scholarly journals Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 891 ◽  
Author(s):  
Ivana Šimić ◽  
Tomaž Mark Zorec ◽  
Ivana Lojkić ◽  
Nina Krešić ◽  
Mario Poljak ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sample Type ◽  
Adeno Associated Virus ◽  
Rhinolophus Ferrumequinum ◽  
Myotis Myotis ◽  
Bacterial Viruses ◽  
The Difference ◽  
Contrasting Habitats ◽  
Myotis Nattereri ◽  
Eptesicus Serotinus

To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown. Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (Myotis myotis, Miniopterus schreibersii, Rhinolophus ferrumequinum, Eptesicus serotinus, Myotis blythii, Myotis nattereri and Myotis emarginatus) conducted in Mediterranean and continental Croatia. Viral nucleic acids were extracted from sample pools, and analyzed using Illumina sequencing. The presence of 63 different viral families representing all seven Baltimore groups were confirmed, most commonly insect viruses likely reflecting the diet of insectivorous bats. Virome compositions of our samples were largely impacted by the sample type: invertebrate-infecting viruses were most frequently found in feces, bacterial viruses in guano, whereas vertebrate-infecting viruses were most common in swabs. Most vertebrate-infecting virus sequences were assigned to retroviruses, parvoviruses, iridoviruses, and poxviruses. We further report the complete genome sequence of a novel adeno-associated virus, densovirus and a near complete length genome sequence of a novel iflavirus. Additionally, one of the most interesting findings in this study was the difference in viromes between two contrasting habitats, the continental and Mediterranean Croatia.

scholarly journals Body Accelerations During the Wingbeat in Six Bat Species: The Function of the Upstroke in Thrust Generation

1987 ◽  
Vol 130 (1) ◽  
pp. 275-293 ◽  
Author(s):  
H. D. J. N. ALDRIDGE
Keyword(s):  
Flight Path ◽  
Rhinolophus Ferrumequinum ◽  
Minimum Power ◽  
Kinematic Pattern ◽  
Horizontal Flight ◽  
Thrust Generation ◽  
Low Speeds ◽  
Myotis Nattereri ◽  
Eptesicus Serotinus

The kinematics and aerodynamics of Rhinolophus ferrumequinum, R. hipposideros, Myotis nattereri, M. mystacinus, Plecotus auritus and Eptesicus serotinus in horizontal flight at various flight speeds are described. Three kinematic patterns can be recognized. At low speeds M. nattereri, M. mystacinus and P. auritus use a ‘tip-reversal’ upstroke in which thrust is generated during the backward ‘flick’ of the chiropatagium. R. hipposideros also uses this kinematic pattern, but does not appear to generate thrust during the upstroke. Both R. ferrumequinum flying at 3.12 m s−1 and E. serotinus flying at 3.44 m s−1 accelerate during the ‘vertical’ upstroke (in which the wings move perpendicularly to the flight path), indicating that their wings are active. When flying at 4.16 m s−1, E. serotinus also uses a ‘vertical’ upstroke, but in this case it decelerates, which suggests that thrust is not being generated. At minimum power speed (4.8 m s−1), R. ferrumequinum uses a ‘reduced-span’ upstroke, thrust is not generated during the upstroke and the animal decelerates.

Şura Mare cave (Romania) - the most important known hibernating roost for Pipistrellus pygmaeus Leach, 1825 (Chiroptera: Vespertilionidae)

2010 ◽  
Vol 53 (1) ◽  
pp. 329-338 ◽  
Author(s):  
Dumitru Murariu ◽  
Victor Gheorghiu
Keyword(s):  
European Union ◽  
The European Union ◽  
Rhinolophus Ferrumequinum ◽  
Pipistrellus Pipistrellus ◽  
Myotis Myotis ◽  
European Union Legislation ◽  
A Priority ◽  
Prevalent Species

Şura Mare cave (Romania) - the most important known hibernating roost for Pipistrellus pygmaeus Leach, 1825 (Chiroptera: Vespertilionidae) The Sura Mare cave from Romania is one of the largest roost for hibernating colonies of bats with more than 40,000 individuals. Pipistrellus pipistrellus and P. pygmaeus are prevalent species with more than 34,000 individuals in mixed colonies. Other 6 bat species are less represented (e.g. Rhinolophus ferrumequinum only 500 individuals) but Miniopterus schreibersii's colony counts 3,500 individuals. From the total of 8 identified bat species, 5 are a priority according to the European Union legislation: Rhinolophus ferrumequinum, Myotis myotis, M. oxygnathus, Barbastella barbastellus and Miniopterus schreibersii.

scholarly journals Bats from Lebanon at the Natural History Museum, Vienna: a cautionary tale on the reliability of museum specimen data (Chiroptera)

2016 ◽  
Vol 47 (1) ◽  
pp. 17-43
Author(s):  
Petr Benda ◽  
Simon Engelberger
Keyword(s):  
Natural History ◽  
Natural History Museum ◽  
Museum Specimen ◽  
Historical Records ◽  
Cautionary Tale ◽  
History Museum ◽  
Rhinolophus Ferrumequinum ◽  
Myotis Myotis ◽  
History Of ◽  
To Come

Abstract Seven historical bat specimens of four species (Rhinolophus ferrumequinum, R. mehelyi, Taphozous nudiventris, Myotis myotis), attributed to originate from the territory of the present-day Lebanon, are deposited and documented in the modern database of the mammal collection of the Natural History Museum, Vienna, Austria (Naturhistorisches Museum Wien). Two of these species (R. mehelyi, T. nudiventris) have never been reported for Lebanon in the existing literature and recent surveys have also failed to find them in this country. Since these bats were collected in the period 1824–1885, the history of the all respective specimens was evaluated in detail. The revision brought rather unexpected results. Only one specimen (R. ferrumequinum) was found to come (most probably) from Lebanon, being collected by W. Hemprich and Ch. Ehrenberg in 1824. In the remaining six specimens, the origin could not be defined, thus rendering the statement that they were collected in Lebanon insecure. This case demonstrates that careful checks of modern interpretations of historical records are necessary when examining past distributions of organisms.

scholarly journals Draft Whole Genome Sequence Analyses on Pseudomonas syringae pv. actinidiae Hypersensitive Response Negative Strains Detected from Kiwifruit Bleeding Sap Samples

2018 ◽  
Vol 108 (5) ◽  
pp. 552-560 ◽  
Author(s):  
Enrico Biondi ◽  
Alan Zamorano ◽  
Ernesto Vega ◽  
Stefano Ardizzi ◽  
Davide Sitta ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Hypersensitive Response ◽  
Time Window ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Optimal Time ◽  
Whole Genome ◽  
Isolation And Identification ◽  
The Difference

Kiwifruit bleeding sap samples, collected in Italian and Chilean orchards from symptomatic and asymptomatic plants, were evaluated for the presence of Pseudomonas syringae pv. actinidiae, the causal agent of bacterial canker. The saps were sampled during the spring in both hemispheres, before the bud sprouting, during the optimal time window for the collection of an adequate volume of sample for the early detection of the pathogen, preliminarily by molecular assays, and then through its direct isolation and identification. The results of molecular analyses showed more effectiveness in the P. syringae pv. actinidiae detection when compared with those of microbiological analyses through the pathogen isolation on the nutritive and semiselective media selected. The bleeding sap analyses allowed the isolation and identification of two hypersensitive response (HR) negative and hypovirulent P. syringae pv. actinidiae strains from different regions in Italy. Moreover, multilocus sequence analysis (MLSA) and whole genome sequence (WGS) were carried out on selected Italian and Chilean P. syringae pv. actinidiae virulent strains to verify the presence of genetic variability compared with the HR negative strains and to compare the variability of selected gene clusters between strains isolated in both countries. All the strains showed the lack of argK and coronatine gene clusters as reported for the biovar 3 P. syringae pv. actinidiae strains. Despite the biologic differences obtained in the tobacco bioassays and in pathogenicity assays, the MLSA and WGS analyses did not show significant differences between the WGS of the HR negative and HR positive strains; the difference, on the other hand, between PAC_ICE sequences of Italian and Chilean P. syringae pv. actinidiae strains was confirmed. The inability of the hypovirulent strains IPV-BO 8893 and IPV-BO 9286 to provoke HR in tobacco and the low virulence shown in this host could not be associated with mutations or recombinations in T3SS island.

scholarly journals Biospeleological notes on fauna in an artificial cave in Përmet (Albania) importance of former military installations for biodiversity

2020 ◽  
Vol 30 (30) ◽  
pp. 57-62
Author(s):  
Maria Naumova
Keyword(s):  
Species Group ◽  
Biodiversity Hotspots ◽  
Military Installations ◽  
Spider Species ◽  
Rhinolophus Ferrumequinum ◽  
Invertebrate Species ◽  
Number Of Species ◽  
Myotis Myotis ◽  
Horseshoe Bat

The subterranean fauna of both natural and artificial caves in Albania remains poorly studied. Cave colonisation can be clarified by investigating the same process in artificial underground sites. The existence of such a process can be judged by the composition of specific vertebrate and invertebrate species in every site. The biospeleological study carried out in an artificial cave in Përmet in June 2019 provided the following results: two bat species, i.e. Greater horseshoe bat Rhinolophus ferrumequinum (Schreber, 1774) and Mouse-eared bat Myotis myotis species group, probably M. blythii (Tomes, 1857) were observed, a specimen of the Balkan stream frog Rana graeca Boulenger, 1891, representing the first amphibian record for the Albanian cave, was discovered deep inside the cave, nine invertebrate species were found (7 spiders, 1 harvestman and 1 moth), with three of the spider species, i.e. Ceratinella brevis (Wider, 1834), Hogna radiata (Latreille, 1817) and Trachyzelotes barbatus (L. Koch, 1866), being the first records for Balkan caves. All recorded species, except Myotis blythii/myotis (both were previously known), are new to the study area. The total number of species recorded in this site, including the data available in literature, has increased to 29. This high number of species shows that artificial caves, including military installations, represent biodiversity hotspots, comparable to natural underground sites and demand much more attention and further investigations.

scholarly journals Visual Variations between Pairs of SARS-CoV-2 Genomes on Integrated Density Matrix

2020 ◽  
Author(s):  
Minghan Zhu ◽  
Jeffrey Zheng
Keyword(s):  
Genome Sequence ◽  
Medical Application ◽  
Virus Genome ◽  
Order Conditions ◽  
Systematic Expansion ◽  
Einstein Distribution ◽  
Transformation Structure ◽  
The Difference ◽  
Difference Calculation ◽  
Bose Einstein

Abstract This paper is the B2 module of the MAS. The quantification matrix is formed according to the four-base arrangement in the genome sequence. The differences in new coronavirus genome sequencing sequences in different samples were demonstrated by using the most concise methods. Using 4 primitive variable value measures, changes in the virus genome sequence base order conditions were determined. When two relatively large genomic sequences are slightly different, the integrated distribution of the difference calculation is subtly similar to the Bose-Einstein distribution, while the sum calculation shows a powerful distribution complexity. It can be formed under the macroscopic angle and can distinguish 16 combinations of supersymmetric structures. In view of the abundant transformation structure in this kind of transformation system, the detailed exploration remains to be followed by the systematic expansion of theory and medical application.

scholarly journals Predation of invasive raccoon (Procyon lotor) on hibernating bats in the Nietoperek reserve in Poland

2020 ◽  
Author(s):  
Jan Cichocki ◽  
Agnieszka Ważna ◽  
Anna Bator-Kocoł ◽  
Grzegorz Lesiński ◽  
Renata Grochowalska ◽  
...  
Keyword(s):  
Invasive Species ◽  
Endangered Species ◽  
Nature Reserve ◽  
Procyon Lotor ◽  
Mammal Species ◽  
Plant Materials ◽  
Local Populations ◽  
Myotis Myotis ◽  
Myotis Nattereri ◽  
Anthropogenic Food

AbstractThe raccoon Procyon lotor is an invasive species inhabiting Europe and its impact on local populations, particularly on endangered species, is not well known. The aim of the study was to determine whether raccoons pose a threat to bats wintering in the Nietoperek nature reserve, one of the largest hibernation sites in Central Europe. In the winter of 2016–2017, 67 raccoon scats were collected in one of the main underground corridors in the reserve. It was confirmed, with the use of molecular methods, that the scats belonged to raccoons. Raccoon prey was identified based on the features of skulls, jaws or hair found in the scats. Analysis of the determinable remains indicates that bats (including Daubenton’s bat/Natterer’s bat/Brandt’s bat M. daubentonii/nattereri/brandtii, Natterer’s bat Myotis nattereri, greater mouse-eared bat Myotis myotis, brown long-eared bat Plecotus auritus) made up the largest percentage of raccoon diet (96%). Remains of other mammal species, lizards Lacerta spp., plant materials and anthropogenic food were also identified in raccoon scats. The results of the research indicate that predation by raccoons can constitute a significant factor in the increasing mortality of bats wintering in Nietoperek.

scholarly journals Reproducibility of Seawater, Inorganic and Organic Carbon 14C Results at NOSAMS

Radiocarbon ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 223-230 ◽  
Author(s):  
Kathryn L. Elder ◽  
Ann P. McNichol ◽  
Alan R. Gagnon
Keyword(s):  
Organic Carbon ◽  
Ocean Circulation ◽  
Storage Time ◽  
Total Error ◽  
World Ocean ◽  
Sample Type ◽  
Machine Error ◽  
Significant Difference ◽  
The Difference ◽  
Seawater Samples

The majority of samples processed at the National Ocean Sciences AMS Facility (NOSAMS) thus far were collected as part of the World Ocean Circulation Experiment (WOCE). Due to the long storage time (2–3 yr) required to analyze thousands of samples on the accelerator mass spectrometer (AMS), a test was designed and implemented to determine the effects, if any, of storage time on 14C concentration. We find no systematic offsets in AMS measurements made over a 5-yr period between a total of 16 replicate sets from surface and deep water collected at the same locality. Furthermore, the average δ14C value from the deepwater AMS replicates (-213.1%, std. dev. 7.3) agrees very closely with the conventional 14C results published for GEOSECS (-212.7%) from station 320 taken 20 yr earlier.A total of 73 WOCE shipboard replicate sets (162 AMS measurements) were analyzed with a mean precision of 4.3%. AMS results from 20 more shipboard replicate sets (44 AMS measurements) submitted as CO2 from the Stable Isotope Laboratory (SIL) at the University of Washington were analyzed with a mean precision of 3.4%. These results suggest no significant difference between water stripping methods used in each preparation lab.To assess reproducibility, we calculate a pooled estimate of σ for replicates called s, which we use as an approximation of σTOT for a given sample type. The s for WOCE seawater replicates is 4.9% and 5.8% for SIL gas replicates. These numbers demonstrate an overall reproducibility of seawater AMS results at NOSAMS that is in line with reported errors. We take the difference between total error s and machine error as the overall standard deviation of combined uncertainties associated with preparation of samples and with AMS. For seawater samples processed at NOSAMS, σSPL is calculated to be 2.4%, and for the SIL gas replicates it is 4.8%.Reproducibility of samples prepared with an acid hydrolysis technique is demonstrated using 24 coral samples submitted in triplicate by Dr. R. G. Fairbanks of Lamont Doherty Earth Observatory. Seventy-two replicates were prepared and analyzed at NOSAMS with a mean reported precision of 1.2%. The pooled estimate s for the Fairbanks triplicates is 2.6%. We calculate a laboratory reproducibility uncertainty for coral hydrolysis samples of 2.2%.In 1993, NOSAMS participated in the Third International Radiocarbon Intercomparison (TIRI) Study. We report here 60 AMS analyses of the six TIRI test materials, five of which are organic carbon samples, to validate sample-processing methods for organic carbon sample AMS analyses at NOSAMS.

scholarly journals Chimeric Capsid Proteins Impact Transduction Efficiency of Haploid Adeno-Associated Virus Vectors

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1138
Author(s):  
Zheng Chai ◽  
Xintao Zhang ◽  
Amanda Lee Dobbins ◽  
Ellie Azure Frost ◽  
R. Jude Samulski ◽  
...  
Keyword(s):  
Fold Increase ◽  
Transduction Efficiency ◽  
Adeno Associated Virus ◽  
Systemic Injection ◽  
Copy Numbers ◽  
C Terminus ◽  
Vector Genome ◽  
Significant Difference ◽  
N Terminus ◽  
The Difference

Our previous studies have demonstrated that haploid AAV vectors made from capsids of two different serotypes induced high transduction and prevented serotype-specific antibody binding. In this study, we explored the transduction efficiency of several haploid viruses, which were made from the VP1/VP2 of one serotype and VP3 of another compatible serotype. After systemic injection of 2 × 1010 vg of AAV vectors into mice, the haploid AAV vectors, composed of VP1/VP2 from serotypes 8 or 9, and VP3 from AAV2, displayed a two to seven-fold increase in liver transduction compared with those of parental AAV2 vectors. Furthermore, a chimeric AAV2/8 VP1/VP2 with N-terminus of VP1/VP2 from AAV2 and C-terminus (VP3 domain) from AAV8 was constructed, and produced the haploid vector 28m-2VP3 with AAV2 VP3. The haploid 28m-2VP3 vector showed a five-fold higher transduction than that of the vectors composed solely of AAV2 VPs. Remarkably, the 28m-2VP3 vectors also induced a significant increase in transgene expression compared to the vectors composed of AAV8 VP1/VP2 with AAV2 VP3. The results suggest that the difference in the VP1/VP2 N-terminal region between AAV2 and AAV8 may allow better “communication” between the VP1/VP2 N-terminus of AAV2 with its cognate VP3. Similarly, the haploid vectors, VP1/VP2 from serotypes 8 or 9 and VP3 from AAV3, achieved higher transductions in multiple tissue types beyond typical tropism compared with those of AAV3 vectors. Consistently, higher vector genome copy numbers were detected in these tissues, indicating that an incorporation of non-cognate VP1/VP2 might influence the cellular tropism of the haploid vectors. However, there was no significant difference or even decreased transductions when compared with those of parental AAV8 or AAV9 vectors. In summary, these studies provide insight into current development strategies of AAV vectors that can increase AAV transduction across multiple tissues.

scholarly journals Establishing Statistical Equivalence of Data from Different Sampling Approaches for Assessment of Bacterial Phenotypic Antimicrobial Resistance

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Heman Shakeri ◽  
Victoriya Volkova ◽  
Xuesong Wen ◽  
Andrea Deters ◽  
Charley Cull ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Antimicrobial Susceptibility ◽  
Antimicrobial Drug ◽  
Equivalence Testing ◽  
Sample Type ◽  
Sample Processing ◽  
Processing Methods ◽  
Content Type ◽  
Statistical Equivalence ◽  
The Difference

ABSTRACTTo assess phenotypic bacterial antimicrobial resistance (AMR) in different strata (e.g., host populations, environmental areas, manure, or sewage effluents) for epidemiological purposes, isolates of target bacteria can be obtained from a stratum using various sample types. Also, different sample processing methods can be applied. The MIC of each target antimicrobial drug for each isolate is measured. Statistical equivalence testing of the MIC data for the isolates allows evaluation of whether different sample types or sample processing methods yield equivalent estimates of the bacterial antimicrobial susceptibility in the stratum. We demonstrate this approach on the antimicrobial susceptibility estimates for (i) nontyphoidalSalmonellaspp. from ground or trimmed meat versus cecal content samples of cattle in processing plants in 2013-2014 and (ii) nontyphoidalSalmonellaspp. from urine, fecal, and blood human samples in 2015 (U.S. National Antimicrobial Resistance Monitoring System data). We found that the sample types for cattle yielded nonequivalent susceptibility estimates for several antimicrobial drug classes and thus may gauge distinct subpopulations of salmonellae. The quinolone and fluoroquinolone susceptibility estimates for nontyphoidal salmonellae from human blood are nonequivalent to those from urine or feces, conjecturally due to the fluoroquinolone (ciprofloxacin) use to treat infections caused by nontyphoidal salmonellae. We also demonstrate statistical equivalence testing for comparing sample processing methods for fecal samples (culturing one versus multiple aliquots per sample) to assess AMR in fecalEscherichia coli. These methods yield equivalent results, except for tetracyclines. Importantly, statistical equivalence testing provides the MIC difference at which the data from two sample types or sample processing methods differ statistically. Data users (e.g., microbiologists and epidemiologists) may then interpret practical relevance of the difference.IMPORTANCEBacterial antimicrobial resistance (AMR) needs to be assessed in different populations or strata for the purposes of surveillance and determination of the efficacy of interventions to halt AMR dissemination. To assess phenotypic antimicrobial susceptibility, isolates of target bacteria can be obtained from a stratum using different sample types or employing different sample processing methods in the laboratory. The MIC of each target antimicrobial drug for each of the isolates is measured, yielding the MIC distribution across the isolates from each sample type or sample processing method. We describe statistical equivalence testing for the MIC data for evaluating whether two sample types or sample processing methods yield equivalent estimates of the bacterial phenotypic antimicrobial susceptibility in the stratum. This includes estimating the MIC difference at which the data from the two approaches differ statistically. Data users (e.g., microbiologists, epidemiologists, and public health professionals) can then interpret whether that present difference is practically relevant.

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