An Anatomical and Phylogenetic Study of the Osteology of the Petrosal of Extant and Extinct Artiodactylans (Mammalia) and Relatives (project)

Gastrointestinal helminths are ubiquitous in both domestic and wild animals. Infections are often sub-clinical except in circumstances of destabilization of host-parasite equilibrium by innate or environmental factors. The present case deals with microscopic and molecular diagnosis of Murshidia linstowi recovered from an elephant. A post-mortem examination of a free-ranging juvenile male elephant calf that had died of electrocution in Athagarh Wildlife Division revealed the presence of slender, whitish nematodes in the stomach. No gross lesions were noticed either in the site of predilection or any other internal organs. The average length of the parasites was 3.8cm. These parasites were collected for further gross as well as microscopic examination following routine parasitological techniques. Temporary mounts prepared after cleaning the nematodes in lactophenol were observed under a microscope. Morphological features such as a well-developed mouth collar, large and globular buccal capsule with fine tubercles, cone shaped oesophageal funnel, short bursa having indistinctly divided lobes and closely apposed ventral rays and stout spicules with club shaped tips bent dorsally corroborated with that of M.linstowi (male). Amplification of the rDNA from the internal transcribed spacer (ITS) region using universal nematode primers NC2 and NC5 revealed a product size of 870bp. The PCR product was subjected to sequencing followed by NCBI-BLAST which revealed 98% homology with M. linstowi. A phylogenetic study showed a maximum similarity with M.linstowi recovered from elephants in Kenya. This particular nematode species belonging to the family Strongylidae and sub-family Cyathostominae appears to be the first documented report in India.

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Janthinobacterium tructae sp. nov., Isolated from Kidney of Rainbow Trout (Oncorhynchus mykiss)

Pathogens ◽

10.3390/pathogens10020229 ◽

2021 ◽

Vol 10 (2) ◽

pp. 229

Author(s):

Won Joon Jung ◽

Sang Wha Kim ◽

Sib Sankar Giri ◽

Hyoun Joong Kim ◽

Sang Guen Kim ◽

...

Keyword(s):

Rainbow Trout ◽

Dna Hybridization ◽

Biochemical Analysis ◽

Major Fatty Acid ◽

Phylogenetic Study ◽

Rainbow Trout Oncorhynchus Mykiss ◽

Close Relatives ◽

Rrna Sequences ◽

Fatty Acid Compositions ◽

Genome Distance

This study presents a novel Janthinobacterium strain, SNU WT3, isolated from the kidney of rainbow trout. A phylogenetic study using 16S rRNA sequences indicated that the strain is closely related to Janthinobacterium svalbardensis JA-1T. However, biochemical analysis found differences in D-xylose adonitol, N-acetylglucosamine, arbutin, and cellobiose. As for genome-to-genome distance and average nucleotide identity values calculated between strain SNU WT3 and other related strains such as J. lividum EIF1, J. svalbardensis PAMC 27463, and J. agaricidamnosum BHSEK were all below the cutoff value between species. DNA-DNA hybridization between strain SNU WT3 and other close relatives indicated the results of J. lividum DSM 1522T (47.11%) and J. svalbardensis JA-1T (38.88%) individually. The major fatty acid compositions of strain SNU WT3 were cylco-C17:0 (41.45%), C16:0 (33.86%) and C12:0 (5.87%). The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, and diphosphatidylglycerol. The quinone system was composed mainly of ubiquinone Q-8. The genome of strain SNU WT3 consists of 6,314,370 bp with a G + C content of 62.35%. Here, we describe a novel species of the genus Janthinobacterium, and the name Janthinobacterium tructae has been proposed with SNU WT3T (=KCTC 72518 = JCM 33613) as the type strain.

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Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia

AMB Express ◽

10.1186/s13568-020-01134-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Maroua Oueslati ◽

Magdalena Mulet ◽

Mohamed Zouaoui ◽

Charlotte Chandeysson ◽

Jorge Lalucat ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Pseudomonas Syringae ◽

Ice Nucleation ◽

Phylogenetic Study ◽

Future Studies ◽

Citrus Orchards ◽

First Time ◽

New Cultivars

Abstract The damages observed in Tunisian citrus orchards have prompted studies on the Pseudomonas spp. responsible for blast and black pit. Prospective orchards between 2015 and 2017 showed that the diseases rapidly spread geographically and to new cultivars. A screening of Pseudomonas spp. isolated from symptomatic trees revealed their wide diversity according to phylogenetic analysis of their housekeeping rpoD and cts genes. The majority of strains were affiliated to Pseudomonas syringae pv. syringae (Phylogroup PG02b), previously described in Tunisia. However, they exhibited various BOX-PCR fingerprints and were not clonal. This work demonstrated, for the first time in Tunisia, the involvement of Pseudomonas cerasi (PG02a) and Pseudomonas congelans (PG02c). The latter did not show significant pathogenicity on citrus, but was pathogenic on cantaloupe and active for ice nucleation that could play a role in the disease. A comparative phylogenetic study of citrus pathogens from Iran, Montenegro and Tunisia revealed that P. syringae (PG02b) strains are closely related but again not clonal. Interestingly P. cerasi (PG02a) was isolated in two countries and seems to outspread. However, its role in the diseases is not fully understood and it should be monitored in future studies. The diversity of pathogenic Pseudomonas spp. and the extension of the diseases highlight that they have become complex and synergistic. It opens questions about which factors favor diseases and how to fight against them efficiently and with sustainable means.

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Emergence of novel SARS-CoV-2 variants in the Netherlands

Scientific Reports ◽

10.1038/s41598-021-85363-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Aysun Urhan ◽

Thomas Abeel

Keyword(s):

The Netherlands ◽

Population Diversity ◽

Genomic Variation ◽

Population Variation ◽

Reference Sequence ◽

Viral Population ◽

Phylogenetic Study ◽

First Case ◽

Novel Variants ◽

Frequent Mutations

AbstractCoronavirus disease 2019 (COVID-19) has emerged in December 2019 when the first case was reported in Wuhan, China and turned into a pandemic with 27 million (September 9th) cases. Currently, there are over 95,000 complete genome sequences of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, in public databases, accompanying a growing number of studies. Nevertheless, there is still much to learn about the viral population variation when the virus is evolving as it continues to spread. We have analyzed SARS-CoV-2 genomes to identify the most variant sites, as well as the stable, conserved ones in samples collected in the Netherlands until June 2020. We identified the most frequent mutations in different geographies. We also performed a phylogenetic study focused on the Netherlands to detect novel variants emerging in the late stages of the pandemic and forming local clusters. We investigated the S and N proteins on SARS-CoV-2 genomes in the Netherlands and found the most variant and stable sites to guide development of diagnostics assays and vaccines. We observed that while the SARS-CoV-2 genome has accumulated mutations, diverging from reference sequence, the variation landscape is dominated by four mutations globally, suggesting the current reference does not represent the virus samples circulating currently. In addition, we detected novel variants of SARS-CoV-2 almost unique to the Netherlands that form localized clusters and region-specific sub-populations indicating community spread. We explored SARS-CoV-2 variants in the Netherlands until June 2020 within a global context; our results provide insight into the viral population diversity for localized efforts in tracking the transmission of COVID-19, as well as sequenced-based approaches in diagnostics and therapeutics. We emphasize that little diversity is observed globally in recent samples despite the increased number of mutations relative to the established reference sequence. We suggest sequence-based analyses should opt for a consensus representation to adequately cover the genomic variation observed to speed up diagnostics and vaccine design.

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