genetic identification
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Author(s):  
A. V. Kobelev ◽  
S. V. Klement'ev ◽  
A. S. Sirotkin

We examine the agglutinating ability of five compounds, namely, A1, A2, A3, A4 and BS1, isolated from activated sludge on selective media typical of a number of dominant microbial cultures that contribute to the formation of microbial aggregates. The morphological properties of the isolates and their lectin activity, as well as the physiological and biochemical properties of individual isolates were studied; microorganisms in their composition were identified. We assessed the capacity of the isolates under study to synthesize an exopolysaccharide matrix, as well as the sedimentation of activated sludge under the action of the native solution and culture liquid of the BS1 isolate. Based on their capacity to agglutinate, the BS1 and A2 isolates were selected for further research as producers of extracellular lectins and objects of agglutination, respectively. The biophysiochemical properties and molecular-genetic identification of the BS1 isolate allowed the degree of identity with r. Bacillus to be defined (96.19%); for the A2 isolate, 92.93% identity with p. Shigella and p. Escherichia was determined. To assess the capacity to synthesize a biofilm matrix, the BS1 and A2 isolates were cultivated on an agar nutrient solution using Congo Red dye. According to the obtained results, the isolates are capable of synthesizing an exopolysaccharide matrix, the main component of bacterial biofilms. The research results on the sedimentation of activated sludge induced by the native solution and culture liquid of BS1 showed the following. The sedimentation rate of activated sludge increased significantly at the beginning of the process upon adding a BS1 cell suspension, while the introduction of the native solution of BS1 intensified the process following 5 minutes of contact. The obtained experimental data suggest that the media containing extracellular bacterial lectins can be effectively used as a coagulant (flocculant) for the sedimentation of activated sludge.


PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0261344
Author(s):  
Youssef Arnaout ◽  
Zouheira Djelouadji ◽  
Emmanuelle Robardet ◽  
Julien Cappelle ◽  
Florence Cliquet ◽  
...  

With more than 1400 chiropteran species identified to date, bats comprise one-fifth of all mammalian species worldwide. Many studies have associated viral zoonoses with 45 different species of bats in the EU, which cluster within 5 families of bats. For example, the Serotine bats are infected by European Bat 1 Lyssavirus throughout Europe while Myotis bats are shown infected by coronavirus, herpesvirus and paramyxovirus. Correct host species identification is important to increase our knowledge of the ecology and evolutionary pattern of bat viruses in the EU. Bat species identification is commonly determined using morphological keys. Morphological determination of bat species from bat carcasses can be limited in some cases, due to the state of decomposition or nearly indistinguishable morphological features in juvenile bats and can lead to misidentifications. The overall objective of our study was to identify insectivorous bat species using molecular biology tools with the amplification of the partial cytochrome b gene of mitochondrial DNA. Two types of samples were tested in this study, bat wing punches and bat faeces. A total of 163 bat wing punches representing 22 species, and 31 faecal pellets representing 7 species were included in the study. From the 163 bat wing punches tested, a total of 159 were genetically identified from amplification of the partial cyt b gene. All 31 faecal pellets were genetically identified based on the cyt b gene. A comparison between morphological and genetic determination showed 21 misidentifications from the 163 wing punches, representing ~12.5% of misidentifications of morphological determination compared with the genetic method, across 11 species. In addition, genetic determination allowed the identification of 24 out of 25 morphologically non-determined bat samples. Our findings demonstrate the importance of a genetic approach as an efficient and reliable method to identify bat species precisely.


Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Shamshidin Abduriyim ◽  
Tuerxunpaxia Kasimu ◽  
Jing-Kai Lan ◽  
Zi-Li Pu ◽  
Jin-Long Bai ◽  
...  

Abstract Species identification is pivotal in taxonomy, systematics, evolutionary biology and conservation biology. We collected bats that died of natural causes in Shihezi city, Xinjiang, China, and carried out morphological and genetic identification. Morphologically, all individuals were adults/subadults or juveniles of Pipistrellus pipistrellus. We found one haplotype for the mitochondrial gene ND1 and five for the mitochondrial gene cytochrome b (Cytb) among six specimens. Phylogenetically, all the Cytb sequences grouped with P. pipistrellus. We confirm this species’ occurrence in Xinjiang, China.


2021 ◽  
Vol 14 (4) ◽  
pp. 20-32 ◽  
Author(s):  
Yana V. Tikhonravova ◽  
Viktor V. Rogov ◽  
Elena A. Slagoda

The advantages and limitations of the petrography method and the relevance of its use for the study of natural ice are reviewed in the present work. The petrographic method of ground ice study is often used for solving paleogeographic issues. The petrofabric analysis of ground ice is not only useful for descriptive purposes but, like the study of cryostructures, helps to infer growth processes and conditions. Different types of natural ice have specific features that can help us to determine ice genesis. Surface ice, such as glacier ice is often presented by foliation formed by large crystals (50-60 mm); lake ice is characterised by the upper zone of small (6 mm x 3 mm) dendritic and equigranular crystals, which change with increasing depth to large (may exceed 200 mm) columnar and prismatic crystals; segregated ice is composed by crystals forming foliation. Ground ice, such as ice wedge is presented by vertical-band appearance and small crystals (2-2.5 mm); closed-cavity ice is often distinguished by radial-ray appearance produced by elongated ice crystals; injection ice is composed by anhedral crystals, showing the movement of water; snowbank ice is presented by a high concentration of circular bubbles and small (0.1-1 mm) equigranular crystals; icing is described by foliation and mostly columnar crystals. Identification of the origin of ground ice is a complicated task for geocryology because it is difficult to distinguish different types of ground ice based on only visual explorations. The simplest way to get an ice texture pattern is by using polarized light. Distinctions between genetic types of ground ice are not always made in studies, and that can produce erroneous inferences. Petrography studies of an ice object are helpful to clarify the data interpretation, e.g., of isotopic analyses. It is particularly relevant for heterogeneous ice wedges’ study.


2021 ◽  
Author(s):  
André Elias Rodrigues Soares ◽  
Nikolaus Boroffka ◽  
Oskar Schröder ◽  
Leonid Sverchkov ◽  
Norbert Benecke ◽  
...  

Central Asia has been an important region connecting the different parts of Eurasia throughout history and prehistory, with large states developing in this region during the Iron Age. Archaeogenomics is a powerful addition to the zooarchaeological toolkit for understanding the relation of these societies to animals. Here, we present the genetic identification of a goitered gazelle specimen (Gazella subgutturosa) at the site Gazimulla-Tepa, in modern-day Uzbekistan, confirming hunting of the species in the region during the Iron Age. The sample was directly radiocarbon dated to 2724-2439 calBP. A phylogenetic analysis of the mitochondrial genome places the individual into the modern variation of G. subgutturosa. Our data does represent both the first ancient DNA and the first nuclear DNA sequences of this species. The lack of genomic resources available for this gazelle and related species prevented us from performing a more in-depth analysis of the nuclear sequences generated. Therefore, we are making our sequence data available to the research community to facilitate other research of this nowadays threatened species which has been subject to human hunting for several millennia across its entire range on the Asian continent.


Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1949
Author(s):  
Andrea Miranda Paez ◽  
Mekala Sundaram ◽  
Janna R. Willoughby

The conservation and management of wildlife requires the accurate assessment of wildlife population sizes. However, there is a lack of synthesis of research that compares methods used to estimate population size in the wild. Using a meta-analysis approach, we compared the number of detected individuals in a study made using live trapping and less invasive approaches, such as camera trapping and genetic identification. We scanned 668 papers related to these methods and identified data for 44 populations (all focused on mammals) wherein at least two methods (live trapping, camera trapping, genetic identification) were used. We used these data to quantify the difference in number of individuals detected using trapping and less invasive methods using a regression and used the residuals from each regression to evaluate potential drivers of these trends. We found that both trapping and less invasive methods (camera traps and genetic analyses) produced similar estimates overall, but less invasive methods tended to detect more individuals compared to trapping efforts (mean = 3.17 more individuals). We also found that the method by which camera data are analyzed can significantly alter estimates of population size, such that the inclusion of spatial information was related to larger population size estimates. Finally, we compared counts of individuals made using camera traps and genetic data and found that estimates were similar but that genetic approaches identified more individuals on average (mean = 9.07 individuals). Overall, our data suggest that all of the methods used in the studies we reviewed detected similar numbers of individuals. As live trapping can be more costly than less invasive methods and can pose more risk to animal well-fare, we suggest minimally invasive methods are preferable for population monitoring when less-invasive methods can be deployed efficiently.


2021 ◽  
Vol 944 (1) ◽  
pp. 012032
Author(s):  
A Sunuddin ◽  
K von Juterzenka ◽  
L M I Sani ◽  
H Madduppa

Abstract The study was conducted to describe the seahorse species based on morphological and molecular characters. The pygmy seahorse in Panggang Island in Kepualuan Seribu was discovered in October 2011. The species was allegedly identified as Hippocampus denise (Family: Syngnathidae) described by Lourie and Randall which published in 2003. The high similarity is based on small morphometric, orange-like color and its association with sea fan Annella sp. Their habitat is fairly shallow at a depth between 13-24 meters compared with their sister species observed in Bali, Nusa Tenggara, and Sulawesi. The phylogenetic analysis constructed with several sequence data of Hippocampus spp. from Genbank shows that sample collected from Panggang Island is in the same clade with Hippocampus denise with 100% bootstrap value. BLAST analysis result also showed a high maximum similar identity (>99%) with the species Hippocampus denise. The seahorse specimen described in this study has a common typology of habitat with Hippocampus denise. This study shows that genetic analysis to determine the Hippocampus denise can be carried out to support species recognition, especially for cryptic species such as Hippocampus spp. There are variations in morphometric and habitat depth levels, indicating local adaptation of pygmy seahorses to the Kepulauan Seribu reefs.


2021 ◽  
Vol 22 (23) ◽  
pp. 12746
Author(s):  
Jing Wang ◽  
Yujuan Xu ◽  
Chunjun Qin ◽  
Jing Hu ◽  
Jian Yin ◽  
...  

The O-antigen is the outermost component of the lipopolysaccharide layer in Gram-negative bacteria, and the variation of O-antigen structure provides the basis for bacterial serological diversity. Here, we determined the O-antigen structure of an Escherichia coli strain, LL004, which is totally different from all of the E. coli serogroups. The tetrasaccharide repeating unit was determined as →4)-β-d-Galp-(1→3)-β-d-GlcpNAc6OAc(~70%)-(1→3)-β-d-GalpA-(1→3)-β-d-GalpNAc-(1→ with monosaccharide analysis and NMR spectra. We also characterized the O-antigen gene cluster of LL004, and sequence analysis showed that it correlated well with the O-antigen structure. Deletion and complementation testing further confirmed its role in O-antigen biosynthesis, and indicated that the O-antigen of LL004 is assembled via the Wzx/Wzy dependent pathway. Our findings, in combination, suggest that LL004 should represent a novel serogroup of E. coli.


2021 ◽  
Vol 12 ◽  
Author(s):  
Jinyu Zhang ◽  
Peng Zhang ◽  
Guohong Zeng ◽  
Guangwei Wu ◽  
Landa Qi ◽  
...  

Siderophores are small molecular iron chelators and participate in the multiple cellular processes in fungi. In this study, biosynthesis gene clusters of coprogens and dimerumic acids were identified by transcriptional level differences of genes related to iron deficiency conditions in Metarhizium robertsii. This leads to the characterization of new coprogen metachelin C (1) and five known siderophores metachelin A (2), metachelin A-CE (3), metachelin B (4), dimerumic acid 11-mannoside (5), and dimerumic acid (6). The structure of metachelin C (1) was elucidated by NMR spectroscopy and HR-ESI-MS analysis. Genetic deletions of mrsidA, and mrsidD abolished the production of compounds 1–6 that implied their involvement in the biosynthesis of coprogen and dimerumic acid. Interestingly, NRPS gene mrsidD is responsible for biosynthesis of both coprogen and dimerumic acid, thus we proposed plausible biosynthetic pathways for the synthesis of coprogen and dimerumic acid siderophores. Therefore, our study provides the genetic basis for understanding the biosynthetic pathway of coprogen and dimerumic acid in Metarhizium robertsii.


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