scholarly journals Nuclear matrix associated RNA datasets of posterior silk glands of Bombyx mori during 5th instar larval development

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Alekhya Rani Chunduri ◽  
Anugata Lima ◽  
Resma Rajan ◽  
Anitha Mamillapalli
Keyword(s):  
Larval Development ◽  
Bombyx Mori ◽  
Nuclear Matrix ◽  
Major Constituent ◽  
Silk Fibre ◽  
Illumina Platform ◽  
Expression Of Genes ◽  
Silk Glands ◽  
Main Component ◽  
And Function

Abstract Objectives Bombyx mori is the key contributor to industrial silk production. The maximum production of silk occurs during 5th instar. The posterior silk glands in the larvae are responsible for the production of the main component of silk fibre—fibroin. The expression of genes and their regulation are dependent on the chromatin architecture. The nuclear matrix supports its structure and function by anchoring specific regions to regulate gene expression. The major constituent of the nuclear matrix, crucial to its structural and temporal maintenance, is its RNA. Therefore, the study of nuclear matrix RNA of the posterior silk glands on different days of 5th instar larval development is essential to understand its association to differential expression of genes. Data description The tissue-specific developmental association of nuclear matrix RNA (NuMat RNA) at the genome level has not been done so far for any organism. Bombyx mori, CSR2 X CSR4 is the most popular dihybrid strain in India. The nuclear matrix RNA was isolated from day 1, day 5 and day 7 of 5th instar posterior silk glands of Bombyx mori. The NuMat RNA was sequenced using Illumina platform. The reads obtained were processed and the datasets were deposited in NCBI.

scholarly journals Carbonic anhydrase generates a pH gradient in Bombyx mori silk glands

2015 ◽  
Vol 65 ◽  
pp. 100-106 ◽  
Author(s):  
L.J. Domigan ◽  
M. Andersson ◽  
K.A. Alberti ◽  
M. Chesler ◽  
Q. Xu ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Bombyx Mori ◽  
Ph Gradient ◽  
Silk Glands ◽  
Bombyx Mori Silk

scholarly journals In-silico prediction and observations of nuclear matrix attachment

2006 ◽  
Vol 11 (2) ◽  
Author(s):  
Adrian Platts ◽  
Amelia Quayle ◽  
Stephen Krawetz
Keyword(s):  
Nuclear Matrix ◽  
In Silico ◽  
Sequence Similarity ◽  
Loop Model ◽  
Simple Loop ◽  
Structural Framework ◽  
The Subject ◽  
In Silico Predictions ◽  
The One ◽  
And Function

AbstractThe nuclear matrix is a functionally adaptive structural framework interior to the nuclear envelope. The nature and function of this nuclear organizer remains the subject of widespread discussion in the epigenetic literature. To draw this discussion together with a view to suggest a way forward we summarize the biochemical evidence for the modalities of DNA-matrix binding alongside the in-silico predictions. Concordance is exhibited at various, but not all levels. On the one hand, both the reiteration and sequence similarity of some elements of Matrix Attachment Regions suggest conservation. On the other hand, in-silico predictions suggest additional unique components. In bringing together biological and sequence evidence we conclude that binding may be hierarchical in nature, reflective of a biological role in replicating, transcribing and potentiating chromatin. Nuclear matrix binding may well be more complex than the widely accepted simple loop model.

scholarly journals Chemical Composition, Antioxidant, Anti-Tyrosinase, Anti-Cholinesterase and Cytotoxic Activities of Essential Oils of Six Algerian Plants

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1710 ◽  
Author(s):  
Kadour Cheraif ◽  
Boulanouar Bakchiche ◽  
Abdelaziz Gherib ◽  
Sanaa K. Bardaweel ◽  
Melek Çol Ayvaz ◽  
...  
Keyword(s):  
Essential Oils ◽  
Cytotoxic Effect ◽  
Food Preservation ◽  
Major Constituent ◽  
Cytotoxic Activities ◽  
Mentha Pulegium ◽  
Antioxidant Power ◽  
Ic50 Values ◽  
Lavandula Officinalis ◽  
Main Component

In this study, the essential oils (EOs) of six Algerian plants (Artemisia campestris L., Artemisia herba-alba Asso, Juniperus phoenicea L., Juniperus oxycedrus L., Mentha pulegium L. and Lavandula officinalis Chaix) were obtained by hydrodistillation, and their compositions determined by GC-MS and GC-FID. The antioxidant activity of the EOS was evaluated via 2,2′-diphenyl-1-picrylhydrazyl (DPPH), ferric-reducing/antioxidant power (FRAP) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid (ABTS) assays. Moreover, their cytotoxic effect was evaluated—as well as their tyrosinase, acetyl- and butyryl-cholinesterase (AChE and BuChE) inhibitory activities. The chemical analyses detected 44, 45, 51, 53, 26 and 40 compounds in EOs of A. campestris, A. herba-alba, J. phoenicea, J. oxycedrus, M. pulegium and L. officinalis, respectively. A. campestris EO was mainly composed of β-pinene (20.7%), while A. herba-alba EO contained davanone D (49.5%) as the main component. α-Pinene (41.8%) was detected as the major constituent in both J. phoenicea (41.8%) and J. oxycedrus (37.8%) EOs. M. pulegium EO was characterized by pulegone as the most abundant (76.9%) compound, while linalool (35.8%) was detected as a major constituent in L. officinalis EO. The antioxidant power evaluation revealed IC50 values ranging from 2.61 to 91.25 mg/mL for DPPH scavenging activity, while the FRAP values ranged from 0.97–8.17 µmol Trolox equivalents (TX)/g sample. In the ABTS assay, the values ranged from 7.01 to 2.40 µmol TX/g sample. In the presence of 1 mg/mL of the samples, tyrosinase inhibition rates ranged from 11.35% to 39.65%, AChE inhibition rates ranged from 40.57% to 73.60% and BuChE inhibition rates ranged from 6.47% to 72.03%. A significant cytotoxic effect was found for A. herba-alba EO. The obtained results support some of the traditional uses of these species in food preservation and for protection against several diseases.

scholarly journals A Novel Adenosine Kinase from Bombyx mori: Enzymatic Activity, Structure, and Biological Function

2019 ◽  
Vol 20 (15) ◽  
pp. 3732 ◽  
Author(s):  
Kai Song ◽  
Yu Li ◽  
Huawei He ◽  
Lina Liu ◽  
Ping Zhao ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Gel Filtration ◽  
Pupal Stage ◽  
Adenosine Monophosphate ◽  
Silk Gland ◽  
Adenosine Kinase ◽  
Site Directed Mutagenesis ◽  
Activity Structure ◽  
Α Helix ◽  
And Function

Adenosine kinase (ADK) is the first enzyme in the adenosine remediation pathway that catalyzes adenosine phosphorylation into adenosine monophosphate, thus regulating adenosine homeostasis in cells. To obtain new insights into ADK from Bombyx mori (BmADK), we obtained recombinant BmADK, and analyzed its activity, structure, and function. Gel-filtration showed BmADK was a monomer with molecular weight of approximately 38 kDa. Circular dichroism spectra indicated BmADK had 36.8% α-helix and 29.9% β-strand structures, respectively. The structure of BmADK was stable in pH 5.0–11.0, and not affected under 30 °C. The melting temperature and the enthalpy and entropy changes in the thermal transition of BmADK were 46.51 ± 0.50 °C, 253.43 ± 0.20 KJ/mol, and 0.79 ± 0.01 KJ/(mol·K), respectively. Site-directed mutagenesis demonstrated G68, S201, E229, and D303 were key amino acids for BmADK structure and activity. In particular, S201A mutation significantly increased the α-helix content of BmADK and its activity. BmADK was located in the cytoplasm and highly expressed in the silk gland during the pre-pupal stage. RNA interference revealed the downregulation of BmADK decreased ATG-8, Caspase-9, Ec-R, E74A, and Br-C expression, indicating it was likely involved in 20E signaling, apoptosis, and autophagy to regulate silk gland degeneration and silkworm metamorphosis. Our study greatly expanded the knowledge on the activity, structure, and role of ADK.

scholarly journals β-Glucosidase genes differentially expressed during composting

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Xinyue Zhang ◽  
Bo Ma ◽  
Jiawen Liu ◽  
Xiehui Chen ◽  
Shanshan Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Environmental Changes ◽  
Cellulose Degradation ◽  
Degradation Mechanism ◽  
Degradation Process ◽  
Global Scale ◽  
Expression Of Genes ◽  
Glucose Tolerant ◽  
Cooling Phase ◽  
And Function

Abstract Background Cellulose degradation by cellulase is brought about by complex communities of interacting microorganisms, which significantly contribute to the cycling of carbon on a global scale. β-Glucosidase (BGL) is the rate-limiting enzyme in the cellulose degradation process. Thus, analyzing the expression of genes involved in cellulose degradation and regulation of BGL gene expression during composting will improve the understanding of the cellulose degradation mechanism. Based on our previous research, we hypothesized that BGL-producing microbial communities differentially regulate the expression of glucose-tolerant BGL and non-glucose-tolerant BGL to adapt to the changes in cellulose degradation conditions. Results To confirm this hypothesis, the structure and function of functional microbial communities involved in cellulose degradation were investigated by metatranscriptomics and a DNA library search of the GH1 family of BGLs involved in natural and inoculated composting. Under normal conditions, the group of non-glucose-tolerant BGL genes exhibited higher sensitivity to regulation than the glucose-tolerant BGL genes, which was suppressed during the composting process. Compared with the expression of endoglucanase and exoglucanase, the functional microbial communities exhibited a different transcriptional regulation of BGL genes during the cooling phase of natural composting. BGL-producing microbial communities upregulated the expression of glucose-tolerant BGL under carbon catabolite repression due to the increased glucose concentration, whereas the expression of non-glucose-tolerant BGL was suppressed. Conclusion Our results support the hypothesis that the functional microbial communities use multiple strategies of varying effectiveness to regulate the expression of BGL genes to facilitate adaptation to environmental changes.

scholarly journals Oleuropein and its peracetylated derivative negatively regulate osteoclastogenesis by controlling the expression of genes involved in osteoclast differentiation and function

2020 ◽  
Vol 11 (5) ◽  
pp. 4038-4048 ◽  
Author(s):  
Maria Angeles Rosillo ◽  
Sergio Montserrat-de-la-Paz ◽  
Rocio Abia ◽  
Maria Luisa Castejon ◽  
Maria Carmen Millan-Linares ◽  
...  
Keyword(s):  
Human Blood ◽  
Osteoclast Differentiation ◽  
Blood Monocytes ◽  
Gene Circuits ◽  
Expression Of Genes ◽  
And Function

OL and Per-OL impair transcriptional gene circuits able to support osteoclastogenesis from human blood monocytes.

scholarly journals Peptide affinity analysis of proteins that bind to an unstructured NH2-terminal region of the osmoprotective transcription factor NFAT5

2016 ◽  
Vol 48 (4) ◽  
pp. 290-305 ◽  
Author(s):  
Jenna F. DuMond ◽  
Kevin Ramkissoon ◽  
Xue Zhang ◽  
Yuichiro Izumi ◽  
Xujing Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Terminal Region ◽  
Hek293 Cells ◽  
The Novel ◽  
Amino Acid Peptide ◽  
Intrinsically Disordered ◽  
Expression Of Genes ◽  
Nuclear Extracts ◽  
And Function ◽  
Peptide Affinity

NFAT5 is an osmoregulated transcription factor that particularly increases expression of genes involved in protection against hypertonicity. Transcription factors often contain unstructured regions that bind co-regulatory proteins that are crucial for their function. The NH2-terminal region of NFAT5 contains regions predicted to be intrinsically disordered. We used peptide aptamer-based affinity chromatography coupled with mass spectrometry to identify protein preys pulled down by one or more overlapping 20 amino acid peptide baits within a predicted NH2-terminal unstructured region of NFAT5. We identify a total of 467 unique protein preys that associate with at least one NH2-terminal peptide bait from NFAT5 in either cytoplasmic or nuclear extracts from HEK293 cells treated with elevated, normal, or reduced NaCl concentrations. Different sets of proteins are pulled down from nuclear vs. cytoplasmic extracts. We used GeneCards to ascertain known functions of the protein preys. The protein preys include many that were previously known, but also many novel ones. Consideration of the novel ones suggests many aspects of NFAT5 regulation, interaction and function that were not previously appreciated, for example, hypertonicity inhibits NFAT5 by sumoylating it and the NFAT5 protein preys include components of the CHTOP complex that desumoylate proteins, an action that should contribute to activation of NFAT5.

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