scholarly journals Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins

2020 ◽  
Author(s):  
Edna María Hernández-Domínguez ◽  
Laura Sofía Castillo-Ortega ◽  
Yarely García-Esquivel ◽  
Virginia Mandujano-González ◽  
Gerardo Díaz-Godínez ◽  
...  
Keyword(s):  
Biological Molecules ◽  
Evolutionary Analysis ◽  
Evolutionary Processes ◽  
Regulation Of Expression ◽  
Computational Mathematics ◽  
Functional Changes ◽  
Sequencing Technologies ◽  
Metabolomic Data ◽  
Changes Over Time

This chapter deals with the topic of bioinformatics, computational, mathematics, and statistics tools applied to biology, essential for the analysis and characterization of biological molecules, in particular proteins, which play an important role in all cellular and evolutionary processes of the organisms. In recent decades, with the next generation sequencing technologies and bioinformatics, it has facilitated the collection and analysis of a large amount of genomic, transcriptomic, proteomic, and metabolomic data from different organisms that have allowed predictions on the regulation of expression, transcription, translation, structure, and mechanisms of action of proteins as well as homology, mutations, and evolutionary processes that generate structural and functional changes over time. Although the information in the databases is greater every day, all bioinformatics tools continue to be constantly modified to improve performance that leads to more accurate predictions regarding protein functionality, which is why bioinformatics research remains a great challenge.

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

scholarly journals Clinical characterization of dysautonomia in long COVID-19 patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicolas Barizien ◽  
Morgan Le Guen ◽  
Stéphanie Russel ◽  
Pauline Touche ◽  
Florent Huang ◽  
...  
Keyword(s):  
Mixed Models ◽  
Repeated Measures ◽  
Physical Medicine ◽  
Persistent Symptoms ◽  
Index Changes ◽  
Changes Over Time ◽  
And Control ◽  
Testing Group ◽  
Over Time

AbstractIncreasing numbers of COVID-19 patients, continue to experience symptoms months after recovering from mild cases of COVID-19. Amongst these symptoms, several are related to neurological manifestations, including fatigue, anosmia, hypogeusia, headaches and hypoxia. However, the involvement of the autonomic nervous system, expressed by a dysautonomia, which can aggregate all these neurological symptoms has not been prominently reported. Here, we hypothesize that dysautonomia, could occur in secondary COVID-19 infection, also referred to as “long COVID” infection. 39 participants were included from December 2020 to January 2021 for assessment by the Department of physical medicine to enhance their physical capabilities: 12 participants with COVID-19 diagnosis and fatigue, 15 participants with COVID-19 diagnosis without fatigue and 12 control participants without COVID-19 diagnosis and without fatigue. Heart rate variability (HRV) during a change in position is commonly measured to diagnose autonomic dysregulation. In this cohort, to reflect HRV, parasympathetic/sympathetic balance was estimated using the NOL index, a multiparameter artificial intelligence-driven index calculated from extracted physiological signals by the PMD-200 pain monitoring system. Repeated-measures mixed-models testing group effect were performed to analyze NOL index changes over time between groups. A significant NOL index dissociation over time between long COVID-19 participants with fatigue and control participants was observed (p = 0.046). A trend towards significant NOL index dissociation over time was observed between long COVID-19 participants without fatigue and control participants (p = 0.109). No difference over time was observed between the two groups of long COVID-19 participants (p = 0.904). Long COVID-19 participants with fatigue may exhibit a dysautonomia characterized by dysregulation of the HRV, that is reflected by the NOL index measurements, compared to control participants. Dysautonomia may explain the persistent symptoms observed in long COVID-19 patients, such as fatigue and hypoxia. Trial registration: The study was approved by the Foch IRB: IRB00012437 (Approval Number: 20-12-02) on December 16, 2020.

scholarly journals Sequencing and Computational Approaches to Identification and Characterization of Microbial Organisms

2013 ◽  
Vol 5 ◽  
pp. BECB.S10886 ◽  
Author(s):  
Brijesh Singh Yadav ◽  
Venkateswarlu Ronda ◽  
Dinesh P. Vashista ◽  
Bhaskar Sharma
Keyword(s):  
Sequence Data ◽  
Microbial Interactions ◽  
Microbial Pathogens ◽  
Nucleotide Sequence Data ◽  
Computational Approaches ◽  
Microbial Detection ◽  
Sequencing Technologies ◽  
Sequencing Platforms ◽  
Identification And Characterization

The recent advances in sequencing technologies and computational approaches are propelling scientists ever closer towards complete understanding of human-microbial interactions. The powerful sequencing platforms are rapidly producing huge amounts of nucleotide sequence data which are compiled into huge databases. This sequence data can be retrieved, assembled, and analyzed for identification of microbial pathogens and diagnosis of diseases. In this article, we present a commentary on how the metagenomics incorporated with microarray and new sequencing techniques are helping microbial detection and characterization.

Hyperpolarized 129Xe Magnetic Resonance Spectroscopy in a Rat Model of Bronchopulmonary Dysplasia

2021 ◽  
Author(s):  
Jordan David Fliss ◽  
Brandon Zanette ◽  
Yonni Friedlander ◽  
Siddharth Sadanand ◽  
Andras A Lindenmaier ◽  
...  
Keyword(s):  
Magnetic Resonance ◽  
Gas Exchange ◽  
Magnetic Resonance Spectroscopy ◽  
Bronchopulmonary Dysplasia ◽  
Rat Model ◽  
Resonance Spectroscopy ◽  
Gas Exchange Parameters ◽  
Functional Changes ◽  
Non Invasive

Premature infants often require mechanical ventilation and oxygen therapy which can result in bronchopulmonary dysplasia (BPD), characterized by developmental arrest and impaired lung function. Conventional clinical methods for assessing the prenatal lung are not adequate for the detection and assessment of long-term health risks in infants with BPD, highlighting the need for a non-invasive tool for the characterization of lung microstructure and function. Theoretical diffusion models, like the Model of Xenon Exchange (MOXE), interrogate alveolar gas exchange by predicting the uptake of inert Hyperpolarized (HP) 129Xe gas measured with HP 129Xe magnetic resonance spectroscopy (MRS). To investigate HP 129Xe MRS as a tool for non-invasive characterization of pulmonary microstructural and functional changes in vivo, HP 129Xe gas exchange data were acquired in an oxygen exposure rat model of BPD that recapitulates the fewer and larger distal airways and pulmonary vascular stunting characteristics of BPD. Gas exchange parameters from MOXE, including airspace mean chord length (L­m), apparent hematocrit in the pulmonary capillaries (HCT), and pulmonary capillary transit time (tx), were compared with airspace mean axis length and area density (MAL and ρ­A) and percentage area of tissue and air (PTA and PAA) from histology. L­m was significantly larger in the exposed rats (p=0.003) and correlated with MAL, ρ­A, PTA, and PAA (0.59<|ρ|<0.66 and p<0.05). Observed increase in HCT (p=0.012) and changes in tx are also discussed. These findings support the use of HP 129Xe MRS for detecting fewer, enlarged distal airways in this rat model of BPD, and potentially in humans.

scholarly journals Study of Osteocyte Behavior by High-Resolution Intravital Imaging Following Photo-Induced Ischemia

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2874
Author(s):  
Hengfeng Yuan ◽  
Wen Jiang ◽  
Yuanxin Chen ◽  
Betty Kim
Keyword(s):  
Imaging Techniques ◽  
Avascular Osteonecrosis ◽  
Functional Changes ◽  
Cellular Processes ◽  
Non Invasive ◽  
Behavioral Dynamics ◽  
Bony Anatomy ◽  
Magnetic Resonance Imaging Mri

Ischemic injuries and local hypoxia can result in osteocytes dysfunction and play a key role in the pathogenesis of avascular osteonecrosis. Conventional imaging techniques including magnetic resonance imaging (MRI) and computed tomography (CT) can reveal structural and functional changes within bony anatomy; however, characterization of osteocyte behavioral dynamics in the setting of osteonecrosis at the single cell resolution is limited. Here, we demonstrate an optical approach to study real-time osteocyte functions in vivo. Using nicotinamide adenine dinucleotide (NADH) as a biomarker for metabolic dynamics in osteocytes, we showed that NADH level within osteocytes transiently increase significantly after local ischemia through non-invasive photo-induced thrombosis of afferent arterioles followed by a steady decline. Our study presents a non-invasive optical approach to study osteocyte behavior through the modulation of local environmental conditions. Thus it provides a powerful toolkit to study cellular processes involved in bone pathologies in vivo.

Spectral-Domain Oct and Microperimeter Characterization of Morphological and Functional Changes in X-Linked Retinoschisis

2009 ◽  
Vol 40 (1) ◽  
pp. 71-74 ◽  
Author(s):  
Muneeswar Gupta Nittala ◽  
Gella Laxmi ◽  
Rajiv Raman ◽  
Padmaja Kumari Rani ◽  
Arun Bhargava ◽  
...  
Keyword(s):  
Spectral Domain ◽  
Functional Changes ◽  
Spectral Domain Oct

MicroRNAs as Therapeutic Agents: The Future of the Battle Against Cancer

2019 ◽  
Vol 18 (30) ◽  
pp. 2544-2554 ◽  
Author(s):  
Sumit Biswas
Keyword(s):  
Drug Resistance ◽  
Cancer Biology ◽  
Therapeutic Agents ◽  
Nucleotide Level ◽  
Target Mrnas ◽  
Sequencing Technologies ◽  
Tumour Suppressors ◽  
The Future ◽  
New Strategies

Since their discovery in the 1990’s, the study of a class of non-coding, single-stranded RNAs, christened the microRNAs has opened up new vistas in the field of cancer biology. MicroRNAs bind to their target mRNAs to act as either oncogenes or tumour suppressors. With the near-complete elucidation of the biogenesis pathway, and the advent of rapid sequencing technologies, microRNAs have slowly cemented their place as essential biomarkers for delineating the progression, metastasis, relapse or drug resistance of cancer. Being crucial players in the cancer pathway, there has been considerable urgency in designing molecules - both at the nucleotide and non-nucleotide level to counter the effects of their binding. A number of different approaches have yielded quite a body of compounds which have been found to be effective in the treatment of various tumours across many different organs. In this study, the focus is on the review of the timeline of discovery and characterization of microRNAs, underlining their importance in different cancers, shedding light on the discovery of anti-microRNA compounds and illustrating their uses in deriving new strategies to combat cancer.

scholarly journals Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea

2020 ◽  
Vol 2020 ◽  
pp. 1-19
Author(s):  
Chenyang Liu ◽  
Dongliang Yuan ◽  
Tong Liu ◽  
Mengge Xing ◽  
Wenying Xu ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Expression Patterns ◽  
Orthologous Gene ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Cultivated Species ◽  
Arachis Duranensis ◽  
Gene Structures ◽  
Wild Peanut

RWP-RK proteins are important factors involved in nitrate response and gametophyte development in plants, and the functions of RWP-RK proteins have been analyzed in many species. However, the characterization of peanut RWP-RK proteins is limited. In this study, we identified 16, 19, and 32 RWP-RK members from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively, and investigated their evolution relationships. The RWP-RK proteins were classified into two groups, RWP-RK domain proteins and NODULE-INCEPTION-like proteins. Chromosomal distributions, gene structures, and conserved motifs of RWP-RK genes were compared among wild and cultivated peanuts. In addition, we identified 12 orthologous gene pairs from the two wild peanut species, 13 from A. duranensis and A. hypogaea, and 13 from A. ipaensis and A. hypogaea. One, one, and seventeen duplicated gene pairs were identified within the A. duranensis, A. ipaensis, and A. hypogaea genomes, respectively. Moreover, different numbers of cis-acting elements in the RWP-RK promoters were found in wild and cultivated species (87 in A. duranensis, 89 in A. ipaensis, and 92 in A. hypogaea), and as a result, many RWP-RK genes showed distinct expression patterns in different tissues. Our study will provide useful information for further functional and evolutionary analysis of the RWP-RK genes.

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