Immunotherapy for microsatellite-instability-high advanced colorectal cancer / 中华胃肠外科杂志

Microsatellite instability-high (MSI-H) colorectal cancer accounts for approximately 10%-15% of all colorectal cancer patients, while in metastatic diseases the MSI-H population accounts for only 5% of patients. Previous studies have shown that early-stage MSI-H colorectal cancer patients have a good prognosis, but those with advanced disease have a poor prognosis and are not sensitive to chemotherapy. The advent of PD-1 antibodies has significantly improved the prognosis and changed treatment landscape in this population, not only achieving good outcomes in late-line therapy, but also significantly outperforming traditional chemotherapy combined with targeted therapy in first-line therapy. How to overcome primary and secondary drug resistance is a key issue in improving the outcome of MSI-H metastatic colorectal cancer, and commonly used approaches include changing chemotherapy regimens, combining with other immunotherapies, combining with anti-angiogenesis, and local treatments (surgery, radiotherapy, or interventional therapy). It is worth noting that immunotherapy has certain lifelong or even lethal toxicity, and the indications for neoadjuvant immunotherapy must be evaluated with caution. Neoadjuvant immunotherapy in MSI-H advantaged population can achieve high rates of pathological complete remission (pCR) and clinical complete remission (cCR). Therefore, for MSI-H patients with a strong intention to preserve anal sphincter and a strict evaluation of cCR after neoadjuvant immunotherapy, the Watch-and-Wait strategy offers an opportunity to preserve sphincter function and improve long-term survival quality in a subset of mid-to-low rectal cancers. Research on adjuvant immunotherapy in the field of colorectal cancer is also in full swing, and the results are worth waiting for.

Neoadjuvant immunotherapy in microsatellite stability or mismatch repair proficient colorectal cancer / 中华胃肠外科杂志

Immunotherapy has become an important treatment option for microsatellite instability-high (MSI-H) and mismatch repair deficient (dMMR) colorectal cancer. From late-line to first-line treatment, and even in neoadjuvant setting for early stage colorectal cancer, promising efficacy was observed with immunotherapy. In microsatellite stability (MSS) or mismatch repair proficient (pMMR) colorectal cancer, the researches of neoadjuvant immunotherapy have been conducted constantly. This paper focuses on the recent researches and progress of neoadjuvant immunotherapy for MSS or pMMR colorectal cancer. Neoadjuvant immunotherapy alone led to a good pathological response in a subset of patients. Studies of induction or consolidation immunotherapy before or after neoadjuvant chemoradiotherapy or concurrent immunotherapy during radiotherapy showed higher pathological complete remission (pCR) rates as compared to standard chemoradiotherapy. Studies on sequential dual immunotherapy after radiochemotherapy and targeted therapy combined with neoadjuvant immunotherapy are ongoing. At present, most of these are pilot studies with small sample size. More researches and long-term follow-up are needed to prove the efficacy of neoadjuvant immunotherapy in MSS or pMMR colorectal cancer.

Analysis of the genetic diversity of Dragon fruit based on ISSR markers in Colombia / Análise da diversidade genética da fruta do dragão com base em marcadores ISSR na Colômbia

Selenicereus megalanthus H. is a tropical fruit belonging to the family Cactaceae, is rich in essential nutrients, antioxidants and bioactive components. It presents wide variability in different characteristics and a great demand in the market; however, genetic studies in Colombia are scarce. The main of this study was to characterize the genetic diversity of 76 yellow pitahaya genotypes with eight ISSR markers. Genetic parameters expected average heterozygosity (He), percentage of polymorphic loci, genetic distances and Fst were estimated with TFPGA. The analysis of the population genetic structure was carried out with the STRUCTURE 2.3.4. As a result, 225 alleles were generated and the number of polymorphic loci ranged 85 (CT, AG) to 90 (GT). High genetic diversity was found, with an average value of heterozygosity was 0.34 with a genetic differentiation coefficient (Fst) of 0.26, indicating that there was a great genetic diversity, similar values than those reported in other studies of pitahaya genetic diversity in Colombia. The 76 genotypes were grouped into K=3 according to geographic location, however, in some groups a mixture of individuals from different origins was observed. The analysis of molecular variance (AMOVA) showed higher variation (75%) within groups than among groups (25%). These results provide information that can be used to develop conservation strategies for dragon fruit and breeding programs to obtain more productive pitahaya genotypes with superior quality, high yield and with resistance to biotic and abiotic factors.

Selenicereus megalanthus H. é uma fruta tropical pertencente à família Cactaceae, rica em nutrientes essenciais, antioxidantes e componentes bioativos. Apresenta grande variabilidade em diferentes características e uma grande demanda no mercado; no entanto, os estudos genéticos na Colômbia são escassos. O principal deste estudo foi caracterizar a diversidade genética de 76 genótipos de pitahaya amarela com oito marcadores ISSR. Parâmetros genéticos esperados de heterozigosidade média (He), porcentagem de locos polimórficos, distâncias genéticas e Fst foram estimados com TFPGA. A análise da estrutura genética da população foi realizada com a ESTRUTURA 2.3.4. Como resultado, 225 alelos foram gerados e o número de loci polimórficos variou de 85 (CT, AG) a 90 (GT). Foi encontrada alta diversidade genética, com um valor médio de heterozigosidade de 0,34 com coeficiente de diferenciação genética (Fst) de 0,26, indicando que havia uma grande diversidade genética, valores semelhantes aos relatados em outros estudos de diversidade genética de pitahaya na Colômbia. Os 76 genótipos foram agrupados em K = 3 de acordo com a localização geográfica, porém, em alguns grupos foi observada uma mistura de indivíduos de diferentes origens. A análise de variância molecular (AMOVA) mostrou maior variação (75%) dentro dos grupos do que entre os grupos (25%). Esses resultados fornecem informações que podem ser utilizadas para desenvolver estratégias de conservação da fruta do dragão e programas de melhoramento para a obtenção de genótipos de pitahaya mais produtivos, com qualidade superior, alto rendimento e com resistência a fatores bióticos e abióticos.

GGAA-Microsatellites of NR0B1 Promoter Region in Ewing's Sarcoma Patients and Healthy Individuals of a Southern Brazilian Population / Microssatélites GGAA na Região Promotora de NR0B1 em Pacientes com Sarcoma de Ewing e Indivíduos Saudáveis de uma População no Sul do Brasil / Microsatélites GGAA en la Región Promotora de NR0B1 en Pacientes con Sarcoma de Ewing y Individuos Sanos de una Población del Sur de Brasil

Introduction: The very aggressive soft tissue and bone pediatric tumor Ewing's sarcoma (ES) is caused in most cases by the chromosomal translocation t(11;22)(q24;q12), which encodes an aberrant chimeric transcription factor (EWS-FLI1) that regulates target genes, including the critical oncogene NR0B1 (Xp21.2),via GGAA-microsatellites. Objective: Analyze the GGAA-microsatellites of NR0B1promoter region of ES patients and healthy subjects in the population investigated. Method: Ten male ES patients and 71 adult healthy males from Rio Grande do Sul state, Brazil, were included in this study. DNA from peripheral blood samples was extracted, amplified by PCR, sequenced by the Sanger method and analyzed by capillary electrophoresis. Total number of GGAA-motifs, length of microsatellite in base pairs, number of segments separated by "A" insertions, and the greatest number of consecutive GGAA-motifs were analyzed as well. Statistical analyses were performed in the SPSS statistical software and p-value <0.05 was considered significant. Results: A total of 21 different alleles was identified in the 81 subjects, with 24.2 allele [(GGAA)7A(GGAA)7A(GGAA)10] being the most frequent, but when comparing the data between the two groups, no significant difference was found. Conclusion: The sample investigated had a wide variation of microsatellite structure, including the presence of rare alleles, allowing the opportunity to describe this population as an essential step to identify genetic implications in ES tumorigenesis

Introdução: O sarcoma de Ewing (ES) é um tumor pediátrico de ossos e partes moles muito agressivo, causado, na maioria das vezes, pela translocação cromossômica t(11;22)(q24;q12), codificando um fator de transcrição quimérico aberrante (EWS-FLI1) que regula genes-alvo, incluindo o oncogene NR0B1 (Xp21.2), via microssatélites GGAA. Objetivo: Analisar os microssatélites GGAA da região promotora de NR0B1 em pacientes com ES e indivíduos saudáveis da população em investigação. Método: Foram incluídos dez pacientes do sexo masculino com diagnóstico de ES e 71 indivíduos adultos hígidos do sexo masculino do Estado do Rio Grande do Sul, Brasil. O DNA foi extraído de sangue periférico e amplificado por PCR, sequenciado pelo método de Sanger e analisado por eletroforese capilar. Foram analisados o número total de repetições GGAA, comprimento total do microssatélite em pares de bases, número de segmentos separados por inserções "A" e maior número de repetições GGAA consecutivas. As análises estatísticas foram realizadas no software estatístico SPSS e o valor de p<0,05 foi considerado significativo. Resultados: Um total de 21 alelos diferentes foi identificado nos 81 indivíduos, com o alelo 24,2 [(GGAA)7A(GGAA)7A(GGAA)10], sendo o mais frequente; mas, ao comparar os dados entre os dois grupos, nenhuma diferença significativa foi encontrada. Conclusão: A amostra estudada é altamente variável em termos de estrutura de microssatélites, incluindo a presença de alelos raros, dando a oportunidade de descrever essa população, o que é uma etapa fundamental na identificação de implicações genéticas na tumorigênese do ES

Introducción: El sarcoma de Ewing (ES) es un tumor pediátrico de huesos y tejidos blandos muy agresivo, que se presenta con mayor frecuencia por translocación cromosómica t(11;22)(q24;q12), que codifica un factor de transcripción quimérico aberrante (EWS-FLI1) que regula los genes diana, incluido el oncogén NR0B1 (Xp21.2), a través de microsatélites GGAA. Objetivo: Analizar los microsatélites GGAA de la región promotora de NR0B1en pacientes con ES y personas sanas de la población investigada. Método: Este estudio incluyó a diez pacientes varones con diagnóstico de ES y 71 varones adultos del estado de Rio Grande do Sul, Brasil. El ADN se extrajo de sangre periférica y se amplificó por PCR, secuenciado por el método de Sanger y analizado por electroforesis capilar. El número total de repeticiones GGAA, longitud total de microsatélites en pares de bases, número de segmentos separados por inserciones "A" y el mayor número de repeticiones GGAA consecutivas fueran analizados. Los análisis estadísticos se realizaron con el software estadístico SPSS y se consideró significativo un valor de p<0,05. Resultados: Se identificaron un total de 21 alelos diferentes en los 81, siendo el alelo 24,2 [(GGAA)7A(GGAA)7A(GGAA)10] el más frecuente, pero al comparar los datos entre los dos grupos, no hubo diferencia estadísticamente significativa. Conclusión: La muestra estudiada es muy variable en cuanto a estructura de microsatélites, incluyendo la presencia de alelos raros, lo que nos permite la oportunidad de describir la población estudiada, lo cual es un paso fundamental en la identificación de implicaciones genéticas en la tumorigénesis de ES

Evaluation of genetic diversity of ginseng fruit color germplasm resources: based on SSR analysis / 中国中药杂志

Illumina Xten was employed for shallow sequencing of Panax ginseng(ginseng) samples, MISA for screening of SSR loci, and Primer 3 for primer design. Polymorphic primers were screened from 180 primers. From the successfully amplified polymorphic primers, 15 primers which featured clear peak shape, good polymorphism, and ease of statistics were selected and used to evaluate the genetic diversity and germplasm resources of 36 ginseng accessions with different fruit colors from Jilin province. The results showed that red-fruit ginseng population had high genetic diversity with the average number of alleles(N_a) of 1.031 and haploid genetic diversity(h) of 0.172. The neighbor-joining cluster analysis demonstrated that the germplasms of red-fruit and yellow-fruit ginseng populations were obviously intermixed, and pick-fruit ginseng germplasms clustered into a single clade. The results of STRUCTURE analysis showed high proportion of single genotype in pick-fruit ginseng germplasm and abundant genotypes in red-fruit and yellow-fruit ginseng germplasms with obvious germplasm mixing. AMOVA revealed that genetic variation occurred mainly within populations(62.00%, P<0.001), and rarely among populations(39%, P<0.001), but homogenization was obvious among different populations. In summary, pink-fruit ginseng population may contain rare genotypes, which is the basis for breeding of high-quality high-yield, and multi-resistance varieties, genetic improvement of varieties, and sustainable development and utilization of ginseng germplasm resources.

Review of genetic diversity and breed identification of black-bone silky fowl / 中国中药杂志

Black-bone silky fowl, sweet, pungent, and hot-natured, is one of the valuable domesticated birds with special economic value in China's genebank of poultry breed, which has a long history of medicinal and edible uses. It has the effects of tonifying liver and kidney, replenishing Qi and blood, nourishing yin, clearing heat, regulating menstruation, invigorating spleen, and securing essence. Therefore, it has remarkable efficacy of enhancing physical strength, tonifying blood, and treating diabetes and gynecological diseases. Various local black-bone silky fowl breeds have been generated due to the differences in environmental conditions, breed selection, and rearing conditions in different areas of China, which are mainly concentrated in Taihe, Wan'an, and Ji'an in Jiangxi province and Putian, Jinjiang, and Yongchun in Fujian province. The indigenous chicken breeds in China have different body sizes, appearance, coat colors, etc. The complex lineages lead to extremely unstable genetic traits. The diverse breeds similar in appearance result in the confusion in the market of silky fowl breeds. With the rapid development of molecular biological technology, the genetics of black-bone silky fowls has been intensively studied. This article reviews the research progress of the germplasm resources, genetic diversity, and breed identification of black-bone silky fowl in China at the morphology, chromosome, protein, and DNA levels. Further, it introduces the principles, application status, and limitations of DNA markers such as mitochondrial DNA, microsatellite markers, and SNPs. This review provides a theoretical basis for the mining of elite trait genes and the protection and utilization of local black-bone silky fowl germplasm resources in China.

Short Tandem Repeats in plants: genomic distribution and function prediction

BACKGROUND: Short Tandem repeats (STRs) existed as popular elements in both eukaryotic and prokaryotic genomes. RESULTS: In this study, we analyzed the characteristics, distributions, and motif features of STRs within whole-genomes of 140 plant species. The results showed that STR density was negatively correlated with the genome size. Hexanucleotide repeat was the most abundant type of STRs. The distribution of algae shows a preference different from that of other plants. By analyzing GC contents of STRs and genome, it was concluded that STR motif was influenced by GC contents. Analysis of the long STRs in genome (length 1000 bp) found that dicots have the more long STRs. For STR types, di- and tri-nucleotide accounted for the highest proportion. Analyzing and designing long STRs in CDS (length 500 bp) was to verify the role of long STRs in Gossypium hirsutum TM-1 and Solanum tuberosum. By comparing the long STRs found in Fragaria x ananassa with other species, some evolutionary characteristics of the long STRs were obtained. CONCLUSIONS: We got the characteristics, distribution, and motif features of STRs in the whole genome of 140 plants and obtained some evolutionary characteristics of long STRs. The study provides useful insights into STR preference, characteristics, and distribution in plants.

Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci

The Neotropical catfish genus Pseudoplatystoma comprises eight species of large size, widely distributed in South American basins. The endangered species P. magdaleniatum is endemic to Magdalena basin (Colombia), experiences high fishing pressure and its population genetics is relatively unknown. To study the genetic status and structure of P. magdaleniatum, 25 species-specific polymorphic microsatellite loci were developed using next-generation sequencing and then tested in samples collected in the Magdalena-Cauca basin. Based on 15 of these loci, P. magdaleniatum showed a high number of alleles per locus (9-10), high values of observed (0.762-0.798) and expected (0.770-0.791) heterozygosities, recent reduction of population size and gene flow. These findings constitute a baseline to measure potential changes in genetic diversity and structure of this commercially important species in a basin undergoing high anthropogenic activities.(AU)

El género de bagres neotropicales Pseudoplatystoma comprende ocho especies de gran tamaño, ampliamente distribuidas en las cuencas de Suramérica. La especie en peligro de extinción P. magdaleniatum es endémica de la Cuenca del Magdalena (Colombia), experimenta una alta presión pesquera y su genética poblacional es relativamente desconocida. Para estudiar el estado y estructura genética de P. magdaleniatum, se desarrollaron 25 loci microsatélites polimórficos especie específicos utilizando secuenciación de próxima generación y se evaluaron en muestras recolectadas en la Cuenca del Magdalena-Cauca. Con base en 15 loci, P. magdaleniatum mostró un alto número de alelos por locus (9-10), valores altos de heterocigosidad observada (0.762-0.798) y esperada (0.770-0.791), reducción reciente del tamaño poblacional y flujo génico. Estos hallazgos constituyen una línea de base para medir cambios potenciales en la diversidad y estructura genética de esta especie comercialmente importante en una cuenca sometida a altas actividades antropogénicas.(AU)

Metapopulation dynamics of the migratory fish Prochilodus lineatus (Characiformes: Prochilodontidae) in a lotic remnant of the Grande River, Southeastern Brazil

River impoundments for electricity generation lead to environmental changes which severely affect fish migration and species richness. However, little is known about their effect on the genetic structure and population dynamics downstream from the reservoir. Here, we analyzed a set of ten microsatellite loci of Prochilodus lineatus, an important South American migratory fish. Specimens (n = 150) were sampled from five sites in a remnant lotic system that includes sections of the Grande, Pardo and Mogi Guaçu rivers, southeastern Brazil. The data showed that all microsatellites were polymorphic with the allele number per locus ranging from 5 to 32, and genetic diversity (H e ) varied from 0.74 to 0.80. Indices of genetic differentiation and Bayesian analysis showed a significant genetic structure and three genetic clusters inhabiting this river system. An asymmetric gene flow suggests source-sink metapopulation dynamics from tributaries (genetic source) to the main river (genetic sink). A genetic cluster that was not detected in the upper Mogi and Pardo rivers tributaries may indicate there is a "trapped gene pool" downstream from the Porto Colômbia dam. Thus, here we provide new insights into the genetic structure and population dynamics of a migratory fish species in a highly dammed river basin.(AU)

Represamento de rios para geração de eletricidade levam a mudanças ambientais que afetam severamente a migração de peixes e riqueza de espécies. No entanto, pouco se sabe sobre seu efeito na estrutura genética e dinâmica populacional a jusante de reservatórios. Aqui, analisamos um conjunto de dez loci de microssatélites de Prochilodus lineatus, um importante peixe migratório sul-americano. Os espécimes (n = 150) foram amostrados em cinco locais de um sistema lótico remanescente que inclui seções dos rios Grande, Pardo e Mogi Guaçu, sudeste do Brasil. Os dados mostraram que todos microssatélites eram polimórficos com o número de alelos por locus variando de 5 a 32 e diversidade genética (H e ) variou de 0,74 a 0,80. Índices de diferenciação genética e análise de agrupamento baseada em modelo bayesiano indicou a presença de três agrupamentos genéticos habitando este sistema fluvial. Um fluxo gênico assimétrico sugere dinâmica metapopulacional de fonte-sumidouro dos tributários (fonte genética) para o rio principal (sumidouro genético). Um agrupamento genético que não foi detectado nos tributários rio Mogi e rio Pardo parecem indicar que há um "trapped gene pool" a jusante da represa de Porto Colômbia. Assim, nós provemos aqui novos conhecimentos sobre a estrutura genética e dinâmica populacional de uma espécie de peixe migratório em um rio altamente fragmentado por barramentos.(AU)

Development of microsatellite loci and population genetics in the bumblebee catfish species Pseudopimelodus atricaudus and Pseudopimelodus magnus (Siluriformes: Pseudopimelodidae)

The Neotropical freshwater catfish Pseudopimelodus atricaudus and Pseudopimelodus magnus are two recently discovered species endemic to the Colombian Magdalena-Cauca River basin. In this study, a set of 13 microsatellite loci were developed by using next generation sequence technology to assess the genetic diversity and population structure in P. atricaudus and test for cross-species amplification in P. magnus. Both species exhibited high genetic diversity (P. atricaudus: Na: 9.000 - 9.769 alleles/locus, Ho: 0.760 - 0.804, HE: 0.804 - 0.840; P. magnus: Na: 12.8 - 5.4 alleles/locus, Ho: 0.638 - 0.683, HE: 0.747 - 0.755) compared to the mean levels of genetic diversity reported for Neotropical Siluriformes, and lack of genetic differentiation among sampling sites within the Cauca River (P. atricaudus: F'ST=0.013 - 0.017, P > 0.05, D'est= -0.004 - 0.023, P > 0.05; P. magnus: F'ST= 0.031, P= 0.055; D'est= 0.045, P= 0.058). This work is the first insight on the diversity and the population genetics of species of the family Pseudopimelodidae and provides a framework to further population genetic and conservation analyses needed in this poorly studied family at the microevolutionary level.(AU)

Los bagres neotropicales Pseudopimelodus atricaudus y Pseudopimelodus magnus son dos especies recientemente descubiertas, endémicas de la cuenca Magdalena-Cauca en Colombia. En este estudio, se desarrollaron 13 loci microsatélites usando tecnología de secuenciación de próxima generación para evaluar la diversidad genética y la estructura poblacional de P. atricaudus y evaluar su amplificación cruzada en P. magnus. Ambas especies exhibieron altos valores de diversidad genética (P. atricaudus: Na: 9.000 - 9.769 alelos/locus, HO: 0.760 - 0.804, HE: 0.804 - 0.840; P. magnus: Na: 12.8 - 5.4 alelos/locus, HO: 0.638 - 0.683, HE: 0.747 - 0.755) comparados con los valores promedios de diversidad genética reportados para Siluriformes neotropicales, y ausencia de estructura genética entre los sitios analizados (P. atricaudus: F'ST= 0.013 - 0.017, P > 0.05, D'est= -0.004 - 0.023, P > 0.05; P. magnus: F'ST= 0.031, P= 0.055; D'est= 0.045, P= 0.058). Este trabajo representa la primera aproximación a la diversidad y genética poblacional de especies de la familia Pseudopimelodidae y proporciona un marco de referencia para futuros estudios genético-poblacionales y de conservación, requeridos en esta familia de bagres poco estudiada en el nivel microevolutivo.(AU)

Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)

Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.(AU)

Pimelodus yuma (anteriormente Pimelodus blochii) es un pez dulceacuícola endémico de las cuencas colombianas Magdalena-Cauca y Caribe que experimenta alteraciones del hábitat como resultado de actividades antropogénicas. Debido a la falta de información sobre la genética poblacional de esta especie, este estudio desarrolló 14 loci microsatélites especie-específicos para evaluar la diversidad genética y la estructura poblacional de muestras de la sección baja del río Cauca. La especie estudiada mostró niveles de diversidad genética más altos que los valores promedio reportados para Siluriformes neotropicales y niveles de endogamia significativos como se describió para algunos congéneres. Además, P. yuma comprende dos grupos genéticos coexistentes que exhiben flujo de genes a lo largo de la sección baja del río Cauca. Esta información constituye una línea base para futuros monitoreos de la diversidad genética y la estructura poblacional en un sector de influencia antrópica de la cuenca Magdalena-Cauca.(AU)

Identificación genética del orégano de Putre (Origanum vulgare L) mediante ITS y microsatélites, una especie reconocida en Chile con Sello de Origen / Genetic identification of the Putre's oregano (Origanum vulgare L) by ITS and microsatellites, a species recognized in Chile with Seal of Origin

Putre ́s oregano (Origanum vulgare L.) is a variety of oregano that grown in the Arica-Parinacota Region. Its organoleptic attributes and unique production conditions have earned it a certification with Geographical Indication (GI). However, the demands of the markets require a scientific-technological support for identification and authentication of materials. In this context, was proposed to identify Putre's oregano by phylogenetic relationships based on the use of molecular markers SSR and "DNA Barcode". The results showed that when comparing materials from different sources of Putre ́s oregano versus information from certified germplasms and GenBank sequences, added to the analysis with nuclear genetic markers, Putre ́s oregano corresponds to the species Origanum vulgare L. subsp virens. This precise identification will support the correct differentiation and authentication of this genotype, serving in addition to supporting the GI.

El orégano de Putre (Origanum vulgare L.) es una variedad de orégano que se cultiva en la Región de Arica y Parinacota. Sus atributos organolépticos y condiciones únicas de producción lo han hecho acreedor de una certificación con Indicación Geográfica (IG). Sin embargo, las exigencias de los mercados requieren de un respaldo científico-tecnológico de identificación y autenticación de materiales. En este contexto, se propuso identificar el orégano de Putre mediante relaciones filogenéticas a partir del uso de marcadores moleculares SSR y "DNA Barcode". Los resultados demostraron que al comparar los materiales de distintas procedencias de orégano de Putre versus la información desde germoplasmas certificados y secuencias de GenBank, sumado al análisis con marcadores genéticos nucleares, el orégano de Putre corresponde a la especie Origanum vulgare L. subsp virens. Esta identificación precisa dará soporte a la correcta diferenciación y autenticación de este genotipo, sirviendo además de apoyo a la IG.

Identificación del fenotipo de inestabilidad microsatelital en carcinoma colorrectal mediante el análisis de la expresión de proteínas reparadoras del ADN: Revisión narrativa / Identification of microsatellite instability phenotype in colorectal carcinoma through expression analysis of DNA mismatch repair proteins: Narrative review

El carcinoma colorrectal (CCR) es de las primeras causas de mortalidad del mundo, presentando Guatemala una incidencia anual de 7.4/millón de habitantes. El síndrome de Lynch se caracteriza clínicamente por un inicio temprano del CCR con lesiones causadas por alteraciones en genes que codifican proteínas reparadoras.Los microsatélites son regiones del ADN con una unidad repetitiva de uno o más nucleótidos y son susceptibles a errores durante la replicación de ADN de los enterocitos. Existe un sistema de reparación que corrige estos errores. Cuando las proteínas reparadoras de este sistema están mutadas o ausentes, dichos errores del ADN persisten. Estas proteínas reparadoras se expresan en el núcleo de las células colónicas normales y son detecta-bles utilizando estudios de inmunohistoquímica (IHQ). Los genes MLH1 y MSH2 pueden encontrarse mutados en el 90% de los casos de cáncer colorrectal y el resto corresponde a MSH6 y PMS2. Esta vía oncogénica se caracteriza por alteración del sistema de reparación de errores durante la replicación del ADN, controlado por los genes MMR (mismatch repair), principalmente MLH1, MSH2, MSH6 y PMS2. Se realizó una revisión extensa de la literatura en PubMed, Springer y JAMA, usando las palabras clave: fenotipo de CCR, Síndrome de Lynch e inestabilidad microsatelital, detectándose 55 artículos. El objetivo de esta revisión es describir la importancia de la identificación del fenotipo del CCR por medios de IHQ y de pruebas moleculares para el eficaz tratamiento con inmunoterapia anti-PD1/PD-L1.

Colorectal cancer (CRC) is one of the leading causes of mortality in the world. In Guatemala it's an important cause of morbidity (7.4 per million inhabitants). Lynch syndrome is clinically characterized by an early onset of nonpolyposis colorectal carcinoma, with multiple lesions and neoplasms. The syndrome is caused by mutations in genes encoding DNA mismatch repair proteins. The microsatellites are regions of the DNA that repeat between one or more nucleotides and are susceptible to errors during replication, these are corrected by a repair system, when genes are mutated, the errors persist. The genes encoding repair proteins are expressed in the nuclei of normal colonic cells which can be observed using immunohistochemical studies. The MLH1, MSH2 genes are found to be mutated in 90% of the cases and the rest corresponds to the MSH6 and PMS2 genes. This oncogenic pathway characteristically consists of an alteration in the DNA repair system that is controlled by mismatch repair genes (MMR). An extensive research was conducted on PubMed, Springer and JAMA, using the keyword: CRC phenotype, Lynch syndrome and microsatellite instability. 55 articles were found. This review«s objective is to understand the mechanisms of nonpolyposis colorectal cancer and the importance of identifying patients with a mutant phenotype as a predictive factor for the efficacy of the anti-PD1/PDL1 immunotherapy and for prognosis.

Genome instability and lymphoma / 中南大学学报(医学版)

Lymphoma is one of the most common malignant tumor of the hematologic system. The genome instability is not only an important molecular basis for the development of lymphoma, but also has important value in the diagnosis and prognosis of lymphoma. There are 2 types of genome instability: Microsatellite instability (MSI/MIN) at gene level and chromosomal instability at chromosome level. Through the study on genes associated with lymphoma, the unstable genes associated with lymphoma could be found, meanwhile the mechanism of its occurrence and development of lymphoma could be explored, and the important basis of molecular biology could also be provided in the field of current hot lymphoma precision medical research.

Genetic polymorphism of 23 autosomal STR loci in Han population from Yuncheng, Shanxi Province / 中南大学学报(医学版)

OBJECTIVES@#Due to the genetic feature of high diversity than other DNA markers, short tandem repeat (STR) plays key roles in forensic, anthropology, and population genetics. Newly introduced multiple STR kit is more valuable because of the greatly improved discriminatory power with the increase in the number of STR loci. The genetic polymorphic data are essential for the application and research in specific population. This study aims to investigate the genetic polymorphism of Han population residing in Yuncheng district, Shanxi Province, to evaluate the application of 23 STR loci in forensic personal identification and paternity test, and to explore the genetic relationship of Han population between Yuncheng and other populations.@*METHODS@#A total of 23 STR loci were amplified from 525 healthy unrelated individuals from the Han nationality in Yuncheng, Shanxi Province using the AGCU EX25 amplification kit. The products were detected and separated by ABI 3500 Genetic Analyzer. Alleles were genotyped by GeneMapper ID (Version 3.2) software, and corresponding frequencies and forensic parameters were calculated. We calculated the genetic distance and plotted the neighboring-joining tree with other 13 population.@*RESULTS@#The allele frequency of the 23 STRs ranged from 0.0010 to 0.5090. No deviation from Hardy-Weinberg equilibrium (@*CONCLUSIONS@#These 23 STRs are highly genetic polymorphic and informative in the Han population of Yuncheng, Shanxi Province, which can provide basic data for forensic personal identification, paternity testing, and population genetic research.

Application of copy number variation sequencing combined with short tandem repeat in analysis of abortion and prenatal diagnosis / 中华医学遗传学杂志

OBJECTIVE@#To explore the cause of abortion and strategy of prenatal diagnosis for pregnant women with high risk for chromosomal abnormalities by using copy number variation sequencing (CNV-seq) and short tandem repeats (STR) analysis.@*METHODS@#A total of 36 samples were collected, including amniotic fluid, abortion tissue, whole blood, chorionic villi and umbilical cord blood. CNV-seq and STR analysis were carried out to detect microdeletions, microduplications, chromosomal aneuploidies, mosaicisms and triploidies.@*RESULTS@#Among all samples, 1 was detected with 4p15.1p16.3 and 14q11.1q22.1 duplication, 1 was detected with 19p13.3 deletion, 8 were detected with chromosomal aneuploidies, 4 were detected with mosaicisms, two were detected with triploidies. No definite pathogenic CNVs were detected in 20 samples, which yielded a positive detection rate of 44.44%.@*CONCLUSION@#As a high-throughput detection method, CNV-seq has the advantages of rapidity, simplicity and high accuracy. It may suit prenatal diagnosis and analysis of abortion factors in combination with STR analysis.

Genetic polymorphisms of 21 non-combined of DNA index system short tandem repeat loci in Hainan Li population / 中华医学遗传学杂志

OBJECTIVE@#To investigate the genetic polymorphisms of 21 non-combined DNA index system short tandem repeat (STR) loci in Hainan Li population.@*METHODS@#DNA samples from 339 unrelated healthy individuals of Li population from Hainan Province were extracted and amplified with fluorescence labeled multiplex PCR system. PCR products were electrophoresed on an ABI3130 Genetic Analyzer following the manufacturer's instructions. Allele designation was performed with a GeneMapper ID-X by comparison with the allele ladder provided by the corresponding kit.@*RESULTS@#A total of 173 alleles and 489 genotypes were observed for the 21 STR loci, respectively. The frequencies of alleles and genotypes were 0.0010-0.5434 and 0.0020-0.3274, respectively. The heterozygosity varied from 0.639 to 0.833. Discrimination power (DP) was 0.803-0.948, power of exclusion for trio-paternity was 0.416-0.584, power of exclusion for duo-paternity was 0.140-0.238, the polymorphism information content(PIC) was 0.57-0.81, respectively. The total discrimination power (TDP), cumulative probability of exclusion for trio-paternity testing(CPE-trio) and cumulative probability of exclusion for duo-paternity testing (CPE-duo) were 0.999 999 999 999 99, 0.999 999 883 211 752, and 0.987 266, respectively.@*CONCLUSION@#The 21 STR loci are highly polymorphic and informative in the studied population and can be employed as supplementary loci in duo-paternity testing or cases with variant circumstances.

Genetic diversity and genetic structures of original plants of Viticis Fructus:an SSR markers-based analysis / 中国中药杂志

The present study aimed to provide the protection strategies for wild germplasm resources of original plants of Viticis Fructus and a theoretical basis for the sustainable use of Viticis Fructus. The genetic diversity and genetic structures of the 232 indivi-duals in 19 populations of Vitex rotundifolia and V. trifolia were analyzed by eight SSR markers with tools such as Popgene32, GenAlex 6.502, and STRUCTURE. Bottleneck effect was detected for the population with more than 10 individuals. The results indicated that 42 and 26 alleles were detected from the populations of V. rotundifolia and V. trifolia, respectively, with average expected heterozygo-sities of 0.448 6 and 0.583 9, which are indicative of low genetic diversity. AMOVA revealed the obvious genetic variation of V. rotundifolia and V. trifolia within population(84.43%, P<0.01; 60.37%, P<0.01). Furthermore, in eight SSR loci, six from V. rotundifolia populations and two from V. trifolia populations failed to meet Hardy-Weinberg equilibrium expectations(P<0.05), which confirmed that the populations experienced bottleneck effect. As assessed by Mantel test, geographical distance posed slight impacts on the genetic variation between the populations of V. rotundifolia and V. trifolia. Principal component analysis(PCA) and STRUCTURE analysis demonstrated evident introgression of genes among various populations. The original plants of Viticis Fructus were confirmed low in genetic diversity and genetic differentiation level. Therefore, the protection of wild resources of original plants of Viticis Fructus should be strengthened to ensure its sustainable use.

Study on Sparganium stoloniferum from different regions in China based on appearance characters and ISSR markers / 中国中药杂志

Based on the characteristics and ISSR molecular marker technology, the study is aimed to compare and perform genetic diversity analysis on Sparganium stoloniferum from 7 regions. Molecular identification method was established for S. stoloniferum from Hunan province. Differences among Sparganii Rhizoma samples from seven habitats were analyzed via measuring weight, length, width and thickness of them. Genetic diversity of S. stoloniferum from 7 regions was analyzed by screening out primers amplifying clear band and showing rich polymorphism, then a cultivars dendrogram was built. The target primer was screened out, and the specific band was sequenced. Nine ISSR primers were selected to amplified clear band, rich polymorphism. A total of 73 bands were amplified by nine ISSR primers selected from 27 ISSR primers. On average, each primer produced 8.0 bands. A total of 38 bands were polymorphic, which occupied 52.8% of all bands. The cultivars dendrogram showed the genetic similarity was 0.54-0.94. Genetic similarity coefficient of S. stoloniferum from Jiangsu province, Anhui province and Jiangxi province was big, indicating the differences among them were slight on genetic level. S. stoloniferum from Hunan province is quite different from samples from the other six habitats on appea-rance and genetic level. A specific band(327 bp) in S. stoloniferum from Hunan province was obtained via ISSR-857 primer, and was sequenced. According BLASTn database, there were few sequences similar to the gene fragment and had little correlation with the growth process of plant. ISSR molecular marker technology provides a new idea for the identification of S. stoloniferum. This result confirmed the particularity of S. stoloniferum from ancient Jingzhou.

Molecular characterization and core collection evaluation of Manihot esculenta Crantz / Caracterização molecular e avaliação de coleção nuclear de Manihot esculenta Crantz

Cassava is one of the most important subsistence crops in tropical regions. It is necessary to preserve and to know the genetic diversity existent for the adequate use of genetic resources. The evaluation of genetic diversity among genotypes results in information about potential parents in breeding programs, allows duplicates identification, and facilitates germplasm exchange between research institutions. The objective of this study was to characterize the genetic diversity of cassava accessions of North Brazil region. A total of 106 accessions were analyzed using ten microsatellite markers. The genetic parameters estimated were: expected heterozygosity (HE), observed heterozygosity (HO) and polymorphic information content (PIC). Clustering was performed using the UPGMA and Neighbor-Joining (NJ) method. Bayesian analysis, analysis of principal coordinates and identification of a core collection were also used. The ten loci amplified 8,40 alleles on average. The average heterozygosity estimates were: HE = 0.71, HO = 0.58 and PIC = 0.72. Genetic distances ranged from 0.158 to 0.908. Six (5,66%) accesses were redundant. Clustering and dispersion analysis didn't differentiate bitter from sweet cassava, and there wasn't correlation between groups and collect origin. The core collection consisted of 22 individuals that represented 94% of total allelic diversity and 20,75% of the base collection. The results indicate high dissimilarity between the accessions and allowed the detection of redundant genotypes, showing the use of genetic markers as informative tools for the management of collections. (AU)

A mandioca é uma das mais importantes culturas de subsistência em países tropicais. É preciso conservar e conhecer a diversidade genética para o uso adequado dos recursos genéticos. A avaliação da diversidade genética entre os genótipos resulta em informações sobre potenciais genitores em programas de melhoramento, possibilita a identificação de duplicatas, além disso, facilita o intercâmbio de germoplasma entre instituições de pesquisa. O objetivo deste trabalho foi caracterizar a diversidade genética dos acessos de mandioca da Região Norte do Brasil. Foram analisados 106 acessos por meio de dez marcadores microssatélites. Os parâmetros de diversidade genética estimados foram: heterozigosidade esperada (HE), heterozigosidade observada (HO) e conteúdo de informação polimórfica (PIC). Agrupamentos foram realizados pelo método UPGMA e Neighbor-Joining (NJ). Utilizou-se também análises bayesianas, dispersão por coordenadas principais e a identificação de uma coleção nuclear. Os dez locos amplificaram 8,40 alelos em média. A média das estimativas de diversidade foram altas: HE = 0,71, HO = 0,58 e PIC = 0,72. As distâncias genéticas variaram de 0,158 a 0,908. Seis (5,66%) acessos estão redundantes. Os agrupamentos e análises de dispersão não evidenciaram distinção entre variedades bravas e mansas e não foi identificada estrutura genética correspondente a origem dos acessos. A coleção nuclear foi formada por 22 indivíduos, que representaram 94% da diversidade alélica total e 20,75% da coleção base. Os resultados indicam alta dissimilaridade entre os acessos e permitiram a detecção de genótipos redundantes, mostrando o uso de marcadores genéticos como ferramentas informativas para o manejo de coleções. (AU)