scholarly journals Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes

2005 ◽  
Vol 33 (13) ◽  
pp. e113-e113 ◽  
Author(s):  
J.-W. Bae
Keyword(s):  
Subtractive Suppression Hybridization ◽  
Subspecies Level

Differentiation and Interrelations of Two Representatives of Laudakia stellio Complex (Reptilia: Agamidae) in Israel

2011 ◽  
Vol 4 (2) ◽  
pp. 102-114 ◽  
Author(s):  
Evgenyi N. Panov ◽  
Larissa Yu. Zykova
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Habitat Preference ◽  
Additional Data ◽  
Near East ◽  
Field Studies ◽  
Subspecies Level ◽  
Limited Gene Flow ◽  
Study Sites ◽  
And Behavior

Field studies were conducted in Central Negev within the breeding range of Laudakia stellio brachydactyla and in NE Israel (Qyriat Shemona) in the range of an unnamed form (tentatively “Near-East Rock Agama”), during March – May 1996. Additional data have been collected in Jerusalem at a distance of ca. 110 km from the first and about 170 km from the second study sites. A total of 63 individuals were caught and examined. The animals were marked and their subsequent movements were followed. Social and signal behavior of both forms were described and compared. Lizards from Negev and Qyriat Shemona differ from each other sharply in external morphology, habitat preference, population structure, and behavior. The differences obviously exceed the subspecies level. At the same time, the lizards from Jerusalem tend to be intermediate morphologically between those from both above-named localities, which permits admitting the existence of a limited gene flow between lizard populations of Negev and northern Israel. The lizards from NE Israel apparently do not belong to the nominate subspecies of L. stellio and should be regarded as one more subspecies within the species.

Detergent fractionation with subsequent subtractive suppression hybridization as a tool for identifying genes coding for plasma membrane proteins

2009 ◽  
Vol 18 (6) ◽  
pp. 527-535 ◽  
Author(s):  
Andreas Lange ◽  
Claudia Kistler ◽  
Tanja B. Jutzi ◽  
Alexandr V. Bazhin ◽  
Claus Detlev Klemke ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Plasma Membrane Proteins ◽  
Subtractive Suppression Hybridization

The types of skippers described by Shu-Iti Murayama (Lepidoptera: Hesperiidae)

Zootaxa ◽  
2020 ◽  
Vol 4801 (2) ◽  
pp. 280-290
Author(s):  
HIDEYUKI CHIBA ◽  
HIROSHI TSUKIYAMA ◽  
JIA-YUAN LIANG ◽  
SHOU-MING WANG ◽  
ZONG-YU SHEN ◽  
...  
Keyword(s):  
Taxonomic Status ◽  
Species Level ◽  
Valid Species ◽  
Subspecies Level ◽  
Subjective Synonym

Fifteen holotypes of Asian Hesperiidae taxa described by Shu-iti Murayama were examined, and their taxonomic status is discussed. We confirm that five are valid names while the rest are synonyms as indicated partially by previous authors. Valid species-level names are Aeromachus matudai (Murayama), Aeromachus bandaishanus Murayama & Shimonoya, Coladenia pinsbukana (Shimonoya & Murayama), and Sebastonyma suthepiana Murayama & Kimura. Valid subspecies-level name is Ochlodes yuchingkina Murayama & Shimonoya. In order to settle the taxonomic status of Pedesta masuriensis cuneomaculata Murayama, masuriensis and tali were studied morphologically and molecularly. As a result, we consider that masuriensis and tali are two different species and treat cuneomaculata as a junior subjective synonym of tali. 

Characterization of Progenitor-Cell-Specific Genes Identified by Subtractive Suppression Hybridization

2004 ◽  
Vol 26 (2-4) ◽  
pp. 131-147 ◽  
Author(s):  
Jingli Cai ◽  
Haipeng Xue ◽  
Ming Zhan ◽  
Mahendra S. Rao
Keyword(s):  
Progenitor Cell ◽  
Subtractive Suppression Hybridization

scholarly journals Taxonomic investigation of representatives of the genus Sphaerotilus: descriptions of Sphaerotilus montanus sp. nov., Sphaerotilus hippei sp. nov., Sphaerotilus natans subsp. natans subsp. nov. and Sphaerotilus natans subsp. sulfidivorans subsp. nov., and an emended description of the genus Sphaerotilus

2011 ◽  
Vol 61 (4) ◽  
pp. 916-925 ◽  
Author(s):  
Elena Gridneva ◽  
Elena Chernousova ◽  
Galina Dubinina ◽  
Vladimir Akimov ◽  
Jan Kuever ◽  
...  
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
Reduced Sulfur Compounds ◽  
Sphaerotilus Natans ◽  
Subspecies Level ◽  
Emended Description ◽  
Taxonomic Approach

Seven strains of the genus Sphaerotilus were obtained from natural thermal sulfide (strains D-501T, D-502, D-504, D-505 and D-507) and low-temperature ferrous (strain HST) springs and from an activated sludge system (strain D-380). These Sphaerotilus isolates and strains of Sphaerotilus natans obtained from the DSMZ (S. natans DSM 6575T, DSM 565 and DSM 566) were studied using a polyphasic taxonomic approach. All strains had Q-8 as the major quinone and C16 : 1ω7, C16 : 0 and C18 : 1ω7 as the major fatty acids. The DNA–DNA hybridization results and 16S rRNA, hsp60 and gyrB gene sequencing experiments showed that isolates D-501T, D-502, D-504, D-505, D-507 and D-380 were closely related to the type strain of S. natans DSM 6575T. However, strains D-501T, D-502, D-504, D-505 and D-507 significantly differed from the heterotrophic strain S. natans DSM 6575T by their capability for lithotrophic growth with reduced sulfur compounds as an electron donor for energy conservation and some other phenotypic features. For this reason, strains D-501T, D-502, D-504, D-505 and D-507 merit a separate taxonomic classification at the subspecies level. The name Sphaerotilus natans subsp. sulfidivorans subsp. nov. (type strain D-501T = DSM 22545T = VKM B-2573T) is proposed. The subspecies Sphaerotilus natans subsp. natans subsp. nov. is automatically created as a result of this proposal. Strain D-380 was phenotypically closely related to S. natans DSM 6575T. Strains D-380 and S. natans DSM 6575T were assigned to the subspecies Sphaerotilus natans subsp. natans subsp. nov. (type strain DSM 6575T = ATCC 13338T). The 16S rRNA, hsp60 and gyrB gene sequences obtained for strains HST and DSM 565 showed very low sequence similarity values of 97.3 %, 89.7 % and 88.4 %, respectively, with S. natans DSM 6575T. Strain HST shared 99 % DNA–DNA relatedness with strain

Dynamic Subspecies Population Structure of Vibrio Cholerae in Dhaka, Bangladesh

2021 ◽  
Author(s):  
Mohammad Islam ◽  
Tania Nasreen ◽  
Kevin Y. H. Liang ◽  
Fatema-Tuz Johura ◽  
Paul C. Kirchberger ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Temporal Dynamics ◽  
Sampling Period ◽  
Amplicon Sequencing ◽  
Rapid Expansion ◽  
Capital City ◽  
Dhaka City ◽  
Physiochemical Parameters ◽  
Subspecies Level ◽  
Abundance And Distribution

Abstract Cholera has been endemic to the Ganges delta for centuries. Although the causative agent, Vibrio cholerae, is autochthonous to coastal and brackish water, cholera occurs continually in Dhaka, the inland capital city of Bangladesh which is surrounded by fresh water. Despite the persistence of this problem, little is known about the environmental abundance and distribution of lineages of V. cholerae, the most important being the pandemic generating lineage (PG) consisting mostly of serogroup O1 strains. To understand spatial and temporal dynamics of PG and other lineages belonging to the V. cholerae species in surface water in and around Dhaka city, we used qPCR and high throughput amplicon sequencing. Seven different freshwater sites across Dhaka were investigated for six consecutive months and physiochemical parameters were measured in situ. Total abundance of V. cholerae was found to be relatively stable throughout the six months sampling period, with 2×105 to 4×105 genome copies/L at six sites and around 5 ×105 genome copies/L at the site located in the most densely populated part of Dhaka city. PG O1 V. cholerae was present in high abundance during the entire sampling period and composed between 24-92% of the total V. cholerae population, only showing occasional but sudden reductions in abundance. In instances where PG O1 lost its dominance, other lineages underwent a rapid expansion while the size of the total V. cholerae population remained almost unchanged. Intraspecies richness of V. cholerae was positively correlated to salinity, conductivity and total dissolved solids (TDS), while it was negatively correlated to dissolved oxygen (DO) concentration in water. Interestingly, negative correlation was observed specifically between PG O1 and salinity, even though the changes in this variable were minor (0-0.8 ppt). Observations in this study suggest that at the subspecies level, population composition of naturally occurring V. cholerae can be influenced by fluctuations in environmental factors, which can lead to altered competition dynamics among the lineages.

scholarly journals Global Patterns and Drivers of Avian Extinctions at the Species and Subspecies Level

PLoS ONE ◽  
2012 ◽  
Vol 7 (10) ◽  
pp. e47080 ◽  
Author(s):  
Judit K. Szabo ◽  
Nyil Khwaja ◽  
Stephen T. Garnett ◽  
Stuart H. M. Butchart
Keyword(s):  
Subspecies Level ◽  
Global Patterns

scholarly journals Discrimination of Streptococcus equi subsp. equi and Streptococcus equi subsp. zooepidemicus using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

2017 ◽  
Vol 29 (5) ◽  
pp. 622-627 ◽  
Author(s):  
Rinosh J. Mani ◽  
Anil J. Thachil ◽  
Akhilesh Ramachandran
Keyword(s):  
Laser Desorption Ionization ◽  
Biochemical System ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Subspecies Level ◽  
Streptococcus Equi ◽  
Level Identification ◽  
Tof Ms

Accurate and timely identification of infectious etiologies is of great significance in veterinary microbiology, especially for critical diseases such as strangles, a highly contagious disease of horses caused by Streptococcus equi subsp. equi. We evaluated a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platform for use in species- and subspecies-level identification of S. equi isolates from horses and compared it with an automated biochemical system. We used 25 clinical isolates each of S. equi subsp. equi and S. equi subsp. zooepidemicus. Using the MALDI-TOF MS platform, it was possible to correctly identify all 50 isolates to the species level. Unique mass peaks were identified in the bacterial peptide mass spectra generated by MALDI-TOF MS, which can be used for accurate subspecies-level identification of S. equi. Mass peaks (mass/charge, m/ z) 6,751.9 ± 1.4 (mean ± standard deviation) and 5,958.1 ± 1.3 were found to be unique to S. equi subsp. equi and S. equi subsp. zooepidemicus, respectively. The automated biochemical system correctly identified 47 of 50 of the isolates to the species level as S. equi, whereas at the subspecies level, 24 of 25 S. equi subsp. equi isolates and 22 of 25 S. equi subsp. zooepidemicus isolates were correctly identified. Our results indicate that MALDI-TOF MS can be used for accurate species- and subspecies-level identification of S. equi.

Population genetics and zoogeography of Australian freshwater golden perch, Macquaria ambigua (Richardson 1845) (Teleostei: Percichthyidae), and electrophoretic identification of a new species from the Lake Eyre basin

1992 ◽  
Vol 43 (6) ◽  
pp. 1585 ◽  
Author(s):  
MK Musyl ◽  
CP Keenan
Keyword(s):  
Drainage Basin ◽  
Gene Pools ◽  
Internal Drainage ◽  
Allopatric Species ◽  
Subspecies Level ◽  
Allelic Differences ◽  
Starch Gel ◽  
Average Gene ◽  
Australian Freshwater ◽  
Two Populations

Populations of golden perch (Macquaria ambigua) were sampled from both sides of the Great Dividing Range (GDR): from the Murray-Darling drainage basin (Murray R., L. Keepit and Condamine R.), the L. Eyre internal drainage basin (Barcoo R. and Diamantina R.), and the internal drainage basin of the Bulloo R.-all to the west of the GDR-and from the Fitzroy drainage basin (Dawson R. and Nogoa R.) east of the GDR. Starch-gel and polyacrylamide electrophoresis of 12 enzyme systems plus two general muscle proteins was used to estimate the genetic variation within and between populations. Of the 18 presumed genetic loci examined, nine were either polymorphic at the P0.99 criterion level or exhibited fixed allelic differences between some of the populations. Within the Murray-Darling drainage basin, there was little indication of heterogeneity. Contingency Χ2 analyses of allelic distributions among drainage basins indicated significant levels of heterogeneity at six variable loci. The isolated L. Eyre population exhibited diagnostic alleles at four loci when compared with the Murray- Darling and Fitzroy populations. The genetic distance of the L. Eyre population (Nei's D=0.23) from these two populations indicates that the L. Eyre golden perch is most probably a previously unrecognized allopatric species. The level of divergence (0 = 0.06) between Fitzroy and Murray-Darling golden perch indicates differentiation at the subspecies level, with no fixed differences observed between these two populations. Finally, golden perch from the Bulloo R. represent either (i) an intermediate evolutionary unit between the presumed ancestral L. Eyre population and the derived Murray-Darling and Fitzroy populations or (ii) a complex hybrid between these populations. Average gene-flow statistics, FST = 0.760 and Nem=0.08, suggest that the populations in each of the four basins can be regarded as separate gene pools that have been isolated for different, and considerable, periods of time.

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