جستجوی مقالات مرتبط با کلیدواژه « dna sequencing » در نشریات گروه « پزشکی »

Immunotherapies that use the immune system to eliminate tumor cells have shown substantial therapeutic effectiveness in several types of human malignancies. Several investigations have emphasized the importance of neoantigens in the recognition of cancer cells by innate T lymphocytes. The identification of neoantigens, which are altered proteins that are selectively produced in tumor cells and not in healthy cells, has resulted in the development of enhanced cancer vaccines. Neoantigen targeting may stimulate anti-tumor T-cell reactions to eliminate tumors while sparing healthy cells from harm. Significant progress in DNA sequencing and computational biology has enabled the identification and development of potent neoantigens for application as therapeutic cancer vaccines. Therapeutic customized vaccines that target neoantigens have demonstrated encouraging outcomes in the field of cancer therapy. Therefore, this study aims to introduce neoantigens and their use in cancer immunotherapy.

The plants with pharmacological potential host potential endophytic fungi having metabolic interaction. Adhatoda vasica Nees, a well-reputed medicinal plant in Asia, has very few investigations on the plant's endophytic fungi available. This study reports the isolation, identification, and bioactive potential determination of the endophytes from the leaf and stem of the plant growing in Bangladesh.

A protocol for fungus isolation was followed, including the significant steps: sample collection, surface sterilization, cultivation, preliminary selection, and purification. The fungal species were identified by morphological and molecular features, and then, small-scale cultivation followed solvent treatment (chloroform) to extract secondary metabolites. The extract's cytotoxic, antimicrobial, and antioxidant activities were determined by brine shrimp lethality bioassay, disc diffusion method, and DPPH free radical scavenging activity, respectively.

Eight endophytic fungi were isolated and identified: four Fusarium sp., two Colletotrichum sp., one Phacidiopycnis sp., one Lasiodiplodia sp. Genome sequence confirmed two novel fungi from the plant: Fusarium solani (OR414980) and Colletotrichum gloeosporioides (OR420097). In bioactivity testing, the fungi from the stem exhibited better activity than the leaf fungi. Among the eight fungi, Lasiodiplodia sp. showed the highest and most significant potential in each bioactivity test. Its extract (100 μg/disc) was approximately 80% susceptible against Gram-negative and Gram-positive bacteria and a fungus A. flavus compared to references (30 μg/disc). The fungus's LC50 (4 h) was 0.45 μg/mL, whereas vincristin sulfate showed nearly half.

The study recorded uncommon fungi of four genera from A. vasica; some showed remarkable bioactivity.

 Methicillin Resistance Staphylococcus aureus (MRSA) causes staph infections, produces numerous toxins and virulence factors, and displays antibiotic resistance. Therefore, this study aimed to detect MRSA and its antibiotic-resistant patterns and evaluate the toxins genes in S. aureus isolates from Baghdad, Iraq.

 Two hundred twenty bacterial samples were collected from different clinical sources in Iraq, 2022-2023. The diagnosis was made using traditional culture, microscopic examinations, and molecular diagnosis using the 16srRNA gene and mecA gene used for Methicillin Resistance detection. In addition, Antibiotic resistance patterns were detected using VITEK-2. Also, the toxins genes were determined by sequencing.

 Fifty isolates were identified as S. aureus, and the strains showed high resistance to Benzylpenicillin, Erythromycin, Oxacillin, and Clindamycin. PCR showed a prevalence of the mecA gene in methicillin resistance S. aureus isolates by 100%, while toxin genes that were present in S. aureus were LukD/E gene 50(100%), eta gene 50(100%), etd gene 47(94%), LukS/F gene 34(68%) and tst gene 21(42%). All isolates tested negative for the etb gene. The results of the sequencing analysis of the studied genes showed that there were no genetic mutations. They were 100% identical except for the eta gene, and the results indicated three genetic mutations.

 All S. aureus isolates had the mecA gene for methicillin resistance, and S. aureus possessed toxin genes. The sequencing analysis of the eta gene indicated the presence of various mutations, including the silent mutations.

Telomere-related tumorigenesis mechanisms in the salivary gland, including mutation in the promoter region of TERT, have been rarely investigated. Therefore, the present study aimed to investigate the mutation in the promoter region of TERT in benign and malignant salivary gland tumors.

This was a descriptive-analytical cross-sectional study. Tissue samples of 54 patients with primary salivary gland tumors sent to the pathology department of Rasool-e-Akram Hospital from September 2017 to September 2021 were examined. Fifteen samples including two groups of the most common benign tumors (n=5; 3 pleomorphic adenomas and 2 Warthin tumors) and four groups of the most common malignant tumors (n=10; 3 mucoepidermoid carcinomas, 3 adenoid cystic carcinomas, 2 acinic cell carcinoma, and 2 salivary duct carcinoma) were selected. The promoter region of TERT, including well-known hot spot regions, is sequenced using the Sanger sequencing method. Data were analyzed using statistical software R version 4.1.2.

Of 15 salivary gland tumor specimens, consisting of  5 benign tumors and 10 malignant tumors after DNA sequencing, TERT promoter region mutation was only seen in one of the adenoid cystic carcinoma samples, located at -146 bp upstream from ATG (chr5: 1,295,250 C>T).

TERT promoter mutation was not different in malignant and benign salivary tumors. Nonetheless, there are a few studies that report TERT promoter mutation in adenoid cystic carcinoma of the salivary gland, necessitating the need for further investigations.

This study was conducted to determine the presence and molecular identify of Acanthamoeba, Naegleria and Vermamoeba in unimproved hot springs.

From Jul to Aug 2017, 54 water samples were collected from hot springs in different parts of the Guilan Province, North Iran. For the isolation of Acanthamoeba, Naegleria and Vermamoeba approximately 500 ml of the water samples were filtered through a cellulose nitrate membrane with a pore size of 0.45 μm. The filter was transferred onto non-nutrient agar plates seeded with Gram-negative bacteria (Escherichia coli) as a food source. The morphological key of page was used to identify free‐living amoebae (FLA) using an inverted microscope, PCR amplification targeting specific genes for each genus and sequencing determined frequent species and genotypes base on NCBI database.

Fifteen of the 54 samples were positive by culture and/or PCR for Acanthamoeba and other FLA from unimproved hot springs. By sequencing the positive isolates, the strains were shown to belong to Acanthamoeba castellanii (12 case isolates belonged to T4 genotype), 4 cases of V. vermiformis, and 3 cases of N. australiensis, 2 cases of N. pagei and 1 cases of N. gruberi.

Although FLA-mediated illnesses are not as high as in environmental distribution, but because of a poor prognosis, more investigations about FLA distribution in hot springs is critical. Hot spring may enhance exposure of the amoebae in individuals. Hence, more attention to unimproved hot springs is needed to prevent free-living amoebae mediated diseases.

Mucopolysaccharidosis VI (MPS VI) or Maroteaux-Lamy syndrome is a rare metabolic disorder, resulting from the deficient activity of the lysosomal enzyme arylsulfatase B (ARSB). The enzymatic defect of ARSB leads to progressive lysosomal storage disorder and accumulation of glycosaminoglycan (GAG) dermatan sulfate (DS), which causes harmful effects on various organs and tissues and short stature. To date, more than 160 different mutations have been reported in the ARSB gene.
Here, we analyzed 4 Iranian and 2 Afghan patients, with dysmorphism indicating MPS VI from North-east Iran. To validate the patients’ type of MPS VI, urine mucopolysaccharide and leukocyte ARSB activity were determined. Meanwhile, genomic DNA was amplified for all 8 exons and flanking intron sequences of the ARSB gene to analyze the spectrum of mutations responsible for the disorder in all patients.
Abnormal excretion of DS and low leukocyte ARSB activity were observed in the urine samples of all 6 studied patients. In direct DNA sequencing, we detected four different homozygous mutations in different exons, three of which seem not to have been reported previously: p.H178N, p.H242R, and p.*534W. All three novel substitutions were found in patients with Iranian breed. We further detected the IVS5>C mutation in Afghan siblings and four different homozygous polymorphisms, which have all been observed in other populations.
results indicated that missense mutations were the most common mutations in the ARSB gene, most of them being distributed throughout the ARSB gene and restricted to individual families, reflecting consanguineous marriages.

Plasmodium vivax apical membrane antigen-1(PvAMA-1) is a surface protein with polymorphic sites. This study was aimed to analyze the polymorphic amino acid residues at PvAMA-1 in different infected age groups. 92 blood samples were collected from south and southeast of Iran. The DNA coding for the domain I (DI), DII, and partial DIII of this antigen was amplified by Nested-PCR, and sequenced. Nucleotide mutations were found in 49 sites and based on the amino acid sequence, 30 variable sites were detected. Age distribution of malaria cases showed that the majority of the patients were between 10 to 30 years old. The scattering plot haplotypes by age showed an increasing incidence rate with age during childhood whereas incidence was the lowest in patients under five years old. Comparison of the polymorphic sites of PvAMA-1 in Iranian isolates with those found in other geographic regions of the world indicated nine common variable positions. In addition, a significant dependence was found between some particular substitutions and age categories. Dependence between particular substitutions and age groups suggests that certain residues in AMA-1 are responsible for clinical attacks in different ages, likely as a result of host immune pressure. The crystal structure of the PvAMA-1 showed that the amino acid substitutions that changed the protein charge were exclusively located in loops and turns where, the interactions with antibodies could occur. These data provide necessary information for an AMA-1 based malaria vaccine design to be effective across all ages.

Despite the high prevalence and drug resistance of disease in Sistan and Baluchestan Province of Iran, the species of cutaneous leishmaniasis (CL) has not been identified. In the present study, cytochrome b (Cyt b) was used in Sistan and Baluchestan to find species of Leishmania in suspected patients of CL using PCR-RFLP and DNA sequencing.
This study was conducted from Oct 2015 to Oct 2016. The samples were collected from the individuals clinically suspected to CL and referred to Iran Shahr, Chabahar, Khash, Zabol, Zahedan, Mirjaveh, and Nikshahr health centers. Overall, 700 Giemsa-Stained slides from the wound of patients suspected of CL were passive collected and examined under a light microscope at×1000. After DNA extraction, positive samples were used for Cyt b detection by PCR-RFLP to determine the parasite species. One hundred positive slides were selected for molecular studies. Among positive samples, 20% were sequenced. To compare the results of sequences, molecular evolutionary genetic analysis (MEGA6) was used.
Overall, 53 samples were identified as L.ý major and 47 samples (47%) L. tropica. Cyt b in L. major and L. tropica is converted to 400 and 480 bp and 130, 215 and 535 bp pieces respectively. In the isolated L. tropica and L. major, nucleotide changes were 3-5 (mainly in wobble site).
Infection was more related to L. major. PCR-RFLP method has a high sensitivity for diagnosis of Leishmania species.

Cystic echinococcosis (CE), called hydatidosis, is caused by the larval stage of Echinococcus granulosus spp. This disease is reported from different parts of Iran, where numerous cyst surgeries are done. It has been determined that there are different genotypes of E. granulosus. A particular genotype of E. granulosus may create different clinical symptoms. Therefore, we used molecular methods to determine the genotypes of hydatid cysts surgically removed in Birjand hospitals.
In this cross-sectional study, all available paraffin-embedded samples (9 cases) of patients during 2006 to 2015 who underwent surgery for hydatidosis were studied. The diagnoses were confirmed retrospectively by pathologists from the department of pathology, Birjand University of Medical Sciences. The profile of cyst size, location, and fertility of the cysts were recorded and their mitochondrial cox1 and nad1 genes were sequenced. The data were analyzed using bioinformatics software to identify their genotypes.
All the human isolates (8/9) except one were genotype G6 of Echinococcus canadensis, while one isolate belonged to G1 genotype (sheep strain) of E. granulosus sensu stricto (s.s.). The localization of the parasite in the patients infected with G6 was determined to be as follows: liver (3), lung (3), and intra-abdominal (2). In the patient infected with genotypes G1 of E. granulosus, the cyst was isolated from the abdominal cavity; only this patient had undergone a previous surgery for the treatment of hydatid cysts. All the nad1 sequences of G6 cysts of E. canadensis belonged to a haplotype, which was the case of cox1 sequences.
It seems that the main cause of human hydatidosis in South Khorasan province is genotype G6 of Echinococcus canadensis. It should be noted that CE caused by G6 genotype grows faster than those caused by G1. Some studies have revealed a higher tendency of this genotype to infect the brain and pulmonary tissue that shows the clinical significance of G6 genotype in this region.

The genus Penicillium contains a large number of ubiquitous environmental taxa, of which some species are clinically important. Identification of Penicillium down to the species level is currently based on polyphasic criteria, including phenotypic features and genetic markers. Biodiversity of the genus Penicillium from Mazandaran and Tehran provinces has not been described.. The current paper focused on the environmental biodiversity of Penicillium isolates within some areas of Mazandaran and Tehran provinces, based on morphological traits and the molecular data from partial sequence of the β-tubulin (BT2) gene.. A total of 400 strains were isolated from the environment and investigated using morphological tests and sequencing of BT2, in order to characterize the spectrum of the Penicillium species.. Sequence analysis of BT2 and morphological criteria of 20 strains representative of 10 species showed that Penicillium chrysogenum was the most prevalent species (n = 6), followed by P. polonicum (n = 3), P. glabrum (n = 2), P. palitans (n = 2), P. melanoconidium (n = 2), and other species, including P. expansum, P. canescense, P. griseofulvum, P. italicum, and P. raistrickii with one case each.. It was shown that partial β-tubulin sequence, as a reliable genetic target, supported specific morphological criteria for identification of the Penicillium species. Like other assessments throughout the world, P. chrysogenum remains the most frequent environmental Penicillium species in Mazandaran and Tehran Provinces..