ARTICLE | doi:10.20944/preprints201610.0121.v1
Subject: Biology, Other Keywords: cytokine; gene expression; osteoclast; root resorption; pediatric dentistry; protein expression
Online: 27 October 2016 (12:10:55 CEST)
The present study was performed to examine that transforming growth factor beta (TGF-β) in root-surrounding tissues on deciduous teeth during the physiological root resorption regulates the differentiation induction into odontoclast. We prepared root-surrounding tissues with (R) or without (N) physiological root resorption scraped off at three regions (R1-R3 or N1-N3) from the cervical area to the apical area of the tooth and measured both TGF-β and the tartrate-resistant acid phosphatase (TRAP) activities. The TGF-β activity level was increased in N1-N3, whereas the TRAP activity was increased in R2 and R3. In vitro experiments for RANKL-mediated osteoclast differentiation revealed that TGF-β in N1-N3 and R1-R3 enhanced the TRAP activity in RAW264 cells. A genetic study indicated that the mRNA level of TGF-β1 in N1 and N2 was significantly increased, and corresponded with that of osteoprotegerin (OPG). In contrast, the expression level of receptor activator of NF-κB ligand (RANKL) was increased in R2 and R3. Our findings suggest that TGF-β is closely related to the regulation of OPG induction and RANKL-mediated odontoclast differentiation depending on the timing of RANKL and OPG mRNA expression in the root-surrounding tissues of deciduous teeth during physiological root resorption.
ARTICLE | doi:10.20944/preprints201701.0120.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: expression recognition; expression triplet; feature optimization; AU weighting; active AU detection.
Online: 26 January 2017 (08:52:52 CET)
Facial expression has lots of applications in human-computer interaction. Although feature extraction and selection have been well studied, the specificity of each expression variation is not fully explored in state-of-the-art works. In this work, the problem of multiclass expression recognition is converted into triplet-wise expression recognition. For each expression triplet, a new feature optimization model based on Action Unit (AU) weighting and patch weight optimization is proposed to represent the specificity of the expression triplet. Sparse representation based approach is then proposed to detect the active AUs of testing sample for better generalization. The algorithm achieved competitive accuracies of 89.67% and 94.09% for Jaffe and CK+ databases, respectively. Better cross-database performance has also been observed.
ARTICLE | doi:10.20944/preprints202008.0322.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: TAP1; transcriptional expression; methylation analysis; survival analysis; co-expression; pathway analysis; health informatics
Online: 14 August 2020 (11:17:29 CEST)
Transporter associated with antigen processing 1 (TAP1) gene codes for a transporter protein, which is responsible for tumor antigen presentation in the MHC I or HLA complex. A defect in the gene results in an inadequate tumor tracking. TAP1 may also influence multi drug resistance, which is an extreme threat in providing treatment by drugs which are chemotherapeutic. The gene of TAP1 was analyzed bioinformatically. It gave us prognostic data as a confirmation of whether it should be used as a biomarker. The expression level and pattern analysis were conducted using ONCOMINE, GENT2 and GEPIA2 online platforms. Samples with different clinical outcomes were investigated for expression and promoter methylation analysis was done in cancer vs normal tissues using UALCAN. The copy number alteration and mutation frequency and expression in different cancer studies were analyzed using cBioPortal. The PrognoScan and KM plotter survival analysis of significant data (p-value<0.05) was representing graphically. Pathway and Gene ontology analysis of gene correlated to TAP1 gene was presented using bar charts. After arranging the data in a single panel and correlating expression to prognosis, understanding mutational and alterations and comparing pathways, TAP1 may be a potential novel target to evade a threat against chemotherapy and the study gives new aspects to consider for immunotherapy in human breast, lung, liver and ovarian cancer.
ARTICLE | doi:10.20944/preprints202104.0521.v1
Subject: Life Sciences, Biochemistry Keywords: Gene expression; Helianthus; microsatellites; transcriptomics
Online: 20 April 2021 (08:21:06 CEST)
Mutations that provide environment dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally significant variation. Some proposed mechanisms that explore the role of cis-regulatory mutations in gene expression divergence involve microsatellites. Microsatellites exhibit high mutation rates and are abundant in both coding and non-coding regions and could influence gene function and products. Here we tested the hypothesis that microsatellites contribute to gene expression divergence among species with 50 individuals from nine closely related Helianthus species using an RNA-seq approach. Differential expression analyses of the transcriptomes revealed that genes containing microsatellites in non-coding regions (UTRs and introns) are more likely to be differentially expressed among species when compared to genes with microsatellites in the coding regions and transcripts lacking microsatellites. We detected a greater proportion of shared microsatellites in 5’UTRs and coding regions compared to 3’UTRs and non-coding transcripts among Helianthus spp. Further, allele frequency differences measured by pairwise FST at single nucleotide polymorphisms (SNPs), indicate greater genetic divergence in transcripts containing microsatellites compared to those lacking microsatellites. A gene ontology (GO) analysis revealed that microsatellite-containing differentially expressed genes are significantly enriched for GO terms associated with regulation of transcription and transcription factor activity. Collectively, our study provides compelling evidence to support the role of microsatellites in gene expression divergence.
ARTICLE | doi:10.20944/preprints202101.0195.v1
Subject: Life Sciences, Biochemistry Keywords: miRNA; Tuberculosis; differential expression analysis
Online: 11 January 2021 (12:59:32 CET)
Molecular studies regarding regulatory elements such as small ncRNAs and their mechanisms are poorly understood in infectious diseases. Tuberculosis is one of the oldest infectious diseases of humanity, and it is still a challenge to prevent and treat it. The control of the infection as well as its diagnosis are still complex, and treatments used are linked to several side effects. This study aimed to investigate miRNA’s expression profile to identify possible biomarkers for tuberculosis. We applied NGS techniques to investigate miRNA’s global expression profile from blood samples of infected patients with tuberculosis, their respective healthy physicians, and external healthy individuals as controls. Samples from 22 individuals run through a differential expression, target genes, gene set enrichment, and miRNA-gene network analysis. We observed 153 altered miRNAs, among which, only three DEmiRNAs (hsa-let-7g-5p, hsa-miR-486-3p and hsa-miR-4732-5p) were found between the investigated patients and their respective physicians. These DEmiRNAs are suggested to play an important role in granuloma regulation and their immune physiopathology. Our results propose that miRNAs may be involved in immune modulation, regulating the repertoire of genes expressed in the immune system’s cells. Our findings encourage the application of miRNAs as potential biomarkers for tuberculosis.
ARTICLE | doi:10.20944/preprints201610.0089.v1
Subject: Mathematics & Computer Science, Analysis Keywords: improper integral; explicit expression; unified expression; beta function; Wallis ratio; integral representation; Catalan number
Online: 21 October 2016 (08:29:08 CEST)
In the paper, the author presents explicit and unified expressions for a sequence of improper integrals in terms of the beta functions and the Wallis ratios. Hereafter, the author derives integral representations for the Catalan numbers originating from combinatorics.
ARTICLE | doi:10.20944/preprints202106.0199.v1
Online: 8 June 2021 (09:15:47 CEST)
The aim of present study was to link the gene expression profile of selected candidate genes with blood profile, growth performance and carcass traits of Barki lambs. Thirty-eight Barki lambs were divided into 3 groups (fast, intermediate and slow growing) according to growth perfor-mance. Body tissues (muscle, liver and fat) were taken from for RNA isolation and Real-time PCR. The results indicated that, the final body weight hot carcass weight were heavier (P ≤ 0.05) in fast (49.9 Kg and 24.57) than intermediate (40.7 and 19.07 Kg) and slow (30.8 and 15.10 Kg) growing animals. The blood profile of total protein, total lipids, calcium, T3 and T4 hormones did not differ among sheep groups. Genes involved in protein biosynthesis (RPL7), fatty acid oxidation (CPT1) and lipolysis (FABP4) were up regulated in fast and intermediate growing lambs in all studied tissues. While, gene-regulating lipogenesis (ADIPOQ) was expressed simi-larly in fat and liver tissues, but increased its expression in muscle of fast and intermediate growing lambs. Expression of CAPN3 was increased in fast and intermediate growing compared to slow growing lambs. In conclusion, the current study providing an evidence for the im-portance of co-expression of these genes in main body tissues linked with growth performance of Barki lambs.
Subject: Life Sciences, Biochemistry Keywords: Cyanobacteria; Gene expression; Regulation; Signalling; Stress
Online: 23 October 2020 (12:26:14 CEST)
Cyanobacteria are highly diverse, widely distributed photosynthetic bacteria inhabiting various environments ranging from deserts to the cryosphere. Throughout this range of niches, they have to cope with various stresses and kinds of deprivation which threaten their growth and viability. In order to adapt to these stresses and survive, they have developed several global adaptive responses which modulate the patterns of gene expression and the cellular functions at work. Sigma factors, two-component systems, transcriptional regulators and small regulatory RNAs acting either separately or collectively, for example, induce appropriate cyanobacterial stress responses. The aim of this review is to summarize our current knowledge about the diversity of the sensors and regulators involved in the perception and transduction of light, oxidative and thermal stresses and nutrient starvation responses. The studies discussed here point to the fact that various stresses affecting the photosynthetic capacity are transduced by common mechanisms.
ARTICLE | doi:10.20944/preprints202008.0670.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: MTHFR; bovine; bioinformatics; gene expression; testes
Online: 30 August 2020 (15:00:47 CEST)
Methylenetetrahydrofolate reductase (MTHFR), an enzyme expressed in mammalian testes exerts direct effect on spermatogenesis; however, its protein characteristics in bovine testes remain unknown. Here, we analysed bovine testicular structure, MTHFR bioinformatics profile, mRNA, and protein expression characteristics in yellow-cattle (y-c) and yak testis using histological procedures, bioinformatics analysis, qRT-PCR, and western blot. Testes from 13 bovines, ≤ 2 years juvenile (y-c, n = 3; yak, n=3) and ≥ 3 years adult (y-c, n = 3; yak, n = 4) were collected and analysed. Anatomical characteristics of testis in y-c and yak were similar except the weight or size for which that of y-c was significantly higher or greater than yak. In y-c, an open reading frame (ORF) for 2600 nucleotides sequence, encoding 655 amino acids showed high homology with zebu cattle (99.51%) and wild yak (98.68%). Secondary and 3D protein structures were similar to that of humans with differences in number of nucleotides, amino acids, and some physico-chemical characteristics. MTHFR mRNA expression in y-c and yak were significantly higher in adult testes compared with juvenile ones. However, its protein expression was higher but not statistically significant in adult y-c and yak compared to the juvenile ones. The highlights and inferences of these and other findings are discussed.
CONCEPT PAPER | doi:10.20944/preprints202004.0259.v1
Subject: Biology, Plant Sciences Keywords: alternative splicing; microRNA; gene expression; Arabidopsis
Online: 16 April 2020 (07:37:32 CEST)
MicroRNA (miRNA) is a typical class of small RNAs that could modulate gene expression in trans at the post-transcriptional level. miRNAs bind to the miRNA binding sites (MBSs) in target mRNAs by sequence complementarity. Alternative splicing (AS) is another commonly occurred process in pre-mRNAs that changes the isoforms of a gene. It is hypothesized that there should be an interaction for gene regulation that involves both AS and miRNA targeting. Studies have verified this hypothesis in the model organism Arabidopsis thaliana. High-throughput sequencing data suggested that in Arabidopsis a considerably large fraction of MBSs are affected by AS events. The overlapping between MBS and AS exceeds the randomly simulated number. Functional experiments have indicated that the AS events are required for the gene expression changes of miRNA targets. Therefore, AS and MBS are mutually favored. The observed expression changes caused by miRNAs could also be contributed by AS events. In the present perspective article, we propose that the AS analysis should be incorporated in the differential-expression analysis of miRNA studies. When defining a differentially-expressed gene, it should be clarified whether the change in gene expression is caused by AS events or solely by miRNA targeting.
ARTICLE | doi:10.20944/preprints201704.0062.v1
Subject: Medicine & Pharmacology, Gastroenterology Keywords: survivin; high expression; gastrointestinal cancer; prognostic
Online: 11 April 2017 (10:51:06 CEST)
Previous studies on the prognostic impact of survivin expression in gastrointestinal (GI) cancer have yielded inconsistent results. This study was initiated to assess the relationship between survivin expression and overall survival (OS) or disease free survival (DFS) in GI cancer patients. We applied system literature searches on EMBASE, PubMed, Web of science, and the Cochrane library to conduct this up-to-date meta-analysis. Thirty studies with totally 3622 GI cancer patients were collected. The prevalence of high survivin expression in GI cancer was 0.57 (95% CI: 0.51-0.63). High survivin expression was significantly associated with shorter OS (HR 1.57, 95% CI: 1.42-1.74) and DFS (HR 1.38, 95% CI: 1.21-1.58). Subgroup analysis also showed significant association between high survivin expression and poorer OS or DFS in gastric cancer or colorectal cancer. In summary, our study indicated that high survivin expression was related to poor prognosis in GI cancer. Well-designed studies with large sample and more convincing data are needed to confirm our conclusion.
REVIEW | doi:10.20944/preprints201905.0330.v1
Subject: Biology, Other Keywords: gene expression; gene regulation; evolution; allele specific expression; eQTL; RNAseq; ChIPseq; chromatin; ATACseq; genotype-phenotype map
Online: 28 May 2019 (10:29:26 CEST)
Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic variation. An exceptional contribution of cis-regulatory evolution has for instance been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and developmental stage-specific expression. We argue that the regulatory context must be considered when studying evolution of gene expression.
ARTICLE | doi:10.20944/preprints202206.0214.v1
Subject: Life Sciences, Genetics Keywords: Adra1b; cardiac ischemia; hypoxia; Crem; gene expression control; gene expression coordination; gene hierarchy; heart failure; transcriptomic stoichiometry
Online: 15 June 2022 (07:37:53 CEST)
Decades of research identified numerous gene biomarkers of cardiac diseases whose restored sequence or/and expression level was hoped to recover the normal cardiac function. However, each human has unique and dynamic pathophysiological characteristics resulting from the unrepeatable combination of favoring factors such are: race, sex, age, medical history, diet, stress, exposure to toxins, habits etc. As such, no treatment fits everybody and finding personalized solutions is a top priority for medicine of 21st century. The Genomic Fabric Paradigm (GFP) provides the most theoretically possible comprehensive characterization of the transcriptome, its alterations in disease and recovery following a treatment. By attaching to each gene the independent average expression level, expression variation and expression coordination with each other gene, GFP delivers thousands times more information than the traditional analysis. This report presents the theoretical bases of the GFP and some applications to our microarray data from mouse models of post ischemic, and constant and intermittent hypoxia-induced heart failure. The GFP analyses revealed novel transcriptomic aspects of the gene expression control and networking under ischemic conditions. Through all-inclusive characterization of the transcriptome and the unrepeatable gene hierarchy in each condition, GFP is an essential avenue towards development of a truly personalized cardiogenomic therapy.
ARTICLE | doi:10.20944/preprints202210.0186.v3
Subject: Life Sciences, Biophysics Keywords: neural; brain; structural intelligence; cell expression; evolution
Online: 4 November 2022 (09:43:59 CET)
This concept paper gives a narrative about intelligence from insects to the human brain, showing where evolution may have been influenced by the structures in these simpler organisms. The ideas also come from the author's own cognitive model, where a number of algorithms have been developed over time and the precursor structures should be codable to some level. Through developing and trying to implement the design, ideas like separating the data from the function have become architecturally appropriate and there have been several opportunities to make the system more orthogonal. Similarly for the human brain, neural structures may work in-sync with the neural functions, or may be slightly separate from them. Each section discusses one of the neural assemblies with a potential functional result, that cover ideas such as timing or scheduling, structural intelligence and neural binding. Another aspect of self-representation or expression is interesting and may help the brain to realise higher-level functionality based on these lower-level processes.
ARTICLE | doi:10.20944/preprints202109.0161.v1
Online: 8 September 2021 (20:25:45 CEST)
For developmental processes we know most of the gene networks controlling specific cell responses. We still have to determine how these networks cooperate and how signals become integrated. The JNK pathway is one of the key elements modulating cellular responses during development. Yet, we still know little on how the core components of the pathway interact with additional regulators or how this network modulates cellular responses in the whole organism in homeostasis or during tissue morphogenesis. We have performed a promoter analysis searching for potential regulatory sequences of puc and identified different specific enhancers directing gene expression in different tissues and at different developmental times. Remarkably, some of these domains respond to the JNK activity, but not all. Altogether, these analyses show that puc expression regulation is very complex and that JNK activities participate in non-previously known processes during the development of Drosophila.
ARTICLE | doi:10.20944/preprints202104.0265.v1
Subject: Medicine & Pharmacology, Allergology Keywords: cancer; hypoxia-inducible factors; HIF3A; expression analysis
Online: 9 April 2021 (14:35:55 CEST)
Background: Hypoxia-inducible factors (HIFs) are transcription factors that get activated and stabilized in the heterodimerized form under hypoxic conditions. The three members of the HIF alpha factors share high structural similarity but have tissue-specific expression patterns. A majority of studies have reported the importance of the HIF1A and HIF2A activity in the survival, proliferation, metastatic potential, and metabolic regulation of hypoxic cancer cells. However, the importance of the expression pattern and activity of HIF3A in a variety of cancers remains unknown. Method and materials: The expression profile of 13 different types of The Cancer Genome Atlas (TCGA) cancer samples were downloaded, normalized and differential gene expression analysis (DGE) was performed to compare the expression pattern of HIF alpha family members in cancer and adjacent normal tissues, as well as at different stages and tumor-sizes. Receiver operating characteristic (ROC) test and survival analysis were carried out to estimate the diagnostic potential of HIF alpha isomers in different cancers, as well as the survival rate of patients with the varying expression levels of HIF alpha factors. Results: The expression status of HIF3A was notably less in all cancer samples in contrast to their adjacent normal tissues. The expression degree of HIF1A varied among distinct types of cancer and the expression degree of HIF2A was lower in nearly all types of cancers. The expression level of HIF alpha isomers did not significantly correlate with different sizes of tumor samples and stages of different tumor tissue samples. HIF3A had very weak diagnostic potential, while HIF2A had better diagnostic potential in most types of cancers compared to HIF1A. Patients who had a higher level of HIF3A had better survival, while the higher expression levels of HIF1A and HIF2A were associated with worse survival in many types of cancers. Conclusion: Our study shows the heterogenous expression pattern of HIF alpha subunits in distinctive kinds of cancers and the influence of HIF3A expression level in the survival of patients with varying types of cancers.
Subject: Biology, Plant Sciences Keywords: BrassicaEDB; Brassica napus; gene expression profile; coexpression
Online: 12 July 2020 (15:25:37 CEST)
The Brassica family contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB, https://biodb.swu.edu.cn/brassica/) for the research community. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including eFP, Treatment, Coexpression, and SRA Project modules based on gene expression profiles and Gene Feature, qPCR Primer, and BLAST modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for Brassica crop researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.
Subject: Biology, Other Keywords: Gene expression; Gene Ontology; Enrichment analysis; Transcriptomics
Online: 2 April 2020 (11:51:32 CEST)
Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome data with respect to their fold changes. FSEA identifies GO terms, which are shared by the group of genes with a similar magnitude of response, and assesses these changes. GO terms found by FSEA are fold-change-specifically (e.g. weakly, moderately or strongly) affected by a stimulus under investigation. We demonstrate that many responses to abiotic factors, mutations, treatments and diseases occur in a fold-change-specific manner. FSEA analyses suggest that there are two prevailing responses of functionally-related gene groups, either weak or strong. Notably, some of the fold-change-specific GO terms are invisible by classical algorithms for functional gene enrichment, SEA and GSEA. These are GO terms not enriched compared to the genome background but strictly regulated by a factor within specific fold-change intervals. FSEA analysis of a cancer-related transcriptome suggested that the gene groups with a tightly coordinated response can be the valuable source to search for possible regulators, markers and therapeutic targets in oncogenic processes. Availability and Implementation: FSEA is implemented as the FoldGO Bioconductor R package and a web-server https://webfsgor.sysbio.cytogen.ru/ .
ARTICLE | doi:10.20944/preprints201810.0331.v1
Subject: Life Sciences, Molecular Biology Keywords: microRNA; mouth neoplasms; expression profile; microarray analysis.
Online: 15 October 2018 (17:59:55 CEST)
MicroRNAs are small non-coding RNAs that are implicated in several physiological processes such as cell development, proliferation, differentiation, apoptosis, immune response and angiogenesis. In the last couple of decades, several studies on miRNA profiling in OSCC have tried to associate miRNAs with clinical characteristics such as relapse, metastasis, and survival, however, the results have been found to vary considerably, sometimes even being contradictory. The main objective of our study was to analyse and verify miRNA expression in oral squamous cell carcinoma in a Spanish population. Second, we attempted to associate the identified deregulated miRNAs with molecular pathways. 8 Oral Squamous Cell Carcinoma patients and 8 healthy control samples were analysed by a microarray Affymetrix® miRNA 4.1 array plate and validated with 8 more cases using RT-qPCR. Deregulated miRNAs were studied using Diana Tools miRPath 3.0 to associate miRNA targets with molecular pathways. Microarray analysis identified 80 deregulated miRNAs (35 over-expressed and 45 under-expressed). Only miR-497-5p and miR-4417 maintained its deregulated expression after validation with qPCR. Among the molecular pathways in which deregulated miRNAs could be implicated, the most statistically significant pathway was ‘proteoglycans in cancer’. No relationship was found between miR-497-5p or miR-4417 expression and clinical or pathological parameters except of nodular affectation (high miR-4417 expression in patients with nodular affectation, p = 0.035) and radiotherapy (diminished miR-497-5p expression in patients who needed radiotherapy, p = 0.05). We have verified the altered expression of miR-497-5p and miR-4417 in Oral Squamous Cell Carcinoma samples and related the deregulated miRNAs with the ‘proteoglycans in cancer’ pathway.
ARTICLE | doi:10.20944/preprints201803.0174.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: gene expression obesity triple negative breast cancer
Online: 20 March 2018 (07:56:33 CET)
Background: Triple negative breast cancer (TNBC) is the most aggressive form of breast cancer with poor outcomes. The molecular basis of TNBC remains poorly understood. The objective of this study was to explore the relationship between obesity and TNBC in premenopausal and postmenopausal Caucasian women using whole genome transcription profiling. Methods: We compared gene expression levels of tumor samples drawn from normal weight, overweight and obese in pre and postmenopausal women diagnosed with TNBC. We performed hierarchical clustering to assess similarity in patterns of gene expression profiles, and conducted network and pathway analysis to identify molecular networks and biological pathways. Results: We discovered gene signatures distinguishing normal weight from obese, normal weight from overweight and overweight from obese individuals in both premenopausal and postmenopausal women. The analysis revealed molecular networks and biological pathways dysregulated in response to obesity. Among the discovered pathways included the unfolded protein response, endoplasmatic reticulum stress, B cell receptor and the autophagy signaling pathways in obese premenopausal women and the integrin, axonal guidance, ERK/MAPK and Glutathione biosynthesis signaling pathways obese postmenopausal women. Conclusions: The results suggest that both overweight and obesity are associated with TNBC, highlighting the need for conformation of these results in independent studies.
ARTICLE | doi:10.20944/preprints201702.0085.v1
Subject: Life Sciences, Molecular Biology Keywords: alfalfa; drought; microRNA; small RNA; differential expression
Online: 23 February 2017 (09:50:07 CET)
Alfalfa, an important legume forage, is an ideal crop for sustainable agriculture and a potential bioenergy plant. Drought, one of the most common environmental stresses, substantially affects plants’ growth, development and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of 4 samples, each with 3 biological replicates. We identified 348 known miRNAs, belonging to 80 miRNA families, from the 12 libraries and 281 novel miRNAs using Mireap software. 18 known miRNAs in roots and 12 known miRNAs in leaves were screened out as drought-responsive miRNAs. Except for miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs were different between roots and leaves in alfalfa. This is the first study discovering miR157a, miR1507, miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 are drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.
ARTICLE | doi:10.20944/preprints202301.0497.v1
Subject: Biology, Other Keywords: matrix metalloproteinases; skin fibrosis; gene expression; laser therapy
Online: 27 January 2023 (07:17:38 CET)
Matrix metalloproteinases (MMPs) are often considered biomarkers of skin fibrosis. At the early stages of the pathological process, an elevation of their enzymatic activity causes significant changes in the composition of the extracellular matrix. MMPs secreted by immune cells facilitate their migration to the site of damage. Then, the immune cells eliminate the affected cells and biomolecules. Moreover, bidirectional changes in the activity of proteolytic enzymes, including MMPs, accompany wound healing. This study aimed to assess changes in the expression of Mmp2, Mmp3, and Mmp9 after treating the mice with laser therapy using the experimental model of bleomycin-induced skin fibrosis. Using immunohistochemistry, we characterized the histological features of scarred skin. We also analyzed changes in the expression of MMPs using real-time polymerase chain reaction before and after the irradiation with laser. We showed that treatment of the mice with CO2 laser partially normalized the histological features of scarred skin. We also noticed a decrease in the expression of Mmp2, Mmp3 (both p < 0.05), and Mmp9 (p = 0.065) during scar healing. The obtained results suggest that normalization of skin homeostasis requires a control of MMPs activities via induction of their genes.
ARTICLE | doi:10.20944/preprints202211.0193.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Flowering; Gene expression; Pod elongation; Soybean; Water deficit
Online: 10 November 2022 (08:34:45 CET)
Drought stress on soybean is a research-demanding matter for negative influence that agricultural drought brings about. This study was designated to evaluate the effect of drought stress on some gene expression in flowering and pod elongation stages in soybean. This experiment was carried out in split-plot format with RCBD design with four replicates. Drought stress as the main factor included three levels (irrigation after 50, 100, and 150 millimeters evaporation from the A-class evaporation pot) of which 50 millimeters evaporation is considered as control. The sub-factor included a factorial combination of 3 varieties (DPX, Sari and WE6) and two sampling stages (flowering and pod elongation). The gene expression analysis was carried out by using the QRT-PCR technique. According to our results, all genes have shown overexpression in drought stress despite this result was not the same for all genotypes and stress levels. Some genes have up-regulated in mediate stress (treatment 100) level (like as Gmdreb 2, Gmdreb 5, GmRD20A, GmaxACD2) and other genes up-regulated in serve stress (treatment 150) level. Between genotypes, DPX cultivar and WE6 line were better than of the sari cultivar for all genes up-regulated.
ARTICLE | doi:10.20944/preprints202210.0299.v1
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: PCOS; Gene expression; Insulin resistance; Diabetes; HOMA-IR
Online: 20 October 2022 (08:25:43 CEST)
Background Polycystic ovary syndrome (PCOS) is a common hormonal disorder worldwide among women of reproductive age. It is characterized by endocrine, reproductive, and metabolic abnormalities. Insulin resistance (IR) is one of its most important clinical features, associated with metabolic disorders and increased risk of type 2 diabetes (T2D). This study aimed to explore the whole blood gene expression profiling related to IR in PCOS patients compared to controls. Methods Blood RNA was extracted from 5 PCOS and 5 non-PCOS women with matched age and BMI. Homeostasis model assessment (HOMA-IR) was used to estimate the IR. The expression of IR genes was analyzed by Profiler PCR array. Results Both groups have similar levels of HOMA-IR (p>0.05). However, differential expression levels were observed between them. Fourteen genes were upregulated and 26 genes were downregulated in PCOS samples. Among the upregulated genes (>2 fold-change, p-value<0.05) are ADIPOQ, ADIPOR1, OLR, IGF-1, and APOE. Downregulated genes (>-2 fold-change, p-value<0.05) include HK-2, IRS1, and SERPINE1. These genes are involved in insulin and adipokines signaling, commonly dysregulated in T2D. They are also involved in innate immunity and inflammatory processes and are essential for lipid and carbohydrate metabolism. Conclusion Our finding suggests that despite both groups having no difference in IR level, there are differentially expressed genes involved in the IR pathway.
ARTICLE | doi:10.20944/preprints202209.0180.v1
Subject: Life Sciences, Endocrinology & Metabolomics Keywords: endometriosis; multi-omics; expression profile; menstrual blood; MenSCs
Online: 13 September 2022 (12:32:56 CEST)
Given the importance of menstrual blood in the pathogenesis of endometriosis and the multifunctional roles of menstrual mesenchymal stem cells (MenSCs) in regenerative medicine, this issue has gained prominence in the scientific community. Moreover, recent reviews highlight how robust the integrated assessment of omics data is for endometriosis. To our knowledge, no study has applied the multi-omics approaches to endometriosis MenSCs. It is a case-control study at a university-affiliated hospital. MenSCs transcriptome and proteome data were obtained by RNA-seq and UHPLC-MS/MS detection. Among the differentially expressed proteins and genes, we emphasize ATF3, ID1, ID3, FOSB, SNAI1, NR4A1, EGR1, LAMC3, and ZFP36 genes and MT2A, TYMP, COL1A1, COL6A2, and NID2 proteins that were already reported in the endometriosis. Our functional enrichment analysis reveals integrated modulating signaling pathways such as epithelial-mesenchymal transition (↑) and PI3K signaling via AKT to mTORC1 (↓in proteome), mTORC1 signaling, TGF beta signaling, TNFA signaling via NFkB, and response to hypoxia via HIF1A targets (↑in transcriptome). Our findings highlight primary changes in the endometriosis MenSCs, suggesting that the chronic inflammatory endometrial microenvironment can modulate these cells, providing opportunities for endometriosis etiopathogenesis. Moreover, they identify challenges for future research leveraging knowledge for regenerative and precision medicine in endometriosis.
ARTICLE | doi:10.20944/preprints202104.0605.v1
Subject: Life Sciences, Biochemistry Keywords: Transcriptome; gene expression; camel; MERS-CoV; vaccine; immunogenicity
Online: 22 April 2021 (10:34:12 CEST)
Middle East Respiratory Syndrome coronavirus (MERS-CoV) infects dromedary camels and zoonotically infects humans, causing a respiratory disease with severe pneumonia and death. With no approved antiviral or vaccine interventions for MERS, vaccines are being developed for camels to prevent virus transmission into humans. We have previously developed a chimpanzee adenoviral vector-based vaccine for MERS-CoV (ChAdOx1 MERS) and reported its strong humoral immunogenicity in dromedary camels. Here, we looked back at total RNA isolated from three immunised dromedaries pre and post-vaccination during the first day; and performed RNA sequencing and bioinformatic analysis in order to shed light on the molecular immune responses following a ChAdOx1 MERS vaccination. Our finding shows that a number of transcripts were differentially regulated as an effect of the vaccination, including genes that are involved in innate and adaptive immunity, such as type I and II interferon responses. The camel Bcl-3 and Bcl-6 transcripts were significantly upregulated, indicating a strong activation of Tfh cells, B cell, and NF-kB pathways. In conclusion, this study gives an overall view of the first changes in the immune transcriptome of dromedaries after vaccination; it supports the potency of ChAdOx1 MERS as a potential camel vaccine to block transmission and prevent new human cases and outbreaks.
ARTICLE | doi:10.20944/preprints202104.0542.v1
Subject: Behavioral Sciences, Applied Psychology Keywords: action unit; aging; emotion; facial expression; facial recognition
Online: 20 April 2021 (12:47:43 CEST)
The ability to express and recognize emotion via facial expressions is well known to change with age. The present study investigated the differences in the facial recognition and facial expression of the elderly (n = 57) and the young (n = 115) and measure how each group uses different facial muscles for each emotion with Facial Action Coding System (FACS). In facial recognition task, the elderly did not recognize facial expressions better than young people and reported stronger feelings of fear and sad from photographs. In making facial expression task, the elderly rated all their facial expressions as stronger than the younger, but in fact, they expressed strong expressions in fear and anger. Furthermore, the elderly used more muscles in the lower face when making facial expressions than younger people. These results help to understand better how the facial recognition and expression of the elderly change, and show that the elderly do not effectively execute the top-down processing concerning facial expression.
ARTICLE | doi:10.20944/preprints202103.0369.v1
Subject: Life Sciences, Biochemistry Keywords: CIPK; Calcium; Chickpea; Structure; Phylogeny; Expression; Stress; Development
Online: 15 March 2021 (11:27:46 CET)
Calcineurin B-like proteins (CBL)-interacting protein kinases (CIPKs) by interacting with CBLs regulate developmental processes, hormone signalling transduction and mediate stress responses in plants. Although the genome of chickpea is available, information of CIPK gene family has been missing in chickpea. Here, a total of 22 CIPK encoding genes were identified in chickpea and characterized by in silico methods. We found a high structural conservation in chickpea CIPK family. Our analysis showed that chickpea CIPKs have evolved with dicots from common ancestors, and extensive gene duplication events have played an important role in evolution and expansion of CIPK family in chickpea. Most chickpea CIPK proteins localize in cytoplasm and nucleus. Promoter analysis revealed various cis-regulatory elements related to plant development, hormone signaling and abiotic stresses. Expression analysis indicated that CIPKs are significantly expressed in a spectrum of developmental stages, tissue/organs that hinted their important role in plant development. Several CIPK genes had specific and overlapping expressions in different abiotic stresses and seed development stages, suggesting the important role of CIPK family in abiotic stress signaling, and seed development in chickpea. Thus, this study provides the avenue for detailed functional characterization of CIPK family in chickpea and other legume crops.
ARTICLE | doi:10.20944/preprints202103.0356.v1
Subject: Life Sciences, Biochemistry Keywords: lncRNA; obesity; fatness, pig; gene expression regulation; miRNA
Online: 12 March 2021 (21:25:35 CET)
Obesity is a problem in the last decades since the development of different technologies forced the submission of a faster pace of life, resulting in nutrition style changes. In turn, domestic pigs are an excellent animal model in recognition of adiposity-related processes, corresponding to the size of individual organs, the distribution of body fat in the organism, and similar metabolism. The present study applied the next-generation sequencing method to identify adipose tissue (AT) transcriptomic signals related to increased fat content by identifying differentially expressed genes (DEGs), included long-non coding RNA molecules. The Freiburg RNA tool was applied to recognise predicting hybridisation energy of RNA-RNA interactions. The results indicated several long non-coding RNAs (lncRNAs) whose expression was significantly positively or negatively associated with fat deposition. lncRNAs play an essential role in regulating gene expression by sponging miRNA, binding transcripts, facilitating translation, or coding other smaller RNA regulatory elements. In the pig fat tissue of obese group, increased expression of lncRNAs corresponding to human MALAT1 was observed that previously recognised in the obesity-related context. Moreover, hybridisation energy analyses pinpointed numerous potential interactions between identified differentially expressed lncRNAs, and obesity-related genes and miRNAs expressed in AT.
ARTICLE | doi:10.20944/preprints202103.0237.v1
Subject: Materials Science, Biomaterials Keywords: graphene oxide; human keratinocytes; proliferation; gene expression; cytotoxicity
Online: 8 March 2021 (16:20:37 CET)
Few-layer graphene oxide (GO) has shown none or very weak cytotoxicity and anti-proliferative effects in a wide range of cell lines such as glyoma cells and human skin HaCaT cells, in concentrations up to 100 µg/mL However, multi-layer GO has been hardly explored in the biomedical field. Thus, multi-layer GO was examined here in human keratinocyte HaCaT cells treated with different concentrations ranging from 0.01 to 150 µg/mL during different periods of times (3, 12 and 24 hours). The results of this study showed a time-concentration dependence with two non-cytotoxic concentrations (0.01 and 0.05 µg/mL) and a median effective concentration value of 4.087 µg/mL at 24 hours of GO exposure. Contrary to what has been reported for few-layer GO, cell proliferation of the HaCaT cells in contact with the multi-layer GO at 0.01 μg/mL showed identical proliferative activity compared to an epidermal growth factor (1.6-fold greater than the control group) after 96 hours. The effects of the multi-layer GO on the expression of 13 genes (SOD1, CAT, MMP1, TGFB1, GPX1, FN1, HAS2, LAMB1, LUM, CDH1, COL4A1, FBN and VCAN) at the non-cytotoxic concentrations of GO in the HaCaT cells were analyzed after 24 hours. Thus, the lowest non-cytotoxic GO concentration was able to up-regulate the CAT, TGFB1, FN1 and CDH1 genes, which confirms the great potential of multi-layer GO in the biomedical field.
ARTICLE | doi:10.20944/preprints202103.0134.v1
Subject: Biology, Anatomy & Morphology Keywords: Bacillus subtilis; NRPS/PKS; amicoumacins; heterologous expression; bioactivities
Online: 3 March 2021 (14:08:28 CET)
Abstract: Bacillus subtilis fmb60, which has broad-spectrum antimicrobial activities was isolated from plant straw compost. A hybrid NRPS/PKS cluster was screened from the genome. Sixteen secondary metabolites produced by the gene cluster were isolated and identified using LC-HRMS and NMR. Three lipoamides D–F (1-3) and two amicoumacin derivatives, amicoumacins D, E (4, 5), were identified, and are reported here for the first time. Lipoamides D–F exhibited strong antibacterial activities against harmful foodborne bacteria, with the MIC ranging from 6.25 to 25 µg/mL. Amicoumacin E scavenged 38.8% of ABTS+ radicals at 1 mg/mL. Direct cloning and heterologous expression of the NRPS/PKS and ace gene cluster identified its importance for the biosynthesis of amicoumacins. This study demonstrated that there is a high potential for biocontrol utilization of B. subtilis fmb60, and genome mining for clusters of secondary metabolites of B. subtilis fmb60 has revealed a greater biosynthetic potential for the production of novel natural products than previously anticipated.
Subject: Life Sciences, Biochemistry Keywords: pig; NREP; gene expression; polymorphism; SNP; meat performance
Online: 1 December 2020 (08:48:46 CET)
The expression microarray technique was performed to investigate the differences in gene expression between Czech Large White pigs and wild boars in the longissimus lumborum et thoracis and biceps femoris muscle tissues. The NREP gene (neuronal regeneration related protein homolog) was selected for detailed study as an expressional and functional candidate gene. NREP plays a role in the transformation of neural, muscle and fibroblast cells and in smooth muscle myogenesis. Quantitative real-time PCR results confirmed that the porcine NREP gene was expressed in both skeletal muscles and significantly overexpressed in Czech Large White pigs compared to wild boars (P < 0.05). We identified 9 polymorphic sites in genomic DNA of NREP gene. Six of these polymorphisms were in complete linkage disequilibrium and therefore only 4 polymorphisms were informative. Associations of these 4 polymorphisms (HF571253:g.103G>A, HF571253:g.134G>A, HF571253:g.179T>C and HF571253:g.402_409delT) with meat performance traits were assessed in Czech Large White pigs. New polymorphisms in NREP gene were significantly associated with parameters of daily weight gain, lean meat and backfat thickness in Czech Large White pigs. Our primary study suggested that porcine NREP may play an important role in skeletal muscle growth, fat metabolism and meat performance traits.
ARTICLE | doi:10.20944/preprints202010.0379.v1
Subject: Biology, Anatomy & Morphology Keywords: qRT-PCR; reference gene; Angelica decursiva; expression stability
Online: 19 October 2020 (12:25:21 CEST)
Angelica decursiva is one of the lending traditional Chinese medicinal plants producing coumarins. Notably, several studies have focused on the biosynthesis and not the qRT-PCR (quantitative real-time reverse transcription polymerase chain reaction) study of coumarins. This qRT-PCR technique has been extensively used to investigate gene expression levels in plants and the selection of reference genes which plays a crucial role in standardizing the data form the qRT-PCR analysis. In our study, 11 candidate reference genes were selected from the existing transcriptome data of Angelica decursiva. Here, four different types of statistical algorithms (geNorm, NormFinder, BestKeeper, and Delta Ct) were used to calculate and evaluate the stability of gene expression under different external treatments. Subsequently, RefFinder analysis was used to determine the geometric average of each candidate gene ranking, and to perform comprehensive index ranking. The obtained results showed that among all the 11 candidate reference genes, SAND family protein (SAND), protein phosphatase 2A gene (PP2A), and polypyrimidine tract-binding protein (PTBP) were the most stable reference genes, where Nuclear cap binding protein 2 (NCBP2), TIP41-like protein (TIP41), and Beta-6-tubulin (TUBA) were the least stable genes. To the best of our knowledge, this work is the first to evaluate the stability of reference genes in the Angelica decursiva which has provided an important foundation on the use of qRT-PCR for an accurate and far-reaching gene expression analysis in this medicinal plant.
ARTICLE | doi:10.20944/preprints202007.0711.v1
Subject: Life Sciences, Molecular Biology Keywords: co-expression network; residual feed intake; RNA-Seq
Online: 30 July 2020 (09:39:36 CEST)
Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from liver, muscle, hypothalamus, pituitary and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.
DATASET | doi:10.20944/preprints201912.0180.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: IBS; BMI; Nanostring; White Blood Cells; RNA expression
Online: 13 December 2019 (10:41:56 CET)
Chronic gastro-abdominal pain with altered bowel habits are associated with pathologies including gastroenteritis, autoimmune and inflammatory bowel disease, and irritable bowel syndrome (IBS). In IBS, diagnostic evidence of infection or inflammation are absent, yet symptoms nonetheless include chronic abdominal pain and alterations of stool frequency and consistency, with most common subtypes including diarrhea-predominant (IBS-D) or constipation predominant (IBS-C). [1, 2] IBS is a common clinical complaint in westernized nations, with females more frequently diagnosed than males . Obesity is also associated with increased likelihood of chronic pain , and is associated with intestinal dysbiosis, and systemic inflammatory signatures . Improving personalized medicine therefore requires patient stratification based on a combination of biological factors contributing to the individual’s symptom and biomarker spectrum. The “buffy coat” method isolates leukocytes and PBMCs from whole blood, comprises the immune cell population in peripheral blood. These cells are relatively inactive but are primed to respond to generalized and localized immune activation signals; they are under active investigation as diagnostic biomarkers . Collection of buffy coat is a standard method in clinical laboratories; detection of immune activation via RNA expression biomarkers will be informative of differential biological response, and be tractable to collect in clinical settings. Results of differential expression, pathway analysis, and cell-type abundance analysis from buffy coat RNA, is presented here using variables for BMI, Gender, and IBS-subtype from publicly available Nanostring RNA expression and phenotypic data from the NCBI GEO database.
Subject: Biology, Plant Sciences Keywords: sunflower; growth-regulating factor; expression pattern; abiotic stress
Online: 11 December 2019 (04:58:22 CET)
Growth-regulating factor (GRF) is a plant-specific transcription factor family, which is involved in nearly all of the central developmental processes in plants. However, little is known about GRF family genes in cultivated sunflower. In this study, 17 GRF genes were identified and characterized from sunflower genome. Their gene structures, conserved motifs, chromosomal distributions and phylogenetic relationships were analyzed. The expression patterns of these genes were detected in various tissues of sunflower inbred line SK02R, which revealed that the 10 seed-specific GRF genes may play important roles during seed development in sunflower. Additionally, transcripts changes of the GRFs under two major abiotic stresses and phytohormones showed that most of the detected GRFs were reduced significantly by GA3 treatment, and other treatments(ABA, NaCl and PEG6000) differently regulated various sunflower growth-regulating factors at different time points. MiR396 target analysis indicated that there may exist a complicated homeostasis between miR396 and its targets GRF and WRKY transcription factor genes in cultivated sunflower. The phylogenetic and expression analyses of the GRF gene family in sunflower would be useful for further cloning and function exploration of the HaGRF genes.
Subject: Keywords: cathepsins; cancer; characterization; cysteine; Escherichia coli; expression; molecular
Online: 27 November 2019 (11:09:52 CET)
Cysteine cathepsins, a class of proteinaceous enzymes, regulate a wide variety of metabolic processes in human including protein breakdown and turnover and immune functions. Eleven cysteine cathepsins have been identified so far and a wide array of studies related to identifying their specific functions, regulation and distribution patterns in tissues have been conducted. However, in recent past, the association of cysteine cathepsins in occurrence and progression of cancers have been identified and this has caused unrest in scientists triggering them to investigate the physiology, biochemical pathways and interactions of these cathepsins in cancer metastasis and therefore has become a noteworthy topic of intensive research. This review focusses and collects together the published work on molecular functional and structural characterization studies that have been done so far on in vitro expression of genes encoding for cysteine cathepsins in the Escherichia coli bacterial expression system. Accordingly, it was found out that all cathepsins except for cathepsins K, C, H, X and W have been expressed this way and the majority of them were found to be expressed in E. coli BL21(DE3) pLysS expression host via pET3 expression vector. In addition, it was also noted that in most of the expression studies, the substrate that was used to validate the enzymatic activity of the recombinant enzyme that was produced was a cysteine residue along with a benzyloxy-carbonyl salt. Through this review, the authors suggest that there is a very high need that all cysteine cathepsins need to be characterized both structurally and functionally on a molecular platform to better understand their interactions including the biochemical pathways. It is also momentous that the mass production of the recombinant forms of these enzymes are facilitated via expression in such bacterial expression systems and in turn, would also provide a strong platform for the development and progression of studies related to human physiology including oncological studies such as cancer metastasis. Moreover, as per biochemical features of the enzymes that could be identified, the production of efficient inhibitors or inducers as per the necessity to improve health and promote wellbeing among the mankind could be facilitated.
ARTICLE | doi:10.20944/preprints201804.0232.v2
Subject: Biology, Physiology Keywords: obesity; plant secondary compound; Clinacanthus nutans; gene expression
Online: 24 April 2018 (10:04:11 CEST)
Obesity is a universal health concern that can lead to serious diseases. The side effects of synthetic anti-obesity drugs necessitate the finding of suitable natural/herbal alternatives. Mother nature offers a wide range of plants with medicinal properties that include crude extracts and isolated compounds which are effective for controlling and reducing weight gain. Obesity was induced in 60, 3-week-old male ICR mice, using high-fat diet (60% dietary energy from fat) for 16-week. The mice were divided at random into six groups with 10 mice: mice fed with high-fat diet (HFD) only, mice fed normal diet only (NC), and orlistat at 15.9 mg/kg (HFD+Orlistat), and mice in three other high-fat diet groups treated with methanolic leaf extract of Clinacanthus nutans (MECN) at 500, 1000 and 1500 mg/kg. After 21-day of the treatment, MECN significantly reduced (P<0.05) the body weight, visceral fat and muscle saturated fatty acid compositions. There was also significant downregulation of HSL, PPAR α and PPAR γ and SCD genes expressions in the obese mice treated with 1500 mg/kg MECN compared to the HFD group. Therefore, MECN is a potentially useful natural supplement for alleviating obesity and obesity-mediated metabolic diseases.
ARTICLE | doi:10.20944/preprints201804.0016.v1
Subject: Life Sciences, Genetics Keywords: colorectal cancer; gene expression; molecular classification; molecular subtyping
Online: 2 April 2018 (09:55:26 CEST)
Molecular classifications of colorectal cancer (CRC) are benefitting cancer research by providing insights into subtype-specific disease prognosis and better therapeutic intervention. So far different conventional DNA markers such as microsatellite instability (MSI), CpG island methylator phenotype (CIMP), chromosomal instability (CIN), and BRAF and KRAS mutations have been used to classify CRC patients but have not shown promising prognostic values. Here, for the first time, we show classification of CRC tumors from Saudi Arabian patients based on gene expression profile (GEP). An existing method of CRC subtyping has been applied to the GEP of tumors from Saudi CRC patients. Survival analysis was carried out on predicted CRC subtypes. In-silico functional analyses were conducted on the gene signature used for subtype prediction. The predicted subtypes showed distinct but statistically insignificant overall survival distribution (log-rank test, p = 0.069). Comparison of predicted subtypes in Saudi CRC patients with that of the French one showed significant dissimilarity in the two populations (Chi-square test, p = 0.0091). Functional analyses of the gene signature used for subtyping suggest their association with “cancer” and “gastrointestinal diseases”. Most of the signature genes were found differentially expressed in CRC tumors compared to adjacent normal tissues. Such a classification framework might help improve the treatment of colorectal cancer patients.
ARTICLE | doi:10.20944/preprints201704.0052.v1
Subject: Medicine & Pharmacology, Nutrition Keywords: lysine; skeletal muscle; transcriptome; gene expression; microarray; pig
Online: 10 April 2017 (06:30:13 CEST)
Nine crossbred finishing barrows randomly assigned to 3 dietary treatments were used to investigate the effects of dietary lysine on muscle growth related metabolic and signaling pathways. Muscle samples were collected from the longissimus dorsi of individual pigs after feeding the lysine-deficient, lysine-adequate, or lysine-excess diet for 5 weeks, and the total RNA was extracted afterwards. Affymetrix Porcine Gene 1.0 ST Array was used to quantify the expression levels of 19,211 genes. A total of 674 transcripts were differentially expressed (P ≤ 0.05); 60 out of 131 transcripts (P ≤ 0.01) were annotated in the NetAffx database. Ingenuity pathway analysis showed that dietary lysine deficiency may lead to (1) increased muscle protein degradation via the ubiquitination pathway as indicated by the up-regulated DNAJA1, HSP90AB1 and UBE2B mRNA, (2) reduced muscle protein synthesis via the up-regulated RND3 and ZIC1 mRNA, (3) increased serine and glycine synthesis via the up-regulated PHGDH and PSPH mRNA, and (4) increased lipid accumulation via the up-regulated ME1, SCD, and CIDEC mRNA. Dietary lysine excess may lead to (1) decreased muscle protein degradation via the down-regulated DNAJA1, HSP90AA1, HSPH1, and UBE2D3 mRNA, and (2) reduced lipid biosynthesis via the down-regulated CFD and ME1 mRNA.
ARTICLE | doi:10.20944/preprints202109.0403.v1
Subject: Life Sciences, Biophysics Keywords: RKIP expression regulation; Stochastic binary regulation of gene expression; Treatment targeting RKIP levels increase; Reduction of heterogeneity of treatment response
Online: 23 September 2021 (11:43:54 CEST)
In this manuscript we use an exactly solvable stochastic binary model for regulation of gene expression to analyse the dynamics of response to a treatment aiming to modulate the number of transcripts of RKIP gene. We demonstrate the usefulness of our method simulating three treatment scenarios aiming to reestablish RKIP gene expression dynamics towards pre-cancerous state: i. to increase the promoter’s ON state duration; ii. to increase the mRNAs’ synthesis rate; iii. to increase both rates. We show that the pre-treatment kinetic rates of ON and OFF promoter switching speeds and mRNA synthesis and degradation will affect the heterogeneity and time for treatment response. Hence, we present a strategy for reducing drug dosage by simultaneously targeting multiple kinetic rates. That enables a reduction of treatment response time and heterogeneity which in principle diminishes the chances of emergence of resistance to treatment. This approach may be useful for inferring kinetic constants related to expression of antimetastatic genes or oncogenes and on the design of multi-drug therapeutic strategies targeting master regulatory genes.
ARTICLE | doi:10.20944/preprints202301.0100.v1
Subject: Biology, Physiology Keywords: Antarctic fish; antioxidant enzymes; oxidative stress; gene expression; PFAS
Online: 5 January 2023 (04:50:42 CET)
Antarctica is the continent with the lowest local human impact, yet it is still vulnerable to contaminants coming from external sources. Emerging pollutants, like PFAS, pose an increasing threat to this environment and therefore require more in-depth investigations to understand their environmental fate and biological impacts. The present study, part of the AntaGPS project, focuses on expression analysis at the transcriptional level of genes coding for 4 antioxidant enzymes (sod1, sod2, gpx1, gpx4) in different organs of an Antarctic fish species, Trematomus newnesi. The kidney showed a higher level of expression than the liver of wildlife specimens. The mRNA levels were also assessed in fish exposed to 1.5 μg/L of PFOA for 10 days. In the liver, the treatment induced an increase in gene expression for all the considered enzymes, while in the kidney it induced a general decrease. The obtained results constitute a starting point for using the expression of antioxidant enzymes as biomarkers, both of oxidative stress and exposure to PFAS, in future biomonitoring campaigns in the Antarctic marine environment.
ARTICLE | doi:10.20944/preprints202211.0223.v1
Subject: Biology, Ecology Keywords: hyacinthus; Caulerpa taxifolia; thermal stress; physiological processes; gene expression
Online: 14 November 2022 (01:05:02 CET)
An increasing ecological phase-shift from coral dominated reefs to macroalgae dominated reefs as a result of anthropogenic impacts, such as eutrophication, sedimentation, and overfishing, has been observed in many reef systems around the world. Ocean warming is a universal threat to both corals and macroalgae, which may alter the outcome of competition between them. Therefore, in order to explore the effects of indirect and direct exposure to macroalgae on the physiological, biochemical, and genetic expression of corals at elevated temperature, the coral Acroproa hyacinthus and highly invasive green algae Caulerpa taxifolia have been chosen. Physiologically, the results exhibited that distinguish from control and direct contact treatments, the density and chlorophyll a content of zooxanthella decreased by 53.1% and 71.2% respectively, when coral indirect contacted with algae at ambient temperature (27°C). Besides, enzyme activities of superoxide dismutase (SOD) and catalase (CAT) in coral tissue were enhanced by interacting with algae. After an increase of 3°C, the density and chlorophyll a content of zooxanthella reduced by 84.4% and 93.8% respectively, whereas the enzmy activities of SOD and CAT increased by 2.3 and 3.1-fold. However, only the zooxanthellae density and pigment content decreased when C.taxifolia co-culture with A.hyacinthus at 30°C. Molecularly, different from the control group, the differentially expressed genes (DEGs) such as Rab family, ATG family and Casp7 were significantly enriched in endocytosis, autophagy and apoptosis pathways , regardless whether A.hyacinthus was indirect or indirect exposure to C.taxifolia at 27°C. Under thermal stress without algae interaction, the DEGs were significantly enriched in microbial immune signal transduction pathways, such as Toll-like receptor signaling pathway and TNF signaling pathway, while multiple cellular immunity (IFI47, TRAF family) and oxidative stress (CAT, SODC, HSP70) genes were up-regulated. Inversely, compared with corals without interaction with algae at 30°C, the DEGs of corals interacted with C.taxifolia at 30°C, were remarkably enriched in apoptosis, NOD-like receptor signaling pathway, including the transcription factors such as Casp family, TRAF family. In conclusion, the density and chlorophyll a content of zooxanthella remained a fading tendency induced by macroalgae at ambient temperature. The oxidative stress and immune response levels of coral has been elevated at 30°C, but macroalgae alleviated the negative effects triggered by thermal stress.
ARTICLE | doi:10.20944/preprints202208.0497.v1
Subject: Life Sciences, Biochemistry Keywords: oxygen; physioxia; hyperoxia; cell culture; transcriptomics; differential gene expression
Online: 29 August 2022 (14:46:44 CEST)
Standard cell culture is routinely performed at supraphysiological oxygen concentrations (~18% O2). Conversely, oxygen levels in most tissues range from 1%–6% (physioxia). Such hyperoxic conditions can alter reactive oxygen species (ROS) production, energy metabolism, mitochondrial network dynamics, and response to drugs and hormones. The aim of this project was to investigate the transcriptional response to different oxygen levels and whether it is similar across cell lines, or cell-line specific. Using RNA-seq, we performed differential gene expression and functional enrichment analyses in four human cancer cell lines, LNCaP, Huh-7, PC-3, and SH-SY5Y cultured at either 5% or 18% oxygen for 14 days. We found that oxygen levels affected transcript abundance of hundreds of genes, with the affected genes having little overlap between cell lines. Functional enrichment analysis also revealed different processes and pathways being affected in each cell line. Interestingly, we found that the top differentially expressed genes are involved in cancer biology. Further, we observed several hypoxia-inducible factor (HIF) targets upregulated at 5% oxygen, suggesting a role of HIF at physiological oxygen conditions. Finally, oxygen strongly induced transcription of mitochondrial genes in most cell lines, in a cell-type specific manner too. We conclude that cellular response to oxygen is widely cell-type specific, emphasizing the importance of maintaining physioxia in cell culture.
ARTICLE | doi:10.20944/preprints202206.0357.v1
Subject: Mathematics & Computer Science, Applied Mathematics Keywords: Unit Step Function; closed - form expression; inverse tangent function
Online: 27 June 2022 (09:34:58 CEST)
In this paper, the author obtains an analytic exact form of the Unit Step Function (or Heaviside step function) which evidently constitutes a fundamental concept of Operational Calculus. This important function is also involved in many other fields of applied and engineering mathematics. Heaviside step function is performed here in a very simple manner, by the use of a finite number of standard operations. In particular it is expressed as the summation of six inverse tangent functions. The novelty of this work when compared with other analytic representations, is that the proposed exact formula contains two arbitrary single - valued continuous functions which satisfy only one restriction. In addition, the proposed explicit representation is not exhibited in terms of miscellaneous special functions, e.g. Bessel functions, Error function, Beta function etc and also is neither the limit of a function, nor the limit of a sequence of functions with point – wise or uniform convergence. Hence, this formula may be much more practical, flexible and useful in the computational procedures which are inserted into Operational Calculus techniques and other engineering practices.
ARTICLE | doi:10.20944/preprints202105.0347.v1
Subject: Biology, Anatomy & Morphology Keywords: Tuberculosis; Mycobacterium tuberculosis; mRNA expression; Cytokine; Human FFPE tissue
Online: 14 May 2021 (15:33:20 CEST)
In the present study, we aimed to investigate whether an automated molecular diagnostic method based on PCR-reverse blot hybridization assay can discriminate between human Mycobacterium tuberculosis (MTB)-positive and -negative FFPE tissues and to compare the relative mRNA expression levels of various host immune markers between MTB-infected and uninfected human tissues using quantitative reverse transcription (qRT) PCR. A total of 52 human FFPE tissue samples from various regions of the body, including the lungs, lymph nodes, tendons, colon, and appendix, were collected and used for the molecular identification of Mycobacterium species and analysis of cytokine mRNA expression. As a result, IFN-γ, TNF-α, IP-10, CXCL9, CXCL11, and GM-CSF mRNA expression levels in MTB-infected tissues were significantly higher than those in uninfected samples. Additionally, the differences in the mRNA expression levels of IFN-γ, CXCL9, and GM-CSF between MTB-infected and uninfected tissues were statistically significant were statistically significant (p < 0.05). Correlation curve analysis indicated that the mRNA expression of IFN-γ was inversely proportional to that of IP-10 and that the mRNA expression levels of IFN-γ, TNF-α, CXCL9, CXCL11, GM-CSF, and TNFR were proportional and well-correlated. Furthermore, to establish marker profiles for detecting MTB infection, the statistically significant expression levels of three markers were combined. We confirmed that the combined profile of IFN-γ, CXCL9, and GM-CSF expression levels was statistically significant (P < 0.001). Although the mRNA expression patterns of host immune markers may vary according to MTB infection status, these patterns may be highly correlated and can be simultaneously used as an additional indicator for diagnosing TB.
REVIEW | doi:10.20944/preprints202009.0604.v1
Subject: Life Sciences, Biochemistry Keywords: Nucleus; Nuclear envelope; Lamins; Genome organization; Chromatin; Gene expression
Online: 25 September 2020 (11:03:59 CEST)
Nuclear lamins are type V intermediate filament proteins that form a filamentous meshwork beneath the inner nuclear membrane. Additionally, a sub-population of A-type and B-type lamins is localized in the nuclear interior. The nuclear lamina protects the nucleus from mechanical stress and mediates nucleo-cytoskeletal coupling. Lamins form a scaffold that partially tethers chromatin at the nuclear envelope. The nuclear lamina also stabilizes protein-protein interactions involved in gene regulation and DNA repair. The lamin-based protein sub-complexes are implicated in both nuclear and cytoskeletal organization, the mechanical stability of the nucleus, genome organization, transcriptional regulation, genome stability, and cellular differentiation. Here we review recent research in the field of nuclear lamins and their role in modulating various nuclear processes and their impact on cell function.
Subject: Life Sciences, Biotechnology Keywords: sulfite oxidase; molybdenum; tungsten; sulfite toxicity; tomato; SO expression
Online: 20 March 2020 (04:16:41 CET)
Plant sulfite oxidase )SO( is a molybdo-enzyme responsible for the oxidation of excess SO2/sulfite into non-toxic sulfate. The effect of toxic sulfite level on leaves and fruits was studied in tomato plants with different SO expression levels: wild-type (WT), SO overexpression (OE) and SO RNA interference (Ri) plants. Leaf discs and ripe fruit of plants lacking SO were more susceptible, whereas SO OE plants were more resistant as revealed by remaining chlorophyll content and tissue damage levels. Application of molybdenum further enhanced the tolerance of leaf discs to sulfite by enhancing SO activity in SO OE lines, but not in WT or Ri plants. Notably, incubation with tungsten, the molybdenum antagonist, overturned the effect of molybdenum spray in SO OE plants, revealed by remaining chlorophyll content and SO activity. The results indicate that SO determines, in tomato leaves and ripe fruits, the resistance to toxic sulfite and the application of molybdenum enhances sulfite resistance in OE plants by increasing SO activity. The results suggest that overexpressing SO mechanism can be employed in agriculture with or without molybdenum application, for the development of more tolerate crops and vegetables to higher concentrations of sulfite/SO2 containing postharvest treatments.
ARTICLE | doi:10.20944/preprints201906.0021.v1
Subject: Life Sciences, Other Keywords: simulated microgravity; radiation; combined effects; gene expression; cell cycle
Online: 3 June 2019 (12:24:59 CEST)
Multiple unique environmental factors such as space radiation and microgravity (µG) pose a serious threat to human gene stability during space travel. Recently, we reported that simultaneous exposure of human fibroblasts to simulated µG and radiation results in more chromosomal aberrations than in cells exposed to radiation alone. However, the mechanisms behind this remain unknown. The purpose of this study was thus to obtain comprehensive data on gene expression using a 3D clinostat synchronized to a carbon (C)-ion or X-ray irradiation system. Human fibroblasts (1BR-hTERT) were maintained under standing or rotating conditions for 3 or 24 h after synchronized C-ion or X-ray irradiation at 1 Gy as part of a total culture time of 2 days. Among 57,773 genes analyzed with RNA sequencing, we focused particularly on the expression of 82 cell cycle-related genes after exposure to the radiation and simulated µG. The expression of cell cycle-suppressing genes (ABL1 and CDKN1A) decreased and that of cell cycle-promoting genes (MKI67, KPNA2, CCNB1, STMN1, and MCM4) increased after C-ion irradiation under µG. The cell cycle may pass through the G1/S and G2 checkpoints with DNA damage due to the combined effects of C-ions and µG, suggesting that increased genomic instability might occur in space.
ARTICLE | doi:10.20944/preprints201904.0277.v1
Subject: Life Sciences, Molecular Biology Keywords: CREB; cryotherapy; gene expression; icing; mitochondria; Pgc-1α; transcription
Online: 25 April 2019 (08:07:44 CEST)
Local cryotherapy is widely used as a treatment for sports-related skeletal muscle injury. However, its molecular mechanisms are unknown. To clarify these mechanisms, in this study, we applied one to three 15-min cold stimulations at 4 °C to various cell lines (in vitro), the tibialis anterior (TA) muscle (ex vivo), and mouse limbs (in vivo). In the in vitro assay, cAMP response element-binding protein 1 (CREB1) was markedly phosphorylated (as pCREB1) and CREB-binding protein (CBP) was recruited to pCREB-1 in response to two or three cold stimulations. In a reporter assay with the cAMP-responsive element, the signals significantly increased after two to three cold stimulations at 4 °C. In the ex vivo study, CREB-targeting genes were significantly upregulated following two or three cold stimulations. The in vivo experiment disclosed that cold stimulation of a mouse limb for 9 days significantly increased mitochondrial DNA copy number and upregulated genes such as Pgc-1α involved in mitochondrial biogenesis. The foregoing results suggest that local cryotherapy increases CREB transcription and upregulates CREB-targeting genes in a manner dependent on cold stimulation frequency and duration. This information may serve as an impetus for further investigations into local cryotherapy as a treatment for sports-related skeletal muscle trauma.
ARTICLE | doi:10.20944/preprints201805.0336.v1
Subject: Materials Science, Biomaterials Keywords: 316L; electrodeposition; nano-hydroxyapatite; carbon nanotubes; osteoblasts; gene expression
Online: 24 May 2018 (06:18:52 CEST)
Herein, we evaluated the electrophoretic deposition of nanohydroxyapatite/superhydrophilic multiwalled carbon nanotube composites (nHAp/MWCNT) onto stainless steel biomedical alloys for applications in bone tissue engineering. First, nHAp/MWCNT composites were dispersed into 0.042 mol L−1 of Ca(NO3)2·4H2O + 0.025 mol L−1 NH4H2PO4 electrolytes (pH = 4.8) at two different concentrations. Next, a voltage of −2 V was applied using 316L stainless steel as a working electrode and (0.27 cm2), a high-purity platinum coil wire as the auxiliary electrode, and an Ag/AgCl(3 M) electrode was used as the reference electrode. The nHAp/MWCNT composites were characterized by transmission electron microscopy. The deposited nHAp and nHAp/MWCNT films were characterized by profilometry, scanning electron microscopy, X-Ray diffractometry and Raman spectroscopy. Human osteoblast cells were cultivated with the different materials, and in vitro cytotoxicity was evaluated using lactate dehydrogenase (LDH) assay. The osteogenesis process was evaluated by mRNA levels of the three genes that are directly related to bone repair: Alkaline Phosphatase, Osteopontin and Osteocalcin. We showed that rough, crystalline apatite thin films containing phases of nHAp were successfully deposited onto 316L stainless steel alloys. Also, we noticed that nHAp/MWCNT thin films deposited onto 316L stainless steel alloys upregulated the expression of important genes related to bone mineralization and maturation. Our results strongly support the possibility of this new alternative to modify the surface of metallic biomedical alloys to promote bone tissue regeneration.
ARTICLE | doi:10.20944/preprints201805.0330.v1
Subject: Life Sciences, Molecular Biology Keywords: fibrillin; cucumber; genome-wide; gene expression; high light stress
Online: 24 May 2018 (05:24:00 CEST)
Fibrillin (FBN) is a plastid lipid-associated protein found in photosynthetic organisms from cyanobacteria to plants. In this study, 10 CsaFBN genes were identified in genomic DNA sequences of cucumber (Chinese long and Gy14) through database searches using the conserved domain of FBN and the 14 FBN genes of Arabidopsis. Phylogenetic analysis of CsaFBN protein sequences showed that there was no counterpart of Arabidopsis and rice FBN5 in the cucumber genome. FBN5 is essential for growth in Arabidopsis and rice; its absence in cucumber may be because of incomplete genome sequences or that another FBN carries out its functions. Among the 10 CsaFBN genes, CsaFBN1 and CsaFBN9 were the most divergent in terms of nucleotide sequences. Most of the CsaFBN genes were expressed in the leaf, stem, and fruit. CsaFBN4 showed the highest mRNA expression levels in various tissues, followed by CsaFBN6, CsaFBN1, and CsaFBN9. High-light stress combined with low temperature decreased photosynthetic efficiency and highly induced transcript levels of CsaFBN1, CsaFBN6, and CsaFBN11, which decreased after 24 h treatment. Transcript levels of the other seven genes were changed only slightly. This result suggests that CsaFBN1, CsaFBN6, and CsaFBN11 may be involved in photoprotection under high-light conditions at low temperature.
ARTICLE | doi:10.20944/preprints201612.0077.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: rule based models; gene expression data; bayesian networks; parsimony
Online: 15 December 2016 (08:21:24 CET)
The comprehensibility of good predictive models learned from high-dimensional gene expression data is attractive because it can lead to biomarker discovery. Several good classifiers provide comparable predictive performance but differ in their abilities to summarize the observed data. We extend a Bayesian Rule Learning (BRL-GSS) algorithm, previously shown to be a significantly better predictor than other classical approaches in this domain. It searches a space of Bayesian networks using a decision tree representation of its parameters with global constraints, and infers a set of IF-THEN rules. The number of parameters and therefore the number of rules are combinatorial to the number of predictor variables in the model. We relax these global constraints to a more generalizable local structure (BRL-LSS). BRL-LSS entails more parsimonious set of rules because it does not have to generate all combinatorial rules. The search space of local structures is much richer than the space of global structures. We design the BRL-LSS with the same worst-case time-complexity as BRL-GSS while exploring a richer and more complex model space. We measure predictive performance using Area Under the ROC curve (AUC) and Accuracy. We measure model parsimony performance by noting the average number of rules and variables needed to describe the observed data. We evaluate the predictive and parsimony performance of BRL-GSS, BRL-LSS and the state-of-the-art C4.5 decision tree algorithm, across 10-fold cross-validation using ten microarray gene-expression diagnostic datasets. In these experiments, we observe that BRL-LSS is similar to BRL-GSS in terms of predictive performance, while generating a much more parsimonious set of rules to explain the same observed data. BRL-LSS also needs fewer variables than C4.5 to explain the data with similar predictive performance. We also conduct a feasibility study to demonstrate the general applicability of our BRL methods on the newer RNA sequencing gene-expression data.
ARTICLE | doi:10.20944/preprints202208.0341.v1
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: Schizophrenia; cell types proportions; differential expression genes; functional pathways; CIBERSORTx
Online: 18 August 2022 (10:54:05 CEST)
Schizophrenia (SCZ) is a severe mental disorder that may result in hallucinations, delusions, and extremely disordered thinking. How each cell type in the brain contributes to SCZ occurrence is still unclear. Here, we leveraged the human dorsolateral prefrontal cortex bulk RNA-seq data, then used the RNA-seq deconvolution algorithm CIBERSORTx to generate SCZ brain single-cell RNA-seq data for a comprehensive analysis to understand SCZ-associated brain cell types and gene expression changes. Firstly, we observed that the proportions of brain cell types in SCZ differed from normal samples. Among these cell types, astrocyte, pericyte, and PAX6 cells were found to have a higher proportion in SCZ patients (astrocyte: SCZ = 0.163, Control = 0.145, P.adj = 4.9×10-4; pericyte: SCZ = 0.057, Control = 0.066, P.adj = 1.1×10-4; PAX6 : SCZ = 0.014, Control = 0.011, P.adj = 0.014), while the L5/6_IT_CAR3 cells and LAMP5 cells are the exact opposite (L5/6_IT_Car3 : SCZ = 0.102, Control = 0.108, P.adj = 0.016; LAMP5 : SCZ = 0.057, Control = 0.066, P.adj = 2.2×10-6). Next, we investigated gene expression in cell types and functional pathways in SCZ. We observed chemical synaptic transmission dysregulation in two types of GABAergic neurons (PVALB and LAMP5), and immune reaction involvement in GABAergic neurons (SST) and non-neuronal cell types (endothelial and oligodendrocyte). Furthermore, we observed that some differential expression genes from bulk RNA-seq displayed cell-type-specific abnormal in the expression of molecules in SCZ. Finally, the cell types with the SCZ-related transcriptomic changes could be considered to belong to the same module since we observed two major similar coordinated transcriptomic changes across these cell types. Together, our results offer novel insights into cellular heterogeneity and the molecular mechanisms underlying SCZ.
ARTICLE | doi:10.20944/preprints202205.0364.v1
Subject: Life Sciences, Molecular Biology Keywords: Hemoglobin switch; BGLT3-lncRNA expression; chromatin conformation; LRF/ZBTB7A overexpression
Online: 26 May 2022 (10:39:49 CEST)
Hemoglobin switch from fetal (HbF) to adult (HbA) has been studied intensively as an essential model for gene’s expression regulation, but also as a beneficial therapeutic approach for β-hemoglobinopathies, towards the objective of reactivating HbF. Transcription factor LRF (Leukemia/lymphoma-related), encoded from ZBTB7A gene has been implicated in fetal hemoglobin silencing, though has a wide range of functions that have not been fully clarified. We thus established LRF/ZBTB7A-overexpressing and ZBTB7A-knockdown K562 (human erythroleukemia cell line) clones and hemoglobin production was evaluated pre- and post-induction. Related effects on the process of hemoglobin switch from fetal to adult were also assessed. Transgenic K562 clones were further developed and studied under the influence of epigenetic chromatin regulators, such as DNA methyl transferase 3 (DNMT3) and Histone Deacetylase 1 (HDAC1), to evaluate LRF’s potential disturbance upon aberrant epigenetic background and provide valuable information of the preferable epigenetic frame, in which LRF unfolds its action on the β-type globin’s expression. ChIP-seq analysis demonstrated that LRF binds το γ-globin genes (HBG2/1) and apparently associates BCL11A for their silencing, but also, during erythropoiesis induction LRF binds BGLT3 gene promoting BGLT3-lncRNA production through the γ-δ intergenic region of β-type globin’s locus, triggering the transcriptional events from γ- to β-globin switch.
ARTICLE | doi:10.20944/preprints202202.0295.v1
Subject: Biology, Plant Sciences Keywords: Alfalfa; bZIP transcription factor; phylogenetic analysis; expression pattern; abiotic stress
Online: 23 February 2022 (13:40:34 CET)
Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies such as differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa. In the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in Arabidopsis thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that particular bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. However, further functional characterization of bZIP transcription factors in alfalfa will help illuminate the role they play in stress tolerance mechanisms in legumes and facilitate the molecular breeding of stress tolerance in alfalfa.
ARTICLE | doi:10.20944/preprints202110.0062.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Bioinformatics analysis; Drought stress; Gene expression; Physiological parameters; Tomato; Transcriptome.
Online: 4 October 2021 (15:01:07 CEST)
Identification of the differentially-expressed genes is important for clarification of the complex molecular mechanisms under drought conditions. In this experiment, transcriptome profiles of sensitive and tolerant tomato genotypes under drought stress were analyzed. Three up-regulated genes were selected, included CAB3 (Chlorophyll a-b binding protein3), SAMDC (S-adenosylmethionine decarboxylase proenzyme), and ACS9 (1-aminocyclopropane-1-carboxylate synthase 9). After bioinformatics analysis, tomato genotypes were subjected to drought stress and gene expression was determined using Real-Time-PCR. Physiological parameters of genotypes were also measured by spectrophotometer-based methods. According to the results, these three genes play a key role in stress tolerance. Expression of the CAB3 gene in both sensitive and tolerant genotypes was not significantly different compared to the control, but the SAMDC gene decreased in both genotypes and the ACS9 gene decreased in sensitive genotype and increased in tolerant genotype. The physiological analysis also showed that under stress conditions, the photosynthetic system of the plant was disrupted and the chlorophyll content was reduced, but, proline content and antioxidant enzymes activity increased, in which their quantity in the tolerant genotype was significantly higher than sensitive. Under drought stress, due to damage to the lipid membrane, Malondialdehyde content also increased, in which the sensitive genotype was more affected.
ARTICLE | doi:10.20944/preprints202105.0424.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Convolutional Neural Network (CNN); Emotion Recognition; Facial Expression; Classification; Accuracy
Online: 18 May 2021 (11:34:19 CEST)
Emotion recognition defined as identifying human emotion and is directly related to different fields such as human-computer interfaces, human emotional processing, irrational analysis, medical diagnostics, data-driven animation, human-robot communi- cation and many more. The purpose of this study is to propose a new facial emotional recognition model using convolutional neural network. Our proposed model, “ConvNet”, detects seven specific emotions from image data including anger, disgust, fear, happiness, neutrality, sadness, and surprise. This research focuses on the model’s training accuracy in a short number of epoch which the authors can develop a real-time schema that can easily fit the model and sense emotions. Furthermore, this work focuses on the mental or emotional stuff of a man or woman using the behavioral aspects. To complete the training of the CNN network model, we use the FER2013 databases, and we test the system’s success by identifying facial expressions in the real-time. ConvNet consists of four layers of convolution together with two fully connected layers. The experimental results show that the ConvNet is able to achieve 96% training accuracy which is much better than current existing models. ConvNet also achieved validation accuracy of 65% to 70% (considering different datasets used for experiments), resulting in a higher classification accuracy compared to other existing models. We also made all the materials publicly accessible for the research community at: https://github.com/Tanoy004/Emotion-recognition-through-CNN.
ARTICLE | doi:10.20944/preprints202101.0342.v1
Subject: Materials Science, Biomaterials Keywords: bismuth vanadium oxide; roots activity; reactive oxygen generation; gene expression
Online: 18 January 2021 (14:06:29 CET)
The excellent properties of nanomaterials have been confirmed in many fields, but the effects on plants are still unclear. In this study, we have found that bismuth vanadium promoted the growth of taproots and the development of lateral roots, increased the roots activity by regulating the expression of polyamine or hormone-related genes and reducing the accumulation of reactive oxygen species in Arabisdopsis thaliana. Meantime, BV had higher antimicrobial effect than that of graphene oxide (GO). These results showed us a new perspective possibility of nanomaterials assisting the development of plants and crops, which is expected to become one of the ways to solve the problem of controlling and promoting the development of plants and crops.
ARTICLE | doi:10.20944/preprints202010.0484.v1
Subject: Biology, Anatomy & Morphology Keywords: inorganic polyphosphate; VTC4; knockout mutant; oxidative stress; gene expression; yeast
Online: 23 October 2020 (10:42:43 CEST)
Inorganic polyphosphate (polyP) is an important factor of stress tolerance in microbial cells. In yeast, the major enzyme of polyP biosynthesis is Vtc4, a subunit of the vacuole transporter chaperone (VTC) complex. In this study, we demonstrated that Vtc4 knockout in Saccharomyces cerevisiae not only decreased polyP content but also caused shifts in the composition of the intracellular polyP pool and changed the stress tolerance profile. In the mutant S. cerevisiae, the level of short-chain acid-soluble polyPs was decreased nearly 10-fold, whereas that of longer acid-insoluble polyPs was decreased only 2-fold, suggesting the existence of other enzymes compensating the production of long-chain polyPs. The Δvtc4 mutant showed inhibition of Mg2+-dependent phosphate uptake and decreased resistance to alkaline stress but increased tolerance to oxidation and heavy metal ions, especially Mn2+. Quantitative PCR revealed the upregulation of the DDR2 gene implicated in multiple stress responses and downregulation of PHO84 encoding a phosphate and Mn2+ transporter, which could account for the effects on phosphate uptake and Mn2+-related stress response in the Δvtc4 mutant. Our study indicates that short-chain polyPs, plays an important role in the regulation of stress response in yeast.
ARTICLE | doi:10.20944/preprints202009.0699.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: SVM; MRMR; Bootstrap; Genes; Gene Expression; Biological Relevance; Subject Classification
Online: 29 September 2020 (09:09:52 CEST)
Selection of biologically relevant genes from high dimensional expression data is a key research problem in gene expression genomics. Most of the available gene selection methods are either based on relevancy or redundancy measure, which are usually adjudged through post selection classification accuracy. Through these methods the ranking of genes was done on a single high-dimensional expression data, which leads to the selection of spuriously associated and redundant genes. Hence, we developed a statistical approach through combining Support Vector Machine with Maximum Relevance and Minimum Redundancy under a sound statistical setup for the selection of biologically relevant genes. Here, the genes are selected through statistical significance values computed using a non-parametric test statistic under a bootstrap based subject sampling model. Further, a systematic and rigorous evaluation of the proposed approach with nine existing competitive methods was carried on six different real crop gene expression datasets. This performance analysis was carried out under three comparison settings, i.e. subject classification, biological relevant criteria based on quantitative trait loci, and gene ontology. Our analytical results showed that the proposed approach selects genes that are more biologically relevant as compared to the existing methods. Moreover, the proposed approach was also found to be better with respect to the competitive existing methods. The proposed statistical approach provides a framework for combining filter, and wrapper methods of gene selection.
REVIEW | doi:10.20944/preprints202009.0013.v1
Subject: Keywords: MicroRNA Expression; Feature Selection; Cancer Diagnosis; Fuzzy Logic; Co-Learning
Online: 1 September 2020 (11:42:35 CEST)
MicroRNAs are used as biomarkers for classification of cancer subtypes since certain miRNAs are differentially expressed in normal and patient samples. Moreover, miRNAs target mRNAs and can heavily influence Gene Expressions. Thus, deregulation of miRNAs is linked to various disorders. Thus, miRNAs can be used for prognosis and developing personalized health solutions for patients. Given the importance of miRNAs, there has been substantial work done in the field. In this paper, recent works in the field of using miRNAs expressions of patients were considered. A total of 20 papers were surveyed which utilized feature selection ensembles, fuzzy logic as well as deep learning. 10 papers have been reported which offer insight into how miRNAs can be utilized for subtype-specific or generalized cancer diagnosis.
ARTICLE | doi:10.20944/preprints202008.0103.v1
Subject: Biology, Animal Sciences & Zoology Keywords: chicken; Newcastle disease; spleen; immune response; gene expression; RNA-seq
Online: 4 August 2020 (16:09:52 CEST)
As a major infectious disease in chickens, Newcastle disease causes considerable economic losses in the poultry industry, especially in developing countries where there is limited access to effective vaccination. Therefore, enhancing resistance to the virus in commercial chickens through breeding is a promising way to promote poultry production. In this study, we investigated gene expression changes at 2 and 6 dpi after infection at day21 with a lentogenic Newcastle disease virus in a commercial egg-laying chicken hybrid using RNA sequencing analysis. By comparing NDV challenged and nonchallenged groups, 526 differentially expressed genes (DEGs) (FDR < 0.05) were identified at 2 dpi, and only 36 at 6 dpi. For the DEGs at 2 dpi, IPA analysis predicted inhibition of multiple signaling pathways in response to NDV that regulate immune cell development and activity, neurogenesis and angiogenesis. Upregulation of Interferon Induced Protein with Tetratricopeptide Repeats 5 (IFIT5) in response to NDV was consistent between the current and most previous studies. Sprouty RTK Signaling Antagonist 1 (SPRY1), a DEG in the current study is located in a significant QTL associated with virus load at 6 dpi in the same population. These identified pathways and DEGs provide potential targets to further study breeding strategy to enhance NDV resistance in chickens.
REVIEW | doi:10.20944/preprints202006.0086.v2
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; Genome organisation and expression; Polyproteins; Prevention strategies
Online: 14 June 2020 (16:49:10 CEST)
COVID-19 manifests regarding extreme acute respiratory conditions caused by a novel beta coronavirus (SARS-CoV-2) which is reported to be the seventh coronavirus to infect humans. Like other SARS-CoVs it has a large positive-stranded RNA genome. But specific furin site in the spike protein, mutation prone and phylogenetically mess Orf1ab separates SARS-CoV-2 from other RNA viruses. Since, the outbreak (February - March 2020) which originated in China, researchers, scientists, and medical professionals are inspecting all possible facts from every possible aspect including its replication, detection, and prevention strategies. This led to the prompt identification of its basic biology, genome characterization, structural based functional information of proteins, and strategies to prevent its spread. Due to the rapid mutation rate, the functional characterization of a few proteins is still lagging. This review summarizes the recent updates on the basic molecular biology of SARS-CoV-2 and prevention strategies undertaken worldwide to tackle COVID-19. This recent information can be implemented for the development and designing of therapeutics against SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202005.0025.v1
Subject: Keywords: linear matrix expression; domain; matrix equation; general solution; generalized inverse
Online: 3 May 2020 (06:23:35 CEST)
One of the typical forms of linear matrix expressions (linear matrix-valued functions) is given by $A + B_1X_1C_1 + \cdots + B_kX_kC_k$, where $X_1, \ldots, X_k$ are independent variable matrices of appropriate sizes, which include almost all matrices with unknown entries as its special cases. The domain of the matrix expression is defined to be all possible values of the matrix expressions with respect to $X_1, \ldots, X_k$. I this article, we approach some problems on the relationships between the domains of two linear matrix expressions by means of the block matrix method (BMM), the matrix rank method (MRM), and the matrix equation method (MEM). As application, we discuss some topics on the relationships among general solutions of some linear matrix equations and their reduced equations.
ARTICLE | doi:10.20944/preprints202002.0051.v3
Subject: Life Sciences, Microbiology Keywords: Wuhan 2019-nCov; ACE2; expression; susceptibility; race; age; gender; smoking; single cell
Online: 2 March 2020 (01:38:52 CET)
In current severe global emergency situation of 2019-nCov outbreak, it is imperative to identify vulnerable and susceptible groups for effective protection and care. Recently, studies found that 2019-nCov and SARS-nCov share the same receptor, ACE2. In this study, we analyzed five large-scale bulk transcriptomic datasets of normal lung tissue and two single-cell transcriptomic datasets to investigate the disparities related to race, age, gender and smoking status in ACE2 gene expression and its distribution among cell types. We didn’t find significant disparities in ACE2 gene expression between racial groups (Asian vs Caucasian), age groups (>60 vs <60) or gender groups (male vs female). However, we observed significantly higher ACE2 gene expression in former smoker’s lung compared to non-smoker’s lung. Also, we found higher ACE2 gene expression in Asian current smokers compared to non-smokers but not in Caucasian current smokers, which may indicate an existence of gene-smoking interaction. In addition, we found that ACE2 gene is expressed in specific cell types related to smoking history and location. In bronchial epithelium, ACE2 is actively expressed in goblet cells of current smokers and club cells of non-smokers. In alveoli, ACE2 is actively expressed in remodelled AT2 cells of former smokers. Together, this study indicates that smokers especially former smokers may be more susceptible to 2019-nCov and have infection paths different with non-smokers. Thus, smoking history may provide valuable information in identifying susceptible population and standardizing treatment regimen.
REVIEW | doi:10.20944/preprints201911.0076.v3
Subject: Life Sciences, Genetics Keywords: phase separation; nuclear bodies; self-assembly; genome organization; gene expression
Online: 11 December 2019 (11:17:34 CET)
The importance of genome organization at the supranucleosomal scale in the control of gene expression is increasingly recognized today. In mammals, Topologically Associating Domains (TADs) and the active / inactive chromosomal compartments are two of the main nuclear structures that contribute to this organization level. However, recent works reviewed here indicate that, at specific loci, chromatin interactions with nuclear bodies could also be crucial to regulate genome functions, in particular transcription. They moreover suggest that these nuclear bodies are membrane-less organelles dynamically self-assembled and disassembled through mechanisms of phase separation. We have recently developed a novel genome-wide experimental method, High-salt Recovered Sequences sequencing (HRS-seq), which allows the identification of chromatin regions associated with large ribonucleoprotein (RNP) complexes and nuclear bodies. We argue that the physical nature of such RNP complexes and nuclear bodies appears to be central in their ability to promote efficient interactions between distant genomic regions. The development of novel experimental approaches, including our HRS-seq method, is opening new avenues to understand how self-assembly of phase separated nuclear bodies possibly contributes to mammalian genome organization and gene expression.
Subject: Biology, Plant Sciences Keywords: soybean; strigolactones; biosynthesis and signaling genes; expression patterns; salt stress
Online: 3 October 2019 (14:01:36 CEST)
Strigolactones (SLs) are a novel emerging plant hormones, which play important roles in regulating plant organ development and environmental stress tolerance. Even though the SL related genes have been identified and well characterized in some plants. The information of SL related genes in soybean is not fully established yet, especially in response to salt stress. In this study, we identified nine SL biosynthesis genes: two D27, two CCD7, two CCD8, and three MAX1, and seven SL signaling genes: two D14, two MAX2 and three D53 in soybean genome. We found that SL biosynthesis and signaling genes are conserved during evolution in different species. Syntenic analysis of these genes revealed their location on nine chromosomes as well as existence of ten pairs of duplication genes. Moreover, plant hormone and stress-responsive elements were identified in the promoter regions of SL biosynthesis and signaling genes. By using quantitative real-time PCR (qRT-PCR), we confirmed that SL genes have different tissue expression in roots, stems and leaves. Further, we also explored the expression profiles of SL biosynthesis and signaling genes under salt stress. These results suggested that SL signaling genes may play important regulatory roles in response to salt stress. In conclusion, we identified and provided valuable information on the soybean SL biosynthesis and signaling genes, and established a foundation for further functional analysis of soybean SL related genes in response to salt stress.
Subject: Physical Sciences, Other Keywords: rumen-protected l-tryptophan; growth performance; metabolites; glucose; gene expression
Online: 29 September 2019 (09:02:27 CEST)
We assessed the growth performance, physiological traits, and gene expressions in steers fed with dietary rumen-protected L-tryptophan (RPT) under cold environment. Eight Korean native steers were assigned to two dietary groups, no RPT (Control) and RPT (0.1% RPT supplementation on a dry matter basis), 6 wks. Maximum and minimum temperatures throughout the experiment were 6.7°C and -7.0°C, respectively. Supplementation of 0.1% RPT to a total mixed ration did not increase body weight but had positive effects of elevating average daily gain (ADG) and reducing the feed conversion ratio (FCR) at day 27 and 48. Metabolic parameter showed higher glucose level (at day 27) in the 0.1% RPT group compared to the control group. Real-time PCR analysis showed no significant differences in the expression of muscle (MYF6, MyoD, and Desmin) metabolism genes between the two groups, whereas the expression of fat (PPARγ, C/EBPα, and FABP4) metabolism genes was lower in the 0.1% RPT group than in the control group. Thus, we demonstrate that long-term (6 wks) dietary supplementation of 0.1% RPT was beneficial owing to enhanced growth performance by increasing ADG and glucose level, decreasing FCR, and maintaining homeostasis in immune responses in beef steers during cold environment.
ARTICLE | doi:10.20944/preprints201901.0263.v1
Subject: Biology, Entomology Keywords: Tenebrio molitor; suppressor of cytokine signaling; insect immunity; gene expression
Online: 26 January 2019 (02:51:45 CET)
Suppressors of cytokine signaling (SOCS) influence cytokine and growth factor signaling by negatively regulating the JAK-STAT pathway. This maintains homeostasis during host immune response. However, functional characterization of SOCS family members in invertebrates is limited. In this study, we discovered the Type-I subfamily of the SOCS genes in the mealworm beetle, T. molitor. The full-length ORFs of TmSOCS5, TmSOCS6, and TmSOCS7 consisted of 1,389, 897 and 1,458 nucleotides, encoding polypeptides of 462, 297 and 485 amino acids, respectively, The C-terminal region of TmSOCS was highly conserved in the SH2 and SOCS box domains. Phylogenetic analysis revealed that the three SOCS genes clustered within the same sub-family and the highest amino acid identity was with the Tribolium castaneum SOCS genes (TcSOCS). While the expression of TmSOCS5 and TmSOCS6 was low in larval, pupal, and adult stages of the insect, TmSOCS7 showed higher expression. The expression of TmSOCS5 and TmSOCS6 was higher in larval hemocytes and adult ovary. The microbes expressed the three TmSOCS genes to varying degrees. C. albicans elicited the strongest response in the host with highest 15-fold expression in TmSOCS7 3 h post-inoculation. Collectively, these data suggest that the Type I TmSOCS could play a role in eliciting host immunity.
ARTICLE | doi:10.20944/preprints201811.0550.v1
Subject: Life Sciences, Virology Keywords: poliovirus 2A protease (PV2Apro); expression; purification; MALDI-TOF; 3D structure
Online: 22 November 2018 (14:41:00 CET)
Poliovirus 2A protease (PV2Apro) plays a vital role in viral replication and down-regulation of host cell protein synthesis. In order to understand more concerning PV2Apro, the protein was over-expressed in bacteria following amplification using sense and antisense primers and cloning in pET15b. Several expression hosts were tested and BL21 (DE3) pLysS cells gave the best expression of PV2Apro with minimal unwanted protein expression following IPTG induction. The 2Apro protein was purified to homogeneity using column chromatography, its solubility determined and its molecular weight and composition determined by MALDI-TOF mass spectrometry. The protease was found in the insoluble fraction and the purified protein had a slightly lower molecular weight than predicted. Moreover, three dimensional structure was modelled using template 1z8r with 58% identity and validated using ramachandran plot. Results revealed that most of the residues lie in favoured and allowed regions. These findings could help in a better understanding of PV2Apro structure and inhibition thus, highlighting potential targets for antiviral drug development.
ARTICLE | doi:10.20944/preprints201811.0416.v1
Subject: Medicine & Pharmacology, Dentistry Keywords: multilevel principal components analysis; shape and image texture; facial expression
Online: 19 November 2018 (04:57:36 CET)
Single-level Principal Components Analysis (PCA) and multi-level PCA (mPCA) methods are applied here to a set of (2D frontal) facial images from a group of 80 Finnish subjects (34 male; 46 female) with two different facial expressions (smiling and neutral) per subject. Inspection of eigenvalues gives insight into the importance of different factors affecting shapes, including: biological sex, facial expression (neutral versus smiling), and all other variations. Biological sex and facial expression are shown to be reflected in those components at appropriate levels of the mPCA model. Dynamic 3D shape data for all phases of a smile made up a second dataset sampled from 60 adult British subjects (31 male; 29 female). Modes of variation reflected the act of smiling at the correct level of the mPCA model. Seven phases of the dynamic smiles are identified: rest pre-smile, onset 1 (acceleration), onset 2 (deceleration), apex, offset 1 (acceleration), offset 2 (deceleration), and rest post-smile. A clear cycle is observed in standardized scores at an appropriate level for mPCA and in single-level PCA. mPCA can be used to study static shapes and images, as well as dynamic changes in shape. It gave us much insight into the question “what’s in a smile?”
ARTICLE | doi:10.20944/preprints201810.0391.v1
Subject: Life Sciences, Other Keywords: wheat; alpha-amylase/trypsin inhibitor; heterologous expression; Pichia pastoris; allergy
Online: 17 October 2018 (17:15:23 CEST)
Although wheat is a staple food for most of human population, some of its components trigger adverse reactions. Among wheat components, the alpha-amylase/trypsin inhibitors (ATI) are important triggers of several allergies and activators of innate immunity. ATI are a group of exogenous protease inhibitors and include several polypeptides. The three ATI polypeptides named CM3, CM16 and 0.28 are considered major allergens, and might also play a role in other common wheat-related pathologies, such as Non Celiac Wheat Sensitivity and even Celiac Disease. On this basis, we pointed to obtain high amounts of them in purity and evaluating their allergenicity potential. We thus isolated the mRNA corresponding to the three ATI genes CM3, CM16 and 0.28 from 28 days post-anthesis wheat kernels and the corresponding cDNAs were used for heterologous expression in Pichia pastoris. The three purified proteins were tested in degranulation assay against human sera of patients with food allergy to wheat. A large range of degranulation values was observed for each protein according to the sera tested. All the three purified proteins CM3, CM16 and 0.28 were active as allergens because able to induce basophils degranulation on wheat allergic patients’ sera, but the highest values of β-hexosaminidase release were observed for CM3 protein.
ARTICLE | doi:10.20944/preprints201808.0399.v1
Subject: Social Sciences, Economics Keywords: Burning Man, festivals, art, public events, self-reliance, radical expression
Online: 22 August 2018 (14:53:56 CEST)
Burning Man is probably the most famous art festival in the world. What started as a bonfire ritual for a small group of friends held on San Francisco beach in 1986, has evolved into an iconic event. Held annually for one week before the Labor Day weekend, the festival attracts over 60,000 participants each year and yields over $8 million in tickets and contributions.This preprint reveals some preliminary results from the economic analysis of Burning Man that is based on the unique data from over 500 surveys collected during several Burning Man events between 2012 and 2018.The paper’s main findings demonstrate that Burning Man is not some hippie get-together with lots of booze and drugs. Instead, it is a lucrative and exclusive event that is attended by bright, wealthy and well-educated people, both from the United States and abroad. A typical Burner is a 32-old childless male with a college degree and an average annual income above $100,000 who attended Burning Man at least two times before and who spends between $5,000 and $6,000 on tickets, fares, gear, and supplies.
ARTICLE | doi:10.20944/preprints201804.0352.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: network inference; data integration; regulatory networks; transcription factor; gene expression
Online: 27 April 2018 (06:34:12 CEST)
Data generation using high throughput technologies has led to the accumulation of diverse types of molecular data.These data have different types (discrete,real,string etc.) and occur in various formats and sizes. Datasets including gene expression, miRNA expression, protein-DNA binding data (ChIP-Seq/ChIP-ChIP), mutation data(copy number variation, single nucleotide polymorphisms), GO annotations, protein-protein interaction and disease-gene association data are some of the commonly used genomic datasets to study biological processes. Each of them provides a unique, complementary and partly independent view of the genome and hence embed essential information about their regulatory mechanisms. In order to understand the functions of genes, proteins and analyze mechanisms arising out of their interactions, information provided by each of these datasets individually may not be sufficient. Therefore integrating these multi-omic data and inferring regulatory interactions from the integrated dataset provides a system level biological insights in predicting gene functions and their phenotypic outcomes. To study genome functionality through interaction networks, different methods have been proposed for collective mining of information from an integrated dataset. We survey here data integration approaches using state-of-the-art techniques such as network integration, Bayesian networks, regularized regression (LASSO) and multiple kernel learning methods.
ARTICLE | doi:10.20944/preprints201703.0208.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: closed expression; Fibonacci number; Fibonacci polynomial; tridiagonal determinant; Hessenberg determinant
Online: 28 March 2017 (03:11:06 CEST)
In the paper, the authors nd a new closed expression for the Fibonacci polynomials and, consequently, for the Fibonacci numbers, in terms of a tridiagonal determinant.
SHORT NOTE | doi:10.20944/preprints201610.0034.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: determinantal expression; recurrence relation; Euler polynomial; Euler number; Hessenberg determinant
Online: 11 October 2016 (10:40:02 CEST)
In the paper, by a very simple approach, the author establishes an expression in terms of a lower Hessenberg determinant for the Euler polynomials. By the determinantal expression, the author finds a recurrence relation for the Euler polynomials. By the way, the author derives the corresponding expression and recurrence relation for the Euler numbers.
ARTICLE | doi:10.20944/preprints201608.0104.v1
Subject: Biology, Horticulture Keywords: Capsicum annuum L.; capsaicinoid synthesis; gene expression; fruit development; MeJA
Online: 10 August 2016 (10:11:50 CEST)
Background: Capsaicinoid are a group of compounds and widely used in the food, medical, and pharmaceutical industries. Capsaicinoid are unique synthesized and accumulated in the pepper fruits. MeJA can enhance the capsaicinoid production. Temporal and spatial expression of capsaicinoid biosynthetic genes are helpful to understand the molecular mechnism of capsaicinoid biosynthesis in the fruits of pepper. Although some of the capsaicinoid biosynthetic genes in pepper have been identified, the expression of these genes at different developing stages of fruit has not been systemically investigated, and little is known about the molecular basis of MeJA inducing capsaicinoid biosynthesis. Results: HPLC study revealed that the capsaicinoid accumulation in the developing fruit of pepper initially appeared at 24 DAP (day after pollination), was actively development at 36 DAP and peaked at 48 DAP. 11 genes that encoded enzymes involved in capsaicinoid biosynthesis were isolated and characterized. Gene expression with quantitative reverse-transcription polymerase chain reaction analysis demonstrated that the CaCS was unique expressed in placenta and the other 10 genes were expressed in all selected tissues and 9 of 11 genes (except CaCa4H and CaCa3H) were strongly expressed in placenta tissue. Spatial expression analysis demostrated that the 11 gene could be collectively grouped into four categories based on the patterns of relative expression of the genes during fruit development. Category I has 2 and they displayed a bell-shaped expression pattern with the peak expression at 24 DAP, Category II contains 5 genes and expression of the 5 genes was constantly increased from 0 to 36 DAP and peaked at 36 DAP. Category III comprises of 2 genes and both genes reached the peak at 48 DAP. Category IV consists of 2 genes and they showed a high expression at 36 and 48 DAF, but unexpressed from 0 to 12 DAP. The gene expressions of the 11 genes were up-regulated by MeJA. 3 genes showed a high expression at 24 h; 4 genes reached the peak at 12 h; the top expression were observed at 18 h; The last one, CaACYase, achieved the highest level at 8 h. Conclusion: The biosynthesis of capsaicinoid in pepper fruit is developmentally regulated. The expression of the majority of capsaicinoid biosynthetic genes is highly consistent with the development accumulation of capsaicinoid in pepper fruit. These results not only provide the initial information on spatial and temporal expression of capsaicinoid biosynthetic genes in pepper developing fruit, but are also valuable to identify the MeJA-induced genes for capsaicinoid biosynthesis and accumulation during pepper fruit development.
ARTICLE | doi:10.20944/preprints202212.0281.v1
Subject: Biology, Plant Sciences Keywords: Water channel; Abiotic stresses; Wheat genes; Post-translation modification; Gene expression
Online: 15 December 2022 (10:07:52 CET)
During the response of plants to adverse stresses, aquaporin (AQP) plays a prominent role in membrane water transport based on received upstream signals. In addition, they have various physical parts for dealing with environmental stresses. Due to the importance of the AQP gene family, studies have been conducted investigating the function and regulatory system of these genes. However, many of their molecular aspects are still unknown. This study aims to carry out a genomic-wide investigation of the AQP gene family in durum wheat using bioinformatics tools and to investigate the expression patterns of some members in response to salt stress. Our results showed that there are 80 TtAQP genes in durum wheat, which are classified into four main groups based on phylogenetic analysis. Many duplications were observed between the members of the TtAQP gene family, and high diversity in response to post-translational modifications was observed between TtAQP family members. The expression pattern of TtAQP genes disclosed that these genes are primarily upregulated in response to salt stress. Besides, qPCR data revealed that TtAQPs are more induced in delayed responses to salinity stress. Overall, our findings illustrate that TtAQP members are diverse in terms of their structure, regulatory systems and expression levels.
ARTICLE | doi:10.20944/preprints202211.0488.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: Capsule network; differential features; deep learning; micro-expression recognition; spatiotemporal features
Online: 28 November 2022 (03:12:12 CET)
Micro-expression (ME) is one of the key psychological stress reactions. It is a modest, spontaneous facial mechanism. ME has significant applicability in a variety of psychologically-related sectors because to its precision and unpredictability with regard to psychological manifestations. Nevertheless, the current Micro-expression recognition (MER) algorithms have poor accuracy and a limited quantity of ME data, and this study issue has not been thoroughly investigated. Therefore, we present an approach for deep learning based on a Spatio-temporal capsule network (STCP-Net). STCP-Net has four components: a jitter reduction module, a differential feature extraction module, an STCP module, and a fully linked layer. The first two modules are aimed to extract diversifying differential features more precisely and to limit the influence of head jitter. The STCP module is used to extract Spatio-temporal features layer by layer, taking the temporal and geographical connection between features into account. This research runs sufficient trials using the Leave One Subject Out (LOSO) methodology for cross-validation using the CASMEII dataset. The conclusion and analysis demonstrate that the algorithm is innovative and efficient.
ARTICLE | doi:10.20944/preprints202210.0317.v1
Subject: Life Sciences, Genetics Keywords: Bioinformatics; Biotic stresses; Regulatory mechanisms; Protein structure; Gene expression; Evolution analysis
Online: 21 October 2022 (03:37:45 CEST)
Sulfate transporters (SULTRs) are responsible for the uptake of the sulfate (SO42−) ions in the rhizosphere by the roots and their distribution in plant organs. In this study, SULTR family members in the genome of the two oilseed crops, Camelina sativa, and Brassica napus, were identified and characterized based on their sequence structure, duplication events, phylogenetic relationships, phosphorylation sites, and expression levels. Herein, 36 and 45 putative SULTR genes were recognized from the genome of C. sativa, and B. napus, respectively. SULTR proteins were predicted as basophilic proteins with low hydrophilicity in both studied species. According to phylogenetic relationships, we divided SULTRs into five groups, in which SULTRs 3 showed highest variation. Besides, several duplication events were observed between SULTRs. The first duplication event was predicted approximately five million years ago between three SULTRs 3.1 in C. sativa. Two subunits were indicated in the 3D structure of SULTRs that the active binding sites differed between C. sativa and B. napus. According to available RNA-seq data, SULTRs showed diverse expression in tissues and response to stimuli. SULTRs 3 showed an expression in all tissues. SULTRs 3.1 were more upregulated in response to abiotic stresses in C. sativa, while SULTRs 3.3, and SULTRs 2.1 showed an upregulation in B. napus. Furthermore, SULTRs 3 and SULTRs 4.1 showed an upregulation in response to biotic stresses in B. napus. Based on the distribution of cis-regulatory elements in the promoter region, we speculated that SULTRs might be controlled by phytohormones such as ABA, and MeJA. Therefore, it seems that SULTR genes in C. sativa have been more influenced by evolutionary processes and have acquired more diversity.
REVIEW | doi:10.20944/preprints202110.0069.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: biology; drug resistance; gene expression profiling; mRNA; multiple myeloma; prognosis; treatment
Online: 5 October 2021 (08:20:44 CEST)
Multiple myeloma (MM) is a genetically complex disease that results from a multistep transformation of normal to malignant plasma cells in the bone marrow. However, the molecular mechanisms responsible for the initiation and heterogeneous evolution of MM remain largely unknown. A fundamental step needed to understand the oncogenesis of MM and its response to therapy is the identification of driver mutations. The introduction of gene expression profiling (GEP) in MM was an important step in elucidating the molecular heterogeneity of MM and its clinical relevance. Since some mutations in myeloma occur in non-coding regions, studies based on the analysis of mRNA provide more comprehensive information on the oncogenic pathways and mechanisms relevant to MM biology. In this review, we discuss the role of gene expression profiling in understanding the biology of multiple myeloma together with the clinical manifestation of the disease, as well as its impact on treatment decisions and future directions.
ARTICLE | doi:10.20944/preprints202109.0281.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: Red Ginseng; Ginsenoside Rg5; Gene expression; IPA pathways; Network pharmacology; Transcriptomics
Online: 16 September 2021 (11:47:52 CEST)
Numerous in vitro studies on isolated cells have been conducted to uncover the molecular mechanisms of action of Panax ginseng Meyer root extracts and purified ginsenosides. However, the concentrations of ginsenosides and the extracts used in these studies were much higher than detected in pharmacokinetic studies in humans and animals orally administered with ginseng preparations at therapeutic doses. Our study aimed to assess: (a) the effects of ginsenoside Rg5, the major "rare" ginsenoside of Red Ginseng, on gene expression in the murine neuronal cell line HT22 in a wide range of concentrations, from 10-4 to 10-18 M, and (b) the effects of differentially expressed genes on cellular and physiological functions in organismal disorders and diseases. Gene expression profiling was performed by transcriptome-wide mRNA microarray analyses in HT22 cells after treatment with ginsenoside Rg5. Ginsenoside Rg5 exhibits soft-acting effects on gene expression of neuronal cells in a wide range of physiological concentrations and strong reversal impact at high (toxic) concentration: significant up- or downregulation of expression of about 300 genes at concentrations from 10-6 M to 10-18 M, and dramatically increased both the number of differentially expressed target genes (up to 1670) and the extent of their expression (fold changes compared to unexposed cells) at a toxic concentration of 10-4 M. Network pharmacology analyses of genes expression profiles using Ingenuity pathway analysis (IPA) software showed that at low physiological concentrations, ginsenoside Rg5 has the potential to activate the biosynthesis of cholesterol and to exhibit predictable effects in senescence, neuroinflammation, apoptosis, and immune response, suggesting soft-acting, beneficial effects on organismal death, movement disorders, and cancer.
ARTICLE | doi:10.20944/preprints202107.0195.v1
Subject: Chemistry, Analytical Chemistry Keywords: Loop-mediated isothermal amplification; AXL over expression; core-shell beads assay
Online: 8 July 2021 (10:57:31 CEST)
The upregulated expression of thyrosine kinase AXL has been reported in several hematologic and solid human tumors including gastric, breast, colorectal, prostate, and ovarian cancers. Thus, AXL can potentially serve as a diagnostic and prognostic biomarker for various cancers. This paper reports the first-ever use of loop-mediated isothermal amplification (LAMP) of the AXL gene as a diagnostic method for ovarian cancer. We demonstrated simple instrumentation toward a point-of-care device to perform LAMP. This paper also reports the first-ever use of core-shell beads as a microreactor to perform LAMP as an attempt to promote environmentally friendly laboratory practices.
ARTICLE | doi:10.20944/preprints202105.0412.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Expression of multilayer network models, oriented graph, multivariate model, nonlinear regression
Online: 18 May 2021 (10:26:19 CEST)
Neural networks models are mostly represented by oriented graphs where only the components, constitutive elements of the graph, are transcribed into mathematical xpression. Indeed, accurate knowledge of the full expression of the model is required in certain situations such as selecting among several reference models, the one that best fits the available data or comparing the explanatory and predictive performance of an established model with respect to some reference models. In this paper, we establish a formalism of the mathematical expression for multilayer perceptron neural network in a general framework, MLP-p-n-q, with p, n and q natural integers and show its restriction to cases where one has a hidden layer and multivariate outputs (MLP-p-1-q), and then a single output (MLP-p-1-1). Then, we give some specific cases of the most commonly used models. An application case is presented in the context of solving a nonlinear regression problem.
ARTICLE | doi:10.20944/preprints202002.0145.v1
Subject: Biology, Other Keywords: parvalbumin; calretinin; calbindin; expression; retina; topography; ganglion cell; calcium buffer protein
Online: 11 February 2020 (11:43:03 CET)
The most prevalent Ca2+-buffer proteins (CaBPs: parvalbumin—PV; calbindin—CaB; calretinin—CaR) are widely expressed by various neurons throughout the brain, including the retinal ganglion cells (RGCs). Even though their retinal expression has been extensively studied, a coherent assessment of topographical variations is missing. To examine this, we performed immunohistochemistry (IHC) in the mouse retina. We found variability in the expression levels and cell numbers for CaR, with stronger and more numerous labels in the dorso-central area. CaBP+ cells contributed to RGCs with all soma sizes, indicating heterogeneity. We separated 4-9 RGC clusters in each area based on expression levels and soma sizes. Besides the overall high variety in cluster number and size, the peripheral half of the temporal retina showed the greatest cluster number, indicating a better separation of RGC subtypes there. Multiple labels showed that 39% of the RGCs showed positivity for a single CaBP, 30% expressed two CaBPs, 25% showed no CaBP expression and 6% expressed all three proteins. Finally, we observed an inverse relation between CaB and CaR expression levels in CaB/CaR dually- and CaB/CaR/PV triple labeled RGCs, suggesting a mutual complementary function.
ARTICLE | doi:10.20944/preprints201910.0249.v1
Subject: Life Sciences, Molecular Biology Keywords: repeats blocks; repeater finder regular expression; tandem repeats of human coronavirus
Online: 22 October 2019 (04:11:40 CEST)
A lot of research studies have been surveyed the completed genomes of prokaryotic and eukaryotic and focused on the correlation between the percentage of microsatellite sequences in completed genomes and the whole size of the organism genomes. There are fewer studies made in repetitive sequences otherwise simple sequence repeats or long tandem repeats of virus genomes. simple sequence repeats (SSRs) are the most important regions for recombination and moving repeats blocks from site to another site in the genomes. A tool was programmed and designed by visual basic 6.0 to find the long tandem repeats in DNA sequences of the small genomes. The tool named “Repeater Finder Regular Expression”, (RFRE) Version 1.0, 2016. The tool was utilized to discover different pattern of long tandem repeats (LTR) motifs on the completed genomes of human corona virus strains by using a joined regular expression language. In this study, a twenty-nine accession numbers of human coronavirus completed genomes, (hku1) strains were retrieved from the Genbank. The researcher can write a different regular expression patterns and joined regular expression patterns through the designed tool to search and find a specific motif of nucleotide sequences inside the complete genomes. The RFRE tool searched and found three different total lengths of a perfect long tandem repeats (240bp, 300bp and 480bp). A Dot plot gave a picture view for the long tandem repeat sequences in the completed genome sequence (KF430201.1) of human coronavirus. The genomic dot plot tool YASS was used as a genomic similarity searching tool to check for the uninterrupted repeats and confirm the sensitivity of the (RFRE) tool. To identify the recombination site in the genomes of human coronavirus the RAT tool was applied to find the recombination sites between the completed genomes of human corona viruses .The RAT tool recognized the recombination site in the nucleotide position (3012) and at the same time this recombination site position (3012) was also recognized as a beginning position of a long tandem repeat. A precise motif was predicted from the translated repeats of Human Corona Virus which found by PRATT tool. There was a relationship between the total length of long tandem repeats and genome size of Human Corona Virus and the correlation value R2 was equal to (0,451). In conclusion, this study presented the importance of finding the long tandem repeats of human coronavirus and gives a relationship between the completed genome size of human coronavirus types and long tandem repeats. The nucleotide position (3012) was a hot spot site for a recombination among the complete genomes of human coronavirus and also identified as a repetitive site in the genomes of human corona virus (hku1). The repeats in human coronavirus (hku1) were predicated to be a main major role of virus evolution.
ARTICLE | doi:10.20944/preprints201609.0062.v1
Subject: Biology, Plant Sciences Keywords: Nicotiana tabacum; solanesol; RNA-seq; solanesyl diphosphate synthase; gene expression; chlorophyll
Online: 18 September 2016 (10:45:27 CEST)
Solanesol is a noncyclic terpene alcohol composed of nine isoprene units and it mainly accumulates in solanaceous plants, especially tobacco (Nicotiana tabacum L.). Here, RNA-seq analyses of tobacco leaves, stems, and roots were used to identify solanesol biosynthesis genes. Six 1-deoxy-d-xylulose 5-phosphate synthase, two 1-deoxy-d-xylulose 5-phosphate reductoisomerase, two 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase, four 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase, two 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase, four 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, two 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase, six isopentenyl diphosphate isomerase, and two solanesyl diphosphate synthase (SPS) genes were identified to be involved in solanesol biosynthesis. Furthermore, the two N. tabacum SPS (NtSPS1 and NtSPS2), which had two conserved aspartate-rich DDxxD domains, were highly homologous with SPS enzymes from other solanaceous plant species. In addition, the solanesol contents of three organs, and leaves from four growing stages, corresponded with the distribution of chlorophyll. Our findings provide a comprehensive evaluation of the correlation between the expression of different biosynthetic genes and the accumulation of solanesol in tobacco.
ARTICLE | doi:10.20944/preprints202212.0307.v1
Subject: Life Sciences, Genetics Keywords: chiasama distibution; mus81; mlh1; ASY1; ZYP1; synaptonemal complex; Allium; GISH; expression profiling
Online: 16 December 2022 (14:12:38 CET)
Meiotic crossovers/chiasmata are not randomly distributed and strictly controlled. The mechanisms behind COs patterning remain largely unknown. In many species COs predominantly occur in the distal 2/3 of the chromosome arm and suppression of COs is observed in the proximal regions. The exceptions are some species, among which Allium fistulosum has strictly localized COs in the proximal region. The ability to manipulate the COs localization can be useful for onion breeding. We investigated the factors that may contribute to the pattern of COs in two closely related onion species A. cepa and A. fistulosum, which differ significantly in the localization of chiasmata, and their F1 diploid and triploid hybrids in pollen mother cells. We demonstrate a significant shift in the COs localization to the distal and interstitial region in F1 triploid hybrid, which has a complete diploid set of A. fistulosum chromosomes and haploid set of A. cepa chromosomes. This observation points to a possible genetic control of COs distribution. We did not find the differences in the assembly and disassembly of ASY1 and ZYP1 between A. cepa and A. fistulosum while the difference between parental species and their hybrids was observed. In diploid F1 hybrids at pachytene the chromosome pairing delay marked by ASY1 was revealed. Immunolocalization of MLH1, a marker for class I of the interference-dependent COs, and MUS81, a marker for class II of the interference-free COs, and mlh1/mus81 gene expression profiling in different stages of meiosis showed a spatiotemporal asymmetry among A. cepa, A. fistulosum and their diploid and triploid F1 hybrids. Our results support the hypothesis of genetic control of CO distribution as one of the players that affect meiotic recombination and exchange of genomic material.
ARTICLE | doi:10.20944/preprints202212.0269.v1
Subject: Social Sciences, Political Science Keywords: Digital media; Pluralism; Freedom of expression; New Constitution; web scrapping; Sentiment Analysis
Online: 15 December 2022 (06:48:44 CET)
There is evidence of constitutional rank in Chile, and not only a sectoral rank, to estimate that the regulation of digital media is in an initial and insufficient phase to properly protect information pluralism as political pluralism. The study aims to investigate the forms of concentration, such as the communicational flow of digital media, to determine the opportunities and information defects of these media due to regulatory deficiencies in this sector. Data collection will be carried out through a qualitative and quantitative methodology. The prospect of the imminent constituent process in Chile provides the opportunity to the evaluate the possibilities to propose changes not only at the legislative level but also at the constitutional level, which are likely to benefit freedom of expression with greater guarantees to such as the pluralism of digital media. The latter also means assessing the relevance of enshrining the right to communication in the future.
ARTICLE | doi:10.20944/preprints202208.0455.v1
Subject: Life Sciences, Biotechnology Keywords: Shock waves; Acoustic cavitation; Gene expression; Aspergillus niger; Cell permeabilization; Fungal germination
Online: 26 August 2022 (09:34:23 CEST)
Shock waves, as used in medicine, can induce cell permeabilization, genetically transforming filamentous fungi; however, little is known on the interaction of shock waves with the cell wall. Because of this, the selection of parameters has been empirical. We studied the influence of shock waves on the germination of Aspergillus niger, to understand their effect on the modulation of four genes related to the growth of conidia. Parameters were varied in the range reported in protocols for genetic transformation. Vials containing conidia in suspension were exposed to either 50, 100 or 200 single-pulse or tandem shock waves, with different peak pressures (approximately 42, 66 and 83 MPa). In the tandem mode, three delays were tested. To equalize the total energy, the number of tandem “events” was halved compared to the number of single-pulse shock waves. Our results demonstrate that shock waves do not generate severe cellular effects on the viability and germination of A. niger conidia. Nevertheless, increase in the aggressiveness of the treatment induced a modification in the four genes tested. Scanning electron microscopy revealed significant changes to the cell wall of the conidia. Under optimized conditions, shock waves could be used for several biotechnological applications, surpassing conventional techniques.
ARTICLE | doi:10.20944/preprints202110.0228.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: flax; Fusarium oxysporum; differential expression genes; GO enrichment analysis; KEGG enrichment analysis
Online: 15 October 2021 (14:32:42 CEST)
A plant’s early response to pathogen stress is a vital indicator of its disease resistance. In order to study the response mechanism of resistant and susceptible flax cultivars to Fusarium oxysporum f. sp. lini (Foln), we applied RNA-sequencing to analyze transcriptomes of flax with Foln 0.5, 2 and 8 hours post inoculation (hpi). We found a significant difference in the number of differential expression genes (DEGs) between resistant and susceptible flax clutivars. The number of DEGs in the Fusarium-resistant cultivar increased dramatically at 2 hpi, and a large number of DEGs participated in the Fusarium-susceptible cultivar response to Foln infection 0.5 hpi. GO enrichment analysis determined that the up-regulated DEGs of both flax cultivars were enriched such as oxidoreductase activity and oxidation-reduction process. At the same time, the genes involved in diterpenoid synthesis were up-regulated in resistant cultivar, while those involved in extracellular region, cell wall and organophosphate ester transport were down-regulated in susceptible cultivar. KEGG enrichment analysis showed the genes encoded WRKY 22 and WRKY33 which involved in MAPK signaling pathway were up-regulated expressed in S-29 and down-regulated expressed in R-7, negatively regulated the disease resistance of flax; The genes encoded Hsp 90 family which in involved in plant pathogen interaction pathway were up-regulated in R-7 and down-regulated in S-29, which positively regulated the disease resistance of flax; The genes encoded MYC2 transcription factor and TIFY proteins which involved in plant hormone signaling pathway were up-regulated in R-7, and regulated the jasmonic acid metabolism of flax and the signal transduction of plant hormones. Meanwhile seven regulatory genes with the most correlation were screened out, Among Lus10025000.g and Lus10026447.g regulated other genes expressed both in plant hormone signal transduction pathway and MAPK signal pathway. In conclusion, these findings will facilitate further studies on the function of these candidate genes in flax of response to Fusarium stress, and the breeding of disease-resistant flax cultivar.
ARTICLE | doi:10.20944/preprints202109.0463.v1
Subject: Life Sciences, Virology Keywords: Artificially designed; chimeric peptides; expression; FMDV; serotype O and A; vaccine candidate
Online: 28 September 2021 (10:56:20 CEST)
Artificially designed, chimeric peptide-based recombinant vaccines are novel approaches to combat the phylogenetically diverse Foot and Mouth Disease (FMD) Virus (FMDV) strains. Among seven distinct serotypes, only serotype O and A are dominantly circulating in Bangladesh and neighbouring countries of Asia, where transboundary transmission, recurrent outbreaks and emergence of novel lineages FMDV are highly prevalent. The objective of this study was to develop multi-epitope recombinant peptides, procuring immunogenicity against circulating diverse subtypes of FMDV serotype O and A. Two chimeric peptides, named B1 (41.0 kDa) and B3 (39.3 kDa), have been designed to incorporate potential B-cell and T-cell epitopes selected from multiple FMDV strains, including previously reported and newly emerged sub-lineages. After expression, characterization and immunization of guineapigs with considerable antigen load of B1 and B3 followed by the serological assays revealed the significant protective immunogenicity, developed from the higher (100 µg) doses of both antigens, against most of the currently prevalent serotype O and A strains of FMDV. The efficient expression, antigenic stability, and multivalent immunogenic potency of the chimeric peptides strongly indicate their credibility as novel vaccine candidates for FMDV serotypes O and A circulating in Bangladesh and surrounding territories.
BRIEF REPORT | doi:10.20944/preprints202109.0349.v1
Subject: Medicine & Pharmacology, Gastroenterology Keywords: RNA-Seq; bioinformatics; web application; gene expression; alternative splicing; visualization; molecular epidemiology
Online: 20 September 2021 (16:56:32 CEST)
Gene expression data is key for the functional annotation of single nucleotide polymorphisms (SNPs) identified in genome-wide association studies (GWAS). Expression and splicing quantitative trait loci (e/sQTLs) in normal colon tissue, such as those from the University of Barcelona and University of Virginia RNA sequencing project (BarcUVa-Seq) and the Genotype-Tissue Expression project (GTEx), are required to gain biological insight of colon-related diseases risk loci. Moreover, transcriptome-wide association studies (TWAS) rely on reference gene expression imputation panels in the tissue of interest to nominate susceptibility genes. Also, it is of high interest to study the relationships between genes in a network framework. For facilitating these analyses, we have updated and expanded the scope of the Colon Transcriptome Explorer (CoTrEx) to the version 2.0. This web-based resource provides exhaustive visualization and analysis of transcriptome-wide gene expression profiles of normal colon tissue from BarcUVa-Seq and GTEx. In addition to the integration of new datasets, CoTrEx 2.0 provides additional e/sQTLs sets, as well as gene expression prediction models and regulatory and co-expression networks. It is freely available at https://barcuvaseq.org/cotrex/. Overall, it is of high interest for researchers aiming to investigate the genetic susceptibility to colon-related complex traits and diseases.
ARTICLE | doi:10.20944/preprints202109.0258.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: Red Ginseng; HRG80TM; Ginsenoside Rg5; Gene expression; IPA pathways; Network pharmacology,; Transcriptomics
Online: 15 September 2021 (12:36:42 CEST)
Panax ginseng C.A.Mey. is an adaptogenic plant traditionally used to enhance mental and physical capacities in cases of weakness, exhaustion, tiredness, loss of concentration, and during recovery. According to ancient records, Red Ginseng root preparations enhance longevity with long-term intake. Recent pharmacokinetic studies of ginsenosides in humans and our in vitro study in neuronal cells suggest that ginsenosides are effective when their level in blood is shallow - at concentrations from 10-6 to 10-18 M. In the present study, we compared the effects of Red Ginseng root preparation HRG80TM(HRG) at concentrations from 0.01 to 10,000 ng/ml with effects of White Ginseng (WG) and purified ginsenosides Rb1, Rg3, Rg5 and Rk1 on gene expression of isolated hippocampal neurons. The aim of this study was to predict the effects of differently expressed genes on cellular and physiological functions in organismal disorders and diseases. Gene expression profiling was performed by transcriptome-wide mRNA microarray analyses in murine HT22 cells after treatment with ginseng preparations. Ingenuity pathway downstream/upstream analysis (IPA) was performed with datasets of significantly up-or downregulated genes, and expected effects on cellular function and disease were identified by IPA software. Ginsenosides Rb1, Rg3, Rg5, and Rk1 have substantially various effects on gene expression profiles (signatures) and are different from signatures of HRG and WG. Furthermore, the signature of HRG is changed significantly with dilution from 10000 to 0.01 ng/ml. Network pharmacological analyses of gene expression profiles showed that HRG exhibits predictable positive effects in neuroinflammation, senescence, apoptosis, and immune response, suggesting beneficial soft-acting effects in cancer, gastrointestinal, and endocrine systems diseases and disorders in a wide range of low concentrations in blood.
ARTICLE | doi:10.20944/preprints202108.0405.v1
Subject: Biology, Anatomy & Morphology Keywords: animal welfare; pigs; deep learning; computer vision; stress detection; facial expression recognition
Online: 19 August 2021 (13:17:08 CEST)
Animal welfare is not only an ethically important consideration in good animal husbandry, but can also have a significant effect on an animal’s productivity. The aim of this paper is to show that a reduction in animal welfare, in the form of increased stress, can be identified in pigs from frontal images of the animals. We train a Convolutional Neural Network (CNN) using a leave-one-out design and show that it is able to discriminate between stressed and unstressed pigs with an accuracy of >90% in unseen animals. Grad-CAM is used to identify the animal regions used, and these support those used in manual assessments such as the Pig Grimace Scale. This innovative work paves the way for further work examining both positive and negative welfare states with a view to the development of an automated system that can be used in precision livestock farming to improve animal welfare.
ARTICLE | doi:10.20944/preprints202105.0333.v1
Subject: Life Sciences, Biochemistry Keywords: genome editing; CRISPR; protoplast; , targeted mutagenesis; TREX2; construct validation; transi-ent expression
Online: 14 May 2021 (13:44:26 CEST)
Cas endonuclease-mediated genome editing provides a long-awaited molecular biological approach to the modification of predefined genomic target sequences in living organisms. Although cas9/guide (g)RNA constructs are straightforward to assemble and can be customized to target virtually any site in the plant genome, the implementation of this technology can be cumbersome, especially in species like Triticale that are difficult to transform, for which only limited genome information is available and/or which carry comparatively large genomes. To cope with these challenges, we have pre-validated cas9/gRNA constructs (1) by frameshift restitution of a reporter gene co-introduced by ballistic DNA transfer to barley epidermis cells, and (2) via transfection in Triticale protoplasts followed by either a T7E1-based cleavage assay or by deep-sequencing of target-specific PCR amplicons. For exemplification, we addressed the Triticale ABA 8’-hydroxylase 1 gene, one of the putative determinants of pre-harvest sprouting of grains. We further show that in-del induction frequency in Triticale can be increased by TREX2 nuclease activity, which holds true for both well- and poorly performing gRNAs. The presented results constitute a sound basis for the targeted induction of heritable modifications in Triticale genes.
REVIEW | doi:10.20944/preprints202011.0060.v1
Subject: Life Sciences, Biochemistry Keywords: Cotton; Fiber initiation; Genomics; Epigenomics; Phytohormones; Transcription factors; MicroRNAs; Gene expression regulation
Online: 2 November 2020 (15:50:39 CET)
The epidermal cells on the surface of the cotton ovules undergo differentiation to produce fibers, which are single-celled hair-like protrusions resembling the plant trichomes. The initiation of these unicellular fibers from the cotton ovule surface is a complex and tightly regulated process. The initiation step is the cell fate-determining stage, which leads to the commitment of cells that eventually developed into fibers, thus becomes the most crucial phase in fiber development. The in-depth knowledge of molecular regulation is a prerequisite to get a clear view of the fiber initiation process's genetic and epigenetic control. The identification and functional validation of cotton fiber initiation-related genes, few fibreless mutants, transcription factors, microRNAs, epigenetic regulators, as well as the elucidation of the role of phytohormones as signaling molecules, has played a significant role in understanding the cotton fiber initiation process at the molecular level. This review focuses on the comprehensive information regarding the genetic and epigenetic regulation of cotton fiber initiation. Thus, the review will provide readers insight into mechanistic details that operate during cotton fiber initiation.
Subject: Life Sciences, Biotechnology Keywords: pathway optimization; machine learning tools; enzyme activity prediction; promoter classification; expression tuning
Online: 26 August 2020 (04:05:47 CEST)
Successful engineering of a microbial host for efficient production of a target product from a given substrate can be viewed as an extensive optimization task. Such a task involves the selection of high activity enzymes as well as their gene expression regulatory control elements (i.e., promoters and ribosome binding sites). Finally, there is also the need to tune expression of multiple genes along a heterologous pathway to relieve constraints from rate-limiting step and help reduce metabolic burden on cells from unnecessary over-expression of high activity enzymes. While the aforementioned tasks could be performed through combinatorial experiments, such an approach incurs significant cost, time and effort, which is a handicap that can be relieved by application of modern machine learning tools. Such tools could attempt to predict high activity enzymes from sequence, but they are currently most usefully applied in classifying strong promoters from weaker ones as well as combinatorial tuning of expression of multiple genes. This perspective reviews the application of machine learning tools to aid metabolic pathway optimization through identifying challenges in metabolic engineering that could be overcome with the help of machine learning tools.
ARTICLE | doi:10.20944/preprints202004.0524.v2
Subject: Biology, Other Keywords: unsupervised learning; tensor decomposition; feature selection; COVID-19; drug discovery; gene expression
Online: 3 June 2020 (05:29:09 CEST)
Background: COVID-19 is a critical pandemic that has affected human communities worldwide, and there is an urgent need to develop effective drugs. Although there are a large number of candidate drug compounds that may be useful for treating COVID-19, the evaluation of these drugs is time-consuming and costly. Thus, screening to identify potentially effective drugs prior to experimental validation is necessary. Method: In this study, we applied the recently proposed method tensor decomposition (TD)-based unsupervised feature extraction (FE) to gene expression profiles of multiple lung cancer cell lines infected with severe acute respiratory syndrome coronavirus 2. We identified drug candidate compounds that significantly altered the expression of the 163 genes selected by TD-based unsupervised FE. Results: Numerous drugs were successfully screened, including many known antiviral drug compounds such as C646, chelerythrine chloride, canertinib, BX-795, sorafenib, sorafenib, QL-X-138, radicicol, A-443654, CGP-60474, alvocidib, mitoxantrone, QL-XII-47, geldanamycin, fluticasone, atorvastatin, quercetin, motexafin gadolinium, trovafloxacin, doxycycline, meloxicam, gentamicin, and dibromochloromethane. The screen also identified ivermectin, which was first identified as an anti-parasite drug and recently the drug was included in clinical trials for SARS-CoV-2. Conclusions: The drugs screened using our strategy may be effective candidates for treating patients with COVID-19.