Strategy for the enrichment of protein biomarkers from diverse bacterial select agents

2021 ◽  
Vol 28 ◽  
Author(s):  
Sasikumar Sabna ◽  
Dev Vrat Kamboj ◽  
Ravi Bhushan Kumar ◽  
Prabhakar Babele ◽  
Sakshi Rajoria ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Species Identification ◽  
Immune Serum ◽  
Tandem Ms ◽  
Environmental Matrices ◽  
Bacterial Proteins ◽  
Conserved Regions ◽  
Groel Protein ◽  
Ms Analysis ◽  
Enrichment Strategy

Background: Some pathogenic bacteria can be potentially used for nefarious applications in the event of bioterrorism or biowarfare. Accurate identification of biological agent from clinical and diverse environmental matrices is of paramount importance for implementation of medical countermeasures and biothreat mitigation. Objective: A novel methodology is reported here for the development of a novel enrichment strategy for the generally conserved abundant bacterial proteins for an accurate downstream species identification using tandem MS analysis in biothreat scenario. Methods: Conserved regions in the common bacterial protein markers were analyzed using bioinformatic tools and stitched for a possible generic immuno-capture for an intended downstream MS/MS analysis. Phylogenetic analysis of selected proteins was carried out and synthetic constructs were generated for the expression of conserved stitched regions of 60 kDa chaperonin GroEL. Hyper-immune serum was raised against recombinant synthetic GroEL protein. Results: The conserved regions of common bacterial proteins were stitched for a possible generic immuno-capture and subsequent specific identification by tandem MS using variable regions of the molecule. Phylogenetic analysis of selected proteins was carried out and synthetic constructs were generated for the expression of conserved stitched regions of GroEL. In a proof-of-concept study, hyper-immune serum raised against recombinant synthetic GroEL protein exhibited reactivity with ~60 KDa proteins from the cell lysates of three bacterial species tested. Conclusion: The envisaged methodology can lead to the development of a novel enrichment strategy for the abundant bacterial proteins from complex environmental matrices for the downstream species identification with increased sensitivity and substantially reduce the time-to-result.

scholarly journals Species Identification and Antifungal Susceptibility Patterns of Species Belonging to Aspergillus Section Nigri

2009 ◽  
Vol 53 (10) ◽  
pp. 4514-4517 ◽  
Author(s):  
Laura Alcazar-Fuoli ◽  
Emilia Mellado ◽  
Ana Alastruey-Izquierdo ◽  
Manuel Cuenca-Estrella ◽  
Juan L. Rodriguez-Tudela
Keyword(s):  
Phylogenetic Analysis ◽  
Species Identification ◽  
Antifungal Susceptibility ◽  
Morphological Features ◽  
Correct Classification ◽  
Paradoxical Effect ◽  
Aspergillus Section Nigri ◽  
Susceptibility Patterns ◽  
Aspergillus Section

ABSTRACT A phylogenetic analysis was performed for 34 Aspergillus strains belonging to section Nigri. Molecular methods allowed for the correct classification into three different clades (A. niger, A. tubingensis, and A. foetidus). Correlation with in vitro itraconazole susceptibility distinguished the following three profiles: susceptible, resistant, and showing a paradoxical effect. A number of different species whose morphological features resemble those of A. niger showed unusual MICs to itraconazole that have never been described for the Aspergillus genus.

Pilaira australis sp. nov. (Mucorales, Mucoromycota) isolated from emu faeces in Australia

Phytotaxa ◽  
2017 ◽  
Vol 329 (3) ◽  
pp. 277 ◽  
Author(s):  
ANDREW S. URQUHART ◽  
PAULINE M. L. COULON ◽  
ALEXANDER IDNURM
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Species Identification ◽  
Internal Transcribed Spacers ◽  
Molecular Phylogenetic Analysis ◽  
Unique Combination ◽  
Dromaius Novaehollandiae ◽  
Molecular Phylogenetic ◽  
Carbon Utilisation ◽  
A New Species

Pilaira australis, a new species of fungus in the coprophilous genus Pilaira, was isolated from emu (Dromaius novaehollandiae) faeces and is described. Morphologically, the species resembles other species in the genus, particularly P. moreaui, except differs in its unique combination of sporangiophore height and sporangiospore length. Molecular phylogenetic analysis indicates that P. australis is distinct from other species in the genus with two regions, the internal transcribed spacers (ITS) and a fragment of the pyrG gene, showing 91% and 90% identity to the nearest species, respectively. Ultrastructure features and carbon utilisation were determined for P. australis, and may provide characteristics for species identification in this genus.

scholarly journals Tandem MS Analysis of Selenamide-Derivatized Peptide Ions

2011 ◽  
Vol 22 (9) ◽  
pp. 1610-1621 ◽  
Author(s):  
Yun Zhang ◽  
Hao Zhang ◽  
Weidong Cui ◽  
Hao Chen
Keyword(s):  
Tandem Ms ◽  
Peptide Ions ◽  
Ms Analysis

scholarly journals Harnessing mtDNA variation to resolve ambiguity in ‘Redfish’ sold in Europe

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3746 ◽  
Author(s):  
Peter Shum ◽  
Lauren Moore ◽  
Christophe Pampoulie ◽  
Cristina Di Muri ◽  
Sara Vandamme ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Species Identification ◽  
Fisheries Management ◽  
North Atlantic ◽  
Molecular Approach ◽  
Mtdna Variation ◽  
Control Region Sequences ◽  
Market Product ◽  
Reference Sequences ◽  
Pacific Rockfish

Morphology-based identification of North AtlanticSebasteshas long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North AtlanticSebastescomprises of four species, commonly known as ‘redfish’, but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from ‘blind’ specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicusandS. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification ofSebastesmarket samples.

scholarly journals Phylogenetic analysis as a means of species identification within Myrmecolacidae (Strepsiptera)

2001 ◽  
Vol 144 (2) ◽  
pp. 179-186 ◽  
Author(s):  
N. R. Halbert ◽  
L. D. Ross ◽  
J. Kathirithamby ◽  
J. B. Woolley ◽  
R. R. Saff ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Species Identification

Phylogenetic analysis of the genus Corotoca, with description of a new genus and species from Brazil (Coleoptera, Staphylinidae, Aleocharinae)

2020 ◽  
pp. 1-45
Author(s):  
Bruno Zilberman
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Species Identification ◽  
New Genus ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Exhaustive Search ◽  
New Genus And Species ◽  
A New Species

Corotoca is a strictly Neotropical genus of termitophilous beetles associated with termites of genus Constrictotermes. A cladistic analysis based on 13 terminal taxa and 60 characters (57 morphological and three behavioral) was conducted. The exhaustive search with equally weighted characters resulted in two most parsimonious trees with 95 steps. Spirachtha is proposed to be the sister group of the monophyletic “subgroup Corotocae” (Corotoca + Cavifonexus gen. nov.), based on eleven synapomorhphies (ten exclusive and one homoplastic). The monophyly of Corotoca is supported here, including six species associated with Constrictotermes cyphergaster: (Corotoca hitchensi sp. nov + (C. melantho + C. pseudomelantho sp. nov.) + ((C. fontesi + (C. phylo + C. araujoi)). A new genus, Cavifronexus gen. nov., is proposed to two species associated with Constrictotermes cavifrons (Holmgren, 1910): Cavifronexus guyanae comb. nov., from Guyana and Brazil, previously described as Corotoca; and a new species, Cavifronexus papaveroi sp. nov., from Brazil. This work also includes descriptions, redescriptions, and illustrations for all species and genera. Keys for genera and species identification in “subgroup Corotocae” are also provided.

Genetic Differentiation and Divergence Time of Chinese Parnassius (Lepidoptera: Papilionidae) Species Based on Nuclear Internal Transcribed Spacer (ITS) Sequence Data

2020 ◽  
Vol 55 (4) ◽  
pp. 520-546
Author(s):  
Chengcai Si ◽  
Keke Chen ◽  
Ruisong Tao ◽  
Chengyong Su ◽  
Junye Ma ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Differentiation ◽  
Species Identification ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Divergence Time ◽  
Time Estimation ◽  
Western China ◽  
Tibet Plateau ◽  
Divergence Time Estimation

Abstract Parnassius (Lepidoptera: Papilionidae) is a genus of attractive butterflies mainly distributed in the mountainous areas of Central Asia, the Himalayas, and western China. In this study, we used the internal transcribed spacer (ITS1 and ITS2) sequence data as DNA barcodes to characterize the genetic differentiation and conduct the phylogenetic analysis and divergence time estimation of the 17 Parnassius species collected in China. Species identification and genetic differentiation analysis suggest that the ITS barcode is an effective marker for Parnassius species identification; additionally, a relatively high level of genetic diversity and low level of gene flow were detected in the five Parnassius species with diverse geographic populations. Phylogenetic analysis indicates that the 17 species studied were clustered in six clades (subgenera), with subgenus Parnassius at the basal position in the phylogenetic trees. Bayesian divergence time estimation shows that the genus originated about 18 million years ago during the early Miocene, correlated with orogenic events in the distribution region, probably southwestern China about 20–10 million years ago. Our estimated phylochronology also suggests that the Parnassius interspecific and intraspecific divergences were probably related with the rapid rising of the Qinghai-Tibet Plateau, the Tibet Movement, the Kunlun-Yellow River Tectonic Movement, and global cooling associated with intensified glaciation in the region during the Quaternary Period.

Currhaeus, a new genus of net-winged beetles and phylogenetic analysis of Eurrhacini (Coleoptera: Lycidae: Lycinae)

Zootaxa ◽  
2020 ◽  
Vol 4869 (3) ◽  
pp. 387-403
Author(s):  
ELYNTON ALVES DO NASCIMENTO ◽  
TAMIRES DINIZ BRESSAN ◽  
MILADA BOCAKOVA
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Likelihood ◽  
Species Identification ◽  
Male Genitalia ◽  
New Genus ◽  
Morphological Data ◽  
Key To Species ◽  
Diagnostic Characters ◽  
Parsimony Trees

A new genus of Neotropical Lycidae, Currhaeus gen. nov., is herein proposed as the second Eurrhacini genus lacking parameres in male genitalia. Seven new species are described: Currhaeus striatus sp. nov., C. nigroapicalis sp. nov., C. championi sp. nov., C. tabascensis sp. nov., C. ruschii sp. nov., C. polegattoi sp. nov., and C. paranaensis sp. nov. Illustrations of diagnostic characters and a key to species identification are presented. Parsimony and maximum likelihood analyses of morphological data demonstrated that Currhaeus gen. nov. belongs in the crown Eurrhacini. Implied weighting parsimony trees recovered Currhaeus as sister to Eurrhacus Waterhouse. 

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