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Molecular Genetics of Assay Technology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 4065

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Guest Editor
National Research Council of Italy (CNR), Department Biomedicine - Institute Biochemistry and Cell Biology (IBBC), Naples, Italy
Interests: aging; dementia; Alzheimer; FTD; progranulin; CD33; TREM2; SIGLEC genes; CRISPR-Cas9; iPSCs Parkinson; neuroinflammation; personalized medicine
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Special Issue Information

Dear Colleagues,

Advancements in molecular genetics have increased both diagnostic and predictive capabilities in healthcare.

Protein misfolding, accumulation, and aggregation are common features in many neurological disorders, including Alzheimer’s disease (AD) and Parkinson disease (PD). Understanding the assays to detect the above as well as how they may improve over time is critical for translational research.

The general principle of proteinopathies is that they change conformation, lose their normal function, and gain toxicity, yet there is no structural understanding of how altered protein conformations or aggregates trigger neuronal dysfunction. IPSCs generate from patients using reprogramming technology may help this understanding. Next-generation sequencing (NGS), droplet digital PCR, and genome-wide sequencing have advanced the field of molecular diagnostics for cell-free nucleic acids analyses.

Chaperones are the leading candidates in the search for factors affecting conformational changes in folding and remodeling the essential folding scene. Ascertaining and validating reliable in vitro and in vivo assays to identify a pool of biological targets will help to develop compounds to interact with these targets and analyze them for their potential for target druggability. Data defining druggable targets and tool compounds are the basis for drug development and personalized medicine. Moreover, human-relevant models for complex biology based on organ-on-chip models enable researchers to more closely emulate human biology by combining human cell sourcing, an organ-specific microenvironment, and tissue-relevant mechanical forces. 

Dr. Emilia Vitale
Guest Editor

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Keywords

  • IPSC next-generation sequencing (NGS)
  • droplet digital PCR
  • target druggability
  • organ-on-a-chip
  • translational medicine

Published Papers (2 papers)

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Research

14 pages, 4212 KiB  
Article
BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning
by Vishwamitra Singh Baisvar, Basdeo Kushwaha, Ravindra Kumar, Murali Sanjeev Kumar, Mahender Singh, Anil Rai and Uttam Kumar Sarkar
Int. J. Mol. Sci. 2022, 23(24), 15958; https://doi.org/10.3390/ijms232415958 - 15 Dec 2022
Cited by 1 | Viewed by 1681
Abstract
Construction of a physical chromosome map of a species is important for positional cloning, targeted marker development, fine mapping of genes, selection of candidate genes for molecular breeding, as well as understanding the genome organization. The genomic libraries in the form of bacterial [...] Read more.
Construction of a physical chromosome map of a species is important for positional cloning, targeted marker development, fine mapping of genes, selection of candidate genes for molecular breeding, as well as understanding the genome organization. The genomic libraries in the form of bacterial artificial chromosome (BAC) clones are also a very useful resource for physical mapping and identification and isolation of full-length genes and the related cis acting elements. Some BAC-FISH based studies reported in the past were gene based physical chromosome maps of Clarias magur (magur) to understand the genome organization of the species and to establish the relationships with other species in respect to genes’ organization and evolution in the past. In the present study, we generated end sequences of the BAC clones and analyzed those end sequences within the scaffolds of the draft genome of magur to identify and map the genes bioinformatically for each clone. A total of 36 clones mostly possessing genes were identified and used in probe construction and their subsequent hybridization on the metaphase chromosomes of magur. This study successfully mapped all 36 specific clones on 16 chromosome pairs, out of 25 pairs of magur chromosomes. These clones are now recognized as chromosome-specific makers, which are an aid in individual chromosome identification and fine assembly of the genome sequence, and will ultimately help in developing anchored genes’ map on the chromosomes of C. magur for understanding their organization, inheritance of important fishery traits and evolution of magur with respect to channel catfish, zebrafish and other species. Full article
(This article belongs to the Special Issue Molecular Genetics of Assay Technology)
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10 pages, 1625 KiB  
Article
SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection
by Dakai Liu, George D. Rodriguez, Hang-Yu Zhou, Ye-Xiao Cheng, Xiaofeng Li, Wenwen Tang, Nishant Prasad, Chun-Cheng Chen, Vishnu Singh, Eric Konadu, Keither K. James, Maria F. Bahamon, Yvonne Chen, Sorana Segal-Maurer, Aiping Wu and William Harry Rodgers
Int. J. Mol. Sci. 2022, 23(11), 6254; https://doi.org/10.3390/ijms23116254 - 2 Jun 2022
Cited by 1 | Viewed by 1850
Abstract
Being in the epicenter of the COVID-19 pandemic, our lab tested 193,054 specimens for SARS-CoV-2 RNA by diagnostic multiplex reverse transcription polymerase chain reaction (mRT-PCR) starting in March 2020, of which 17,196 specimens resulted positive. To investigate the dynamics of virus molecular evolution [...] Read more.
Being in the epicenter of the COVID-19 pandemic, our lab tested 193,054 specimens for SARS-CoV-2 RNA by diagnostic multiplex reverse transcription polymerase chain reaction (mRT-PCR) starting in March 2020, of which 17,196 specimens resulted positive. To investigate the dynamics of virus molecular evolution and epidemiology, whole genome amplification (WGA) and Next Generation Sequencing (NGS) were performed on 9516 isolates. 7586 isolates with a high quality were further analyzed for the mutation frequency and spectrum. Lastly, we evaluated the utility of the mRT-PCR detection pattern among 26 reinfected patients with repeat positive testing three months after testing negative from the initial infection. Our results show a continuation of the genetic divergence in viral genomes. Furthermore, our results indicate that independent mutations in the primer and probe regions of the nucleocapsid gene amplicon and envelope gene amplicon accumulate over time. Some of these mutations correlate with the changes of detection pattern of viral targets of mRT-PCR. Our data highlight the significance of a continuous genetic divergence on a gene amplification-based assay, the value of the mRT-PCR detection pattern for complementing the clinical diagnosis of reinfection, and the potential for WGA and NGS to identify mutation hotspots throughout the entire viral genome to optimize the design of the PCR-based gene amplification assay. Full article
(This article belongs to the Special Issue Molecular Genetics of Assay Technology)
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