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  • Open access
  • 9 Reads
The glyphosate target enzyme 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) contains several EPSPS-associated domains in fungi

The 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. Glyphosate is a multi-spectrum herbicide largely utilized to control weeds, which targets the EPSPS enzyme and inhibits the production of these essential amino acids. In most plants and prokaryotes, the EPSPS protein is constituted by a single domain, whereas in fungi contains the EPSPS and several EPSPS-associated domains. Here, we perform a comprehensive analysis of 391 EPSPS proteins of fungi gathered from the Pfam database. We analyze our dataset with a bipartite graph (Cytoscape) and dollon parsimony (Count) to determine the distribution and the evolution of the 22 EPSPS-associated domains in fungi. The EPSPS-associated domains can be classified into four partially overlapping groups: shikimate pathway, other enzymes, gene expression and structural proteins. The most frequent EPSPS-associated domains are shikimate kinase, 3-dehydroquinate synthase, 3-dehydroquinate dehydratase, shikimate dehydrogenase substrate binding domain and shikimate DH. These domains are present in 56% of the proteins analyzed and 34% of proteins contain shikimate DH at the end of sequence. The most common domain architecture of the EPSPS enzyme in fungi contains 5-6 domains. A parsimony analysis suggests that a 6-domain protein is the ancestral form of the EPSPS in fungi and that alternative architectures are due to domain losses (also some gains) and duplications. The results of this study will be useful to determine the impact of glyphosate in fungi and to quantify its putative differential effects on alternative domain architectures.

  • Open access
  • 12 Reads
OMICs role in Heridatarian prostate cancer.
Sergio Cuenca-Lopez, Patricia 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, Maria Jesus Alvarez-Cubero

Prostate cancer (PC) is one of the most prevalent tumors in the world, however, the hereditary (Hereditary PC; HPC) form is a rare pathology (ORPHA: 1331), without exceeding 6%. Despite its very low incidence, a family history of PC in a first-degree relative multiplies the risk to suffer from PC approximately twofold. Therefore, the search for genetic variables associated with detection, monitoring and treatment is unavoidable.

Although the study of the genome and its expression have provided us with valuable information, it has not been able to describe biomarkers that help us resolve the appearance and evolution of the tumor. With this study, we make a deep analysis in data of exome and miRNAs analyzed by Next-generation sequencing (NGS) analysis in search of new biomarkers as variants of aggressiveness of this tumor. We performed this analysis in a family of a high incidence of PC.

Our data revealed that some genes such as HIBCH and DPP4 are just 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.

  • Open access
  • 9 Reads
Determination of expression signature and proportion of mtDNA in plasma fractions in patients with Renal Cell Carcinoma.
ELENA ARANCE, AlMUDENA SABIO BONILLA, Mª Yarmila Gª Iglesias, ROCÍO LOPEZ CINTAS, SARA MARTÍN ESTEBAN, GINESA LÓPEZ TORRES, CORTÉS VALVERDE, LUIS MARTÍNEZ GONZÁLEZ

Renal Cell Carcinoma (RCC) is the third most common urologic malignancy,remains 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 mitocondrial DNA (mtDNA) copy number alteration in peripheral blood and risk of developing RCC, we conducted a case-control study 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 the copy numbers of nuclear regions and mitochondrial genes (in hypervariable and conserved regions) in each plasma fraction.

  • Open access
  • 16 Reads
Chromosome-level genome assemblies expanded capabilities of conservation biology
Azamat Totickov, Andrei Tomarovsky, Lorena Derezanin, Olga Dudchenko, Erez Lieberman-Aiden, Klaus Koepfli, Sergei Kliver

Conservation biology aims to keep and restore biodiversity on genetic, species and ecosystem levels, prevent species extinction and protect their habitats. One of the important aspects of a conservation is genetic diversity assessed within endangered populations or species. Reduction in sequencing costs facilitated estimation of the genetic diversity in multiple individuals on the whole genome level even with a very limited budget. However, whole genome approach requires generation of reference genome assembly of suitable quality first. Current trend is to use chromosome-level assemblies offering a set of useful advantages.

We compared genetic diversity in endangered species (cheetah, sea otter and others) for both old highly fragmented and recently generated chromosome-level assemblies. New contiguous assemblies allowed to calculate more precisely broadly used indicators of genetic diversity such as length and number of ROHs (runs of homozygosity) and visualize regions of low heterozygosity in the genome. In addition, we located known microsatellite loci previously used in STR-fingerprinting on chromosomes to understand diversity of what regions were estimated in previous diversity studies.

Chromosome level genome assemblies provide better estimates of genetic diversity, better understanding for results of previous studies and new possibilities for visualization of results. Another new opportunity is the simple and cheap procedure for development of comprehensive STR-arrays or microarrays with known localization of each locus to use it for diversity estimates in multiple (hundreds and thousands) individuals and in low quality samples.

  • Open access
  • 4 Reads
Influence of a major mountainous landscape barrier (Mount Cameroon) on the spread of metabolic (GSTe2) and target-site (Rdl) resistance alleles in the African malaria vector Anopheles funestus
Nathalie Amvongo-Adjia, Jacob M. Riveron, Flobert Njiokou, Samuel Wanji, Charles S. Wondji

Increased levels of insecticide resistance in major malaria vectors such as Anopheles funestus is threatening the continued effectiveness of insecticide-based control programmes. Understanding the ecological factors impacting the spread of resistance alleles in necessary to design suitable resistance management strategies. Here we examined the influence of the highest mountain in West Africa (4,100 meters elevation) on the spread of both metabolic and target-site resistance alleles in An. funestus sensu stricto (s.s) populations. High frequencies of both 296S-Rdl (49% - 90%) and 119F-GSTe2 (67% - 81%) resistance alleles were observed An. funestus s.s. populations across Mount Cameroon. Genetic variability parameters suggested that these resistance markers underwent high levels of polymorphisms with 16 to 12 haplotypes identified respectively. However, neutrality tests were not consistent with recent expansion or resistance genes being under selection. Analysis of the maximum likelihood phylogenetic trees of haplotypes indicated that populations primarily clustered according to resistance patterns, whereas the neighbour joining trees of distances suggested that landscape variations could potentially be associated with the risk of presence and insecticide resistance for malaria vectors. These raise the need for further investigations covering different bioecological zones for a detailed report on current status of insecticide resistance in malaria vectors.

  • Open access
  • 158 Reads
Genetic analysis algorithm for the study of patients with Multiple Congenital Anomalies and isolated Congenital Heart Disease
Marisol Delea, Lucia Massara, Lucia Espeche, María Bidondo, Jaen Oliveri, Paloma Brun, Mónica Fabbro, Micaela Galain, Cecilia Fernandez, Melisa Taboas, Carlos Bruque, Emilio Kolomenski, Agustin Izquierdo, Ariel Berenstein, Pablo Barbero, Viviana Cosentino, Celeste Martinoli, Mariana Vilas, Mónica Rittler, Rodrigo Mendez, Lilian Furforo, Rosa Liascovich, Boris Groisman, Sandra Rozental, Liliana Dain

Introduction: Congenital anomalies (CA) affects 3-5 % of newborns, representing the second leading cause of infant mortality in Argentina. Newborns presenting multiple congenital anomalies (MCA) have a prevalence of 2,26/1000 births while congenital heart diseases (CHD) are the most frequent CA, with a prevalence of 4,06/1000 births. The goal of this work was to identify the genetic causes in patients with MCA and isolated CHD (iCHD) from Argentina.

Material and Methods: We recruited 368 patients (174 MCA and 194 iCHD) born between June 2015 and August 2019 from 13 public hospitals participating in the National Network of Congenital Anomalies of Argentina (RENAC). DNA from peripheral blood was obtained from all patients while karyotyping was performed for those patients presenting with MCA. Samples from patients presenting with conotruncal CHD (cCHD) or DiGeorge phenotype (n=137) were analyzed by MLPA. Ninety-two MCA samples were selected for array-CGH analysis and 18 for targeted or exome next generation sequencing (NGS).

Results: A total of 276 patients were studied by at least one technique. Cytogenetic abnormalities were present in 16 MCA patients, while 16 had clinically relevant imbalances detected by array-CGH. Among cCHD patients, 26 presented 22q11 deletions or duplications and one a TBX1 gene deletion. After NGS analysis, 12 patients presented clinically relevant nucleotide variants, 5 of them novels in KAT6B, SHH, MYH11, MYH7 and EP300 genes.

Conclusions: Using this algorithm that combines a technical and clinical strategy, 28% of the patients analyzed were diagnosed.

  • Open access
  • 117 Reads
A new nomenclature for the chromosome-specific probes of white hawk (Leucopternis albicollis)

The white hawk (Leucopternis albicollis) is a diurnal bird of prey (Accipriformes, Accipitridae). This species has a karyotype with a low diploid number (2n=66), however, the comparison with Gallus gallus (2n=78) and the putative avian ancestral karyotype indicates the occurrence of extensive chromosome fissions in the ancestral macrochromosomes. Hence, it is likely that fusions involving microchromosomes underly the decrease in the diploid number in the white hawk. Considering that the ancestral macrochromosomes are fissioned, the chromosome-specific probes made for each of the chromosome segments resulting from the fissions allow the detection of intrachromosomal rearrangements in species with conserved karyotype. Using this strategy, whole chromosome probes from the white hawk have been exploited as a cytogenetic tool for phylogenetic studies in birds since 2010. However, some problems were detected with this first set of probes. Here, we have constructed new probes of the white hawk in order to improve the previous set. Additionally, we have employed bacterial artificial chromosome (BAC) hybridization for chromosome 17-28 to confirm the expected microchromosome fusions. Our results show that microchromosomes 17-28 were involved in fusion events with macrochromosomes. In addition, a new nomenclature has been proposed for the new set of probes and some previous inaccuracies corrected. As an example, ancestral chromosome GGA1 is now shown to have homology to seven white hawk chromosomes rather than five, as homologies to two small chromosomes were missed. In conclusion, the new complete set of chromosome probes will improve the value of this tool for avian comparative cytogenetics.

  • Open access
  • 13 Reads
Study of some candidate genes for treatment in prostate cancer.
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, Luis Javier Martinez-Gonzalez

Prostate cancer (PC) is the most frequent tumour in men in Spain and the second worldwide. The activation of the cytosolic androgen receptor (AR) by the androgenic signalling pathway is essential for carcinogenesis and tumour development. 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)]. Thereby, candidate genetic positions involved in pathways implicated in the development of resistance against ADT were selected. The search of single nucleotide polymorphisms (SNPs) was carried out to establish a possible connection between the genotype of each patient and the response to treatment.

The statistical analysis revealed a certain tendency to resistance in A/G carriers in rs1004446 (IGF2), although a relationship with statistical significance was not confirmed. Furthermore, a significant statistical relation between aggressive phenotypes was confirmed in SNP rs10877012 (CYP27B1, p=0.013). These results open up a wide range of possibilities for the future.

  • Open access
  • 21 Reads
First draft genome sequence of Salmonella enterica subsp. enterica serovar enteritidis isolated from the chicken meat in Russia
Alexey Rakov, Anatoly Yakovlev, Viacheslav Sinkov

Salmonella enterica subsp. enterica serovar Enteritidis is one of the most common zoonotic pathogens. Specifically, Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) represented 61.2% of all reported serovars of confirmed human cases in 2017 in the European Union and about 70% of all reported serovars of confirmed human cases in 1988-2018 in Russia. Chickens known to be the main reservoir for S. Enteritidis (EFSA and ECDC 2018). However, there is a lack of information on full-genome sequences of S. Enteritidis, isolated in Russia. 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 4,565 coding genes, 4 rRNAs, 62 tRNAs, and 14 noncoding RNAs were predicted. To our knowledge, this is the first publically deposited annotated genome of this serovar isolated from chicken in Russia. The Salmonella Enteritidis S-25048 genome is suitable for use as a reference strain of Salmonella Enteritidis isolated in Russia.

  • Open access
  • 11 Reads
NGS screening for identification of novel pexophagy-related mutant in Arabidopsis thaliana

Nowadays, there is a strong interest to study autophagy mechanisms in plants, as it is one of the main cellular degradation and recycling pathways involved in the adaptation of organisms to stress conditions. 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. Although most of peup mutants are identified as the mutants defective in autophagy-related (ATG) genes, the causative genes of several mutants are still staying undiscovered.

The aim of this study is 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.

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