Detekcija polimorfizama jednog nukleotida (SNP-a) u HER2, MUC1, ESR1 i BRCA1 gena povezanih s tumorom mliječne žlijezde kuja

Worldwide, canine mammary cancer (CMC) is the most frequent type of neoplasia in female dogs, and it is three times more frequent in dogs than in humans. In Colombia, CMC is the second most frequent type of cancer, after skin neoplasia. Genetics is one of the most important factors involved in any type of cancer, and the genetic basis of this disease is reflected through line breeding due to changes in allelic frequencies that are traceable using molecular markers. This study aimed to detect single nucleotide polymorphisms (SNPs) associated with CMC in blood samples collected from collected from healthy and CMC female dogs at Diego Villegas Toro Veterinary Hospital of Universidad de Caldas (Manizales, Colombia). We designed primers using Primer-BLAST and Primer3, and gene fragments from HER2, MUC1, ESR1, and BRCA1 were amplified to identify SNPs through genome mapping using the UCSC Genome Institute genome browser. We used the genome of Canis lupus familaris Boxer breed [GCF_000002285.3, (CanFam 3.1)] as a reference to compare the gene fragments and SNPs. We associated SNPs with the CMC and control groups by testing odds ratios (OR) through Fisher’s exact tests to determine an association or risk for CMC. We detected two SNPs for ESR1, three for MUC1, six for HER2, and one for BRCA1. MUC1 was the only gene to display an SNP in an exonic region that resulted in an amino acid substitution (Pro>Thr). No significant differences based on the OR were found, though the majority of SNPs, with the exception of four, were found in females with CMC. We report a novel molecular marker for HER2 that amplifies exons 25–26 and introns 24-25, and highlight the importance of conducting further studies on MUC1 and elucidating the role of introns and splicing in candidate genes associated with CMC.Diljem svijeta, tumor mliječne žlijezde kuja (CMC) najčešća je skupina neoplazija kuja te je tri puta učestalija u pasa nego u ljudi. U Kolumbiji, CMC je bio druga najčešća vrsta tumora, nakon neoplazija na koži. Nadalje, genetika je jedan od najvažnijih čimbenika uključenih u bilo koju vrstu tumora, a genetska baza ove bolesti održava se kroz linijski uzgoj uslijed promjena alelnih frekvencija, koje se mogu pratiti preko molekularnih markera. Ova studija imala je za cilj detektirati polimorfizme jednog nukleotida (SNP-e) povezane s CMC-om u uzorcima krvi prikupljenih od kuja s CMC-om i zdravih kuja u veterinarskoj bolnici Diego Villegas Toro Sveučilišta Caldas (Manizales, Kolumbija). Dizajnirali smo početnice uporabom Primer-BLAST i Primer3 te su fragmenti gena HER2, MUC1, ESR1 i BRCA1 pojačani za identifikaciju SNP-a preko mapiranja genoma uporabom preglednika genoma Instituta za genom Sveučilišta Santa Cruz u Kaliforniji (UCSC). Rabili smo genom Canis lupus familaris pasmine bokser [GCF_000002285.3, (CanFam 3.1)] kao referencu za usporedbu fragmenata gena i SNP-a. Povezali smo SNP-e s CMC-om i kontrolnim skupinama testiranjem omjera izgleda (OR) pomoću Fisherovih egzaktnih testova za određivanje povezanosti ili rizika od CMC-a. Detektirali smo dva SNP-a za ESR1, tri za MUC1, šest za HER2 i jedan za BRCA1. MUC1 je bio jedini gen koji je pokazao SNP u regiji egzona što je rezultiralo supstitucijom aminokiseline (Pro>Thr). Nismo pronašli značajne razlike na temelju OR-a, premda je većina SNP-a, izuzev četiri, pronađena u kuja s CMC-om. Prijavljujemo novi molekularni marker za HER2 koji pojačava egzone 25 - 26 i introne 24 - 25 te naglašavamo važnost provođenja dodatnih studija na MUC1, kao i pojašnjenja uloge introna i izrezivanja u gena kandidata poveznih s CMC-om

Procjena gama-aktina, beta-aktina, gliceraldehid-3-fosfat dehidrogenaze i 18S kao referentnih gena za qRT-PCR uporabom uzoraka krvi u istraživanju mliječnih žlijezda kujica

Mammary tumours are the most frequent group of neoplasia in female dogs. Tumorigenesis is associated with gene expression changes in a wide variety of genes. For this reason, real-time quantitative PCR (qRT-PCR) is used in routine diagnostic procedures in clinical practice due to its the specificity, sensitivity, simplicity, and high performance. qRT-PCR is also widely used to measure the expression of target genes compared to reference genes in several tissues. We collected blood samples from healthy female dogs and females with canine mammary cancer in Manizales, Colombia between June 2018 and January 2019, and mRNA was isolated from each sample for cDNA synthesis. qRT-PCR-based expression assays were performed using primers designed for gamma-actin, beta-actin, GAPDH, and 18S genes. We calculated the amplification efficiency, specificity, and stability using geNorm, NormFinder, BestKeeper, and the ΔCt comparative method. We obtained linear regressions to verify constant gene expression and conducted an ANOVA to detect expression differences regarding Ct values and healthy vs. ill conditions. We found stability for primers 18S-1, GAPDH-1, GAPDH-NM, and Gamma-actin-1 (in increasing order). Furthermore, these genes showed constant expression levels in patients (R2>0.80). We report novel primers for gamma-actin and GAPDH, which proved to be efficient endogenous control genes for qRT-PCR applications in blood tissue. These primers are useful for gene expression research in canine mammary cancer.Tumori mliječnih žlijezda najčešća su skupina neoplazija u kujica. Tumorogeneza je povezana s promjenama u ekspresiji gena u širokom rasponu gena. Iz tog razloga se rabi kvantitativna lančana reakcija polimerazom u stvarnom vremenu (qRT-PCR) u rutinskim dijagnostičkim postupcima u kliničkoj praksi, uslijed specifičnosti, osjetljivosti, jednostavnosti i visoke učinkovitosti ove tehnike. qRT-PCR se široko rabi i za mjerenje ekspresije ciljanih gena u usporedbi s referentnim genima u više vrsta tkiva. Prikupili smo uzorke krvi zdravih kujica i kujica s tumorom mliječnih žlijezda u Manizalesu, Kolumbiji, od lipnja 2018. do siječnja 2019. godine. Izolirali smo mRNK iz svakog uzorka za cDNK sintezu. Pokusi ekspresije na bazi qRT-PCR obavljeni su uporabom primera dizajniranih za gama-aktin, beta-aktin, gliceraldehid- 3-fosfat dehidrogenazu (GAPDH) i 18S gene. Izračunali smo pojačanu učinkovitost, specifičnost i stabilnost uporabom geNorm, NormFinder, BestKeeper i ΔCt komparativne metode. Dobili smo linearne regresije za potvrđivanje stalne ekspresije gena i proveli smo analizu varijance (ANOVA) za detekciju razlika u ekspresiji s obzirom na Ct vrijednosti te zdrava u usporedbi s bolesnim stanjima. Otkrili smo i stabilnost za primere 18S-1, GAPDH-1, GAPDH-NM i Gamma-actin-1 (rastućim redoslijedom). Nadalje, ovi geni su pokazali konstantne razine ekspresije u pacijenata (R2>0,80). Izvještavamo o novim primerima za gama-aktin i GAPDH, koji su se pokazali učinkovitim endogenim kontrolnim genima za qRT-PCR primjene u krvnom tkivu. Ti primeri su korisni za istraživanje ekspresije gena u tumora psećih mliječnih žlijezda

“In Silico” Characterization of 3-Phytase A And 3-Phytase B from Aspergillus niger

Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of −0,304 and −0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H59 and H63 act as nucleophiles and that D339 and D319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions.PubMedScopu

Kinetic constants complete results.

Enzyme kinetics of pure recombinant POXA 1B was characterized using ABTS as a substrate. Maximum velocity values (V_max), substrate affinity or Michaelis constant (Km), catalytic constant or turnover number (K_cat), and kinetic efficiency (specificity constant K_cat/Km) also were found

Covid-19: consecuencias y desafíos en la economía colombiana. Una mirada desde las universidades

Este libro reúne diferentes hallazgos, perspectivas y efectos ante un fenómeno que, más de un año después, todavía representa un reto científico, médico y social para todos. Igualmente, esta obra representa el objetivo de la Red Investigadores de Economía: aunar esfuerzos para encontrar respuestas y para fortalecer la investigación en el país, aumentar la difusión de trabajos de calidad y propiciar el encuentro entre académicos, universidades y el Banco de la República. Las investigaciones expuestas en este libro pasaron por un proceso de selección por parte del comité científico, asegurando que hubiese una pluralidad de miradas y de instituciones educativas, además del Banco, donde se relacionaran los efectos de la pandemia y la actividad económica en el país, las consecuencias sociales y regionales. El texto está dividido en cuatro partes. En la primera se hace un análisis macroeconómico de los efectos de la pandemia; para ello se examinan los efectos de la emergencia sanitaria a nivel nacional y regional mediante modelos macroeconómicos que permiten obtener respuestas ante preguntas muy relevantes. La segunda sección trata sobre el impacto en el mercado laboral, el efecto del Covid-19 en la distribución del ingreso y el efecto de corto plazo en el mercado urbano. La tercera parte aborda los efectos de la pandemia en los agentes económicos y en otros mercados. Ello incluye la exposición del empleo al Covid-19, la vulnerabilidad económica de los hogares en el país y su respuesta en el consumo, patrones de actividad laboral y salud mental, efectos en la educación, inseguridad alimentaria de la población migrante, entre otros. Por último, el cuarto segmento hace un énfasis especial en los efectos diferenciales entre las regiones del país y la heterogeneidad de dicho impacto; para ello se analizan temas de informalidad, vulnerabilidad, fuerza de trabajo disponible, entre otros, en distintas regiones del país

New insights into the genetic etiology of Alzheimer’s disease and related dementias

Characterization of the genetic landscape of Alzheimer’s disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/‘proxy’ AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele