scholarly journals CORSID enables de novo identification of transcription regulatory sequences and genes in coronaviruses

2021 ◽  
Author(s):  
Chuanyi Zhang ◽  
Palash Sashittal ◽  
Mohammed El-Kebir
Keyword(s):  
Prior Information ◽  
De Novo ◽  
Critical Role ◽  
Gene Identification ◽  
Regulatory Sequences ◽  
Gene Annotations ◽  
Sequence Identifier ◽  
Simultaneous Identification ◽  
Discontinuous Transcription ◽  
First Time

Genes in coronaviruses are preceded by transcription regulatory sequences (TRSs), which play a critical role in gene expression mediated by the viral RNA-dependent RNA-polymerase via the process of discontinuous transcription. In addition to being crucial for our understanding of the regulation and expression of coronavirus genes, we demonstrate for the first time how TRSs can be leveraged to identify gene locations in the coronavirus genome. To that end, we formulate the TRS AND GENE IDENTIFICATION (TRS-GENE-ID) problem of simultaneously identifying TRS sites and gene locations in unannotated coronavirus genomes. We introduce CORSID (CORe Sequence IDentifier), a computational tool to solve this problem. We also present CORSID-A, which solves a constrained version of the TRS-GENE-ID problem, the TRS IDENTIFICATION (TRS-ID) problem, identifying TRS sites in a coronavirus genome with specified gene annotations. We show that CORSID-A outperforms existing motif-based methods in identifying TRS sites in coronaviruses and that CORSID outperforms state-of-the-art gene finding methods in finding genes in coronavirus genomes. We demonstrate that CORSID enables de novo identification of TRS sites and genes in previously unannotated coronaviruses. CORSID is the first method to perform accurate and simultaneous identification of TRS sites and genes in coronavirus genomes without the use of any prior information.

scholarly journals PAX2 Gene Mutation in a Family with Isolated Renal Hypoplasia

2001 ◽  
Vol 12 (8) ◽  
pp. 1769-1772
Author(s):  
KAORI NISHIMOTO ◽  
KAZUMOTO IIJIMA ◽  
TAKU SHIRAKAWA ◽  
KOUSAKU KITAGAWA ◽  
KENICHI SATOMURA ◽  
...  
Keyword(s):  
Nonsense Mutation ◽  
De Novo ◽  
Direct Sequencing ◽  
Critical Role ◽  
Transactivation Domain ◽  
Renal Anomalies ◽  
Renal Hypoplasia ◽  
Renal Coloboma Syndrome ◽  
Ophthalmologic Examination ◽  
First Time

Abstract. The PAX2 gene encodes a transcription factor that plays a critical role in the development of the urogenital tract, eyes, ears, and central nervous system. Recently, renal hypoplasia was observed to be part of the renal-coloboma syndrome, which is caused by heterozygous mutations of the PAX2 gene. The renal-coloboma syndrome is a rare autosomal dominant syndrome that involves optic nerve colobomas and renal anomalies. For investigation of whether PAX2 mutations occur in patients with isolated renal hypoplasia, patient DNA was analyzed for PAX2 mutations, by using PCR and direct sequencing. The study involved 20 patients with bilateral renal hypoplasia associated with decreased renal function. Heterozygous PAX2 mutations were detected in two patients, i.e., a novel nonsense mutation (C to A transversion at position 1566 in exon 9) in patient 1 and another novel nonsense mutation (C to T transversion at position 1318 in exon 7) in patient 2. The nucleotide changes for patients 1 and 2 directly introduced stop codons, presumably resulting in a message for a truncated PAX2 protein that lacked a partial transactivation domain. An ophthalmologic examination revealed a very mild, asymptomatic coloboma in patient 2, whereas the fundus was normal for patient 1. The mutation cosegregated with the presence of renal hypoplasia in the family of patient 1, appearing de novo in the mother of the patient, which strongly suggests that this mutation was the cause of renal hypoplasia in this family. This study demonstrates for the first time that PAX2 mutations can be responsible for isolated renal hypoplasia.

Non-Plasmonic SERS with Silicon: Is It Really Safe? New Insights into Opto-Thermics of Core/Shell Microbeads

2018 ◽  
Author(s):  
Nicolò Bontempi ◽  
Irene Vassalini ◽  
Stefano Danesi ◽  
Matteo Ferroni ◽  
Paolo Colombi ◽  
...  
Keyword(s):  
Critical Role ◽  
Raman Laser ◽  
Core Shell ◽  
Thermal Coupling ◽  
Melting Points ◽  
Experimental Proof ◽  
Weakly Coupled ◽  
Light Management ◽  
Laser Sources ◽  
First Time

<p>Here we investigate for the first time the opto-thermal behavior of SiO<sub>2</sub>/Si core/shell microbeads (Si-rex) irradiated with three common Raman laser sources (lambda=532, 633, 785 nm) under real working conditions. We obtained an experimental proof of the critical role played by bead size and aggregation in heat and light management, demonstrating that in the case of strong opto-thermal coupling the temperature can exceed that of the melting points of both core and shell components. In addition, we also show that weakly coupled beads can be utilized as stable substrates for plasmon-free SERS experiments.</p>

scholarly journals Induction of Promoter DNA Methylation Upon High-Pressure Spraying of Double-Stranded RNA in Plants

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 789
Author(s):  
Athanasios Dalakouras ◽  
Ioannis Ganopoulos
Keyword(s):  
High Pressure ◽  
De Novo ◽  
Epigenetic Changes ◽  
Double Stranded Rna ◽  
Rna Molecules ◽  
Promoter Sequences ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
First Time ◽  
De Novo Methylation

Exogenous application of RNA molecules is a potent method to trigger RNA interference (RNAi) in plants in a transgene-free manner. So far, all exogenous RNAi (exo-RNAi) applications have aimed to trigger mRNA degradation of a given target. However, the issue of concomitant epigenetic changes was never addressed. Here, we report for the first time that high-pressure spraying of dsRNAs can trigger de novo methylation of promoter sequences in plants.

Synthesis of an azadioxa-planar triphenylborane and investigation of its structural and photophysical properties

2021 ◽  
Author(s):  
Y. Kitamoto ◽  
K. Oda ◽  
K. Ogino ◽  
K. Hiyama ◽  
H. Kita ◽  
...  
Keyword(s):  
Photophysical Properties ◽  
Critical Role ◽  
Molecular Properties ◽  
Bridging Groups ◽  
First Time

An azadioxa-planar triphenylborane was synthesized for the first time and it was found that bridging groups have a critical role in changing its molecular properties.

scholarly journals De Novo Partial 13q22-q34 Trisomy with Typical Neurological and Immunological Findings: A Case Report with New Genetic Insights

2020 ◽  
Vol 11 (1) ◽  
pp. 21
Author(s):  
Claudia Brogna ◽  
Valentina Milano ◽  
Barbara Brogna ◽  
Lara Cristiano ◽  
Giuseppe Rovere ◽  
...  
Keyword(s):  
Case Report ◽  
De Novo ◽  
Partial Trisomy ◽  
Cerebral Vasculitis ◽  
Radiological Findings ◽  
Cerebral Lesions ◽  
Brain Malformations ◽  
Vermian Hypoplasia ◽  
Callosal Dysgenesis ◽  
First Time

The partial trisomy 13q encompasses an extensive variability of phenotypic and radiological findings including leukoencephalopathy and brain malformations such as holoprosencephaly, callosal dysgenesis, hippocampal hypoplasia, olfactory hypoplasia, and vermian hypoplasia. We report for the first time a case of a 23-year-old patient affected by de novo partial 13q22.1q34 trisomy (41.7 Mb, 72,365,975-114,077,122x3) presenting with hemiparesis related to both ischemic and haemorrhagic cerebral lesions compatible with cerebral vasculitis due to a possible combination of genetic and immunological interaction.

scholarly journals Prediction of IL4 Inducing Peptides

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Sandeep Kumar Dhanda ◽  
Sudheer Gupta ◽  
Pooja Vir ◽  
G. P. S. Raghava
Keyword(s):  
Mhc Class Ii ◽  
Critical Role ◽  
Interleukin 4 ◽  
Th2 Response ◽  
Data Set ◽  
T Helper 2 ◽  
Cell Responses ◽  
Antibody Class ◽  
First Time ◽  
Motif Information

The secretion of Interleukin-4 (IL4) is the characteristic of T-helper 2 responses. IL4 is a cytokine produced by CD4+ T cells in response to helminthes and other extracellular parasites. It has a critical role in guiding antibody class switching, hematopoiesis and inflammation, and the development of appropriate effector T-cell responses. In this study, it is the first time an attempt has been made to understand whether it is possible to predict IL4 inducing peptides. The data set used in this study comprises 904 experimentally validated IL4 inducing and 742 noninducing MHC class II binders. Our analysis revealed that certain types of residues are preferred at certain positions in IL4 inducing peptides. It was also observed that IL4 inducing and noninducing epitopes differ in compositional and motif pattern. Based on our analysis we developed classification models where the hybrid method of amino acid pairs and motif information performed the best with maximum accuracy of 75.76% and MCC of 0.51. These results indicate that it is possible to predict IL4 inducing peptides with reasonable precession. These models would be useful in designing the peptides that may induce desired Th2 response.

Updating the knowledge of the flower flies (Diptera: Syrphidae) from Chile: Illustrated catalog, extinction risk and biological notes

Zootaxa ◽  
2021 ◽  
Vol 4959 (1) ◽  
pp. 1-178
Author(s):  
RODRIGO M. BARAHONA-SEGOVIA ◽  
PAMELA RIERA ◽  
LAURA PAÑINAO-MONSÁLVEZ ◽  
VICENTE VALDÉS GUZMÁN ◽  
PATRICIA HENRÍQUEZ-PISKULICH
Keyword(s):  
Extinction Risk ◽  
Critical Role ◽  
Floral Biology ◽  
Iucn Red List ◽  
Decomposition Of Organic Matter ◽  
Management Plans ◽  
Flower Flies ◽  
Iucn Red List Criteria ◽  
Definition Of ◽  
First Time

Syrphidae, more commonly known as flower flies, are considered one of the most important Diptera families worldwide because of their critical role in pollination, biological control and decomposition of organic matter. The study of these flies in Chile has stagnated due to a lack of local experts as well as the absence of an updated catalog of species. This study is an attempt to remedy the latter of these issues by providing an illustrated and updated catalog to the Syrphidae of Chile. Species are presented under currently accepted names, with synonyms and previous combinations listed and original references. Type localities, world and Chilean distribution by geopolitical Chilean regions, taxonomic and biological notes, a complete record of bibliographic references and extinction risk under IUCN Red List criteria are provided. This catalog recognizes 132 species of Syrphidae, belonging to four subfamilies (Eristalinae, Microdontinae, Pipizinae and Syrphinae), 13 tribes and 47 genera. A total of 46 species (34.84 %) is restricted to the geopolitical territory of Chile. Eight species are considered exotic, one is considered incertae sedis and three are based on doubtful records. Seventeen species of 10 different genera (Copestylum Macquart, 1846; Dolichogyna Macquart, 1842; Eosalpingogaster Hull, 1949b; Eupeodes Osten Sacken, 1877; Meromacrus Rondani, 1848; Palpada Macquart, 1834; Paragus Latreille, 1804; Sphiximorpha Rondani, 1850; Sterphus Philippi, 1865 and Toxomerus Macquart, 1855) are reported from Chile for the first time. A total of 44 species (33.33 %) reported from Chile are directly threatened by human activities such as agriculture, forestry, mining and/or urbanization and indirectly by climate change. The gaps found in the geographic distribution of Chilean flower fly species and what it means for its use by disciplines such as ecology, floral biology and agronomy, are discussed. In addition, the use of this illustrated catalog for biological conservation, the potential definition of priority areas and ecosystem management plans based on this group of Diptera are also discussed. 

The vitamin K–dependent γ-glutamyl carboxylase gene contains a TATA-less promoter with a novel upstream regulatory element

Blood ◽  
2003 ◽  
Vol 102 (4) ◽  
pp. 1333-1339 ◽  
Author(s):  
Elizabeth E. Romero ◽  
Umaima Marvi ◽  
Zachary E. Niman ◽  
David A. Roth
Keyword(s):  
Blood Coagulation ◽  
Dna Sequence ◽  
Vitamin K ◽  
Nuclear Protein ◽  
Regulatory Element ◽  
Hepatoma Cell ◽  
Critical Role ◽  
Developmental Expression ◽  
Regulatory Sequences ◽  
Developmentally Regulated

Abstract The expression of the vitamin K–dependent γ-glutamyl carboxylase gene in liver is developmentally regulated. Since the gene product catalyzes an essential post-translational modification of the vitamin K–dependent blood coagulation proteins, the regulation of carboxylase expression is critical for hemostasis. We analyzed the activity of the rat carboxylase gene 5′-regulatory DNA sequences in rat hepatoma cell lines at different states of differentiation. These studies demonstrated that the 2.6-kb 5′-flanking sequence has differentiation-dependent transcriptional activity. Transient gene expression assays, examining the effects of nested deletions and site-directed mutagenesis of putative regulatory sequences, together with electrophoretic mobility shift assays (EMSAs) were used to identify sequences critical for the developmentally regulated transcription of the rat carboxylase gene. We identified a DNA sequence (–76 to –65; GTTCCGGCCTTC) not known to bind to transcription factors, yet which functions as an upstream promoter element. In vivo genomic DNA footprinting confirms the presence of nuclear protein–DNA interactions at this site in the endogenous carboxylase gene in differentiated hepatoma cells. Therefore, this DNA sequence has specific nuclear protein–binding activity and functional properties consistent with a regulatory element that plays a critical role in the developmental expression of the carboxylase gene, and hence the regulation of vitamin K–dependent blood coagulation protein synthesis.

scholarly journals Consistency and Stability of Motor Subtype Classifications in Patients With de novo Parkinson’s Disease

2021 ◽  
Vol 15 ◽  
Author(s):  
Jingru Ren ◽  
Chenxi Pan ◽  
Yuqian Li ◽  
Lanting Li ◽  
Ping Hua ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
De Novo ◽  
Classification Systems ◽  
Motor Symptoms ◽  
Chi Squared ◽  
Baseline Evaluation ◽  
The Stability ◽  
First Time ◽  
Non Motor Symptoms

ObjectivePatients with Parkinson’s disease (PD) are commonly classified into subtypes based on motor symptoms. The aims of the present study were to determine the consistency between PD motor subtypes, to assess the stability of PD motor subtypes over time, and to explore the variables influencing PD motor subtype stability.MethodsThis study was part of a longitudinal study of de novo PD patients at a single center. Based on three different motor subtype classification systems proposed by Jankovic, Schiess, and Kang, patients were respectively categorized as tremor-dominant/indeterminate/postural instability and gait difficulty (TD/indeterminate/PIGD), TDS/mixedS/akinetic-rigidS (ARS), or TDK/mixedK/ARK at baseline evaluation and then re-assessed 1 month later. Demographic and clinical characteristics were recorded at each evaluation. The consistency between subtypes at baseline evaluation was assessed using Cohen’s kappa coefficient (κ). Additional variables were compared between PD subtype groups using the two-sample t-test, Mann–Whitney U-test or Chi-squared test.ResultsOf 283 newly diagnosed, untreated PD patients, 79 were followed up at 1 month. There was fair agreement between the Jankovic, Schiess, and Kang classification systems (κS = 0.383 ± 0.044, κK = 0.360 ± 0.042, κSK = 0.368 ± 0.038). Among the three classification systems, the Schiess classification was the most stable and the Jankovic classification was the most unstable. The non-motor symptoms questionnaire (NMSQuest) scores differed significantly between PD patients with stable and unstable subtypes based on the Jankovic classification (p = 0.008), and patients with a consistent subtype had more severe NMSQuest scores than patients with an inconsistent subtype.ConclusionFair consistency was observed between the Jankovic, Schiess, and Kang classification systems. For the first time, non-motor symptoms (NMSs) scores were found to influence the stability of the TD/indeterminate/PIGD classification. Our findings support combining NMSs with motor symptoms to increase the effectiveness of PD subtypes.

scholarly journals Obesity Accelerates Age-Associated Defects in Human B Cells Through a Metabolic Reprogramming Induced by the Fatty Acid Palmitate

2022 ◽  
Vol 2 ◽  
Author(s):  
Daniela Frasca ◽  
Maria Romero ◽  
Denisse Garcia ◽  
Alain Diaz ◽  
Bonnie B. Blomberg
Keyword(s):  
Fatty Acid ◽  
B Cells ◽  
Critical Role ◽  
Metabolic Reprogramming ◽  
Autoimmune Antibodies ◽  
Human B Cells ◽  
Initial Hypothesis ◽  
First Time ◽  
Culture Supernatants

We have measured the secretion of autoimmune antibodies in plasma samples and in culture supernatants of blood-derived B cells from four groups of individuals: young lean (YL), elderly lean (EL), young obese (YO) and elderly obese (EO). We found secretion comparable in YO and EL individuals, suggesting that obesity accelerates age-associated defects in circulating B cells. To define at least one possible molecular pathway involved, we used an in vitro model in which B cells from YL and EL individuals have been stimulated with the Fatty Acid (FA) palmitate, the most common saturated FA in the human body. The rationale to use palmitate is that there is a chronic increase in circulating levels of palmitate, due to increased spontaneous lipolysis occurring during aging and obesity, and this may induce autoimmune B cells. Results herein show that in vitro incubation of B cells from YL and EL individuals with the FA palmitate induces mRNA expression of T-bet, the transcription factor for autoimmune antibodies, as well as secretion of autoimmune IgG antibodies, with B cells from YL individuals looking similar to B cells from EL individuals, confirming our initial hypothesis. The generation of autoimmune B cells in the presence of the FA palmitate was found to be associated with a metabolic reprogramming of B cells from both YL and EL individuals. These results altogether show the critical role of the FA palmitate in inducing human B cell immunosenescence and show for the first time the importance of metabolic pathways in this process.

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