initiation, progression, treatment, and prognosis. This summary of the current knowledge about AS will contribute to our understanding of CRC initiation and development. This study will help in the discovery of novel biomarkers and therapeutic targets for CRC prognosis and treatment.
Jianyi Wang, Chuhan Wang, Le Li, Lirui Yang, Shuoshuo Wang, Xuelian Ning, Shuangshu Gao, Lili Ren, Anita Chaulagain, Jing Tang, Tianzhen Wang

1621 related Products with: Alternative splicing: An important regulatory mechanism in colorectal carcinoma.



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#33629733   2021/02/22 To Up

Molecular characterization of the prostaglandin E receptor subtypes 2a and 4b and their expression patterns during embryogenesis in zebrafish.

The molecular expression profiles of zebrafish ep2a and ep4b have not been defined to-date. Phylogenetic trees of EP2a and EP4b in zebrafish and other species revealed that human EP4 and zebrafish EP4b were more closely related than EP2a. Zebrafish EP2a is a 281 amino acid protein with high identity to that of human (43%), mouse (44%), rat (43%), dog (44%), cattle (41%), and chicken (41%). Zebrafish EP4b encoded a precursor of 497 amino acids with high amino acid identity to that of mammals, including human (57%), mouse (54%), rat (55%), dog (55%), cattle (56%), and chicken (54%). Whole-mount in situ hybridization revealed that ep2a was robustly expressed in the anterior four somites at the 10-somites stages, but was absent in the somites at 19 hpf. It was observed again in the pronephric duct at 24 hpf, in the intermediate cell mass located in the trunk, and in the rostral blood island at 30 hpf. Ep2a was also expressed in the notochord at 48 hpf. During somitogenesis, ep4b was highly expressed in the eyes, somites, and the trunk neural crest. From 30 to 48 hpf, ep4b could be detected in the posterior cardinal vein and the neighboring ICM. From these data, we conclude that ep2a and ep4b are conserved in vertebrates and that the presence of ep2a and ep4b transcripts during developmental stages infers their role during early zebrafish larval development. In addition, the variable expression of the two receptor isoforms was strongly suggestive of divergent roles of molecular regulation.
Yongjun Han, Hongbo Chang, Hong Wu

2769 related Products with: Molecular characterization of the prostaglandin E receptor subtypes 2a and 4b and their expression patterns during embryogenesis in zebrafish.

5mg200ul100ug96T0.1 mg50 ug 100ug100 μg96 wells (1 kit)200

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#33629462   2021/02/24 To Up

Distinct and dementia-related synaptopathy in the hippocampus after military blast exposures.

Explosive shockwaves, and other types of blast exposures, are linked to injuries commonly associated with military service and to an increased risk for the onset of dementia. Neurological complications following a blast injury, including depression, anxiety, and memory problems, often persist even when brain damage is undetectable. Here, hippocampal explants were exposed to the explosive 1,3,5-trinitro-1,3,5-triazinane (RDX) to identify indicators of blast-induced changes within important neuronal circuitries. Highly controlled detonations of small, 1.7-gram RDX spherical charges reduced synaptic markers known to be downregulated in cognitive disorders, but without causing overt neuronal loss or astroglial responses. In the absence of neuromorphological alterations, levels of synaptophysin, GluA1, and synapsin IIb were significantly diminished within 24 hr, and these synaptic components exhibited progressive reductions following blast exposure as compared to their stable maintenance in control explants. In contrast, labeling of the synapsin IIa isoform remained unaltered, while neuropilar staining of other markers decreased, including synapsin IIb and neural cell adhesion molecule (NCAM) isoforms, along with evidence of NCAM proteolytic breakdown. NCAM displayed a distinct decline after the RDX blasts, whereas NCAM and NCAM exhibited smaller or no deterioration, respectively. Interestingly, the extent of synaptic marker reduction correlated with AT8-positive tau levels, with tau pathology stochastically found in CA1 neurons and their dendrites. The decline in synaptic components was also reflected in the size of evoked postsynaptic currents recorded from CA1 pyramidals, which exhibited a severe and selective reduction. The identified indicators of blast-mediated synaptopathy point to the need for early biomarkers of explosives altering synaptic integrity with links to dementia risk, to advance strategies for both cognitive health and therapeutic monitoring.
Michael F Almeida, Thuvan Piehler, Kelly E Carstens, Meilan Zhao, Mahsa Samadi, Serena M Dudek, Christopher J Norton, Catherine M Parisian, Karen L G Farizatto, Ben A Bahr

2280 related Products with: Distinct and dementia-related synaptopathy in the hippocampus after military blast exposures.

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#33629224   2021/02/24 To Up

StCaM2, a calcium binding protein, alleviates negative effects of salinity and drought stress in tobacco.

Overexpression of StCaM2 in tobacco promotes plant growth and confers increased salinity and drought tolerance by enhancing the photosynthetic efficiency, ROS scavenging, and recovery from membrane injury. Calmodulins (CaMs) are important Ca sensors that interact with effector proteins and drive a network of signal transduction pathways involved in regulating the growth and developmental pattern of plants under stress. Herein, using in silico analysis, we identified 17 CaM isoforms (StCaM) in potato. Expression profiling revealed different temporal and spatial expression patterns of these genes, which were modulated under abiotic stress. Among the identified StCaM genes, StCaM2 was found to have the largest number of abiotic stress responsive promoter elements. In addition, StCaM2 was upregulated in response to some of the selected abiotic stress in potato tissues. Overexpression of StCaM2 in transgenic tobacco plants enhanced their tolerance to salinity and drought stress. Accumulation of reactive oxygen species was remarkably decreased in transgenic lines compared to that in wild type plants. Chlorophyll a fluorescence analysis suggested better performance of photosystem II in transgenic plants under stress compared to that in wild type plants. The increase in salinity stress tolerance in StCaM2-overexpressing plants was also associated with a favorable K/Na ratio. The enhanced tolerance to abiotic stresses correlated with the increase in the activities of anti-oxidative enzymes in transgenic tobacco plants. Overall, our results suggest that StCaM2 can be a novel candidate for conferring salt and drought tolerance in plants.
Meenakshi Raina, Ashish Kumar, Nikita Yadav, Sumita Kumari, Mohd Aslam Yusuf, Ananda Mustafiz, Deepak Kumar

1593 related Products with: StCaM2, a calcium binding protein, alleviates negative effects of salinity and drought stress in tobacco.

96tests100.00 ug100.00 ug100 μg1000 TESTS/0.65ml100.00 ug0.05 mg100.00 ug100.00 ug 100ul1 Set1 Set

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#33628608   2020/02/11 To Up

Copper induces transcription of laccase gene in phytopathogenic fungus, .

Laccases are one of many groups of inducible enzymes produced by the filamentous fungus, during colonisation of host plant tissues. While the processes involved in laccase induction are not fully understood, Cupric ions (e.g. CuSO) and gallic acid (GA) have been reported as laccase inducers. This study investigates laccases activities and the expression of three laccase genes () in three isolates grown in laccase-inducing medium (LIM) supplemented with CuSO and GA. Laccase activity in culture filtrates with CuSO increased after 48 h of growth in LIM at 24°C. The induction of transcription was greatest at a concentration of 0.6 mM CuSO, concentrations greater than 0.6 mM inhibited fungal growth. In contrast, no laccase induction was observed in the presence of GA. Liquid chromatography-mass spectroscopy (NanoLC ESI MS/MS) analysis confirmed the presence of a 63.4 kDa protein, the isoform in the culture filtrate with 0.6 mM CuSO. Analysis of mRNA transcripts further showed was also inducible and the expression of and was isolate-dependent. In conclusion, CuSO induces a 63.4 kDa laccase in by induced transcription of the gene.
U V A Buddhika, S Savocchia, C C Steel

1606 related Products with: Copper induces transcription of laccase gene in phytopathogenic fungus, .

2 Pieces/Box100 96T 25UG96T5ug2ug300 units1 Set2ug1 Set

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#33628092   2021/01/21 To Up

Nonionic surfactant attenuates acute lung injury by restoring epithelial integrity and alveolar fluid clearance.

Acute lung injury (ALI) has a great impact and a high mortality rate in intensive care units (ICUs). Excessive air may enter the lungs, causing pulmonary air embolism (AE)-induced ALI. Some invasive iatrogenic procedures cause pulmonary AE-induced ALI, with the presentation of severe inflammatory reactions, hypoxia, and pulmonary hypertension. Pulmonary surfactants are vital in the lungs to reduce the surface tension and inflammation. Nonionic surfactants (NIS) are a kind of surfactants without electric charge on their hydrophilic parts. Studies on NIS in AE-induced ALI are limited. We aimed to study the protective effects and mechanisms of NIS in AE-induced ALI. Five different groups (n = 6 in each group) were created: sham, AE, AE + NIS pretreatment (0.5 mg/kg), AE + NIS pretreatment (1 mg/kg), and AE + post-AE NIS (1 mg/kg). AE-induced ALI was introduced by the infusion of air via the pulmonary artery. Aerosolized NIS were administered via tracheostomy. Pulmonary AE-induced ALI showed destruction of the alveolar cell integrity with increased pulmonary microvascular permeability, pulmonary vascular resistance, pulmonary edema, and lung inflammation. The activation of nuclear factor-κB (NF-κB) increased the expression of pro-inflammatory cytokines, and sodium-potassium-chloride co-transporter isoform 1 (NKCC1). The pretreatment with NIS (1 mg/kg) prominently maintained the integrity of the epithelial lining and suppressed the expression of NF-κB, pro-inflammatory cytokines, and NKCC1, subsequently reducing AE-induced ALI. NIS maintained the integrity of the epithelial lining and suppressed the expression of NF-κB, pro-inflammatory cytokines, and NKCC1, thereby reducing hyperpermeability, pulmonary edema, and inflammation in ALI.
Po-Chun Hsieh, Chan-Yen Kuo, Chin-Pyng Wu, Chung-Tai Yue, Chung-Kan Peng, Kun-Lun Huang, Chou-Chin Lan

2205 related Products with: Nonionic surfactant attenuates acute lung injury by restoring epithelial integrity and alveolar fluid clearance.

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