scholarly journals Genetic analysis confirms the presence of Dicrocoelium dendriticum in the Himalaya ranges of Pakistan

2020 ◽  
Author(s):  
Muhammad Asim Khan ◽  
Kiran Afshan ◽  
Muddassar Nazar ◽  
Sabika Firasat ◽  
Umer Chaudhry ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Fasciola Hepatica ◽  
Species Variation ◽  
Nucleotide Polymorphisms ◽  
Species Identity ◽  
Liver Flukes ◽  
Species Specific ◽  
Ribosomal Cistron ◽  
The Himalaya ◽  
Cox 1

AbstractLancet liver flukes of the genus Dicrocoelium (Trematoda: Digenea) are recognised parasites of domestic and wild herbivores. The aim of the present study was to address a lack of knowledge of lancet flukes in the Himalaya ranges of Pakistan by characterising Dicrocoelium species collected from the Chitral valley. The morphology of 48 flukes belonging to eight host populations was examined in detail and according to published keys, they were identified as either D. dendriticum or Dicrocoelium chinensis. PCR and sequencing of fragments of ribosomal cistron DNA, and cytochrome oxidase-1 (COX-1) and NADH dehydrogenase-1 (ND-1) mitochondrial DNA from 34, 14 and 3 flukes revealed 10, 4 and 1 unique haplotypes, respectively. Single nucleotide polymorphisms in these haplotypes were used to differentiate between D. chinensis and D. dendriticum, and confirm the molecular species identity of each of the lancet flukes as D. dendriticum. Phylogenetic comparison of the D. dendriticum rDNA, COX-1 and ND-1 sequences with those from D. chinensis, Fasciola hepatica and Fasciola gigantica species was performed to assess within and between species variation and validate the use of species-specific markers for D. dendriticum. Genetic variations between D. dendriticum populations derived from different locations in the Himalaya ranges of Pakistan illustrate the potential impact of animal movements on gene flow. This work provides a proof of concept for the validation of species-specific D. dendriticum markers and is the first molecular confirmation of this parasite species from the Himalaya ranges of Pakistan. The characterisation of this parasite will allow research questions to be addressed on its ecology, biological diversity, and epidemiology.

Species identity matters: Functional responses to warming in congeneric turfs differ from those of a canopy algae but are species-specific

2021 ◽  
pp. 107396
Author(s):  
Isabella Provera ◽  
Cristina Piñeiro-Corbeira ◽  
Rodolfo Barreiro ◽  
Laura Díaz-Acosta ◽  
Pilar Díaz-Tapia
Keyword(s):  
Functional Responses ◽  
Species Identity ◽  
Species Specific ◽  
Canopy Algae

scholarly journals Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cooper J. Park ◽  
Nicole A. Caimi ◽  
Debbie C. Buecher ◽  
Ernest W. Valdez ◽  
Diana E. Northup ◽  
...  
Keyword(s):  
New Mexico ◽  
Genetic Manipulation ◽  
Distinct Species ◽  
Biosynthetic Gene Cluster ◽  
Genomic Variation ◽  
Species Variation ◽  
Nucleotide Polymorphisms ◽  
Peptide Synthetases ◽  
Genome Wide ◽  
Diversity Estimates

Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.

scholarly journals Across-species differences in pitch perception are consistent with differences in cochlear filtering

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Kerry MM Walker ◽  
Ray Gonzalez ◽  
Joe Z Kang ◽  
Josh H McDermott ◽  
Andrew J King
Keyword(s):  
Fundamental Frequency ◽  
Species Differences ◽  
Pitch Perception ◽  
Species Variation ◽  
Opposite Pattern ◽  
Auditory Periphery ◽  
Cochlear Tuning ◽  
Animal Vocalizations ◽  
Species Specific ◽  
Relative Salience

Pitch perception is critical for recognizing speech, music and animal vocalizations, but its neurobiological basis remains unsettled, in part because of divergent results across species. We investigated whether species-specific differences exist in the cues used to perceive pitch and whether these can be accounted for by differences in the auditory periphery. Ferrets accurately generalized pitch discriminations to untrained stimuli whenever temporal envelope cues were robust in the probe sounds, but not when resolved harmonics were the main available cue. By contrast, human listeners exhibited the opposite pattern of results on an analogous task, consistent with previous studies. Simulated cochlear responses in the two species suggest that differences in the relative salience of the two pitch cues can be attributed to differences in cochlear filter bandwidths. The results support the view that cross-species variation in pitch perception reflects the constraints of estimating a sound’s fundamental frequency given species-specific cochlear tuning.

scholarly journals Wind drives drought responses of green roof vegetation in two substrates

2018 ◽  
Author(s):  
Arkadiusz Przybysz ◽  
Konstantin Sonkin ◽  
Arne Sæbø ◽  
Hans Martin Hanslin ◽  
Keyword(s):  
Biological Diversity ◽  
Green Roof ◽  
Green Roofs ◽  
Plant Performance ◽  
Succulent Plant ◽  
Hieracium Pilosella ◽  
Key Factor ◽  
Substrate Moisture ◽  
Species Specific ◽  
Functional And Phylogenetic Diversity

The multifunctionality and delivery of ecosystem services from green roofs is improved by biological diversity of the roof vegetation. However, the frequency and intensity of drought episodes on extensive green roofs may limit the use of non-succulent species and the potential functional and phylogenetic diversity of the vegetation. Wind accelerates water use by plants and desiccation of the green roof substrate, and may be a key factor in selection of non-succulent plant species for green roofs. In this study, we tested wind interactions with green roof substrate composition and the effects on plant and substrate water balance, overall plant performance, and wilting and survival of three non-succulent species (Plantago maritima L., Hieracium pilosella L., and Festuca rubra L.) under realistic prolonged water deficit conditions. We found that, regardless of species or substrate tested, wind accelerated drought response. Drought-stressed plants exposed to wind wilted and died earlier, mostly due to more rapid desiccation of the growth substrate (critical substrate moisture content was 6-8%). The moderate wind levels applied did not affect plant performance when not combined with drought. Species with contrasting growth forms showed similar responses to treatments, but there were some species-specific responses. This highlights the importance of including wind to increase realism when evaluating drought exposure in non-succulent green roof vegetation.

scholarly journals Species Identity of Large Trees Affects the Composition and the Spatial Structure of Adjacent Trees

Forests ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1162
Author(s):  
Olga Cholewińska ◽  
Andrzej Keczyński ◽  
Barbara Kusińska ◽  
Bogdan Jaroszewicz
Keyword(s):  
Spatial Structure ◽  
Biological Diversity ◽  
Nearest Neighbor ◽  
Linear Models ◽  
Point Of View ◽  
Species Identity ◽  
Large Tree ◽  
Large Trees ◽  
Old Trees ◽  
Temperate Forest Ecosystem

Large trees are keystone structures for the functioning and maintenance of the biological diversity of wooded landscapes. Thus, we need a better understanding of large-tree–other-tree interactions and their effects on the diversity and spatial structure of the surrounding trees. We studied these interactions in the core of the Białowieża Primeval Forest—Europe’s best-preserved temperate forest ecosystem, characterized by high abundance of ancient trees. We measured diameter and bark thickness of the monumental trees of Acer platanoides L., Carpinus betulus L., Picea abies (L.) H. Karst, Quercus robur L., and Tilia cordata Mill., as well as the diameter and distance to the monumental tree of five nearest neighbor trees. The effects of the monumental tree on arrangements of the surrounding trees were studied with the help of linear models. We revealed that the species identity of a large tree had, in the case of C. betulus and T. cordata, a significant impact on the diversity of adjacent tree groupings, their distance to the central tree, and frequency of the neighboring trees. The distance between the neighbor and the large trees increased with the increasing diameter of the central tree. Our findings reinforce the call for the protection of large old trees, regardless of their species and where they grow from the geographical or ecosystem point of view.

scholarly journals Specific Detection of Fasciola hepatica and F. gigantica in Infected Domesticated Animals Using High-Resolution Melting Analysis (HRM)

2020 ◽  
Author(s):  
Zeinab MOGHADAMIZAD ◽  
Ahmad HOSSEINI-SAFA ◽  
Mehdi MOHEBALI ◽  
Peyman HEYDARIAN ◽  
Mojgan ARYAEIPOUR ◽  
...  
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
Fasciola Hepatica ◽  
High Resolution Melting Analysis ◽  
Universal Primers ◽  
Specific Primer ◽  
Universal Primer ◽  
Melting Analysis ◽  
Liver Flukes ◽  
Fasciola Spp

Background: It is difficult to make an exact morphological distinction between Fasciola hepatica and Fasciola gigantica. We used High Resolution Melting analysis (HRM) method to differentiate the F. hepatica species from F. gigantica in order to differentiate them. Methods: Overall, 80 adult liver flukes were collected from infected slaughtered animals including cattle, sheep and goats from Lorestan Province, western Iran from Sep 2015 to Aug 2017. Genomic DNA was extracted using commercial DNA extraction kit. The multilocus sequences of mDNA including COX1, COX3 and ND6 were amplified employing real-time PCR & HRM analysis. Specific and universal primer pairs were designed for differentiation Fasciola spp. Results: Universal primers cannot be used to distinguish between these two species, but in the contrary, specific primer pairs of each species could differentiate them properly. Molecular identification using specific primer pairs were consistent. Conclusion: HRM is a simple, fast and reliable method for detecting and differentiating F. hepatica from F. gigantica and can be used for diagnostic and epidemiological purposes.

scholarly journals Genome-wide markers reveal differentiation between and within the cryptic sister species, sunset and vermilion rockfish

2021 ◽  
Author(s):  
Gary C. Longo ◽  
John Harms ◽  
John R. Hyde ◽  
Matthew T. Craig ◽  
Ana Ramón-Laca ◽  
...  
Keyword(s):  
Management Strategies ◽  
Cost Effective ◽  
Sister Species ◽  
Nucleotide Polymorphisms ◽  
Relative Contribution ◽  
Genetic Groups ◽  
Cost Effective Method ◽  
Species Population ◽  
Single Complex ◽  
Species Specific

AbstractThe vermilion rockfish complex, which consists of the cryptic sister species vermilion and sunset rockfish, is one of the most valuable recreational fisheries on the U.S. West Coast. These species are currently managed as a single complex, and because of uncertainty surrounding the relative contribution of each species within existing data sources, the stock status of each species is not fully known. A reliable and cost-effective method is needed to disentangle these species that will allow for the development of abundance indices, life history profiles, and catch histories that may potentially support species-specific stock assessments. Using restriction-site associated DNA sequence (RADseq) markers we generated 10,003 polymorphic loci to characterize the vermilion rockfish complex. PCA and Bayesian clustering approaches based on these loci clearly distinguished between sunset and vermilion rockfishes and identified hybrid individuals. These loci included 203 highly differentiated (FST ≥ 0.99) single nucleotide polymorphisms, which we consider candidates in the planned development of a diagnostic assay capable of distinguishing between these cryptic species. In addition to clearly delineating to species, subsets of the interspecific markers allowed for insight into intraspecific differentiation in both species. Population genetic analyses for sunset rockfish identified two weakly divergent genetic groups with similar levels of genetic diversity. Vermilion rockfish, however, were characterized by three distinct genetic groups with much stronger signals of differentiation and significantly different genetic diversities. Collectively, these data will contribute to well-informed, species-specific management strategies to protect this valuable species complex.

scholarly journals Interaction between COX-1 and COX-2 increases susceptibility to ischemic stroke in a Chinese population

2019 ◽  
Author(s):  
Lei Zhao ◽  
Jinghuan Fang ◽  
Muke Zhou ◽  
Jie Zhou ◽  
Lihua Yu ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Gene Interaction ◽  
Additive Effect ◽  
Large Artery ◽  
Nucleotide Polymorphisms ◽  
Vessel Occlusion ◽  
Single Nucleotide ◽  
Ischemic Stroke Risk ◽  
Cox 2 ◽  
Cox 1

Abstract Background Mutations of cyclooxygenase gene (COX gene) may increase the susceptibility of ischemic stroke. We investigated five variants (rs5788, rs1330344, rs3842788, rs20417, and rs689466) of two COX genes to explain the association between these polymorphisms and ischemic stroke risk determine whether gene–gene interaction between these genes increase the susceptibility of ischemic stroke or its subtypes. Methods A total of 1981 study subjects (1078 cases and 903 control subjects) were recruited. The interaction of multiple factors was investigated using Multifactor Dimensionality Reduction and additive effect of single nucleotide polymorphisms on ischemic stroke or its subtypes were analyzed by multiple factor logistic regression. Results At COX-1(rs1330344), AA genotype carriers had a lower susceptibility of ischemic stroke (OR=0.657, 95%CI= 0.437-0.988, P = 0.044), and A allele carriers had a lower susceptibility of ischemic stroke (OR=0.812, 95%CI= 0.657-0.978, P = 0.029). At COX-1(rs3842788), AA genotype carriers had a higher susceptibility of ischemic stroke (OR =5.203, 95% CI=1.519-5.159, P =0.016). At COX-2 (rs689466), AA genotype carriers had a higher susceptibility of large-artery atherosclerosis (OR =1.404, 95% CI=1.019-1.934, P =0.038). COX-1(rs1330344, rs3842788) and COX-2 rs689466 interacted in SVO, but had no additive effect with ischemic stroke or its subtypes. Conclusions At rs1330344, AA genotype may reduce the susceptibility of ischemic stroke. At rs3842788, AA genotype may increase the susceptibility of ischemic stroke. At rs689466, AA genotype may increase the susceptibility of large-artery atherosclerosis (LAA). COX-1(rs1330344, rs3842788) and COX-2 rs689466 interacted in small vessel occlusion (SVO), but had no additive effect with ischemic stroke or its subtypes.

scholarly journals The return to water in ancestral Xenopus was accompanied by a novel mechanism for producing and shaping vocal signals

2018 ◽  
Author(s):  
Ursula Kwong-Brown ◽  
Martha L. Tobias ◽  
Damian O. Elias ◽  
Ian C. Hall ◽  
Coen P.H. Elemans ◽  
...  
Keyword(s):  
Sound Production ◽  
Neuromuscular Control ◽  
Current Theory ◽  
Species Divergence ◽  
Species Identity ◽  
Rapid Separation ◽  
Resonance Modes ◽  
Acoustic Signature ◽  
Vocal Signals ◽  
Species Specific

AbstractSpecies-specific vocal signals allow listeners to locate potential mates. During the tetrapod transition from water to land, lungs replaced gills, allowing expiration to drive sound production. Several groups, e.g. cetaceans and some frogs, then returned to water. Here we explore how air-driven sound production changed upon re-entry and how essential acoustic information on species identity was preserved in the secondarily aquatic frog Xenopus. We filmed movements of cartilage and muscles during evoked sound production in isolated larynges. Our results refute the current theory for Xenopus vocalization, cavitation, and instead favor sound production by mechanical excitation of laryngeal resonance modes following rapid separation of laryngeal arytenoid discs. The resulting frequency resonance modes (dyads) are intrinsic to the larynx rather than due to neuromuscular control. We show that dyads are a distinctive acoustic signature across species. While dyad component frequencies overlap across species, their ratio is shared within each Xenopus clade and thus provide information on species identity, potentially facilitating both conspecific localization and ancient species divergence.

Characterisation of two calmodulin-like proteins from the liver fluke, Fasciola hepatica

2007 ◽  
Vol 388 (6) ◽  
pp. 593-599 ◽  
Author(s):  
Sean L. Russell ◽  
Neil V. McFerran ◽  
Elizabeth M. Hoey ◽  
Alan Trudgett ◽  
David J. Timson
Keyword(s):  
Metal Binding ◽  
Metal Ion ◽  
Liver Fluke ◽  
Fasciola Hepatica ◽  
Expression Vectors ◽  
Metal Ion Binding ◽  
Ion Sensing ◽  
Calcium Magnesium ◽  
Ion Binding Sites ◽  
Liver Flukes

Abstract Calmodulin is a calcium ion-sensing signalling protein found in eukaryotics. Two calmodulin-like gene sequences were identified in an EST library from adult liver flukes. One codes for a protein (FhCaM1) homologous to mammalian calmodulins (98% identity), whereas the other protein (FhCaM2) has only 41% identity. These genes were cloned into expression vectors and the recombinant proteins were expressed in Escherichia coli. Gel shift assays showed that both proteins bind to calcium, magnesium and zinc ions. Homology models have been built for both proteins. As expected, FhCaM1 has a highly similar structure to other calmodulins. Although FhCaM2 has a similar fold, its surface charge is higher than FhCaM1. One of the potential metal ion-binding sites has lower metal-ion co-ordination capability, while another has an adjacent lysine residue, both of which may decrease the metal-binding affinity. These differences may reflect a specialised role for FhCaM2 in the liver fluke.

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