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1558 KiB

Open AccessProceeding Paper

Revising the Chromosome-Specific Probes of White Hawk (Leucopternis albicollis)

by Ivanete Furo, Rafael Kretschmer, Jorge Pereira, Darren Griffin, Rebecca O’Connor, Patricia C. M. O’Brien, Malcolm Ferguson-Smith and Edivaldo H. C. de Oliveira

Proceedings 2021, 76(1), 1; https://doi.org/10.3390/IECGE-07152 - 2 Nov 2020

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Abstract

Leucopternis albicollis is a diurnal bird of prey with extensive karyotype reorganization. Chromosome-specific probes from this species have been used successfully to detect intrachromosomal rearrangements in different species of bird since 2010. However, some gaps were detected in this first set of probes. [...] Read more.

Leucopternis albicollis is a diurnal bird of prey with extensive karyotype reorganization. Chromosome-specific probes from this species have been used successfully to detect intrachromosomal rearrangements in different species of bird since 2010. However, some gaps were detected in this first set of probes. Here, we have obtained a new set of whole chromosome probes in order to improve the previous one; also, we have performed experiments using bacterial artificial chromosome (BAC) from chicken microchromosomes. Our results demonstrated that the microchromosomes were involved in fusion events. In addition, a new nomenclature has been proposed for the new set of probes and some inaccurate data were corrected. Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

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177 KiB

Open AccessExtended Abstract

First Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis Isolated from the Chicken Meat in Russia

by Alexey V. Rakov, Anatoly A. Yakovlev and Viacheslav V. Sinkov

Proceedings 2021, 76(1), 2; https://doi.org/10.3390/IECGE-07154 - 2 Nov 2020

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Abstract

Salmonella enterica subsp. enterica serovar Enteritidis is one of the most common zoonotic pathogens. We report here the genome sequence of Salmonella enterica subsp. enterica serovar Enteritidis S-25048 isolated from chicken (Gallus gallus domesticus) meat in Artyom, Russia. The assembled genome [...] Read more.

Salmonella enterica subsp. enterica serovar Enteritidis is one of the most common zoonotic pathogens. We report here the genome sequence of Salmonella enterica subsp. enterica serovar Enteritidis S-25048 isolated from chicken (Gallus gallus domesticus) meat in Artyom, Russia. The assembled genome size was 4,695,145 bp. A total of 4565 coding genes, four rRNAs, 62 tRNAs, and 14 noncoding RNAs were predicted. To our knowledge, this is the first publically deposited annotated genome of this serovar isolated in Russia. The Salmonella Enteritidis S-25048 genome is suitable for use as a reference strain of Salmonella Enteritidis isolated in Russia. Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

214 KiB

Open AccessProceeding Paper

Study of Some Candidate Genes for Treatment in Prostate Cancer

by Veronica Arenas-Rodriguez, Patricia Maria Porras-Quesada, Victor Sanchez-Conde, Ignacio Puche-Sanz, Fernando Vazquez-Alonso, Sergio Cuenca-Lopez, Blanca Cano-Gutierrez, Sara Martin-Esteban, Maria Jesus Alvarez-Cubero and Luis Javier Martinez-Gonzalez

Proceedings 2021, 76(1), 3; https://doi.org/10.3390/IECGE-07153 - 2 Nov 2020

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Abstract

The androgenic signalling pathway is essential for carcinogenesis and tumour development in prostate cancer (PC). The importance of that pathway makes it the main target of treatments against PC, among which androgen deprivation therapy (ADT) stands out. The heterogeneity of the response against [...] Read more.

The androgenic signalling pathway is essential for carcinogenesis and tumour development in prostate cancer (PC). The importance of that pathway makes it the main target of treatments against PC, among which androgen deprivation therapy (ADT) stands out. The heterogeneity of the response against the same treatment shows the importance of the search for molecular biomarkers, which enable the prediction of the response to the therapy in each case. This work focuses on the characterization of the response to treatment in several patients of PC through the analysis of different genetic variants (rs10877012 (CYP27B1); rs3768490 (GSTM5); rs1004446 (IGF2)). The statistical analysis revealed a certain tendency to resistance in A/G genotype carriers in rs1004446 (IGF2). Furthermore, a significant statistical relation between aggressive phenotypes was confirmed in single nucleotide polymorphism (SNP) rs10877012 (CYP27B1, p = 0.013). Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

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445 KiB

Open AccessProceeding Paper

Cytomorphological, Molecular Diagnosis and Evaluation of Insertion of the LINE-1 Element in the C-MYC Gene in Canine Transmissible Venereal Tumor: Applicability in Veterinary Clinical Routine

by Faro Thamirys Aline Silva, Ferreira Wallax Augusto Silva and De Oliveira Edivaldo Herculano Correa

Proceedings 2021, 76(1), 4; https://doi.org/10.3390/IECGE-07156 - 2 Nov 2020

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Abstract

Canine transmissible venereal tumor (CTVT) is the oldest known cancer in the world. Cytomorphologically, the cases are classified into three types. Previous studies have shown that the insertion of the transposable element LINE-1 in the MYC gene has diagnostic importance. Therefore, we characterized [...] Read more.

Canine transmissible venereal tumor (CTVT) is the oldest known cancer in the world. Cytomorphologically, the cases are classified into three types. Previous studies have shown that the insertion of the transposable element LINE-1 in the MYC gene has diagnostic importance. Therefore, we characterized this insertion in samples of the three different cytomorphological types of CTVT, in order to verify whether there were any differences concerning the presence or location of the insertion and the size of the fragment. Our results showed that LINE-1 was inserted in all the samples analyzed, in the same position and presenting the same size (400 bp). We conclude that even though it is important for the oncogenesis process, this insertion has no influence on the cytomorphological type and the observed clinical differences. Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

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309 KiB

Open AccessProceeding Paper

OMICs Role in Hereditarian Prostate Cancer

by Sergio Cuenca-Lopez, Patricia Maria Porras-Quesada, Fernando Vazquez-Alonso, Victor Sanchez-Conde, Maria del Pilar Gomez-Matas, Adoracion Aneas-Alaminos, Veronica Arenas-Rodriguez, Blanca Cano-Gutierrez, Luis Javier Martinez-Gonzalez and Maria Jesus Alvarez-Cubero

Proceedings 2021, 76(1), 5; https://doi.org/10.3390/IECGE-07147 - 2 Nov 2020

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Abstract

Prostate cancer (PC) is one of the most prevalent tumours in the world, however, the hereditary (Hereditary PC; HPC) form is a rare pathology, that does not exceed 6%. Despite its very low incidence, a family history of PC in a first-degree relative [...] Read more.

Prostate cancer (PC) is one of the most prevalent tumours in the world, however, the hereditary (Hereditary PC; HPC) form is a rare pathology, that does not exceed 6%. Despite its very low incidence, a family history of PC in a first-degree relative multiplies the risk of suffering from PC by approximately two-fold. Therefore, the search for genetic variables associated with the detection, monitoring and treatment of the condition is paramount. In this study, we conduct deep screening of exomes by next-generation sequencing (NGS) analysis in search of new biomarkers. We performed this analysis in a family with a high incidence of PC. Our data reveal that variants in some genes, such as HIBCH and DPP4, are present in all HPC patients. Moreover, high-risk patients have unique additional variants, such as FANK1, TUBA3FP and ALDH3B2. These results provide a new set of promising biomarkers in HCP. Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

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977 KiB

Open AccessProceeding Paper

The Glyphosate Target Enzyme 5-Enolpyruvyl Shikimate 3-Phosphate Synthase (EPSPS) Contains Several EPSPS-Associated Domains in Fungi

by Tuomas Tall and Pere Puigbò

Proceedings 2021, 76(1), 6; https://doi.org/10.3390/IECGE-07146 - 2 Nov 2020

Cited by 3 | Viewed by 1955

Abstract

5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the central enzyme of the shikimate pathway to synthesize three aromatic amino acids in fungi, plants and prokaryotes. This enzyme is the target of the herbicide glyphosate. In most plants and prokaryotes, the EPSPS protein is constituted by [...] Read more.

5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the central enzyme of the shikimate pathway to synthesize three aromatic amino acids in fungi, plants and prokaryotes. This enzyme is the target of the herbicide glyphosate. In most plants and prokaryotes, the EPSPS protein is constituted by a single domain, whereas in fungi, it contains several EPSPS-associated domains. Here, we perform a comprehensive analysis of 390 EPSPS proteins of fungi to determine the distribution and the evolution of the EPSPS-associated domains. The results of this study will be useful to determine the potential differential impact of glyphosate on alternative domain architectures in fungi. Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

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371 KiB

Open AccessProceeding Paper

NGS Screening for Identification of Novel Pexophagy-Related Mutation in Arabidopsis thaliana

by Katarzyna Sieńko, Kacper Żukowski, Kenji Yamada and Shino Goto-Yamada

Proceedings 2021, 76(1), 7; https://doi.org/10.3390/IECGE-07155 - 2 Nov 2020

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Abstract

Peroxisomes are the type of organelles in eukaryotic cells that are involved in different biochemical pathways depending on the type of cell. We have isolated a number of peroxisome unusual positioning (peup) mutants, which display the accumulation of abnormal peroxisomes, and [...] Read more.

Peroxisomes are the type of organelles in eukaryotic cells that are involved in different biochemical pathways depending on the type of cell. We have isolated a number of peroxisome unusual positioning (peup) mutants, which display the accumulation of abnormal peroxisomes, and demonstrated that autophagy is involved in removing damaged organelles. These peup mutants also show defects of other autophagy-related processes, such as the recovery from dark-senescence, and also failed to induce vacuole-related vesicle formations during microautophagy under nutrient deprivations. The aim of this study was to identify the causative gene of the peup33 mutant using next-generation sequencing (NGS) as a tool. Identification of mutations with NGS will allow us to save time compared to the conventional mapping method. Here, we present the workflow of the experiment, the procedure of bioinformatic analysis and the software applied to the sequence data produced by NGS. Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

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252 KiB

Open AccessProceeding Paper

Genetic Analysis Algorithm for the Study of Patients with Multiple Congenital Anomalies and Isolated Congenital Heart Disease

by Marisol Delea, Lucía S. Massara, Lucía D. Espeche, María P. Bidondo, Pablo Barbero, Jaen Oliveri, Paloma L. Brun, Mónica Fabro, Micaela Galain, Cecilia S. Fernández, Melisa Taboas, Carlos D. Bruque, Emilio Kolomenski, Agustín Izquierdo, Ariel J. Berenstein, Viviana Cosentino, María C. Martinoli, Mariana Vilas, Mónica Rittler, Rodrigo Mendez, Lilian Furforo, Rosa Liascovich, Boris Groisman, Sandra Rozental, Liliana B. Dain and the PID ACM-CC Group Show full author list Hide full author list

Proceedings 2021, 76(1), 8; https://doi.org/10.3390/IECGE-07151 - 2 Nov 2020

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Abstract

In this work, we aim to identify the genetic causes of pathogenesis in Argentinean patients with multiple congenital anomalies (MCA) and isolated Congenital Heart Disease (iCHD). We recruited 174 MCA and 194 iCHD patients from 15 public hospitals. Karyotyping was performed for MCA [...] Read more.

In this work, we aim to identify the genetic causes of pathogenesis in Argentinean patients with multiple congenital anomalies (MCA) and isolated Congenital Heart Disease (iCHD). We recruited 174 MCA and 194 iCHD patients from 15 public hospitals. Karyotyping was performed for MCA patients, and MLPA for conotruncal CHD or suspected 2q11 Deletion Syndrome (22q11DS). Selected samples were analyzed by array-CGH (Comparative genomic hybridization) (n = 89) and/or Next-Generation Sequencing (NGS) (n = 18). We successfully analyzed 252/368 patients: 14 had cytogenetic abnormalities, 27 had imbalances in 22q11, and 16 had other clinically relevant copy number variations (CNVs). NGS revealed 12 relevant nucleotide variants (five novels). Combining molecular, clinical and genetic evaluations, the diagnostic yield was 26.2%. Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

454 KiB

Open AccessProceeding Paper

Determination of Expression Signature and Proportion of mtDNA in Plasma Fractions in Patients with Renal Cell Carcinoma

by Elena Arance-Criado, Fernando Vázquez-Alonso, Mª Yarmila García-Iglesias, Rocío López-Cintas, Sara Martín-Esteban, Ginesa López-Torres, Ana Isabel Cortés-Valverde, María Jesús Alvarez-Cubero and Luis Javier Martínez-Gonzalez

Proceedings 2021, 76(1), 9; https://doi.org/10.3390/IECGE-07148 - 2 Nov 2020

Cited by 1 | Viewed by 1217

Abstract

Renal Cell Carcinoma (RCC) is the third most common urologic malignancy, remaining one of the most lethal urological malignancies, preferably in developed countries. The incidence and mortality rates differ significantly according to sex, race, age and external factors such as smoking, obesity and [...] Read more.

Renal Cell Carcinoma (RCC) is the third most common urologic malignancy, remaining one of the most lethal urological malignancies, preferably in developed countries. The incidence and mortality rates differ significantly according to sex, race, age and external factors such as smoking, obesity and hypertension increasing RCC risk. The use of novel predictive biomarkers is currently being increased as these improve the diagnosis, progression and prognosis of RCC. Since recent studies have demonstrated a promising association between mitochondrial DNA (mtDNA) copy number alteration in peripheral blood and the risk of developing RCC, we conducted a case-control study into a cohort of 15 controls and 13 patients to determine exosomes mtDNA content in plasma fractions as a potential novel non-invasive biomarker in liquid biopsy in order to monitor the RCC status in patients. In this way, plasma fractions highly purified in exosomes were obtained from blood samples from controls and RCC cases, and relative mtDNA content was measured by quantitative real-time polymerase chain reaction (qPCR). Our results show fragment size distribution profile and we observed that in phase F; with a higher content of exosomal mtDNA; p value shows statistically significant differences in mitochondrial genes HV long and CYB long. Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

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1877 KiB

Open AccessProceeding Paper

Chromosome-Level Genome Assemblies: Expanded Capabilities for Conservation Biology Research

by Azamat Totikov, Andrey Tomarovsky, Lorena Derezanin, Olga Dudchenko, Erez Lieberman-Aiden, Klaus Koepfli and Sergei Kliver

Proceedings 2021, 76(1), 10; https://doi.org/10.3390/IECGE-07149 - 2 Nov 2020

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Abstract

Genome assemblies are becoming increasingly important for understanding genetic diversity in threatened species. However, due to limited budgets in the area of conservation biology, genome assemblies, when available, tend to be highly fragmented with tens of thousands of scaffolds. The recent advent of [...] Read more.

Genome assemblies are becoming increasingly important for understanding genetic diversity in threatened species. However, due to limited budgets in the area of conservation biology, genome assemblies, when available, tend to be highly fragmented with tens of thousands of scaffolds. The recent advent of high throughput chromosome conformation capture (Hi-C) makes it possible to generate more contiguous assemblies containing scaffolds that are length of entire chromosomes. Such assemblies greatly facilitate analyses and visualization of genome-wide features. We compared genetic diversity in seven threatened species that had both draft genome assemblies and newer chromosome-level assemblies available. Chromosome-level assemblies allowed better estimation of genetic diversity, localization, and, especially, visualization of low heterozygosity regions in the genomes. Full article

(This article belongs to the Proceedings of The 1st International Electronic Conference on Genes: Theoretical and Applied Genomics)

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