Characterization and phylogenetic analysis of chloroplast genome of Cynanchum wallichii and Cynanchum otophyllum / 药学学报

italic>Cynanchum wallichii and Cynanchum otophyllum belong to the genus Cynanchum in the family Apocynaceae, and are important medicinal plants. In this study, we sequenced and assembled the chloroplast genomes of C. wallichii and C. otophyllum, and performed a phylogenetic analysis of the structural characteristics of their chloroplast genomes and their phylogenetic positions. The results showed that the chloroplast genomes of both C. wallichii and C. otophyllum had a typical tetrad structure, with 133 genes annotated, and the total GC contents of both were similar. Codon preference analysis showed that the relative synonymous codon usage in the chloroplast genomes of C. wallichii and C. otophyllum differed slightly, but the differences were not significant, and there was a strong A or U preference at the third codon position. In both chloroplast genomes, 91 and 103 simple sequence repeats were detected respectively, and the largest proportion of A/T type repeats. Nucleotide polymorphism analysis showed that the nucleotide diversity of the intergenic sequences in the chloroplast genome of genus Cynanchum were generally higher than those of the common gene sequences. A pair of primers was designed based on the high variation region of the chloroplast genome to identify C. wallichii and C. otophyllum. The phylogenetic analysis showed that the C. wallichii and Cynanchum thesioides were the closest relatives, while the C. otophyllum, Cynanchum bungei and Cynanchum wilfordii formed a stable monophyletic clade within the genus Cynanchum, and the three species were closely related. The comparative analysis of the chloroplast genomic characteristics and phylogeny of C. wallichii and C. otophyllum will provide a theoretical basis for the species identification of the two plants and for the study of genetic diversity and phylogeny of the genus Cynanchum.

Genetic counseling for hearing loss today / 临床耳鼻咽喉头颈外科杂志

Genetic counseling for hearing loss today originated from decoding the genetic code of hereditary hearing loss, which serves as an effective strategy for preventing hearing loss and constitutes a crucial component of the diagnostic and therapeutic framework. This paper described the main principles and contents of genetic counseling for hearing loss, the key points of counseling across various genetic models and its application in tertiary prevention strategies targeting hearing impairment. The prospects of an AI-assisted genetic counseling decision system and the envisions of genetic counseling in preventing hereditary hearing loss were introduced. Genetic counseling for hearing loss today embodies the hallmark of a new era, which is inseparable from the advancements in science and technology, and will undoubtedly contribute to precise gene intervention!

Characteristics of the chloroplast genome of Camellia insularis / 生物工程学报

In this study, the chloroplast genome of Camellia insularis Orel & Curry was sequenced using high-throughput sequencing technology. The results showed that the chloroplast genome of C. insularis was 156 882 bp in length with a typical tetrad structure, encoding 132 genes, including 88 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Codon preference analysis revealed that the highest number of codons coded for leucine, with a high A/U preference in the third codon position. Additionally, 67 simple sequence repeats (SSR) loci were identified, with a preference for A and T bases. The inverted repeat (IR) boundary regions of the chloroplast genome of C. insularis were relatively conserved, except for a few variable regions. Phylogenetic analysis indicated that C. insularis was most closely related to C. fascicularis. Yellow camellia is a valuable material for genetic engineering breeding. This study provides fundamental genetic information on chloroplast engineering and offers valuable resources for conducting in-depth research on the evolution, species identification, and genomic breeding of yellow Camellia.

Identification of banana ADA1 gene family members and their expression profiles under biotic and abiotic stresses / 生物工程学报

The Spt-Ada-Gcn5-acetyltransferase (SAGA) is an ancillary transcription initiation complex which is highly conserved. The ADA1 (alteration/deficiency in activation 1, also called histone H2A functional interactor 1, HFI1) is a subunit in the core module of the SAGA protein complex. ADA1 plays an important role in plant growth and development as well as stress resistance. In this paper, we performed genome-wide identification of banana ADA1 gene family members based on banana genomic data, and analyzed the basic physicochemical properties, evolutionary relationships, selection pressure, promoter cis-acting elements, and its expression profiles under biotic and abiotic stresses. The results showed that there were 10, 6, and 7 family members in Musa acuminata, Musa balbisiana and Musa itinerans. The members were all unstable and hydrophilic proteins, and only contained the conservative SAGA-Tad1 domain. Both MaADA1 and MbADA1 have interactive relationship with Sgf11 (SAGA-associated factor 11) of core module in SAGA. Phylogenetic analysis revealed that banana ADA1 gene family members could be divided into 3 classes. The evolution of ADA1 gene family members was mostly influenced by purifying selection. There were large differences among the gene structure of banana ADA1 gene family members. ADA1 gene family members contained plenty of hormonal elements. MaADA1-1 may play a prominent role in the resistance of banana to cold stress, while MaADA1 may respond to the Panama disease of banana. In conclusion, this study suggested ADA1 gene family members are highly conserved in banana, and may respond to biotic and abiotic stress.

Genome-wide association analysis of agronomic traits related to eggplant fruits: a review / 生物工程学报

Eggplant is an important horticultural crop and one of the most widely grown vegetables in the Solanaceae family. Eggplant fruit-related agronomic traits are complex quantitative traits with low efficiency and long cycle time for traditional breeding selection. With the rapid development of high-throughput sequencing technology and bioinformatics tools, genome-wide association study (GWAS) has shown great application potential in analyzing the genetic rules of complex agronomic traits related to eggplant fruits. This paper first reviews the progress of genome-wide association analysis in eggplant fruit shape, fruit color and other fruit-related agronomic traits. Subsequently, aiming at the problem of missing heritability, which is common in the genetic studies of eggplant quantitative traits, this paper puts forward the development strategies of eggplant GWAS in the future based on the hot spots of application of four GWAS strategies in the research of agronomics traits related to eggplant fruits. Lastly, the application of GWAS strategy in the field of eggplant molecular breeding is expected to provide a theoretical basis and reference for the future use of GWAS to analyze the genetic basis of various eggplant fruit-related traits and to select fruit materials that meet consumer needs.

Application of Mendelian randomization in liver cancer / 临床肝胆病杂志

In recent years， the research method of Mendelian randomization based on genome-wide association studies has been widely used for etiological exploration in the medical field， which can effectively overcome the confounding biases and interference of reverse causalities in traditional observational researches with its unique advantages of the distributive randomness and timing priority of genetic variants. This article reviews the method of Mendelian randomization and its application in liver cancer， in order to provide new ideas for the research on causal association in liver cancer.

Bidirectional casual effects between periodontitis and Sjögren's syndrome: a Mendelian randomization study / 口腔疾病防治

Objective@#To evaluate the bidirectional association between periodontitis and Sjögren's syndrome using the Mendelian randomization (MR) method.@*Methods@#Genome-wide association study (GWAS) data of periodontitis (N = 45 563) and Sjögren's syndrome (N = 214 435) were selected to meet the requirements of the same ethnicity and different regions. Inverse variance-weighted (IVW), MR-Egger, and weighted median (WM) tests were used to evaluate the causal effect. Cochran's Q statistics, MR-Egger intercept, MR-PRESSO and leave-one-out analysis were used as sensitivity analyses to assess the stability and reliability of the results.@*Results@#After screening, the GWAS data of Sjögren's syndrome were based on the Finnish region, and the periodontitis GWAS data were based on the UK region, both of which originated from European ancestry. Using IVW (OR = 1.017, 95% CI = 0.956-1.082), MR-Egger (OR = 0.985, 95% CI= 0.956-1.082), and WM (OR =1.021, 95% CI = 0.948-1.099), no causal effect of Sjögren's syndrome on periodontitis was found using any of the three methods. Conversely, no causal effect of periodontitis on Sjögren's syndrome was found (IVW, OR = 1.024, 95% CI = 0.852-1.230; MR-Egger, OR = 0.978, 95% CI = 0.789-1.212; WM, OR = 1.024, 95% CI = 0.846-1.260). The sensitivity analyses indicated that the results were stable and reliable. Cochran's Q test and MR-PRESSO revealed that there was no significant heterogeneity among the instrumental variables, which included single nucleotide polymorphisms (SNPs). The intercept of MR-Egger regression indicated no pleiotropy in the included SNPs. No individual SNP was found that significantly affected the results using the leave-one-out method.@*Conclusion@#This study does not support a bidirectional causal effect between periodontitis and Sjögren's syndrome.

Specific DNA barcodes screening, germplasm resource identification, and genetic diversity analysis of Platycodon grandiflorum / 药学学报

Platycodonis Radix is the dry root of Platycodon grandiflorum of Campanulaceae, which has a variety of pharmacological effects and is a commonly used bulk Chinese medicine. In this study, the chloroplast genome sequences of six P. grandiflorum from different producing areas has been sequenced with Illumina HiSeq X Ten platform. The specific DNA barcodes were screened, and the germplasm resources and genetic diversity were analyzed according to the specific barcodes. The total length of the chloroplast genome of 6 P. grandiflorum samples was 172 260-172 275 bp, and all chloroplast genomes showed a typical circular tetrad structure and encoded 141 genes. The comparative genomics analysis and results of amplification efficiency demonstrated that trnG-UCC and ndhG_ndhF were the potential specific DNA barcodes for identification the germplasm resources of P. grandiflorum. A total of 305 P. grandiflorum samples were collected from 15 production areas in 9 provinces, for which the fragments of trnG-UCC and ndhG_ndhF were amplificated and the sequences were analyzed. The results showed that trnG-UCC and ndhG_ndhF have 5 and 11 mutation sites, respectively, and 5 and 7 haplotypes were identified, respectively. The combined analysis of the two sequences formed 13 haplotypes (named Hap1-Hap13), and Hap4 is the main genotype, followed by Hap1. The unique haplotypes possessed by the three producing areas can be used as DNA molecular tags in this area to distinguish from the germplasm resources of P. grandiflorum from other areas. The haplotype diversity, nucleotide diversity and genetic distance were 0.94, 4.79×10-3 and 0.000 0-0.020 3, respectively, suggesting that the genetic diversity was abundant and intraspecific kinship was relatively close. This study laid a foundation for the identification of P. grandiflorum, the protection and utilization of germplasm resources, and molecular breeding.

A Rapid PCR-RFLP Method for Assessing Heterozygosity of Murraya paniculata Germplasm / 中国实验方剂学杂志

ObjectiveTo establish a rapid method for evaluating the heterozygosity of Murraya paniculata germplasm materials and provide as a foundation for developing germplasm breeding and innovation measures for M. paniculata. MethodSingle nucleotide polymorphisms （SNPs） were screened from the genome resequencing data of 65 plants of M. paniculata. A self-written script was used to transform 20 SNPs into restriction fragment length polymorphism （RFLP） markers. Polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP） was employed to detect the 20 RFLP markers in 12 M. paniculata germplasm accessions， and the heterozygosity of M. paniculata germplasm accessions was calculated based on the number of enzyme-cutting bands at the 20 RFLP marker sites. Plink was used to calculate the whole genome heterozygosity of 12 M. paniculata germplasm accessions， and the results obtained with different methods were compared. ResultThere was no significant difference in the heterozygosity calculated by the PCR-RFLP method and the genome resequencing method. The PCR-RFLP and genome resequencing methods identified 8 and 9 germplasm accessions， respectively， with a heterozygosity level less than 30%. Seven germplasm accessions with heterozygosity less than 30.00% were calculated by both methods. ConclusionThe PCR-RFLP method established in this study for evaluating the heterozygosity of M. paniculata germplasm demonstrates the precision of 87.5% and the accuracy of 77.8%. This method serves as a reference for developing heterozygosity evaluation methods in other medicinal plant germplasm resources.

La viruela sísmica aspectos relacionados a la fisiopatología, genoma, patogénesis, transmisión, replicación e inmunología / Aspects Related to pathophysiology, Genome, Pathogenesis, Transmission, Replication and Immunology of Monkeypox

Introducción: La viruela símica es una enfermedad zoonótica identificada por primera vez en 1958. El virus es un miembro del género Orthopoxvirus, de la familia Poxviridae. Infecta a una amplia variedad de mamíferos y se desconoce su reservorio natural. Objetivos: Describir los aspectos importantes relacionados a la fisiopatología, genoma, patogénesis, transmisión, replicación e inmunología de la viruela símica. Métodos: Se realizó una búsqueda de artículos originales, reportes de casos, revisiones bibliográficas y sistemáticas en el Portal Regional de la BVS, PubMed, Science, Nature y Lancet. Se consultaron los informes de la Organización Mundial de la Salud y la Organización Panamericana de la Salud sobre la viruela símica. Resultados: La propagación del virus de la viruela símica puede ocurrir a través del contacto cercano con lesiones, fluidos corporales, gotitas respiratorias y objetos contaminados. Una vez dentro del organismo, el virus infecta mucosas, células epiteliales y células inmunitarias de los tejidos adyacentes. El virus se replica y disemina rápidamente a través del sistema hemático y linfático. Las células T desempeñan un papel importante en la regulación de la respuesta inmunitaria contra el virus. Sin embargo, los Orthopoxvirus han desarrollado varios mecanismos para la evasión de la respuesta inmunitaria. Conclusiones: Los aspectos importantes descritos que se tuvieron en cuenta acerca de la transmisión de la viruela símica han tenido cambio significativo con el tiempo. El brote mundial de viruela símica de 2022 presentó una cadena de transmisión principalmente entre humanos asociada al contacto sexual(AU).

Introduction: Monkeypox is a zoonotic disease that was first identified in 1958. The virus is a member of Orthopoxvirus genus, of Poxviridae family. It infects wide variety of mammals and its natural reservoir is unknown. Objectives: To describe the important aspects related to pathophysiology, genome, pathogenesis, transmission, replication and immunology of monkeypox. Methods: A search of original articles, case reports, bibliographic and systematic reviews was carried out in VHL Regional Portal, PubMed, Science, Nature and Lancet. Reports from the World Health Organization and the Pan American Health Organization on monkeypox were consulted. Results: Spread of monkeypox virus can occur through close contact with lesions, body fluids, respiratory droplets, and contaminated objects. Once inside the body, the virus infects mucous membranes, epithelial cells and immune cells of adjacent tissues. The virus replicates and spreads rapidly through the blood and lymphatic system. T cells play an important role in regulating the immune response against the virus. However, Orthopoxviruses have developed several mechanisms to evade the immune response. Conclusions: The important aspects described, taken into account about monkeypox transmission, have significantly changed over time. 2022 global monkeypox outbreak presented a chain of transmission primarily among humans associated with sexual contact(AU)

Candida auris: a global pathogen that has taken root in Colombia / Candida auris: un agente patógeno global que se ha arraigado en Colombia

Candida auris has been recognized as an emerging multidrug-resistant pathogen with a significant public health burden, causing cases of invasive infection and colonization due to its persistence on inanimate surfaces, ability to colonize skin of some patients, and high transmissibility in healthcare settings. The first sporadic report of the isolation of this species from the ear canal of a patient in Asia was in 2009 and reports from other regions of the world soon followed. However, it was not until 2015 that global epidemiological alerts were communicated as a result of an increasing number of reports of invasive infections caused by C. auris in several countries. Colombia was soon added to this list in 2016 after an unusual increase in the number of C. haemulonii isolates was reported, later confirmed as C. auris. Since the issuing of a national alert by the Colombian National Institute of Health together with the Ministry of Health in 2016, the number of cases reported reached over 2,000 by 2022. Colombian isolates have not shown pan resistance to available antifungals, unlike C. auris strains reported in other regions of the world, which leaves patients in Colombia with therapeutic options for these infections. However, increasing fluconazole resistance is being observed. Whole-genome sequencing of Colombian C. auris isolates has enhanced molecular epidemiological data, grouping Colombian isolates in clade IV together with other South American isolates. Data from Colombia showed that public health authorities, scientific community, and the general public need to be aware of fungal diseases as they present an often-deadly threat to patients.

Candida auris ha sido reconocido como un agente patógeno multirresistente emergente con una carga significativa en la salud pública. Genera casos de infección invasiva y colonización debido a su persistencia en superficies inanimadas, su capacidad para colonizar fácilmente la piel de algunos pacientes y su alta transmisibilidad en el ambiente hospitalario. El primer reporte esporádico de esta especie fue en Asia en el 2009 cuando se realizó su aislamiento a partir del conducto auditivo de un paciente, y pronto le siguieron reportes en otras regiones del mundo. Sin embargo, no fue hasta 2015 que se conocieron las alertas epidemiológicas a nivel mundial debido a un aumento en el número de casos de infecciones causadas por C. auris en varios países. Colombia se sumó a la lista en 2016 luego de un aumento inusual en el número de aislamientos de C. haemulonii informados, que luego se confirmaron como C. auris. Desde que el Instituto Nacional de Salud junto con el Ministerio de Salud emitieron la Alerta Nacional en el 2016, el número de casos reportados superó los 2.000 en el 2022. Los aislamientos colombianos no han mostrado resistencia generalizada a los antifúngicos disponibles, contrario a lo reportado para cepas de C. auris en algunas regiones del mundo, por lo que los pacientes en Colombia aún cuentan con opciones terapéuticas para estas infecciones. No obstante, se ha observado un aumento en la resistencia al fluconazol. La secuenciación del genoma completo agrupó los aislamientos colombianos en el Ciado IV, junto con otros sudamericanos de C. auris, y aportó al conocimiento de los datos epidemiológicos moleculares de esta especie. Los datos de Colombia evidencian que las autoridades de salud pública, la comunidad científica y el público en general deben ser conscientes de las enfermedades fúngicas, ya que a menudo representan una amenaza mortal para los pacientes.

First molecular characterization of Escherichia coli O157:H7 isolates from clinical samples in Paraguay using whole-genome sequencing Molecular characterization of Escherichia coli O157 isolates from Paraguay / Primera caracterización molecular de aislamientos de Escherichia coli O157:H7 provenientes de muestras clínicas en Paraguay utilizando secuenciación de genoma completo

Abstract Escherichia coli O157:H7 is a foodborne pathogen implicated in numerous outbreaks worldwide that has the ability to cause extra-intestinal complications in humans. The Enteropathogens Division of the Central Public Health Laboratory (CPHL) in Paraguay is working to improve the genomic characterization of Shiga toxin-producing E. coli (STEC) to enhance laboratory-based surveillance and investigation of foodborne disease outbreaks. Whole genome sequencing (WGS) is proposed worldwide to be used in the routine laboratory as a high-resolution tool that allows to have all the results in a single workflow. This study aimed to carry out for the first time, the genomic characterization by WGS of nine STEC O157:H7 strains isolated from human samples in Paraguay. We were able to identify virulence and resistance mechanisms, MLST subtype, and even establish the phylogenetic relationships between isolates. Furthermore, we detected the presence of strains belonging to hypervirulent clade 8 in most of the isolates studied.

Resumen Escherichia coli O157:H7 es un patógeno transmitido por alimentos implicado en numerosos brotes en todo el mundo y es capaz de causar complicaciones extraintestinales en humanos. La sección de «Enteropatógenos¼ del Laboratorio Central de Salud Pública trabaja en mejorar la caracterización genómica de STEC, de modo de potenciar la vigilancia laboratorial y la investigación de brotes de enfermedades transmitidas por alimentos. La secuenciación de genoma completo (WGS, por sus siglas en inglés) se propone a nivel mundial como una herramienta de alta resolución para ser utilizada en el laboratorio de rutina, ya que permite obtener todos los resultados en un único proceso. El objetivo de este trabajo fue llevar a cabo, por primera vez, la caracterización genómica por WGS de nueve cepas STEC O157:H7 aisladas en Paraguay a partir de muestras de origen humano. Pudimos identificar los factores de virulencia, los mecanismos de resistencia, el subtipo MLST, e incluso pudimos establecer la relación filogenética entre los aislamientos. Además, detectamos que la mayoría de las cepas pertenecían al clado hipervirulento 8.

Advancements in Genetic Diversity and Genome Characteristics of Durians (Durio spp.)

Durian is one of the important fruit crops in Southeast Asia with its unique flavor and important economic benefits. Breeding programs have produced hundreds of different cultivars of durian. These cultivars are classified mainly by fruit and flower characteristics, which cannot be observed at the vegetative stage. Therefore, molecular biology is a powerful tool to approach and explore the genetic characteristics of durians. Many studies based on barcoded DNA and molecular markers have been conducted and valuable data have been exploited. Thanks to the advancement of sequencing technology, the plastid genome and the whole genome were sequenced in some durian cultivars. The data revealed reliable data on the structure and function of several genes. This review aims to update recent studies on the durian genome attributes and potential applications in the conservation of germplasm, authentication, and exploration of the gene structure and function of this specialty plant.

Web-tools for the genomic analysis of the 2022 Monkeypox virus global outbreak / Herramientas web para el análisis genómico del virus de la viruela símica durante el brote mundial de 2022

Abstract The resources and platforms available on the internet for collecting and sharing information and performing genomic sequence analysis have made it possible to follow closely the evolution the evolution of SARS-CoV-2. However, the current monkeypox outbreak in the world brings us back to the need to use these resources to appraise the extent of this outbreak. The objective of this work was an analysis of the information presented so far in the genomic database GISAID EpiPox™, using various tools available on the web. The results indicate that the monkeypox outbreak is referred as MPXV clade II B.1 lineage and sub-lineages, isolated from male patients mainly from the European and American continents. In the current scenario, the access to genomic sequences, epidemiological information, and tools available to the scientific community is of great importance for global public health in order to follow the evolution of pathogens.

Resumen Los recursos y plataformas disponibles en Internet para recopilar, compartir información y realizar análisis de secuencias genómicas han permitido seguir de cerca la evolución del SARS-CoV-2. El actual brote global de viruela del mono en el mundo, requiere de nuevo utilizar estos recursos para conocer el alcance de este brote. El objetivo de este trabajo fue un análisis de la información presentada hasta el momento en la base de datos genómica EpiPox™ de GISAID, utilizando diversas herramientas disponibles en la web. Los resultados indican que el brote de la viruela del mono o símica está referido al linaje y sub-linajes B.1 del clado II de MPXV, aislado principalmente de pacientes hombres de Europa y América. En el escenario actual, el acceso a las secuencias genómicas, la información epidemiológica, y las herramientas disponibles para la comunidad científica son de gran importancia para la salud pública mundial con el fin de seguir la evolución de los patógenos.

Genomic monitoring unveils a high prevalence of severe acute respiratory syndrome coronavirus 2 Omicron variant in vaccine breakthrough cases in Bahia, Brazil

SUMMARY OBJECTIVE: Genome sequencing has been proved to be an excellent tool to monitor the molecular epidemiology of the disease caused by severe acute respiratory syndrome coronavirus 2, i.e., coronavirus disease 2019. Some reports of infected, vaccinated individuals have aroused great interest because they are primarily being infected with circulating variants of concern. To investigate the cases of infected, vaccinated individuals in Salvador, Bahia, Brazil, we performed genomic monitoring to estimate the magnitude of the different variants of concern in these cases. METHODS: Nasopharyngeal swabs from infected (symptomatic and asymptomatic), vaccinated or unvaccinated individuals (n=29), and quantitative reverse transcription polymerase chain reaction cycle threshold value (Ct values) of ≤30 were subjected to viral sequencing using nanopore technology. RESULTS: Our analysis revealed that the Omicron variant was found in 99% of cases and the Delta variant was found in only one case. Infected, fully vaccinated patients have a favorable clinical prognosis; however, within the community, they become viral carriers with the aggravating factor of viral dissemination of variants of concern not neutralized by the currently available vaccines. CONCLUSION: It is important to acknowledge the limitations of these vaccines and to develop new vaccines to emergent variants of concern, as is the case of influenza vaccine; going through new doses of the same coronavirus vaccines is "more of the same."

Viruela símica: una revisión narrativa de la fisiopatología

La viruela símica es una enfermedad zoonótica identificada por primera vez en 1958. El virus es un miembro del género Orthopoxvirus, de la familia Poxviridae. Infecta a una amplia variedad de mamíferos, pero se desconoce su reservorio natural. El virus del brote de 2022 pertenece a los clados IIa y IIb. Es probable que la aparición del brote actual se deba a las importaciones del brote de Nigeria de 2017-2018. La propagación de persona a persona puede ocurrir a través del contacto cercano con lesiones, fluidos corporales, gotitas respiratorias y objetos contaminados. Una vez dentro del organismo, el virus infecta las mucosas, células epiteliales y células inmunitarias de los tejidos adyacentes. Luego, el virus se replica y disemina rápidamente a través del sistema hemático y linfático. Las células T desempeñan un papel importante en la regulación de la respuesta inmunitaria contra el virus. Sin embargo, los Orthopoxvirus han desarrollado varios mecanismos para la evasión de la respuesta inmunitaria. La vigilancia de la enfermedad es un factor crucial en la evaluación de riesgo del virus y del control del brote. Para esta revisión se realizó la búsqueda de los principales artículos relacionados a la patogenia del virus, publicados hasta la fecha. El artículo destaca la necesidad de nuevos estudios sobre transmisibilidad y patogenicidad de las cepas asociadas al brote de 2022.

Monkeypox is a zoonotic disease first identified in 1958. The virus is a member of the genus Orthopoxvirus, family Poxviridae. It infects a wide variety of mammals, but its natural reservoir is unknown. The virus in the 2022 outbreak belongs to clades IIa and IIb. The emergence of the current outbreak is likely to be due to importations from the 2017-2018 Nigerian outbreak. Person to person spread can occur through close contact with lesions, body fluids, respiratory droplets and contaminated objects. Once inside the body, the virus infects mucous membranes, epithelial cells and immune cells in adjacent tissues. The virus then replicates and spreads rapidly through the blood and lymphatic system. Tcells play an important role in regulating the immune response against the virus. However, Orthopoxvirus have evolved several mechanisms for evasion of the immune response. Disease surveillance is a crucial factor in virus risk assessment and outbreak control. For this review we searched for the main articles related to the pathogenesis of the virus published to date. The article highlights the need for further studies on transmissibility and pathogenicity of the strains associated with the 2022 outbreak.

Screening of specific DNA barcode, identification of germplasm resources, and analysis of genetic diversity of Atractylodes chinenesis / 药学学报

italic>Atractylodes chinensis has important medicinal and economic values. In this study, the chloroplast genome sequences of four A. chinensis samples from different producing areas were sequenced using the Illumina platform. The specific DNA barcodes were screened and the germplasm resources of A. chinensis samples from different producing areas and the genetic diversity of the population were analyzed basing on the specific barcodes. The whole chloroplast genomes of the four A. chinensis samples had a typical cyclic tetrad structure, with 112 genes annotated. The comparative genomics results indicated that ccsA and trnC-GCA_petN were potential specific DNA barcodes for intraspecific identification of A. chinensis. Polymerase chain reaction (PCR) analysis of ccsA and trnC-GCA_petN was performed on 256 samples from 14 areas in 9 provinces, and the amplification efficiency was 100%. Sequence analysis showed that ccsA and trnC-GCA_petN had 11 and 22 variant positions, which could identify 16 and 22 haplotypes, respectively. The combined sequence analysis identified 39 haplotypes, named Hap1-Hap39, of which the most abundant and widely distributed genotype was Hap9. Haplotype diversity (Hd) = 0.896 and nucleotide diversity (Pi) = 0.002 22 indicated high genetic diversity at the species level in A. chinensis. The genetic distances of the haplotypes were 0.000 00-0.004 88, indicating that there were small genetic differences among the haplotypes. The results of phylogenetic tree analysis showed that 39 haplotypes had very close genetic relationship, and formed two obvious branches with other groups of the same genus except Atractylodes macrocephala. This study plays an important role in the identification of the origin of A. chinensis and the protection and breeding of germplasm resources.

Comparative and phylogeny analysis of Asarum caudigerum and A. cardiophyllum complete chloroplast genomes / 药学学报

The complete chloroplast genome of medicinal plant Asarum caudigerum Hance and its close relative A. cardiophyllum Franchet were sequenced using Illumina Hiseq technology, and assembled, annotated, and characterized by bioinformatic methods in this study. Then phylogenetic analysis of the complete chloroplast genomes of A. caudigerum, A. cardiophyllum, and twelve published species was conducted. The results indicated that the chloroplast genomes ranged from 186 215-186 985 bp in length, with a large single copy (LSC, 89 445-90 169 bp) and two inverted repeats (IRa/IRb, 48 387-48 408 bp). The overall GC content was 37.4%-37.5%. A total of 144 chloroplast genes were annotated, including 98 protein coding genes, 38 tRNA genes and 8 rRNA genes. In addition, complex genomic rearrangements were detected in the chloroplast genome of Asarum. Meanwhile, visual evaluation of the discrete type of the sequence indicated that the variation level of non-coding region was higher than that of coding region. Phylogenetic analyses suggested that A. caudigerum and A. cardiophyllum were clustered into a single clade and A. cardiophyllum, A. sieboldii var. seoulense, A. misandrum and A. maculatum were clustered into another single branch. These two clade were sister species. This study provides a scientific basis for the identification, phylogenetic relationship, molecular breeding of Asarum species.

Correlation analysis between SLC52A2 gene expression and prognosis of patients with uveal melanoma / 国际眼科杂志(Guoji Yanke Zazhi)

AIM: To analyze the correlation between SLC52A2 and uveal melanoma(UM)based on the cancer genome atlas(TCGA)database, and preliminarily explore the influence of SLC52A2 on the prognosis of UM patients and potential mechanism.METHODS: The clinical information on 80 patients with UM and mRNA expression data of SLC52A2 were collected from TCGA database. According to the expression level of SLC52A2, 80 patients were divided into high and low expression groups by median method. The relationship between the expression of SLC52A2 and clinical pathological features, as well as the prognosis was analyzed. The age, sex, clinical stage, pathological stage, and mRNA expression of SLC52A2 were analyzed by univariate and multivariate Cox analysis to search the prognostic factors of UM. Enrichment analyses were used to predict the possible regulatory pathway of SLC52A2 in UM.RESULTS: The survival prognosis of patients with low expression of SLC52A2 was better than that of patients with high expression of SLC52A2(P<0.05). The level of SLC52A2 has no significant correlation with the age, sex, clinical stage, and pathological stage of patients in both groups(P>0.05). Multivariate Cox analysis showed that the high expression of SLC52A2 was a risk factor for poor prognosis. The nomogram prediction model developed by combining the expression of SLC52A2 with clinical pathological features could accurately predict the survival probability of UM patients. The infiltration abundance of Th2 and Treg cells in both groups has difference(all P<0.001). GSEA analysis showed that the gene of JAK-STAT(FDR=0.028, P=0.004)and PI3K/AKT(FDR=0.017, P=0.002)were rich in samples with high expression of SLC52A2.CONCLUSION: The high expression of SLC52A2 is a risk factor for the prognosis of UM patients. SLC52A2 can be used as a biomarker to predict the prognosis and to become a new target for the treatment of patients with UM.