DNA markers are used as a size reference and sample loading control during gel electrophoresis. Most markers are designed for conventional gel electrophoresis to separate DNA smaller than 20 kb. For ...larger molecules, pulsed-field gel electrophoresis (PFGE) marker is required. Limited PFGE markers are available because large DNA are prone to nicking and degradation, causing smeary bands. Here, we developed a robust marker based on bacterial artificial chromosomes (BACs) with bands up to 184 kb. This marker could consistently confer intense and distinct bands for accurate gel analysis in molecular biology studies, laboratory validations or clinical diagnosis.
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•PFGE marker is prone to DNA degradation, which gives smeary banding patterns, causing difficulties in gel analysis.•We have developed a set of low-range PFGE markers based on restriction endonuclease fragments of bacterial artificial chromosomes.•Instead of giving only single banding pattern, this method offers almost endless possible combinations of customizable bands up to 184 kb.•It gives distinct band distribution and accurate quantification of nucleic acid compared to traditional markers.
Medicinal plants have been used worldwide for centuries to maintain health and to treat diseases, more so chronic diseases. However, adulteration and use of spurious materials as substitutes have ...become a major concern for users and industry for reasons of safety and efficacy. Therefore, authentication of medicinal plants is of utmost importance. Morphological, anatomical, chemical and DNA markers solve the problem by differentiating the genuine material from the adulterants, substitutes and spurious drugs. DNA markers use nucleotide sequences to identify species; it takes preference over the other two markers being not age dependent, tissue specific and having a higher discriminating power. Therefore, characterization of plants with such markers is an ideal approach for identification of medicinal plant species and populations/varieties of the same species. Availability of certified taxonomic specimens in herbaria is certainly required for unambiguous confirmation through final visual comparison and analysis.
•DNA markers have upper hand in indentifying medicinal plants compared to other markers•Of the various DNA markers, LAMP, SCAR and DNA barcoding are ideal for authentication•DNA markers are used to build a reference library of traditional medicine.
Colorectal cancer (CRC) is among the most common cancers. In fact, it is placed in the third place among the most diagnosed cancer in men, after lung and prostate cancer, and in the second one for ...the most diagnosed cancer in women, following breast cancer. Moreover, its high mortality rates classifies it among the leading causes of cancer‑related death worldwide. Thus, in order to help clinicians to optimize their practice, it is crucial to introduce more effective tools that will improve not only early diagnosis, but also prediction of the most likely progression of the disease and response to chemotherapy. In that way, they will be able to decrease both morbidity and mortality of their patients. In accordance with that, colon cancer research has described numerous biomarkers for diagnostic, prognostic and predictive purposes that either alone or as part of a panel would help improve patient's clinical management. This review aims to describe the most accepted biomarkers among those proposed for use in CRC divided based on the clinical specimen that is examined (tissue, faeces or blood) along with their restrictions. Lastly, new insight in CRC monitoring will be discussed presenting promising emerging biomarkers (telomerase activity, telomere length and micronuclei frequency).
The novel machine learning technique Random Forest (RF) was used to test if the genetic differentiation of populations of marine species may be related to any of the key environmental variables known ...to shape species distributions. The study was performed in North and Baltic Sea characterized by strong gradients of environmental factors and almost continuous distributions of Mytilus mussel populations. Assessment of the species identity was performed using four nuclear DNA markers, and previously published single nucleotide polymorphism (SNP) data. A general pattern of cline variation was observed with increasing Mytilus trossulus share towards the eastern Baltic Sea. Average allele share rose to 61% in Höga Kusten, Gulf of Bothnia. All Baltic Sea samples revealed a strong introgression of Mytilus edulis and a limited introgression of M. trossulus through the Danish Straits.
The studied environmental variables described 67 and 68% of the variability in the allele frequencies of M. edulis and M. trossulus. Salinity defined over 50% of the variability in the gene frequencies of the studied Mytilus spp. populations. Changes along this environmental gradient were not gradual but instead a significant shift from gene dominance was found at a salinity of 12 PSU. Water temperature and the trophic status of the sea area had only moderate association with the gene frequencies. The obtained results showed that the novel machine learning technique can be successfully used for finding correlations between genetic differentiation of populations and environmental variables and for defining the functional form of these linkages.
Background: Current study was designed to provide a better insight into the circulating genotypes, genetic diversity, and population structure of Echinococcus spp. between southeast of Iran and ...Pakistan. Methods: From Jun 2020 to Dec 2020, 46 hydatid cysts were taken from human (n: 6), camel (n: 10), goat (n: 10), cattle (n: 10) and sheep (n: 10) in various cities of Sistan and Baluchestan Province of Iran, located at the neighborhood of Pakistan. DNA samples were extracted, amplified, and subjected to sequence analysis of cox1 and nad1 genes. Results: The phylogeny inferred by the Maximum Likelihood algorithm indicated that G1 genotype (n: 19), G3 genotype (n: 14) and G6 genotype (n: 13) assigned into their specific clades. The diversity indices showed a moderate (nad1: Hd: 0.485) to high haplotype diversity (cox1: Hd: 0.867) of E. granulosus s.s. (G1/G3) and low nucleotide diversity. The negative value of Tajima’s D and Fu’s Fs test displayed deviation from neutrality indicating a recent population expansion. A parsimonious network of the haplotypes of cox1 displayed star-like features in the overall population containing IR9/PAK1/G1, IR2/PAK2/G3 and IR18/G6 as the most common haplotypes. A pairwise fixation index (Fst) indicated that E. granulosus s.s. populations are genetically moderate differentiated between southeast of Iran and Pakistan. The extension of haplotypes PAK18/G1 (sheep) and PAK26/G1 (cattle) toward Iranian haplogroup revealed that there is dawn of Echinococcus flow due to a transfer of alleles between mentioned populations through transport of livestock or their domestication. Conclusion: The current findings strengthen our knowledge concerning the evolutionary paradigms of E. granulosus in southeastern borders of Iran and is effective in controlling of hydatidosis.
Herbal products, such as dietary supplements, have become a subject of increasing global importance for their health benefits and economic considerations. However, they have also been targets of ...adulteration practices, being the accurate identification of botanicals in herbal products of utmost importance to protect the health and expectations of consumers. Particularly, in the case of dietary supplements, which can have different types of formulations, the identification of plant material used in their production is often a research challenge. DNA‐based techniques have played a crucial role on the development of a wide range of tools for the authentication of herbal products. Therefore, this review intends to describe their main progresses, critically discussing their advantages and drawbacks when applied to authenticate herbal products, focusing on dietary supplements. DNA barcoding is particularly emphasized because it has provided the highest number of applications, followed by the advances on high‐resolution melting analysis combined with DNA barcodes. A special emphasis is also given to the promising approaches relying on DNA metabarcoding and isothermal amplification.
Recent phylogenetic reconstructions in the Ceropegieae (Apocynaceae-Asclepiadoideae) show that the 357 species of highly succulent stapeliads and four lineages of the 141 species of Brachystelma ...R.Br. ex Sims are nested within the 219 species of Ceropegia L.
The stapeliads, shown convincingly to be nested within Ceropegia, are primarily characterized by their non-climbing, highly succulent, tuberculate stems with fleshy flowers with a mostly short corolla-tube. However, highly succulent, tuberculate stems are not restricted to the stapeliads and are present in four lineages of Ceropegia. Furthermore, tubular flowers are also found among the stapeliads and are not restricted to Ceropegia. Since a slender, tubular corolla is extremely homoplasious within Brachystelma, Ceropegia and the stapeliads, we move away from this as defining Ceropegia to recognize some sections in which there is a range from slender, tubular flowers to almost flat flowers.
To re-establish a monophyletic Ceropegia, we propose a new classification in which Brachystelma and all genera of the stapeliads are placed in a greatly enlarged Ceropegia. This new concept of Ceropegia is defined by the lack of hard, wiry roots, the softly fleshy tissue of the peduncles and pedicels, the absence of any corolline corona, the presence of two well-developed series of the staminal corona and the presence of a compitum in the style-head leading to the fertilization of both ovaries. We transfer the species of Brachystelma into several sections of Ceropegia and reduce the 31 stapeliad genera to sections of Ceropegia, after which Ceropegia has 63 sections. Sect. Chamaesiphon H.Huber is the largest with 115 species, two sections among the stapeliads each contain over 50 species but the remaining sections are mostly considerably smaller. We provide diagnostic descriptions, lists of included species and distributions for each of the subdivisions that we recognise. Over 400 new combinations are made in Ceropegia.
•Vegetative, floral and molecular characters show Brachystelma and the stapeliads nested inside Ceropegia.•Brachystelma is polyphyletic, the stapeliads are monophyletic and Ceropegia is paraphyletic.•We argue for expanding the present concept of Ceropegia to recover a monophyletic Ceropegia.
Thirteen microsatellite markers were developed for one of the vulnerable snake species Indian Rat snake (Ptyas mucosa) in Indian ecosystems that are now subject to much restoration efforts. All loci ...were polymorphic when tested across 25 individuals. The average number of alleles per locus varied from 4 to 7 (mean 5.2). Observed and expected heterozygosity ranged from 0.76 to 1.00 and 0.59–0.94, respectively and the average polymorphic information content is 0.664 were identified demonstrating the utility of these markers for the investigation of the population genetic structure and diversity of this species.
species exhibit a broad distribution in nature and play a crucial role in human and ecological environments.
Two
species isolated from the ancient Great Wall loess in the Mentougou District of ...Beijing, China, were identified and described as new species, namely,
and
, based on morphological characteristics and phylogenetic analyses of multiple genes including ITS,
,
and
genes.
Phylogenetic analyses showed that both novel species formed a distinctive lineage and that they were most closely related to
and
, respectively.
is characterized by biverticillate conidiophores that produce globose conidia and is distinguished from similar species by its capacity to grow on CYA at 30°C.
is typically recognized by its restricted growth and floccose colony texture. The description of these two new species provided additional knowledge and new insights into the ecology and distribution of
.
The recent outbreak of the Olive Quick Decline Syndrome (OQDS), caused by
Xylella fastidiosa
subsp.
pauca
(
Xf
), is dramatically altering ecosystem services in the peninsula of Salento (Apulia ...Region, southeastern Italy). Here we report the accomplishment of several exploratory missions in the Salento area, resulting in the identification of thirty paucisymptomatic or asymptomatic plants in olive orchards severely affected by the OQDS. The genetic profiles of such putatively resistant plants (PRPs), assessed by a selection of ten simple sequence repeat (SSR) markers, were compared with those of 141 Mediterranean cultivars. Most (23) PRPs formed a genetic cluster (K1) with 22 Italian cultivars, including ‘Leccino’ and ‘FS17’, previously reported as resistant to
Xf
. The remaining PRPs displayed relatedness with genetically differentiated germplasm, including a cluster of Tunisian cultivars. Markedly lower colonization levels were observed in PRPs of the cluster K1 with respect to control plants. Field evaluation of four cultivars related to PRPs allowed the definition of partial resistance in the genotypes ‘Frantoio’ and ‘Nocellara Messinese’. Some of the PRPs identified in this study might be exploited in cultivation, or as parental clones of breeding programs. In addition, our results indicate the possibility to characterize resistance to
Xf
in cultivars genetically related to PRPs.
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