molecular analysis
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2022 ◽  
Vol 43 (2) ◽  
pp. 585-598
Author(s):  
Ana Paula Molinari Candeias ◽  
◽  
Gabrieli Maria Huff ◽  
Adriana Fiorini Rosado ◽  
André Luis Vriesman Beninca ◽  
...  

The objective of this study is to compare the direct fecal smear (DFS) and centrifugal sedimentation (CS) methods in the detection of Cryptosporidium spp. oocysts in fecal samples of dairy calves. One hundred and fourteen fecal samples were collected from calves aged up to six months from 10 dairy farms located in Palotina and Francisco Alves, Paraná, Brazil. The microscopic analysis revealed the presence of Cryptosporidium spp. oocysts in 51.75% (59/114) of the samples in both methods. In CS, 48.25% (55/114) of the samples were positive, while in DFS slides, only 6.14% (7/114) were positive. Only 4 samples were positive exclusively in DFS. To ensure that there were no false-negative results in the microscopic analysis, the 55 samples that were negative in both DFS and CS were selected for molecular analysis using the nested PCR (nPCR). Of these 55 samples, 24% (13/55) were positive and forwarded for sequencing part of the genome, which made it possible to identify C. parvum, C. bovis and C. ryanae. Besides the characterization of the Cryptosporidium species, it was possible to identify bacteria of the genus Acinetobacter interfering directly in the analyzed samples. The microscopic analysis also revealed higher sensitivity when CS was used to make the fecal smears. However, some samples that were negative in this technique had positive PCR results. Thus, molecular analysis is indicated to confirm cases of Cryptosporidium spp. Further studies are necessary to prove the specificities of the used primers since the results obtained in nPCR were positive for the protozoan but, when genetic sequencing was performed, Acinetobacter spp. was identified.


ESMO Open ◽  
2022 ◽  
Vol 7 (1) ◽  
pp. 100308
Author(s):  
M. Simbolo ◽  
G. Centonze ◽  
G. Ali ◽  
G. Garzone ◽  
S. Taormina ◽  
...  

Author(s):  
Lucas Henrique Fantin ◽  
Ana Lúcia de Souza Madureira Felício ◽  
Ciro Hideki Sumida ◽  
Ricardo Marcelo Gonçalves ◽  
Karla Braga ◽  
...  

2022 ◽  
Vol 17 (12) ◽  
Author(s):  
Ana Carolina Almeida de Oliveira Ferreira ◽  
Erika da Silva Monteiro ◽  
David de Oliveira Sousa ◽  
Calliandra Maria de Souza Silva ◽  
Izabel Cristina Rodrigues Da Silva ◽  
...  

Tilapia (Oreochromis niloticus) is the most cultivated and consumed freshwater fish in Brazil. The present study aimed to evaluate the microbiological quality of ice and fresh tilapia samples commercialized in the Federal District. Tilapia samples were tested for counts of mesophilic and psychrotrophic bacteria, determination of total and thermotolerant coliforms, Staphylococcus aureus counts and presence of Salmonella. Ice samples were analyzed for determination of total coliforms and thermotolerant coliforms and presence of Escherichia coli. Of the 20 samples of fresh tilapia analyzed, ten samples (50%) presented Salmonella (genetically confirmed through the presence of the invA gene) and, therefore, were unfit for consumption. S. aureus was found in 11 samples (55%), and one sample of fillet presented S. aureus counts (3.15 CFU/g) above the limit allowed by Brazilian legislation (3 log CFU/g). S. aureus colonies were confirmed by detection of CoA gene in molecular analysis. Of the 14 ice samples analyzed, 12 samples (85.7%) were unfit for use in fish conservation due to the presence of total coliforms and 9 ice samples (64.3%) were also contaminated with thermotolerant coliforms. E. coli was isolated from 6 ice samples (42.9%) and confirmed in the molecular analysis through the amplification of the MalB gene. In conclusion, the high contamination of tilapia samples with Salmonella and of the ice used for its conservation with coliforms and E. coli indicates the need for better hygienic practices in the tilapia production chain, to increase its quality and microbiological safety.


Phytotaxa ◽  
2022 ◽  
Vol 531 (1) ◽  
pp. 1-17
Author(s):  
WICHARUJ TONGKHAM ◽  
SUPALAK PUMIKONG ◽  
NUTTHA POTAPOHN ◽  
WEENUN BUNDITHYA

A new endemic slipper orchid in the family Orchidaceae from Northern Thailand was described according to morphological and molecular analyses. Morphological information specifies the new slipper orchid Paphiopedilum charlesworthii var. lannaense to be similar to Paphiopedilum charlesworthii (Rolfe) Pfitzer 1895, with the exception of its staminode being obovate-obcordate with yellow color, glittery and rough surface. Molecular analysis by AFLP technique indicates that Paphiopedilum charlesworthii var. lannaense can be included as a member of section Paphiopedilum and is closely related to Paphiopedilum coccineum Perner, H. & Herrmann, R. (2000) (syn. Paphiopedilum barbigerum var. coccineum), from which it differs morphologically by dorsal sepal and petal characters. The morphological and molecular evidence supported that Paphiopedilum charlesworthii var. lannaense is a new slipper orchid in the genus Paphiopedilum (Cypripedioideae, Orchidaceae).


Author(s):  
Ingrid M. D. Di Benedetto ◽  
Valeria N. Debarbora ◽  
Alicia P. Benitez Ibalo ◽  
Elena B. Oscherov ◽  
Analía G. Autino ◽  
...  

In this study two species of soft ticks belonging to the genus Ornithodoros were recorded in three areas in the province of Corrientes, Argentina. Four larvae were identified as Ornithodoros hasei (Schulze, 1935) on Molossus molossus (Molossidae) in Paraje Tres Cerros (Department of San Martín), while 56 larvae were identified as Ornithodoros sp. cf. O. mimon Kohls, Clifford & Jones, 1969 on Eptesicus furinalis and Myotis levis (Vespertilionidae) in Paraje Galarza (Department of Santo Tomé) and Colonia Carlos Pellegrini (Department of San Martín). These last two locations are found within the Esteros del Iberá eco-region.  The known distribution range of O. hasei and O. cf. O. mimon is expanded to include the province of Corrientes. Two new ectoparasite-host associations were recorded for Argentina between O. hasei on M. molossus and O. cf. O. mimon on M. levis. The morphological differences together with the results of the phylogenetic analysis show that O. hasei presents genetic similarity with specimens from Brazil, and in Argentina, with ticks from Santa Fe. Instead, Ornithodoros sp. cf. O. mimon recorded in Corrientes and Uruguay belong to a different taxon than the O. mimon recorded in Brazil and Santa Fe, Argentina. Based on this, O. mimon should be considered a complex of species in which the specimens from Corrientes are provisionally considered as Ornithodoros sp. cf. O. mimon until their taxonomic status can be determined.


Author(s):  
Dinh Minh Tran ◽  
To Uyen Huynh ◽  
Thi Huyen Nguyen ◽  
Tu Oanh Do ◽  
Quang-Vinh Nguyen ◽  
...  

Author(s):  
Sibtain Ahmed ◽  
Fizza Akbar ◽  
Amyna Jaffar Ali ◽  
Bushra Afroze

Abstract Objectives Evaluation of clinical, biochemical and molecular analysis of Pakistani patients with hepatic GSDs. Methods Medical charts, biochemical, histopathological and molecular results of patients with hepatic GSD were reviewed. Results Out of 55 GSD patients, 41 (74.5%) were males and 14 (25.5%) were females with consanguinity in 50 (91%) patients. The median age of initial symptoms, clinic diagnosis and molecular diagnosis were 450 (IQR: 270–960), 1,095 (IQR: 510–1,825) and 1717 (IQR: 796–3,011) days, respectively. Molecular analysis and enzyme activity was available for 33 (60%) and two patients, respectively. GSD III (n=9) was most prevalent followed by GSD Ib (n=7), GSD IXc (n=6), GSD VI (n=4), GSD Ia (n=3), GSD XI (n=3), GSD IXb (n=2) and GSD IXa (n=1). In patients (n=33) who underwent molecular analysis; 19 different variants in eight genes associated with GSD were identified. We also report five novel variants, two in SLC37A4, one in AGL and two in PYGL contributing to the diagnosis of GSD Ib, GSD III and GSD VI, respectively. Conclusions Fifty-five patients of GSDs in 26 families from a single care provider indicate a relatively high frequency of GSD in Pakistan, with multiple unrelated families harboring identical disease-causing variants, on molecular analysis, including two known pathogenic variants in SLC37A4 and PHKG2, and a novel variant in AGL.


2022 ◽  
Vol 10 (1) ◽  
pp. 103
Author(s):  
Colin R. Tinsley ◽  
Noémie Jacques ◽  
Marine Lucas ◽  
Cécile Grondin ◽  
Jean-Luc Legras ◽  
...  

Geotrichum candidum is an environmental yeast, also found as part of the cheese surface microbiota, where it is important in the ripening of many traditional cheeses, such as Camembert. We have previously developed a Multi Locus Sequence Typing (MLST) scheme, which differentiated five clades, of which one contained only environmental isolates, two were composed almost entirely of dairy isolates, and two others contained a mixture of dairy, environmental, and miscellaneous food isolates. In order to provide a simple method to uniquely type G. candidum strains, and in addition to permit investigation of the population structure at a fine level, we describe here a molecular analysis using a set of twelve highly discriminating microsatellite-like markers. The present study consolidates the previously suggested division between dairy and environmental strains, and in addition distinguishes a specifically European group of environmental strains. This analysis permitted the discrimination of 72 genotypes from the collection of 80 isolates, while retaining the underlying meaningful phylogenetic relation between groups of strains.


Cancers ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 233
Author(s):  
Szilvia Lilla Csoma ◽  
Judit Bedekovics ◽  
Gergő Veres ◽  
Anita Árokszállási ◽  
Csilla András ◽  
...  

Biliary tract cancer (BTC) is a rare malignancy with a long disease course and an overall poor prognosis. Despite multiple chemotherapy agents, there is no defined second-line treatment opportunity for advanced BTCs. In the era of precision oncology, NGS plays an important role in identifying mutations that may predict the molecular pathomechanism and manage the BTC therapy. The peripheral blood liquid biopsy (LB) of cancer patients represents variable amounts of cell-free DNA (cfDNA) released from tumor foci of any anatomical location. Our study aimed to identify somatic mutations and tumor variant burden (TVB) in cell-free and matched tumor DNA. We found a positive correlation between the estimated tumor volume and cfDNA yield (r = 0.9326, p < 0.0001). Comparing tissue and LB results, similar TVB was observed. SNVs were proven in 84% of the cases, while in two cases, only the LB sample was informative for molecular analysis. The most important aberrations in BTCs, such as FGFR2, IDH1, IDH2, KRAS, and TP53, could be detected in matched LB samples. Our prospective study demonstrates a minimally invasive testing approach to identify molecular genetic alterations in cholangiocarcinoma and gallbladder cancers. Clinical applications of cfDNA reflect by capturing the outstanding spatial tumor heterogeneity and guarantee novel aspects for the precision oncology treatment.


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