Displaying publications 1 - 20 of 1023 in total

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  1. Fulltext H19: An Oncogenic Long Non-coding RNA in Colorectal Cancer
    Chowdhury PR, Salvamani S, Gunasekaran B, Peng HB, Ulaganathan V
    Yale J Biol Med, 2023 Dec;96(4):495-509.
    PMID: 38161577 DOI: 10.59249/TDBJ7410
    Colorectal cancer (CRC) has been recorded amongst the most common cancers in the world, with high morbidity and mortality rates, and relatively low survival rates. With risk factors such as chronic illness, age, and lifestyle associated with the development of CRC, the incidence of CRC is increasing each year. Thus, the discovery of novel biomarkers to improve the diagnosis and prognosis of CRC has become beneficial. Long non-coding RNAs (lncRNAs) have been emerging as potential players in several tumor types, one among them is the lncRNA H19. The paternally imprinted oncofetal gene is expressed in the embryo, downregulated at birth, and reappears in tumors. H19 aids in CRC cell growth, proliferation, invasion, and metastasis via various mechanisms of action, significantly through the lncRNA-microRNA (miRNA)-messenger RNA (mRNA)-competitive endogenous RNA (ceRNA) network, where H19 behaves as a miRNA sponge. The RNA transcript of H19 obtained from the first exon of the H19 gene, miRNA-675 also promotes CRC carcinogenesis. Overexpression of H19 in malignant tissues compared to adjacent non-malignant tissues marks H19 as an independent prognostic marker in CRC. Besides its prognostic value, H19 serves as a promising target for therapy in CRC treatment.
    Matched MeSH terms: Gene Expression Regulation, Neoplastic/genetics
  2. Targeting notch-related lncRNAs in cancer: Insights into molecular regulation and therapeutic potential
    Siddique R, Gupta G, Mgm J, Kumar A, Kaur H, Ariffin IA, et al.
    Pathol Res Pract, 2024 May;257:155282.
    PMID: 38608371 DOI: 10.1016/j.prp.2024.155282
    Cancer is a group of diseases marked by unchecked cell proliferation and the ability for the disease to metastasize to different body areas. Enhancements in treatment and early detection are crucial for improved outcomes. LncRNAs are RNA molecules that encode proteins and have a length of more than 200 nucleotides. LncRNAs are crucial for chromatin architecture, gene regulation, and other cellular activities that impact both normal growth & pathological processes, even though they are unable to code for proteins. LncRNAs have emerged as significant regulators in the study of cancer biology, with a focus on their intricate function in the Notch signaling pathway. The imbalance of this pathway is often linked to a variety of malignancies. Notch signaling is essential for cellular functions like proliferation, differentiation, and death. The cellular response is shaped by these lncRNAs through their modulation of essential Notch pathway constituents such as receptors, ligands, and downstream effectors around it. Furthermore, a variety of cancer types exhibit irregular expression of Notch-related lncRNAs, underscoring their potential use as therapeutic targets and diagnostic markers. Gaining an understanding of the molecular processes behind the interaction between the Notch pathway and lncRNAs will help you better understand the intricate regulatory networks that control the development of cancer. This can open up new possibilities for individualized treatment plans and focused therapeutic interventions. The intricate relationships between lncRNAs & the Notch pathway in cancer are examined in this review.
    Matched MeSH terms: Gene Expression Regulation, Neoplastic/genetics
  3. Expressing banana transcription factor MaERFVII3 in Arabidopsis confers enhanced waterlogging tolerance and root growth
    Teoh EY, Teo CH, Baharum NA, Tan BC
    PeerJ, 2024;12:e17285.
    PMID: 38708359 DOI: 10.7717/peerj.17285
    BACKGROUND: Waterlogging poses a significant threat to plant growth and yield worldwide. Identifying the genes responsible for mitigating waterlogging stress is crucial. Ethylene-responsive factors (ERFs) are transcriptional regulators that respond to various biotic and abiotic stresses in plants. However, their roles and involvement in responding to waterlogging stress remain largely unexplored. Hence, this study aimed to elucidate the role of ERFs in enhancing banana plant resilience to waterlogging.

    METHODS: We hypothesized that introducing a group VII ERF transcription factor in Arabidopsis could enhance waterlogging stress tolerance. To test this hypothesis, we isolated MaERFVII3 from banana roots, where it exhibited a significant induction in response to waterlogging stress. The isolated MaERFVII3 was introduced into Arabidopsis plants for functional gene studies.

    RESULTS: Compared with wild-type plants, the MaERFVII3-expressing Arabidopsis showed increased survival and biomass under waterlogging stress. Furthermore, the abundance of transcripts related to waterlogging and hypoxia response showed an elevation in transgenic plants but a decrease in wild-type and empty vector plants when exposed to waterlogging stress. Our results demonstrate the significant contribution of MaERFVII3 to waterlogging tolerance in Arabidopsis, providing baseline data for further exploration and potentially contributing to crop improvement programs.

    Matched MeSH terms: Gene Expression Regulation, Plant*
  4. lncRNAs'p potential roles in the pathogenesis of cancer via interacting with signaling pathways; special focus on lncRNA-mediated signaling dysregulation in lung cancer
    Shelash SI, Shabeeb IA, Ahmad I, Saleem HM, Bansal P, Kumar A, et al.
    Med Oncol, 2024 Nov 08;41(12):310.
    PMID: 39516331 DOI: 10.1007/s12032-024-02536-w
    Lung cancer ranks among the most lethal types of cancer globally, with a high occurrence and fatality rate. The spread of cancer to other parts of the body, known as metastasis, is the primary cause of treatment failure and death in lung cancer cases. Current approaches for treating advanced lung cancer typically involve a combination of chemotherapy and targeted therapy. However, the majority of patients ultimately develop resistance to these treatments, leading to a worsened prognosis. In recent years, cancer biology research has predominantly focused on the role of protein-encoding genes in cancer development. Long non-coding RNAs (lncRNAs) are transcripts over 200 nucleotides in length that do not encode proteins but are crucial RNA molecules involved in numerous biological functions. While many functions of lncRNAs remain unknown, some have been linked to human diseases, including cancer. Studies have demonstrated that lncRNAs interact with other large molecules in the cell, such as proteins, DNA, and RNA, influencing various critical aspects of cancer. LncRNAs play a significant role in regulating gene expression and have a crucial function in the transcriptional regulation of cancer cells. They mediate various biological and clinical processes such as invasion, metastasis, apoptosis, and cell proliferation. Dysregulation of lncRNAs has been found to impact the process of carcinogenesis through advanced technologies like RNA sequencing and microarrays. Collectively, these long non-coding RNAs hold promise as potential biomarkers and therapeutic targets for human cancers. In this segment, we provide a comprehensive summary of the literature on the characteristics and formation of lncRNAs, along with an overview of their current known roles in lung cancer.
    Matched MeSH terms: Gene Expression Regulation, Neoplastic*
  5. Non-coding RNAs as key regulators of Gasdermin-D mediated pyroptosis in cancer therapy
    Gupta G, Afzal M, Moglad E, Ali H, Singh TG, Kumbhar P, et al.
    Pathol Res Pract, 2024 Sep;261:155490.
    PMID: 39126977 DOI: 10.1016/j.prp.2024.155490
    Pyroptosis is an inflammatory programed cell death process that plays a crucial role in cancer therapeutic, while Gasdermin-D is a critical effector protein for pyroptosis execution. This review discusses the intricate interactions between Gasdermin-D and some non-coding RNAs (lncRNA, miRNA, siRNA) and their potential application in the regulation of pyroptosis as an anticancer therapy. Correspondingly, these ncRNAs significantly implicate in Gasdermin-D expression and function regarding the pyroptosis pathway. Functioning as competing endogenous RNAs (ceRNAs), these ncRNAs might regulate Gasdermin-D at the molecular level, underlying fatal cell death caused by cancer and tumor propagation. Therefore, these interactions appeal to therapeutics, offering new avenues for cancer treatment. It address this research gap by discussing the possible roles of ncRNAs as mediators of gasdermin-D regulation. It suggest therapeutic strategies based on the current research findings to ensure the interchange between the ideal pyroptosis and cancer cell death.
    Matched MeSH terms: Gene Expression Regulation, Neoplastic
  6. Fulltext Perigone Lobe Transcriptome Analysis Provides Insights into Rafflesia cantleyi Flower Development
    Lee XW, Mat-Isa MN, Mohd-Elias NA, Aizat-Juhari MA, Goh HH, Dear PH, et al.
    PLoS One, 2016;11(12):e0167958.
    PMID: 27977777 DOI: 10.1371/journal.pone.0167958
    Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to address this issue, we have generated and characterised the transcriptome of the Rafflesia cantleyi flower, and performed a comparison with the transcriptome of its floral bud to predict genes that are expressed and regulated during flower development. Approximately 40 million sequencing reads were generated and assembled de novo into 18,053 transcripts with an average length of 641 bp. Of these, more than 79% of the transcripts had significant matches to annotated sequences in the public protein database. A total of 11,756 and 7,891 transcripts were assigned to Gene Ontology categories and clusters of orthologous groups respectively. In addition, 6,019 transcripts could be mapped to 129 pathways in Kyoto Encyclopaedia of Genes and Genomes Pathway database. Digital abundance analysis identified 52 transcripts with very high expression in the flower transcriptome of R. cantleyi. Subsequently, analysis of differential expression between developing flower and the floral bud revealed a set of 105 transcripts with potential role in flower development. Our work presents a deep transcriptome resource analysis for the developing flower of R. cantleyi. Genes potentially involved in the growth and development of the R. cantleyi flower were identified and provide insights into biological processes that occur during flower development.
    Matched MeSH terms: Gene Expression Regulation, Plant/genetics
  7. Fulltext CRNDE: A Pivotal Oncogenic Long Non-Coding RNA in Cancers
    Hor YZ, Salvamani S, Gunasekaran B, Yian KR
    Yale J Biol Med, 2023 Dec;96(4):511-526.
    PMID: 38161583 DOI: 10.59249/VHYE2306
    Colorectal Neoplasia Differentially Expressed (CRNDE), a long non-coding RNA that was initially identified as aberrantly expressed in colorectal cancer (CRC) has also been observed to exhibit elevated expression in various other human malignancies. Recent research has accumulated substantial evidence implicating CRNDE as an oncogenic player, exerting influence over critical cellular processes linked to cancer progression. Particularly, its regulatory interactions with microRNAs and proteins have been shown to modulate pathways that contribute to carcinogenesis and tumorigenesis. This review will comprehensively outline the roles of CRNDE in colorectal, liver, glioma, lung, cervical, gastric and prostate cancer, elucidating the mechanisms involved in modulating proliferation, apoptosis, migration, invasion, angiogenesis, and radio/chemoresistance. Furthermore, the review highlights CRNDE's potential as a multifaceted biomarker, owing to its presence in diverse biological samples and stable properties, thereby underscoring its diagnostic, therapeutic, and prognostic applications. This review aims to provide comprehensive insights of CRNDE-mediated oncogenesis and identify CRNDE as a promising target for future clinical interventions.
    Matched MeSH terms: Gene Expression Regulation, Neoplastic/genetics
  8. Fulltext A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system
    Govender N, Senan S, Mohamed-Hussein ZA, Wickneswari R
    Sci Rep, 2018 Jun 15;8(1):9211.
    PMID: 29907786 DOI: 10.1038/s41598-018-27493-z
    The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes. Using the reference genome-based mapping approach, a total of 64 361 genes was identified in all samples and the data was annotated against the non-redundant database by the BLAST2GO Pro. Suite. After removing the outlier genes and samples, a total of 12 734 genes across 17 samples were subjected to gene co-expression network construction using petal, an R library. A gene co-expression network model built with scale-free and small-world properties extracted four vicinity networks (VNs) with putative involvement in yield-related biological processes as follow; heat stress tolerance, floral and shoot meristem differentiation, biosynthesis of chlorophyll molecules and laticifers, cell wall metabolism and epigenetic regulations. Our VNs revealed putative key players that could be adapted in breeding strategies for J. curcas shoot system improvements.
    Matched MeSH terms: Gene Expression Regulation, Plant/physiology*
  9. Transcriptome analysis and molecular characterization of novel small RNAs in Mycobacterium tuberculosis Lineage 1
    Jumat MI, Chin KL
    World J Microbiol Biotechnol, 2024 Jul 25;40(9):279.
    PMID: 39048776 DOI: 10.1007/s11274-024-04089-6
    Mycobacterium tuberculosis (Mtb), the tuberculosis-causing agent, exhibits diverse genetic lineages, with known links to virulence. While genomic and transcriptomic variations between modern and ancient Mtb lineages have been explored, the role of small non-coding RNA (sRNA) in post-translational gene regulation remains largely uncharted. In this study, Mtb Lineage 1 (L1) Sabahan strains (n = 3) underwent sRNA sequencing, revealing 351 sRNAs, including 23 known sRNAs and 328 novel ones identified using ANNOgesic. Thirteen sRNAs were selected based on the best average cut-off value of 300, with RT-qPCR revealing significant expression differences for sRNA 1 (p = 0.0132) and sRNA 29 (p = 0.0012) between Mtb L1 and other lineages (L2 and L4, n = 3) (p > 0.05). Further characterization using RACE (rapid amplification of cDNA ends), followed by target prediction with TargetRNA3 unveils that sRNA 1 (55 base pairs) targets Rv0506, Rv0697, and Rv3590c, and sRNA 29 (86 base pairs) targets Rv33859c, Rv3345c, Rv0755c, Rv0107c, Rv1817, Rv2950c, Rv1181, Rv3610c, and Rv3296. Functional characterization with Mycobrowser reveals these targets involved in regulating intermediary metabolism and respiration, cell wall and cell processes, lipid metabolism, information pathways, and PE/PPE. In summary, two novel sRNAs, sRNA 1 and sRNA 29, exhibited differential expression between L1 and other lineages, with predicted roles in essential Mtb functions. These findings offer insights into Mtb regulatory mechanisms, holding promise for the development of improved tuberculosis treatment strategies in the future.
    Matched MeSH terms: Gene Expression Regulation, Bacterial*
  10. The synthesis of papaya fruit flavor-related linalool was regulated by CpTPS18 and CpNAC56
    Yao Y, Fu W, Yu Y, Wan S, Zhang W, Ming R
    Plant Reprod, 2024 Sep;37(3):295-308.
    PMID: 37966580 DOI: 10.1007/s00497-023-00486-3
    Papaya is a tropical fruit crop renowned for its rich nutrition, particularly pro-vitamin A. Aroma substances are a major component of fruit quality. While extensive research has been conducted on papaya aroma, there has been a notable lack of in-depth research into a specific class of substances. To bridge this gap, our study focused on analyzing the aroma components of various papaya varieties and their biosynthesis pathways. We compared the volatile components of three papaya varieties with distinct flavors at various ripeness stages. A continuous accumulation of linalool, a volatile compound, in the 'AU9' fruit was detected as it matured. The linalool content reached 56% of the total volatile components upon full ripening. Notably, this percentage was significantly higher than that observed in the other two varieties, 'ZhongBai' and 'Malaysian 7', indicating that linalool serves as the primary component influencing the papaya's odor. Subsequently, we identified CpTPS18, a gene associated with linalool biosynthesis, and demonstrated its ability to catalyze linalool production from GPP and enhance its accumulation through overexpression in papaya fruits, both in vivo and in vitro. Based on transcriptomic analysis, it was predicted that CpMYB56 and CpNAC56 may transcriptionally activate the expression of CpTPS18. Subsequent yeast one-hybrid assay and dual luciferase analysis revealed that CpNAC56 activates the transcription of CpTPS18. Transient overexpression in vivo demonstrated that this gene could upregulate the expression of CpTPS18 and promote linalool accumulation. These results uncovered the primary volatile molecule responsible for papaya fruit odor and identified two major genes influencing its biosynthesis. The genomic resources and information obtained from this study will expedite papaya improvement for fruit quality.
    Matched MeSH terms: Gene Expression Regulation, Plant*
  11. Fulltext Potential regulatory role of gibberellic and humic acids in sprouting of Chlorophytum borivilianum tubers
    Nakasha JJ, Sinniah UR, Puteh A, Hassan SA
    ScientificWorldJournal, 2014;2014:168950.
    PMID: 24688363 DOI: 10.1155/2014/168950
    Tubers of safed musli (Chlorophytum borivilianum) were immersed in three different concentrations of gibberellic acid (GA3) or humic acid (HA) prior to planting. The highest concentration of GA3 (20 mg L(-1)) and all concentrations of HA (5, 10, and 15%) appeared to hasten tuber sprouting and promote uniform sprouting pattern. The use of 20 mg L(-1) GA3 or 15% HA successfully improved sprouting and mean sprouting time. Safed musli growth and development was improved through the increase in the number of leaves, total leaf area, leaf area index, and total fibrous root length. This directly influenced the number of new tubers formed. The use of 20 mg L(-1) GA3 or 15% HA gave similar response with nonsignificant difference among them. However, due to the cost of production, the result from this study suggests that 15% HA should be used to obtain improved sprouting percentage, homogeneous stand establishment, efficient plant growth and development, and increased yield of safed musli.
    Matched MeSH terms: Gene Expression Regulation, Plant/physiology*; Gene Expression Regulation, Developmental/physiology*
  12. Reconstructing gene regulatory networks from knock-out data using Gaussian Noise Model and Pearson Correlation Coefficient
    Mohamed Salleh FH, Arif SM, Zainudin S, Firdaus-Raih M
    Comput Biol Chem, 2015 Dec;59 Pt B:3-14.
    PMID: 26278974 DOI: 10.1016/j.compbiolchem.2015.04.012
    A gene regulatory network (GRN) is a large and complex network consisting of interacting elements that, over time, affect each other's state. The dynamics of complex gene regulatory processes are difficult to understand using intuitive approaches alone. To overcome this problem, we propose an algorithm for inferring the regulatory interactions from knock-out data using a Gaussian model combines with Pearson Correlation Coefficient (PCC). There are several problems relating to GRN construction that have been outlined in this paper. We demonstrated the ability of our proposed method to (1) predict the presence of regulatory interactions between genes, (2) their directionality and (3) their states (activation or suppression). The algorithm was applied to network sizes of 10 and 50 genes from DREAM3 datasets and network sizes of 10 from DREAM4 datasets. The predicted networks were evaluated based on AUROC and AUPR. We discovered that high false positive values were generated by our GRN prediction methods because the indirect regulations have been wrongly predicted as true relationships. We achieved satisfactory results as the majority of sub-networks achieved AUROC values above 0.5.
    Matched MeSH terms: Gene Expression Regulation
  13. Draft genome sequence of Vitellibacter vladivostokensis KMM 3516(T): a protease-producing bacterium
    Thevarajoo S, Selvaratnam C, Chan KG, Goh KM, Chong CS
    Mar Genomics, 2015 Oct;23:49-50.
    PMID: 25957696 DOI: 10.1016/j.margen.2015.04.009
    Type strain Vitellibacter vladivostokensis KMM 3516(T) (=NBRC 16718(T)) belongs to the phylum Cytophaga-Flavobacterium-Bacteroides. To date, no genomes of the Vitellibacter spp. have been reported, and their metabolic pathways are unknown. This study reports the draft genome sequence of V. vladivostokensis. Moreover, mining of genes associated with proteolytic enzymes was performed to provide insights for further enzyme characterization.
    Matched MeSH terms: Gene Expression Regulation, Bacterial/physiology; Gene Expression Regulation, Enzymologic/physiology
  14. ADAP is a possible negative regulator of glucosinolate biosynthesis in Arabidopsis thaliana based on clustering and gene expression analyses
    Harun S, Rohani ER, Ohme-Takagi M, Goh HH, Mohamed-Hussein ZA
    J Plant Res, 2021 Mar;134(2):327-339.
    PMID: 33558947 DOI: 10.1007/s10265-021-01257-9
    Glucosinolates (GSLs) are plant secondary metabolites consisting of sulfur and nitrogen, commonly found in Brassicaceae crops, such as Arabidopsis thaliana. These compounds are known for their roles in plant defense mechanisms against pests and pathogens. 'Guilt-by-association' (GBA) approach predicts genes encoding proteins with similar function tend to share gene expression pattern generated from high throughput sequencing data. Recent studies have successfully identified GSL genes using GBA approach, followed by targeted verification of gene expression and metabolite data. Therefore, a GSL co-expression network was constructed using known GSL genes obtained from our in-house database, SuCComBase. DPClusO was used to identify subnetworks of the GSL co-expression network followed by Fisher's exact test leading to the discovery of a potential gene that encodes the ARIA-interacting double AP2-domain protein (ADAP) transcription factor (TF). Further functional analysis was performed using an effective gene silencing system known as CRES-T. By applying CRES-T, ADAP TF gene was fused to a plant-specific EAR-motif repressor domain (SRDX), which suppresses the expression of ADAP target genes. In this study, ADAP was proposed as a negative regulator in aliphatic GSL biosynthesis due to the over-expression of downstream aliphatic GSL genes (UGT74C1 and IPMI1) in ADAP-SRDX line. The significant over-expression of ADAP gene in the ADAP-SRDX line also suggests the behavior of the TF that negatively affects the expression of UGT74C1 and IPMI1 via a feedback mechanism in A. thaliana.
    Matched MeSH terms: Gene Expression Regulation, Plant
  15. Fulltext Implisit judul berita pilihan raya umum ke-14
    Faris Fakhira Tauran, Zaitul Azma Zainon Hamzah
    Malaysian Journal of Social Sciences and Humanities, 2019;4(6):32-44.
    MyJurnal
    Kemenangan parti pembangkang dalam pilihan raya umum (PRU) kali ke-14 telah memecahkan tampuk pimpinan kerajaan lama yang telah memerintah selama 60 tahun. Pelbagai isu mengenai pilihan raya umum disiarkan menerusi media massa terutamanya media cetak. Media cetak seperti surat khabar juga tidak terlepas daripada menyiarkan pelbagai judul berita yang menarik. Walau bagaimanapun, terdapat beberapa judul berita yang ditulis menggunakan perkataan yang mempunyai makna implisit. Penggunaan perkataan yang mempunyai makna implisit ini akan menyukarkan pembaca untuk memahami judul yang dipaparkan. Kajian ini bertujuan untuk mengenal pasti dan membincangkan perkataan implisit yang terdapat dalam judul berita PRU ke-14. Kaedah yang dipilih bagi melaksanakan kajian ini ialah kaedah kualitatif. Selain itu, bahan kajian yang digunakan ialah surat khabar Berita Harian keluaran bulan April dan Mei bagi tahun 2018. Namun, berita yang dipilih hanya berfokus kepada berita PRU ke-14 yang mempunyai perkataan implisit sahaja. Setiap data yang dikumpul akan dikateorikan mengikut bentuk kata iaitu kata tunggal, kata terbitan dan kata majmuk. Data yang telah dikategorikan akan dianalisis dengan menggunakan teori semiotik. Hasil dapatan menunjukkan bahawa terdapat 28 judul berita PRU ke-14 yang menggunakan perkataan implisit. Kebanyakan perkataan implisit ini terdiri daripada kata majmuk iaitu sebanyak 18 judul, diikuti kata tunggal sebanyak 8 judul dan kata terbitan sebanyak 2 judul. Penggunaan perkataan implisit ini adalah bertujuan untuk menarik perhatian pembaca supaya membaca berita yang disiarkan. Justeru, kajian ini secara tidak langsung dapat menunjukkan bahawa berita bergenre politik juga turut menggunakan perkataan implisit dalam penulisan judul berita.
    Matched MeSH terms: Gene Expression Regulation, Bacterial
  16. Analysis of differentially expressed proteins in cancerous and normal colonic tissues
    Gam LH, Leow CH, Man CN, Gooi BH, Singh M
    World J Gastroenterol, 2006 Aug 21;12(31):4973-80.
    PMID: 16937492
    AIM: To identify and analyze the differentially expressed proteins in normal and cancerous tissues of four patients suffering from colon cancer.

    METHODS: Colon tissues (normal and cancerous) were homogenized and the proteins were extracted using three protein extraction buffers. The extraction buffers were used in an orderly sequence of increasing extraction strength for proteins with hydrophobic properties. The protein extracts were separated using the SDS-PAGE method and the images were captured and analyzed using Quantity One software. The target protein bands were subjected to in-gel digestion with trypsin and finally analyzed using an ESI-ion trap mass spectrometer.

    RESULTS: A total of 50 differentially expressed proteins in colonic cancerous and normal tissues were identified.

    CONCLUSION: Many of the identified proteins have been reported to be involved in the progression of similar or other types of cancers. However, some of the identified proteins have not been reported before. In addition, a number of hypothetical proteins were also identified.

    Matched MeSH terms: Gene Expression Regulation*; Gene Expression Regulation, Neoplastic*
  17. Metabolic engineering of Lactococcus lactis influence of the overproduction of lipase enzyme
    Raftari M, Ghafourian S, Bakar FA
    J Dairy Res, 2013 Nov;80(4):490-5.
    PMID: 24063299 DOI: 10.1017/S0022029913000435
    The dairy industry uses lipase extensively for hydrolysis of milk fat. Lipase is used in the modification of the fatty acid chain length, to enhance the flavours of various chesses. Therefore finding the unlimited source of lipase is a concern of dairy industry. Due to the importance of lipase, this study was an attempt to express the lipase from Burkholderia cepacia in Lactococcus lactis. To achieve this, a gene associated with lipase transport was amplified and subcloned in inducible pNZ8148 vector, and subsequently transformed into Lc. lactis NZ9000. The enzyme assay as well as SDS-PAGE and western blotting were carried out to analysis the recombinant lipase expression. Nucleotide sequencing of the DNA insert from the clone revealed that the lipase activity corresponded to an open reading frame consisting of 1092 bp coding for a 37·5-kDa size protein. Blue colour colonies on nile blue sulphate agar and sharp band on 37·5-kD size on SDS-PAGE and western blotting results confirm the successful expression of lipase by Lc. lactis. The protein assay also showed high expression, approximately 152·2 μg/ml.h, of lipase by recombinant Lc. lactis. The results indicate that Lc. lactis has high potential to overproduce the recombinant lipase which can be used commercially for industrially purposes.
    Matched MeSH terms: Gene Expression Regulation, Bacterial/physiology*; Gene Expression Regulation, Enzymologic/physiology*
  18. Targeting and regulation of autophagy in hepatocellular carcinoma: revisiting the molecular interactions and mechanisms for new therapy approaches
    Hashemi M, Nadafzadeh N, Imani MH, Rajabi R, Ziaolhagh S, Bayanzadeh SD, et al.
    Cell Commun Signal, 2023 Feb 09;21(1):32.
    PMID: 36759819 DOI: 10.1186/s12964-023-01053-z
    Autophagy is an evolutionarily conserved process that plays a role in regulating homeostasis under physiological conditions. However, dysregulation of autophagy is observed in the development of human diseases, especially cancer. Autophagy has reciprocal functions in cancer and may be responsible for either survival or death. Hepatocellular carcinoma (HCC) is one of the most lethal and common malignancies of the liver, and smoking, infection, and alcohol consumption can lead to its development. Genetic mutations and alterations in molecular processes can exacerbate the progression of HCC. The function of autophagy in HCC is controversial and may be both tumor suppressive and tumor promoting. Activation of autophagy may affect apoptosis in HCC and is a regulator of proliferation and glucose metabolism. Induction of autophagy may promote tumor metastasis via induction of EMT. In addition, autophagy is a regulator of stem cell formation in HCC, and pro-survival autophagy leads to cancer cell resistance to chemotherapy and radiotherapy. Targeting autophagy impairs growth and metastasis in HCC and improves tumor cell response to therapy. Of note, a large number of signaling pathways such as STAT3, Wnt, miRNAs, lncRNAs, and circRNAs regulate autophagy in HCC. Moreover, regulation of autophagy (induction or inhibition) by antitumor agents could be suggested for effective treatment of HCC. In this paper, we comprehensively review the role and mechanisms of autophagy in HCC and discuss the potential benefit of targeting this process in the treatment of the cancer. Video Abstract.
    Matched MeSH terms: Gene Expression Regulation, Neoplastic
  19. Revealing holistic metabolic responses associated with lipid and docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1
    Prabhakaran P, Raethong N, Thananusak R, Nazir MYM, Sapkaew C, Soommat P, et al.
    Biochim Biophys Acta Mol Cell Biol Lipids, 2023 May;1868(5):159306.
    PMID: 36907245 DOI: 10.1016/j.bbalip.2023.159306
    Aurantiochytrium sp. SW1, a marine thraustochytrid, has been regarded as a potential candidate as a docosahexaenoic acid (DHA) producer. Even though the genomics of Aurantiochytrium sp. are available, the metabolic responses at a systems level are largely unknown. Therefore, this study aimed to investigate the global metabolic responses to DHA production in Aurantiochytrium sp. through transcriptome and genome-scale network-driven analysis. Of a total of 13,505 genes, 2527 differentially expressed genes (DEGs) were identified in Aurantiochytrium sp., unravelling the transcriptional regulations behinds lipid and DHA accumulation. The highest number of DEG were found for pairwise comparison between growth phase and lipid accumulating phase where a total of 1435 genes were down-regulated with 869 genes being up-regulated. These uncovered several metabolic pathways that contributing in DHA and lipid accumulation including amino acid and acetate metabolism which involve in the generation of crucial precursors. Upon applying network-driven analysis, hydrogen sulphide was found as potential reporter metabolite that could be associated with the genes related to acetyl-CoA synthesis for DHA production. Our findings suggest that the transcriptional regulation of these pathways is a ubiquitous feature in response to specific cultivation phases during DHA overproduction in Aurantiochytrium sp. SW1.
    Matched MeSH terms: Gene Expression Regulation
  20. Oncoinformatic screening of the gene clusters involved in the HER2-positive breast cancer formation along with the in silico pharmacodynamic profiling of selective long-chain omega-3 fatty acids as the metastatic antagonists
    Morshed AKMH, Al Azad S, Mia MAR, Uddin MF, Ema TI, Yeasin RB, et al.
    Mol Divers, 2023 Dec;27(6):2651-2672.
    PMID: 36445532 DOI: 10.1007/s11030-022-10573-8
    The HER2-positive patients occupy ~ 30% of the total breast cancer patients globally where no prevalent drugs are available to mitigate the frequent metastasis clinically except lapatinib and neratinib. This scarcity reinforced researchers' quest for new medications where natural substances are significantly considered. Valuing the aforementioned issues, this research aimed to study the ERBB2-mediated string networks that work behind the HER2-positive breast cancer formation regarding co-expression, gene regulation, GAMA-receptor-signaling pathway, cellular polarization, and signal inhibition. Following the overexpression, promotor methylation, and survivability profiles of ERBB2, the super docking position of HER2 was identified using the quantum tunneling algorithm. Supramolecular docking was conducted to study the target specificity of EPA and DHA fatty acids followed by a comprehensive molecular dynamic simulation (100 ns) to reveal the RMSD, RMSF, Rg, SASA, H-bonds, and MM/GBSA values. Finally, potential drug targets for EPA and DHA in breast cancer were constructed to determine the drug-protein interactions (DPI) at metabolic stages. Considering the values resulting from the combinational models of the oncoinformatic, pharmacodynamic, and metabolic parameters, long-chain omega-3 fatty acids like EPA and DHA can be considered as potential-targeted therapeutics for HER2-positive breast cancer treatment.
    Matched MeSH terms: Gene Expression Regulation
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