scholarly journals Isolation and Characterization of 27 Novel Microsatellite Loci in Critically Endangered Wyoming Toad

2019 ◽  
Vol 10 (2) ◽  
pp. 563-566
Author(s):  
Renee M. Martin ◽  
Heidi Meador ◽  
Lee Bender ◽  
Lacey Hopper

Abstract Wyoming toad Anaxyrus baxteri is a federally endangered amphibian endemic to the Laramie basin in southwestern Wyoming, USA. A captive breeding program propagates A. baxteri, and the monitoring of genetic diversity in the captive stock can assist in guiding conservation measures of this species. Illumina paired-end sequencing lead to 27 species-specific polymorphic microsatellite genetic markers being developed. Across 24 samples, A. baxteri exhibited two to eight alleles per locus, and observed and expected heterozygosities per locus ranged from 0.292 to 0.958 and from 0.344 to 0.787, respectively. Tests for Hardy–Weinberg equilibrium were nonsignificant except for Abax_13 and Abax_39. These microsatellite markers will be useful for genetic monitoring to aid recovery efforts of A. baxteri captive and wild populations as well as other amphibians in the family Bufonidae.

2016 ◽  
Vol 31 (1) ◽  
pp. 17
Author(s):  
Celia Isabel Bisbal -Pardo ◽  
Miguel Ángel Del Río -Portilla ◽  
Ana Yonori Castillo -Paéz ◽  
Axayácatl Rocha-Olivares

The geoduck Panopea globosa is a long-lived and large endemic infaunal clam sustaining a growing fishery in the Northwest coast of México that, in spite of its increasing demand in Asian markets very little is known about its biology. In order to provide genetic markers to support genetic research of wild populations, nine novel microsatellite loci (di-, tri-, and tetranucleotide repeats) were developed using shotgun sequencing with next generation technology (Illumina). The number of alleles per locus ranged from 3 to 16 and the observed and expected heterozygosity ranged from 0.286 to 0.650 and 0.504 to 0.906, respectively. Five loci were found to be significantly deviated from the Hardy-Weinberg equilibrium and three pairs showed evidence of linkage disequilibrium. Most loci are highly informative for population genetics and linkage analyses according to their polymorphism information content (> 0.5) and will be useful for increasing our understanding of the wild population structure and developing a sustainable fishery management. Aislamiento y caracterización de nuevos marcadores microsatelitales en la almeja generosa (Panopea globosa) La almeja generosa Panopea globosa es una especie infáunica longeva y de gran tamaño que mantiene una pesquería creciente en la costa del Noroeste de México. A pesar de su demanda creciente en los mercados asiáticos, se conoce muy poco acerca de su biología. Con la finalidad de proveer nuevos marcadores genéticos para la caracterización de poblaciones silvestres, se desarrollaron nueve marcadores microsatelitales nuevos (con patrones repetidos de di-, tri-, y tetranucleotídicos) utilizando secuenciación genómica aleatoria con tecnología de secuenciación de siguiente generación (Illumina). El número de alelos por locus varió de 3 a 16 y los valores de heterocigosidad observada y esperada variaron de 0.286 a 0.650 y 0.504 a 0.906, respectivamente. Cinco microsatelites se desvían del equilibrio de Hardy-Weinberg y tres pares de microsatélites mostraron evidencia de desequilibrio de ligamiento. La mayoría de los loci son altamente informativos para estudios poblacionales y análisis de ligamiento de acuerdo con su contenido de información de polimorfismos (> 0.5) y serán útiles para incrementar el conocimiento de la estructura genética de las poblaciones silvestres de esta almeja y para coadyuvar en su pesquería sustentable.


2020 ◽  
Vol 21 (9) ◽  
pp. 3160 ◽  
Author(s):  
Pilar Domingo-Calap ◽  
Beatriz Beamud ◽  
Lucas Mora-Quilis ◽  
Fernando González-Candelas ◽  
Rafael Sanjuán

The emergence of multidrug-resistant bacteria is a major global health concern. The search for new therapies has brought bacteriophages into the spotlight, and new phages are being described as possible therapeutic agents. Among the bacteria that are most extensively resistant to current antibiotics is Klebsiella pneumoniae, whose hypervariable extracellular capsule makes treatment particularly difficult. Here, we describe two new K. pneumoniae phages, πVLC5 and πVLC6, isolated from environmental samples. These phages belong to the genus Drulisvirus within the family Podoviridae. Both phages encode a similar tail spike protein with putative depolymerase activity, which is shared among other related phages and probably determines their ability to specifically infect K. pneumoniae capsular types K22 and K37. In addition, we found that phage πVLC6 also infects capsular type K13 and is capable of striping the capsules of K. pneumoniae KL2 and KL3, although the phage was not infectious in these two strains. Genome sequence analysis suggested that the extended tropism of phage πVLC6 is conferred by a second, divergent depolymerase. Phage πVLC5 encodes yet another putative depolymerase, but we found no activity of this phage against capsular types other than K22 and K37, after testing a panel of 77 reference strains. Overall, our results confirm that most phages productively infected one or few Klebsiella capsular types. This constitutes an important challenge for clinical applications.


2019 ◽  
Vol 24 (2) ◽  
pp. 7-16
Author(s):  
Nabin Rana ◽  
Saraswoti Khadka ◽  
Bishnu Prasad Marasini ◽  
Bishnu Joshi ◽  
Pramod Poudel ◽  
...  

 Realizing myxobacteria as a potential source of antimicrobial metabolites, we pursued research to isolate myxobacteria showing antimicrobial properties. We have successfully isolated three strains (NR-1, NR-2, NR-3) using the Escherichia coli baiting technique. These isolates showed typical myxobacterial growth characteristics. Phylogenetic analysis showed that all the strains (NR-1, NR-2, NR-3) belong to the family Archangiaceae, suborder Cystobacterineae, and order Myxococcales. Furthermore, 16S rRNA gene sequence similarity searched through BLAST revealed that strain NR-1 showed the closest similarity (91.8 %) to the type strain Vitiosangium cumulatum (NR-156939), NR-2 showed (98.8 %) to the type of Cystobacter badius (NR-043940), and NR-3 showed the closest similarity (83.5 %) to the type of strain Cystobacter fuscus (KP-306730). All isolates showed better growth in 0.5-1 % NaCl and pH around 7.0, whereas no growth was observed at pH 9.0 and below 5.0. All strains showed better growth at 32° C and hydrolyzed starch, whereas casein was efficiently hydrolyzed by NR-1 and NR-2. Besides, preliminary antimicrobial tests from crude extracts showed activities against Gram-positive, Gram-negative bacteria, and fungi. Our findings suggest that the arcane soil habitats of Nepal harbor myxobacteria with the capability to produce diverse antimicrobial activities that may be explored to overcome the rapidly rising global concern about antibiotic resistance.


Parasitology ◽  
1996 ◽  
Vol 112 (3) ◽  
pp. 331-338 ◽  
Author(s):  
X. Q. Hong ◽  
J. Santiago Mejia ◽  
S. Kumar ◽  
F. B. Perler ◽  
C. K. S. Carlow

SUMMARYDirofilaria immitis is an important filarial parasite of dogs and cats, and a useful model for human filariasis. Current diagnostic tests for heartworm infection in animals rely on the presence of fecund female worms (usually found 6·5 months post-infection or later) and therefore fail to detect pre-patent infections. Putative pepsin inhibitors from 2 filarial parasites of humans namely Onchocerca volvulus (Ov33, Oc3.6, OvDSB) and Brugia malayi (Bm33), have been shown to be useful in diagnosis of onchocerciasis and lymphatic filariasis, respectively. Previous studies have suggested that a homologue exists in D. immitis (DiT33), which may have potential in diagnosis of heartworm infection. In this study, the isolation and characterization of a cDNA clone encoding DiT33 is described.‡ This cDNA contains 12 bases of the nematode-specific 22 nucleotide spliced leader sequence and encodes a 26·4 kDa-protein with a high level of similarity (87–89%) to other filarial members of the family. DJT33 was over-expressed in E. coli as a fusion with the maltose-binding protein and serological analysis was performed using a panel of clinically defined dog sera. The findings of this study indicate that DiT33 is a promising antigen for the early detection of D. immitis and may be a valuable tool in the control and management of heartworm infection.


2004 ◽  
Vol 70 (2) ◽  
pp. 704-711 ◽  
Author(s):  
Keizo Nagasaki ◽  
Yuji Tomaru ◽  
Noriaki Katanozaka ◽  
Yoko Shirai ◽  
Kensho Nishida ◽  
...  

ABSTRACT A novel single-stranded RNA (ssRNA) virus specifically infecting the bloom-forming diatom Rhizosolenia setigera (R. setigera RNA virus [RsRNAV]) was isolated from Ariake Sea, Japan. Viral replication occurred within the cytoplasm, and the virus particle was icosahedral, lacked a tail, and was 32 nm in diameter on average. The major nucleic acid extracted from the RsRNAV particles was an ssRNA molecule 11.2 kb in length, although smaller RNA molecules (0.6, 1.2, and 1.5 kb) were occasionally observed. The major structural proteins of RsRNAV were 41.5, 41.0, and 29.5 kDa. Inter- and intraspecies host specificity tests revealed that RsRNAV is not only species specific but also strain specific and that its intraspecies host specificity is diverse among virus clones. The latent period of RsRNAV was 2 days, and the burst sizes were 3,100 and 1,010 viruses per host cell when viruses were inoculated into the host culture at the exponential and stationary growth phases, respectively, at 15°C under a 12-h-12-h light-dark cycle of ca. 110 μmol of photons m−2 s−1 with cool white fluorescent illumination. To our knowledge, this is the first report describing the biological properties of a virus infecting a diatom. Further studies on RsRNAV will be helpful in understanding the ecological relationship between diatoms and viruses in nature.


2007 ◽  
Vol 7 (4) ◽  
pp. 701-704 ◽  
Author(s):  
MARTINA VYSKOČILOVÁ ◽  
MARKÉTA ONDRAČKOVÁ ◽  
ANDREA ŠIMKOVÁ ◽  
JEAN-FRANÇOIS MARTIN

2010 ◽  
Vol 79 (3) ◽  
pp. 437-442
Author(s):  
Daniel Šperling ◽  
František Čada ◽  
Alois Čížek

The objectives of this study were to establish the prevalence of intestinal Spirochetes of the genusBrachyspirain Czech dogs and to determine the susceptibility of obtainedB. pilosicoliisolates to selected antibacterial substances. Spirochetes were diagnosed microscopically in 23 out of 1139 samples of dogs’ excrements, primarily intended for a parasitological testing. The cultivation of positive samples provided 10 brachyspira isolates, which were, on the basis of their biochemical activity and the results of the species-specific PCR, identified asB. pilosicoli(9 isolates) andB. hyodysenteriae(1 isolate). These dogs came from households. All the 7 tested isolatesB. pilosicoliwere sensitive to metronidazole and doxycycline, uniformly resistant to erythromycin, partly sensitive to cefazoline, lincomicine and ampicilline except for one isolate ofB. pilosicoli, which was resistant to ampicilline. The second part of study was focused on dogs with diarrhoea that came from animal shelters, where a high prevalence of 58% (10/17) ofB. pilosicoliwas found.


2013 ◽  
Vol 59 (1) ◽  
pp. 39-45 ◽  
Author(s):  
Chao Gong ◽  
Spencer Heringa ◽  
Randhir Singh ◽  
Jinkyung Kim ◽  
Xiuping Jiang

The objectives of this study were to isolate and characterize bacteriophages specific to hydrogen-sulfide-producing bacteria (SPB) from raw animal materials, and to develop a SPB-specific bacteriophage cocktail for rendering application. Meat, chicken offal, and feather samples collected from local supermarkets and rendering processing plants were used to isolate SPB (n = 142). Bacteriophages (n = 52) specific to SPB were isolated and purified from the above samples using 18 of those isolated SPB strains as hosts. The host ranges of bacteriophages against 5 selected SPB strains (Escherichia coli, Citrobacter freundii, and Hafnia alvei) were determined. Electron microscopy observation of 9 phages selected for the phage cocktail revealed that 6 phages belonged to the family of Siphoviridae and 3 belonged to the Myoviridae family. Restriction enzyme digestion analysis with endonuclease DraI detected 6 distinguished patterns among the 9 phages. Phage treatment prevented the growth of SPB for up to 10 h with multiplicity of infection ratios of 1, 10, 100, and 1000 in tryptic soy broth at 30 °C, and extended the lag phase of SPB growth for 2 h at 22 °C with multiplicities of infection of 10, 100, and 1000. These results suggest that the selected bacteriophage cocktail has a high potential for phage application to control SPB in raw animal materials destined for the rendering process.


2000 ◽  
Vol 74 (7) ◽  
pp. 3156-3165 ◽  
Author(s):  
Richard Molenkamp ◽  
Babette C. D. Rozier ◽  
Sophie Greve ◽  
Willy J. M. Spaan ◽  
Eric J. Snijder

ABSTRACT Equine arteritis virus (EAV), the type member of the family Arteriviridae, is a single-stranded RNA virus with a positive-stranded genome of approximately 13 kb. EAV uses a discontinuous transcription mechanism to produce a nested set of six subgenomic mRNAs from which its structural genes are expressed. We have generated the first documented arterivirus defective interfering (DI) RNAs by serial undiluted passaging of a wild-type EAV stock in BHK-21 cells. A cDNA copy of the smallest DI RNA (5.6 kb) was cloned. Upon transfection into EAV-infected BHK-21 cells, transcripts derived from this clone (pEDI) were replicated and packaged. Sequencing of pEDI revealed that the DI RNA was composed of three segments of the EAV genome (nucleotides 1 to 1057, 1388 to 1684, and 8530 to 12704) which were fused in frame with respect to the replicase reading frame. Remarkably, this DI RNA has retained all of the sequences encoding the structural proteins. By insertion of the chloramphenicol acetyltransferase reporter gene in the DI RNA genome, we were able to delimitate the sequences required for replication/DI-based transcription and packaging of EAV DI RNAs and to reduce the maximal size of a replication-competent EAV DI RNA to approximately 3 kb.


2015 ◽  
Vol 90 (1) ◽  
pp. 76-91 ◽  
Author(s):  
Nicole A. Doria-Rose ◽  
Jinal N. Bhiman ◽  
Ryan S. Roark ◽  
Chaim A. Schramm ◽  
Jason Gorman ◽  
...  

ABSTRACT The epitopes defined by HIV-1 broadly neutralizing antibodies (bNAbs) are valuable templates for vaccine design, and studies of the immunological development of these antibodies are providing insights for vaccination strategies. In addition, the most potent and broadly reactive of these bNAbs have potential for clinical use. We previously described a family of 12 V1V2-directed neutralizing antibodies, CAP256-VRC26, isolated from an HIV-1 clade C-infected donor at years 1, 2, and 4 of infection (N. A. Doria-Rose et al., Nature 509:55–62, 2014, http://dx.doi.org/10.1038/nature13036 ). Here, we report on the isolation and characterization of new members of the family mostly obtained at time points of peak serum neutralization breadth and potency. Thirteen antibodies were isolated from B cell culture, and eight were isolated using trimeric envelope probes for differential single B cell sorting. One of the new antibodies displayed a 10-fold greater neutralization potency than previously published lineage members. This antibody, CAP256-VRC26.25, neutralized 57% of diverse clade viral isolates and 70% of clade C isolates with remarkable potency. Among the viruses neutralized, the median 50% inhibitory concentration was 0.001 μg/ml. All 33 lineage members targeted a quaternary epitope focused on V2. While all known bNAbs targeting the V1V2 region interact with the N160 glycan, the CAP256-VRC26 antibodies showed an inverse correlation of neutralization potency with dependence on this glycan. Overall, our results highlight the ongoing evolution within a single antibody lineage and describe more potent and broadly neutralizing members with potential clinical utility, particularly in areas where clade C is prevalent. IMPORTANCE Studies of HIV-1 broadly neutralizing antibodies (bNAbs) provide valuable information for vaccine design, and the most potent and broadly reactive of these bNAbs have potential for clinical use. We previously described a family of V1V2-directed neutralizing antibodies from an HIV-1 clade C-infected donor. Here, we report on the isolation and characterization of new members of the family mostly obtained at time points of peak serum neutralization breadth and potency. One of the new antibodies, CAP256-VRC26.25, displayed a 10-fold greater neutralization potency than previously described lineage members. It neutralized 57% of diverse clade viral isolates and 70% of clade C isolates with remarkable potency: the median 50% inhibitory concentration was 0.001 μg/ml. Our results highlight the ongoing evolution within a single antibody lineage and describe more potent and broadly neutralizing members with potential clinical utility, particularly in areas where clade C is prevalent.


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