Characterization of Chromosomal and Repetitive Elements in the Genome of “Rana nigrovittata” (Anura, Ranidae): Revealed by Classical and Molecular Techniques

2021 ◽  
Vol 55 (6) ◽  
pp. 583-589
Author(s):  
Sumalee Phimphan ◽  
Surachest Aiumsumang ◽  
Alongklod Tanomtong
Keyword(s):  
Repetitive Elements ◽  
Molecular Techniques

scholarly journals Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 405
Author(s):  
Anna Matysiak ◽  
Michal Kabza ◽  
Justyna A. Karolak ◽  
Marcelina M. Jaworska ◽  
Malgorzata Rydzanicz ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Ocular Surface ◽  
Molecular Techniques ◽  
Corneal Tissue ◽  
Rna Seq ◽  
Microbiome Composition ◽  
Viral Sequences ◽  
Pcr Techniques ◽  
Unmapped Reads

The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria, Firmicutes, and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.

scholarly journals Biosorption potential and molecular characterization of metal resistant autochthonous microbes from tannery solid waste

2021 ◽  
Author(s):  
Hajira Younas ◽  
Aisha Nazir ◽  
Zakia Latif ◽  
Janice E Thies ◽  
Muhammad Shafiq ◽  
...  
Keyword(s):  
Solid Waste ◽  
Its Region ◽  
Metal Resistance ◽  
Molecular Techniques ◽  
Bacterial Strains ◽  
Fungal Strains ◽  
Resistant Strains ◽  
Tannery Solid Waste ◽  
Clean Metal

This study encompasses isolation and screening of heavy metal-resistant fungal and bacterial strains from tannery solid waste (TSW). Twelve fungal strains and twenty-five bacterial strains were isolated from TSW. The growth of fungal strains was observed against different heavy metals ranging from 10 mg L -1 to 1050 mg L -1 and the growth of bacteria was observed in metal concentrations ranging from 10 mg L -1 to 1200 mg L -1 . Five multi-metal resistant fungal isolates belonging to the genus Trichoderma and ten bacterial isolates belonging to the genus Bacillus showed good metal resistance and biosorption potential. They were identified through molecular techniques, fungi based on ITS region ribotyping, and bacteria based on 16S rRNA ribotyping. The fungal strains were characterized as T. hamatum (TSWF-06), T. harzianum (TSWF-11), T. lixii (TSWF-02) and T. pseudokoningii (TSWF-03, TSWF-10). The bacterial strains were characterized as Bacillus xiamenensis (TSW-02), B. velezensis (TSW-05), B. piscis (TSW-06), B. safensis (TSW-10), B. subtilis (TSW-14, TSW-15, TSW-17) B. licheniformis (TSW-19), B. cereus (TSW-20) and B. thuringiensis (TSW-22). The fungal strains namely, T. pseudokoningii (TSWF-03) and T. harzianum proved to be two multi-metal resistant strains with good biosorption efficiency. Unlike fungi, bacterial strains showed metal specific resistance. The strains Bacillus xiamenensis , B. subtilis (TSW-14) and B. subtilis (TSW-15) showed good biosorption efficiency against Cr, B. safensis against Cu, B. piscis and B. subtilis (TSW-17) against Pb and B. licheniformis and B. thuringiensis against Zn. The autochthonous fungal and bacterial strains can therefore be employed to clean metal contaminated environments.

scholarly journals Characterization of Five New Earthworm Mitogenomes (Oligochaeta: Lumbricidae): Mitochondrial Phylogeny of Lumbricidae

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 580
Author(s):  
Hongyi Liu ◽  
Yufeng Zhang ◽  
Wei Xu ◽  
Yu Fang ◽  
Honghua Ruan
Keyword(s):  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Morphological Characteristics ◽  
Molecular Techniques ◽  
Phylogenetic Studies ◽  
Octolasion Tyrtaeum ◽  
Eisenia Nordenskioldi ◽  
Novel Strategy

Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendrobaena octaedra, Eisenia andrei, Eisenia nordenskioldi, and Octolasion tyrtaeum) with lengths ranging from 14,977 to 15,715 were presented. Each mitogenome possessed a putative control region that resided between tRNA-Arg and tRNA-His. All of the PCGs were under negative selection according to the value of Ka/Ks. The phylogenetic trees supported the classification of Eisenia and Lumbricus; however, the trees based on cox1 did not. Through various comparisons, it was determined that cox1 fragments might be more suitable for molecular identification. These results lay the foundation for further phylogenetic studies on Lumbricidae.

scholarly journals Massive sequencing of artisan cheeses from raw sheep’s milk

2019 ◽  
Vol 6 (5) ◽  
pp. 236-240
Author(s):  
Ruiz Julia ◽  
Etcheverria Analia ◽  
Padola Nora ◽  
Kruger Alejandra ◽  
Medina Luis
Keyword(s):  
Dairy Products ◽  
Food Industry ◽  
Streptococcus Thermophilus ◽  
Molecular Techniques ◽  
Native Flora ◽  
Three Samples ◽  
Massive Sequencing ◽  
Traditional Fermentation ◽  
Antibacterial Capacity

Lactic acid bacteria (LAB) are used in the food industry to confer aromatic characteristics and their antibacterial capacity. In this study the native flora of LAB that participates in the traditional fermentation of semi-hard cheeses made with raw sheep's milk from the region of Andalusia, Spain was analyzed. Three samples of four different commercial cheeses were taken. Massive sequencing was carried out to identify the lactic and accompanying flora. Predominant lactic flora was Lactococcus lactis, Streptococcus thermophilus, Lactobacillus paracasei and Lactococcus raffinolactis, and to a lesser extent other species of the genera Lactobacillus, Streptococcus, Pediococcus and Leuconestoc. The accompanying flora was composed of species of the genera Mycoplasma, Pseudomonas, Acinetobacter, Chryseobacterium, Mannheimia, Trueperella, Enterococcus, Vibrio, Serratia, Macrococcus, Staphylococcus, Massilia, Flavobacterium, Yersinia, Gallaecimonas, Hafnia, Leclercia, Obesumbacterium, Morganella and Kluyvera. These results show that modern molecular techniques are very good tools to identify natural LABs of artisanal dairy products. The characterization of the native flora of the artisanal cheese allows us to evaluate the microbiological diversity of the natural population of LAB and the symbiosis with another type of flora.

Morphological and molecular characterization of adult worms of Leucochloridium paradoxum Carus, 1835 and L. perturbatum Pojmańska, 1969 (Digenea: Leucochloridiidae) from the great tit, Parus major L., 1758 and similarity with the sporocyst stages

2013 ◽  
Vol 88 (4) ◽  
pp. 506-510 ◽  
Author(s):  
I. Rząd ◽  
P. Hofsoe ◽  
R. Panicz ◽  
J.K. Nowakowski
Keyword(s):  
Parus Major ◽  
Morphological Characters ◽  
Great Tit ◽  
Molecular Techniques ◽  
Morphological Identification ◽  
The Baltic Sea ◽  
The Baltic ◽  
Morphological And Molecular Characterization ◽  
Sea Coast

AbstractUnlike the sporocyst stages, adult leucochloridiid digeneans are difficult to differentiate. Sporocyst broodsacs can be identified on the basis of their colour and banding pattern, but in the absence of broodsacs and when experimental infection cannot be performed, tentative morphological identification needs to be verified, and molecular techniques offer a tool to do this. In this study, adult leucochloridiid digeneans were collected from the great tit (Parus major) found dead at three localities at or near the Baltic Sea coast (Hel, Bukowo-Kopań and Szczecin) in northern Poland. On the basis of differences in their morphological characters, Hel specimens were tentatively assigned to Leucochloridium perturbatum, Bukowo-Kopań and Szczecin specimens being identified tentatively as L. paradoxum. Subsequent ribosomal DNA sequence analysis confirmed the identification of these leucochloridiid flukes. Nucleotide sequences discriminating between the two species were identical to those used by earlier authors as characteristic of two distinctly different sporocyst broodsacs representing L. perturbatum and L. paradoxum.

scholarly journals Prevalence and Molecular Epidemiological Data onDirofilaria immitisin Dogs from Northeastern States of India

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Sonjoy Kumar Borthakur ◽  
Dilip Kumar Deka ◽  
Saidul Islam ◽  
Dilip Kumar Sarma ◽  
Prabhat Chandra Sarmah
Keyword(s):  
Epidemiological Data ◽  
Elisa Test ◽  
Molecular Techniques ◽  
Diagnostic Methods ◽  
Molecular Tools ◽  
Stray Dogs ◽  
Concentration Technique ◽  
Working Dogs ◽  
Polymerase Chain

The aim of the present study was to determine the prevalence ofDirofilaria immitisin stray, pet, and working dogs (n=413, 266, and 103, resp.) from Guwahati (Assam) and Aizawl (Mizoram), areas located in two Northeastern States of India. Diagnostic methods applied were microscopy (wet film and Knott’s concentration technique), immunological test (Ag ELISA by SNAP 4Dx ELISA kit), and molecular tools (polymerase chain reaction and sequencing), which evidenced 11.38, 18.03, and 13.93% of positive animals, respectively. No significant differences were observed by area (18.23% versus 17.68%) nor by sex (18.1% versus 17.9%), whereas stray dogs proved more infected than other groups (P<0.05). ELISA test evidenced an overall 22.69% of occult infections, mainly in working dogs (60%), and molecular techniques detectedDirofilaria (Nochtiella) repensin 4 stray dogs from Guwahati. Characterization ofD. immitisisolates for ITS-2 region showed close identity with South Asian isolates.

scholarly journals Genetic and Morphological Characterization of Mangifera indica L. Growing in Egypt

HortScience ◽  
2018 ◽  
Vol 53 (9) ◽  
pp. 1266-1270 ◽  
Author(s):  
Nader R. Abdelsalam ◽  
Hayssam M. Ali ◽  
Mohamed Z.M. Salem ◽  
Elsayed G. Ibrahem ◽  
Mohamed S. Elshikh
Keyword(s):  
Genetic Diversity ◽  
Mangifera Indica ◽  
Morphological Characteristics ◽  
Morphological Characterization ◽  
Molecular Techniques ◽  
Germplasm Management ◽  
Fruit Crops ◽  
The Family ◽  
High Diversity

Mango (Mangifera indica L.) is a fruit crops belong to the family Anacardiaceae and is the oldest cultivated tree worldwide. Cultivars maintained in Egypt have not been investigated previously. Mango was first brought to Egypt from South Asia. Morphological and molecular techniques were used to identify the genetic diversity within 28 mango cultivars. SSR and EST-SSR were used for optimizing germplasm management of mango cultivars. Significant variations were observed in morphological characteristics and genetic polymorphism, as they ranged from 0.71% to 100%. High diversity was confirmed as a pattern of morphological and genotypes data. Data from the present study may be used to calculate the mango relationship and diversity currently grown in Egypt.

Molecular Characterization of Some Equine Vector-Borne Pathogens and Identification of Their Vectors in Egypt

2020 ◽  
Author(s):  
Hend H.A.M. Abdullah ◽  
Dina Aboelsoued ◽  
Tarek K Farag ◽  
Kadria N Abdel Megeed ◽  
Sobhy Abdel-Shafy ◽  
...  
Keyword(s):  
Molecular Techniques ◽  
Ixodid Ticks ◽  
Morphological Identification ◽  
Vector Borne Diseases ◽  
Maldi Tof ◽  
Vector Borne ◽  
First Time ◽  
Multiple Pathogens ◽  
Apparently Healthy

Abstract Background Equine vector borne diseases (EVBD) have been considered emerging and reemerging diseases transmitted by arthropods and most of these diseases have zoonotic concern. This study was designed to screen EVBD in equines and their vectors using molecular analyses and identify vectors by MALDI-TOF and molecular techniques.Methods A total of 335 blood samples were collected from apparently healthy equines (320 from horses and 15 from donkeys) from Cairo and Beni-Suef provinces in Egypt. A total of 166 arthropods (105 sucking flies and 61 ticks) were collected from the same animals. MALDI-TOF and molecular techniques were used to confirm the findings of morphological identification of vector. Quantitative PCR and Standard PCR coupled with sequencing were performed in equines and vectors DNA for screening multiple pathogens.Results MALDI-TOF and molecular techniques confirmed that Hippoposca equina (louse fly), Rhipicephalus annulatus (Rh. annulatus) and Rh. microplus ixodid ticks were found. In vectors, we identified Anaplasma marginale (A. marginale; 1.6%), A. platys-like (1.6%) and a new Ehrlichia sp. (4.9%) in Rh. microplus, while Ehrlichia rustica (E. rustica) was found in Rh. microplus and Rh. annulatus. Likewise, Borrelia theileri was identified in Rh. microplus (3.3%). For H. equina, Anaplasma and Borrelia sp. DNA were detected by qPCR only. In equines, A. marginale (0.6%), A. ovis (0.6%) and Theileria ovis (T. ovis; 0.6%) were found in donkeys. In horses, T. equi (1.2%) and a new Theileria sp. Africa (2.7%) were identified.Conclusions For the first time, we reported here the presence of Rh. microplus as a competent tick for Rh. annulatus in Egypt using MALDI-TOF and molecular identification. To the best of our knowledge, we provided the first detection of different pathogens as A. marginale, A. platys-like, E. rustica, new Ehrlichia sp., B. theileri in Rh. microplus, A. marginale, A. ovis and T. ovis in donkeys and a new Theileria sp. Africa in horses in Egypt.

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