scholarly journals Ebony Wood Identification to Battle Illegal Trade

2019 ◽  
Vol 3 ◽  
Author(s):  
Mehrdad Jahanbanifard ◽  
Barbara Gravendeel ◽  
Frederic Lens ◽  
Fons Verbeek
Keyword(s):  
Global Market ◽  
Musical Instruments ◽  
Species Level ◽  
Eastern Africa ◽  
Wood Identification ◽  
Accurate Identification ◽  
Specific Chemical ◽  
Molecular Barcoding ◽  
Species Specific ◽  
Tof Ms

Illegal logging is a serious global issue. It is not only a great threat to rare forest species, but also contributes to the current biodiversity crisis and climate change. Despite international agreements, 10-30% of all imported wood has been illegally logged. Many of these trees, especially rosewood (Dalbergia) and ebony (Diospyros), are very important for the global market because of their high economic value. Ebony is a common name for the black heartwood (inner parts of the stem) of some Diospyros species. These woods are used in products such as acoustic musical instruments. The genus Diospyros includes over 700 species globally. More than 200 of them are endemic to Madagascar, which is a one of the richest regions in terms of biodiversity. This island is situated in the Indian Ocean off the coast of Eastern Africa and is known for its unique biodiversity. Due to over-harvesting in recent decades, many Malagasy species of Diospyros are listed as endangered under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES; CITES checklist for Diospyros). Trade of these species requires CITES permits. All described Malagasy ebony species under Appendix II meaning that, while not currently threatened with extinction they may become so if trade is not controlled. Controlling the logging trade is often more difficult than it seems. Labels are easily switched, different species of wood can be mixed, permits can be falsified, and many more tricks are used to get illegally logged wood onto the global market. One of the most commonly used techniques to identify timber products is the assessment of species-specific cellular patterns (White et al. 1991). Wood anatomy has been practiced for more than 200 years, and automated tools have been developed to identify wood at the genus and species level over the past decade (Figueroa-Mata et al. 2018, Hafemann et al. 2014, Koch et al. 2011, Ravindran et al. 2018). However, the lack of sufficient resolution for species-level identification, especially for speciose genera such as Diospyros, is the main drawback of this method. Identification using molecular barcoding is an alternative but challenging method as timber is composed mainly of dead cells and the few living cells often have poor DNA quality. A third identification method is direct analysis in real time time-of-flight mass spectrometry (DART TOF MS; Espinoza et al. 2015, Evans et al. 2017). This method analyses the chemical composition of a wood sample, resulting in a species-specific chemical fingerprint. DART TOF MS has already been successfully applied to several tree genera including Dalbergia (rosewood), Aquilaria (agarwood), and Quercus (oak). The main disadvantage of this method is that it can only be applied to heartwood samples from the inner part of the trunk. In order to develop a comprehensive and accurate identification tool to identify Malagasy ebony woods, we are working towards building an image recognition model based on wood anatomical microscopic images. As a case study, we successfully trained our classifier using a public dataset (Martins et al. 2012) such that our model was able to distinguish different tree genera of that dataset with 93% accuracy. We are currently extending this work to the subgeneric level of Diospyros. This will be used to establish the presence of ebony woods in acoustic musical instruments based on reference samples from wood specimens preserved in natural history musea. To achieve sufficient accuracy, we are focusing on the microscopic features of transverse and tangential orientation planes in ebony woods. Our database will include very high resolution images of Diospyros species, and can help wood anatomist at wood identification institute and customs officers at harbours to increase the accuracy of the identification of illegally logged ebony woods.

scholarly journals Performance of Five Commercial Identification Platforms for Identification of Staphylococcus delphini

2019 ◽  
Vol 57 (11) ◽  
Author(s):  
Matthew C. Canver ◽  
Tsigereda Tekle ◽  
Samantha T. Compton ◽  
Katrina Callan ◽  
Eileen M. Burd ◽  
...  
Keyword(s):  
Distinct Species ◽  
Human Infection ◽  
Species Level ◽  
Accurate Identification ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Staphylococcus Intermedius ◽  
Animal Pathogens ◽  
Tof Ms

ABSTRACT The Staphylococcus intermedius group (SIG) is a collection of coagulase-positive staphylococci consisting of four distinct species, namely, Staphylococcus cornubiensis, Staphylococcus delphini, Staphylococcus intermedius, and Staphylococcus pseudintermedius. SIG members are animal pathogens and rare causes of human infection. Accurate identification of S. pseudintermedius has important implications for interpretation of antimicrobial susceptibility testing data and may be important for other members of the group. Therefore, we sought to evaluate the performance of five commercially available identification platforms with 21 S. delphini isolates obtained from a variety of animal and geographic sources. Here, we show that automated biochemical platforms were unable to identify S. delphini to the species level, a function of its omission from their databases, but could identify isolates to the SIG level with various degrees of success. However, all automated systems misidentified at least one isolate as Staphylococcus aureus. One matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system was able to identify S. delphini to the species level, suggesting that MALDI-TOF MS is the best option for distinguishing members of the SIG. With the exception of S. pseudintermedius, it is unclear if other SIG members should be routinely identified to the species level; however, as our understanding of their role in animal and human diseases increases, it may be necessary and important to do so.

scholarly journals Accuracy of conventional identification methods used for Enterobacteriaceae isolates in three Nigerian hospitals

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2511 ◽  
Author(s):  
Christiana Jesumirhewe ◽  
Peter Oladejo Ogunlowo ◽  
Mitsan Olley ◽  
Burkhard Springer ◽  
Franz Allerberger ◽  
...  
Keyword(s):  
Multidrug Resistant ◽  
Species Level ◽  
Accurate Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Maldi Biotyper ◽  
Identification Of Bacteria ◽  
Identification Techniques ◽  
Tof Ms

BackgroundEnterobacteriaceae are ubiquitously present in nature and can be found in the intestinal tract of humans and animals as commensal flora. Multidrug-resistant Enterobacteriaceae are increasingly reported and are a threat to public health implicating a need for accurate identification of the isolates to species level. In developing countries, identification of bacteria basically depends on conventional methods: culture and phenotypic methods that hamper the accurate identification of bacteria. In this study, matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technique was compared to conventional identification techniques.Materials and MethodsIn total, 147 Enterobacteriaceae isolates were collected from March to May 2015 from three medical microbiology laboratories of hospitals in Edo state, Nigeria, after being tested according to the individual laboratories standard operating procedures. All isolates were stored at −20°C until tested centrally by MALDI-TOF MS.ResultsOne hundred and forty five (98.6%) isolates had a MALDI Biotyper best score > or =2.0, indicating a secure genus and probable species identification; and 2(1.36%) isolates had a best score <2.0 indicating probable genus identification. Isolates with best scores of > or =2.0 comprised nine genera and 10 species, respectively. A total of 57.2% and 33.1% of isolates identified had agreement between MALDI-TOF MS and conventional techniques for identification at genus and species level, respectively, when analyzing bacteria with MALDI Biotyper best scores > or =2.0.ConclusionThe results of our study show that the applied conventional identification techniques for Enterobacteriaceae in the investigated Nigerian hospitals are not very accurate. Use of state-of-the-art identification technologies for microorganisms is necessary to guarantee comparability of bacteriological results.

scholarly journals Unraveling the Olfactory Biases of Male Euglossine Bees: Species-Specific Antennal Responses and Their Evolutionary Significance for Perfume Flowers

2021 ◽  
Vol 9 ◽  
Author(s):  
Katharina Brandt ◽  
Stefan Dötterl ◽  
Santiago R. Ramírez ◽  
Florian Etl ◽  
Isabel Cristina Machado ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Chemical Compounds ◽  
Species Level ◽  
Evolutionary Significance ◽  
Euglossine Bees ◽  
Specific Chemical ◽  
Antennal Response ◽  
Euglossine Bee ◽  
Species Specific ◽  
Antennal Responses

Male euglossine bees exhibit unique adaptations for the acquisition and accumulation of chemical compounds from “perfume flowers” and other sources. During courtship display, male bees expose perfume mixtures, presumably to convey species-specific recognition and/or mate choice signals to females. Because olfaction regulates both signal production (in males) and signal detection (in females) in this communication system, strong selective pressures are expected to act on the olfactory system, which could lead to sensory specialization in favor of an increased sensitivity to specific chemical compounds. The floral scents of euglossine-pollinated plants are hypothesized to have evolved in response to the preexisting sensory biases of their male euglossine bee pollinators. However, this has never been investigated at the peripheral olfactory circuitry of distinct pollinating genera. Here, we present a comparative analysis using electroantennography (EAG) of males across the phylogeny of 29 euglossine bee species, among them Euglossa and Eulaema species. First, we tested whether antennal responses differ among different euglossine genera, subgenera and species. Secondly, we conducted a comparative phylogenetic analysis to investigate the macroevolutionary patterns of antennal responses across the euglossine bee phylogeny. We found that antennal response profiles are very unique on the species level and differ on the subgenus and the genus level. The differences can be explained by chemical compounds typically found in the floral scent bouquets of perfume flowers and specific compounds of species either pollinated by Euglossa (e.g., ipsdienol) or Eulaema bees (e.g., (−)-(E)-carvone epoxide). Also, we detected a phylogenetic signal in mean antennal responses and found that especially at the species level of our simulation the overall antennal responses exhibit greater disparity relative to a null model of pure Brownian-motion across the phylogeny. Altogether, our results suggest that (1) euglossine bee species exhibit species-specific antennal responses that differ among euglossine genera and subgenera, (2) antennal responses diverge early after speciation events, and (3) scent composition of perfume flowers evolved in response to pollinator-mediated selection imposed by preexisting sensory biases in euglossine bees.

scholarly journals Development of a One-Step Multiplex PCR Assay for Differential Detection of Four species (Enterobacter cloacae, Enterobacter hormaechei, Enterobacter roggenkampii, and Enterobacter kobei) Belonging to Enterobacter cloacae Complex With Clinical Significance

2021 ◽  
Vol 11 ◽  
Author(s):  
Yang Ji ◽  
Peihong Wang ◽  
Tingting Xu ◽  
Yanzi Zhou ◽  
Rongchang Chen ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Clinical Significance ◽  
Enterobacter Cloacae ◽  
Species Level ◽  
Specific Primers ◽  
Accurate Identification ◽  
Multiplex Pcr Assay ◽  
Specificity And Sensitivity ◽  
One Step ◽  
Species Specific

Enterobacter cloacae complex (ECC) is composed of multiple species and the taxonomic status is consecutively updated. In last decades ECC is frequently associated with multidrug resistance and become an important nosocomial pathogen. Currently, rapid and accurate identification of ECC to the species level remains a technical challenge, thus impedes our understanding of the population at the species level. Here, we aimed to develop a simple, reliable, and economical method to distinguish four epidemiologically prevalent species of ECC with clinical significance, i.e., E. cloacae, E. hormaechei, E. roggenkampii, and E. kobei. A total of 977 ECC genomes were retrieved from the GenBank, and unique gene for each species was obtained by core-genome comparisons. Four pairs of species-specific primers were designed based on the unique genes. A total of 231 ECC clinical strains were typed both by hsp60 typing and by species-specific PCRs. The specificity and sensitivity of the four species-specific PCRs ranged between 96.56% and 100% and between 76.47% and 100%, respectively. The PCR for E. cloacae showed the highest specificity and sensitivity. A one-step multiplex PCR was subsequently established by combining the species-specific primers. Additional 53 hsp60-typed ECC and 20 non-ECC isolates belonging to six species obtained from samples of patients, sewage water and feces of feeding animals were tested by the multiplex PCR. The identification results of both techniques were concordant. The multiplex PCR established in this study provides an accurate, expeditious, and cost-effective way for routine diagnosis and molecular surveillance of ECC strains at species level.

scholarly journals Identification of Adult Fasciola spp. Using Matrix-Assisted Laser/Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry

2020 ◽  
Vol 9 (1) ◽  
pp. 82
Author(s):  
Issa Sy ◽  
Lena Margardt ◽  
Emmanuel O. Ngbede ◽  
Mohammed I. Adah ◽  
Saheed T. Yusuf ◽  
...  
Keyword(s):  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Specific Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Species Specific ◽  
Tof Ms ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

Fascioliasis is a neglected trematode infection caused by Fasciola gigantica and Fasciola hepatica. Routine diagnosis of fascioliasis relies on macroscopic identification of adult worms in liver tissue of slaughtered animals, and microscopic detection of eggs in fecal samples of animals and humans. However, the diagnostic accuracy of morphological techniques and stool microscopy is low. Molecular diagnostics (e.g., polymerase chain reaction (PCR)) are more reliable, but these techniques are not routinely available in clinical microbiology laboratories. Matrix-assisted laser/desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a widely-used technique for identification of bacteria and fungi; yet, standardized protocols and databases for parasite detection need to be developed. The purpose of this study was to develop and validate an in-house database for Fasciola species-specific identification. To achieve this goal, the posterior parts of seven adult F. gigantica and one adult F. hepatica were processed and subjected to MALDI-TOF MS to create main spectra profiles (MSPs). Repeatability and reproducibility tests were performed to develop the database. A principal component analysis revealed significant differences between the spectra of F. gigantica and F. hepatica. Subsequently, 78 Fasciola samples were analyzed by MALDI-TOF MS using the previously developed database, out of which 98.7% (n = 74) and 100% (n = 3) were correctly identified as F. gigantica and F. hepatica, respectively. Log score values ranged between 1.73 and 2.23, thus indicating a reliable identification. We conclude that MALDI-TOF MS can provide species-specific identification of medically relevant liver flukes.

scholarly journals An analysis of the population of Cryptococcus neoformans strains isolated from animals in Poland, in the years 2015–2019

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Magdalena Florek ◽  
Urszula Nawrot ◽  
Agnieszka Korzeniowska-Kowal ◽  
Katarzyna Włodarczyk ◽  
Anna Wzorek ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Species Level ◽  
Molecular Type ◽  
Animal Group ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Severe Infections ◽  
Resistant Strains ◽  
World Distribution ◽  
Tof Ms

AbstractFungi belonging to the Cryptococcus neoformans/C. gattii species complex (CNGSC) are pathogens causing severe infections in humans and animals, that for humans may result in a mortality rate ranging up to 70%. The CNGSC is divided into eight major molecular types, that may differ in their virulence and susceptibility. In order to fully understand the epidemiology of cryptococcosis, it is important to study the world distribution and population structure of these pathogens. The present study is the first presenting a population of strains isolated in Poland and one of the few using a multi-species animal group as a source of the specimen. The pathogen was present in 2.375% of the tested animals. The URA5-RFLP and MALDI-TOF MS analyses have revealed that the population consisted exclusively of C. neoformans strains, with a predominance of major molecular type VNIV (C. neoformans var. neoformans). The MALDI-TOF MS was used to perform the CNGSC strains identification on both the species and sub-species level. Despite the fact that the animals providing the specimens were not treated with 5-fluorocytosine, around 10% of the tested population presented MIC values exceeding 64 mg/L, indicating the existence of the 5-fluorocytosine-resistant strains in the environment.

scholarly journals Identification of the ‘Streptococcus anginosus group’ by matrix-assisted laser desorption ionization – time-of-flight mass spectrometry

2014 ◽  
Vol 63 (9) ◽  
pp. 1143-1147 ◽  
Author(s):  
Katherine Woods ◽  
David Beighton ◽  
John L. Klein
Keyword(s):  
Species Level ◽  
Direct Transfer ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Streptococcus Anginosus ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Transfer Method ◽  
Tof Ms

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) provides rapid, accurate and cost-effective identification of a range of bacteria and is rapidly changing the face of routine diagnostic microbiology. However, certain groups of bacteria, for example streptococci (in particular viridans or non-haemolytic streptococci), are less reliably identified by this method. We studied the performance of MALDI-TOF MS for identification of the ‘Streptococcus anginosus group’ (SAG) to species level. In total, 116 stored bacteraemia isolates identified by conventional methods as belonging to the SAG were analysed by MALDI-TOF MS. Partial 16S rRNA gene sequencing, supplemented with sialidase activity testing, was performed on all isolates to provide ‘gold standard’ identification against which to compare MALDI-TOF MS performance. Overall, 100 % of isolates were correctly identified to the genus level and 93.1 % to the species level by MALDI-TOF MS. However, only 77.6 % were correctly identified to the genus level and 59.5 % to the species level by a MALDI-TOF MS direct transfer method alone. Use of a rapid in situ extraction method significantly improved identification rates when compared with the direct transfer method (P<0.001). We recommend routine use of this method to reduce the number of time-consuming full extractions required for identification of this group of bacteria by MALDI-TOF MS in the routine diagnostic laboratory. Only 22 % (1/9) of Streptococcus intermedius isolates were reliably identified by MALDI-TOF MS to the species level, even after full extraction. MALDI-TOF MS reliably identifies S. anginosus and Streptococcus constellatus to the species level but does not reliably identify S. intermedius.

scholarly journals Matrix-assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a Reliable Tool to Identify Species of Catalase-negative Gram-positive Cocci not Belonging to the Streptococcus Genus

2016 ◽  
Vol 10 (1) ◽  
pp. 202-208 ◽  
Author(s):  
Marisa Almuzara ◽  
Claudia Barberis ◽  
Viviana Rojas Velázquez ◽  
Maria Soledad Ramirez ◽  
Angela Famiglietti ◽  
...  
Keyword(s):  
Extraction Methods ◽  
Species Level ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Genus Level ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Level Identification ◽  
Gram Positive Cocci ◽  
Tof Ms

Objective:To evaluate the performance of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) by using 190 Catalase-negative Gram-Positive Cocci (GPC) clinical isolates.Methods:All isolates were identified by conventional phenotypic tests following the proposed scheme by Ruoff and Christensen and MALDI-TOF MS (Bruker Daltonics, BD, Bremen, Germany). Two different extraction methods (direct transfer formic acid method on spot and ethanol formic acid extraction method) and different cut-offs for genus/specie level identification were used. The score cut-offs recommended by the manufacturer (≥ 2.000 for species-level, 1.700 to 1.999 for genus level and <1.700 no reliable identification) and lower cut-off scores (≥1.500 for genus level, ≥ 1.700 for species-level and score <1.500 no reliable identification) were considered for identification. A minimum difference of 10% between the top and next closest score was required for a different genus or species.MALDI-TOF MS identification was considered correct when the result obtained from MS database agreed with the phenotypic identification result.When both methods gave discordant results, the 16S rDNA orsodAgenes sequencing was considered as the gold standard identification method. The results obtained by MS concordant with genes sequencing, although discordant with conventional phenotyping, were considered correct. MS results discordant with 16S orsodA identification were considered incorrect.Results:Using the score cut-offs recommended by the manufacturer, 97.37% and 81.05% were correctly identified to genus and species level, respectively. On the other hand, using lower cut-off scores for identification, 97.89% and 94.21% isolates were correctly identified to genus and species level respectively by MALDI-TOF MS and no significant differences between the results obtained with two extraction methods were obtained.Conclusion:The results obtained suggest that MALDI-TOF MS has the potential of being an accurate tool for Catalase-negative GPC identification even for those species with difficult diagnosis asHelcococcus,Abiotrophia,Granulicatella, among others. Nevertheless, expansion of the library, especially including more strains with different spectra on the same species might overcome potential “intraspecies” variability problems. Moreover, a decrease of the identification scores for species and genus-level identification must be considered since it may improve the MALDI-TOF MS accuracy.

ISSR-Derived Species-Specific SCAR Marker for Rapid and Accurate Authentication of Ocimum tenuiflorum L.

Planta Medica ◽  
2017 ◽  
Vol 84 (02) ◽  
pp. 117-122 ◽  
Author(s):  
Amit Kumar ◽  
Vereena Rodrigues ◽  
Priyanka Mishra ◽  
Kuppusamy Baskaran ◽  
Ashutosh Shukla ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
High Volume ◽  
Inter Simple Sequence Repeat ◽  
Rapid Identification ◽  
Medicinal Species ◽  
Accurate Identification ◽  
Sequence Characterized Amplified Region ◽  
Medicinal Value ◽  
Ocimum Tenuiflorum ◽  
Species Specific

Abstract Ocimum tenuiflorum has been widely used in traditional medicine and has high medicinal value. High volume trade of this potential medicinal plant species led to unscrupulous adulteration of both crude drugs as well as formulations. Morphology-based authentication is difficult in cases of incomplete or damaged samples and in dried herbal materials. In such cases, PCR-based molecular methods may aid in accurate identification. The present study aimed at developing species-specific DNA marker(s) for the authentication of O. tenuiflorum. A species-specific amplicon (279 bp) generated through an inter-simple sequence repeat marker (UBC 835) in all individuals of O. tenuiflorum was cloned, sequenced, and a primer pair was developed (designated as CIM-OT-835F/CIM-OT-835R). The newly developed sequence characterized amplified region marker was validated through PCR amplification in all available seven species of Ocimum, and its specificity for O. tenuiflorum was confirmed with the consistent generation of an amplicon of 177 bp. The developed marker can be used for accurate and rapid identification of the species for certification purposes and will be useful in quality control of medicinal preparations containing this important medicinal species.

scholarly journals The megalopa stage of Portunus spinimanus Latreille, 1819 and Portunus gibbesii (Stimpson, 1859) (Decapoda, Brachyura, Portunidae) from the southeastern Atlantic coast of the United States

Zootaxa ◽  
2007 ◽  
Vol 1638 (1) ◽  
pp. 21-37 ◽  
Author(s):  
MARIA LUCIA NEGREIROS-FRANSOZO ◽  
NADIA MEYERS ◽  
VÍVIAN FRANSOZO ◽  
SUSAN THORTON-DE VICTOR
Keyword(s):  
South Carolina ◽  
Atlantic Coast ◽  
Relative Size ◽  
The United States ◽  
Species Level ◽  
Crab Larvae ◽  
Juvenile Instar ◽  
Species Specific ◽  
Swimming Crabs ◽  
Southeastern Atlantic

The identification of megalopae from plankton samples is difficult, because this larval stage is the least well known among crab larvae, unknown in some species and poorly described in others. Wild megalopa specimens of some swimming crabs (family Portunidae Rafinesque, 1815) were captured alive from neuston samples obtained during summer surveys near the coast of Charleston, South Carolina (U.S.A). For identification purposes, larvae were reared to the 8th juvenile instar. After reaching the 5th juvenile instar, the juvenile crabs exhibited morphological features suitable for identification to the species level. The specimens belonged to two species of Portunidae, Portunus spinimanus Latreille, 1819 and P. gibbesii (Stimpson, 1859). Their megalopae were described in detail and compared to other portunid megalopae known from the southeastern Atlantic coast of the U.S.A. Species-specific characters of portunid megalopae are the number of carpal spines on the chelipeds, the relative size of the sternal spines (7th sternite), the number of antennal flagellum segments, and the setation of mouthparts.

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