Two New Haplotypes of Bartonella sp. Isolated from Lipoptena fortisetosa (Diptera: Hippoboscidae) in SE Poland

Insects of the genus Lipoptena are parasitic arthropods with a broad host range. Due to the type of parasitism (hematophagy), their potential role as vectors of pathogens, i.e., Bartonella sp., Anaplasma phagocytophilum, Rickettsia spp., and Borrelia burgdorferi is considered. As the range of their occurrence has been changing dynamically in recent years and infestations of humans have increasingly been reported, these organisms are now the subject of numerous studies. Our research aimed to present the molecular characteristics of Bartonella sp. detected in Lipoptena fortisetosa parasitizing wild cervids in south-eastern Poland. Adults of Lipoptena spp. were collected from carcasses of roe deer and red deer between spring and autumn in 2013. The PCR method was used to detect Bartonella sp. in the insects. We report two new haplotypes of the rpoB gene of Bartonella sp. isolated from L. fortisetosa feeding on wild cervids in south-eastern Poland and the presence of this invasive ectoparasitic species in the studied area since 2013. Phylogenetic analyses of newly obtained Bartonella sp. haplotypes confirmed their unique position on the constructed tree and network topology. The rpoB gene sequences found belonging to lineage B support the view that this phylogenetic lineage represents a novel Bartonella species.

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Lower Recovery of Nontuberculous Mycobacteria from Outdoor Hawai’i Environmental Water Biofilms Compared to Indoor Samples

Microorganisms ◽

10.3390/microorganisms9020224 ◽

2021 ◽

Vol 9 (2) ◽

pp. 224

Author(s):

Ravleen Virdi ◽

Melissa E. Lowe ◽

Grant J. Norton ◽

Stephanie N. Dawrs ◽

Nabeeh A. Hasan ◽

...

Keyword(s):

Pulmonary Disease ◽

Environmental Samples ◽

Nontuberculous Mycobacteria ◽

Phylogenetic Analyses ◽

Environmental Water ◽

Rpob Gene ◽

The United States ◽

Indoor Environments ◽

Respiratory Specimens ◽

Rpob Sequence

Nontuberculous mycobacteria (NTM) are environmental organisms that can cause opportunistic pulmonary disease with species diversity showing significant regional variation. In the United States, Hawai’i shows the highest rate of NTM pulmonary disease. The need for improved understanding of NTM reservoirs led us to identify NTM from patient respiratory specimens and compare NTM diversity between outdoor and indoor locations in Hawai’i. A total of 545 water biofilm samples were collected from 357 unique locations across Kaua’i (n = 51), O’ahu (n = 202), Maui (n = 159), and Hawai’i Island (n = 133) and divided into outdoor (n = 179) or indoor (n = 366) categories. rpoB sequence analysis was used to determine NTM species and predictive modeling applied to develop NTM risk maps based on geographic characteristics between environments. M. chimaera was frequently identified from respiratory and environmental samples followed by M. chelonae and M. abscessus; yet significantly less NTM were consistently recovered from outdoor compared to indoor biofilms, as exemplified by showerhead biofilm samples. While the frequency of M. chimaera recovery was comparable between outdoor and indoor showerhead biofilms, phylogenetic analyses demonstrate similar rpoB gene sequences between all showerhead and respiratory M. chimaera isolates, supporting outdoor and indoor environments as possible sources for pulmonary M. chimaera infections.

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New olenelline trilobites from the Northwest Territories, Canada, and the phylogenetic placement of Judomia absita Fritz, 1973

Zootaxa ◽

10.11646/zootaxa.2918.1.2 ◽

2011 ◽

Vol 2918 (1) ◽

pp. 15 ◽

Cited By ~ 1

Author(s):

I. WESLEY GAPP ◽

BRUCE S. LIEBERMAN ◽

MICHAEL C. POPE ◽

KELLY A. DILLIARD

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Northwest Territories ◽

Phylogenetic Analyses ◽

Geographic Range ◽

Early Cambrian ◽

Phylogenetic Placement ◽

The Subject ◽

Three New Species ◽

One New Species

The Early Cambrian olenelline trilobites are a diverse clade and have been the subject of several phylogenetic analyses. Here, three new species of Bradyfallotaspis Fritz, 1972 (B. coriae, B. nicolascagei, and B. sekwiensis) and one new species of Nevadia Walcott, 1910 (N. saupeae) are described from the Sekwi Formation of the Mackenzie Mountains, Northwest Territories, Canada. In addition, new specimens potentially referable to Nevadia ovalis McMenamin, 1987 were recovered that may expand that species’ geographic range, which was thought to be restricted to Sonora, Mexico. The results of a phylogenetic analysis incorporating several olenelline taxa, including Judomia absita Fritz, 1973 from the Sekwi Formation, are also presented herein. This species has been assigned to various olenelline genera, including Judomia Lermontova, 1951 and Paranevadella Palmer & Repina, 1993. Phylogenetic analysis suggests this species is closely related to Judomia tera Lazarenko, 1960 from Siberia. This phylogenetic relationship provides further support for the hypothesis that a close biogeographic relationship existed between Laurentia and Siberia during the Cambrian.

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Biological and Molecular Characteristics of a Novel Partitivirus Infecting the Edible Fungus Lentinula edodes

Plant Disease ◽

10.1094/pdis-07-16-0951-re ◽

2017 ◽

Vol 101 (5) ◽

pp. 726-733 ◽

Cited By ~ 15

Author(s):

Mengpei Guo ◽

Yinbing Bian ◽

Jinjie Wang ◽

Gangzheng Wang ◽

Xiaolong Ma ◽

...

Keyword(s):

Lentinula Edodes ◽

Control Strategies ◽

Phylogenetic Analyses ◽

Pcr Analysis ◽

Molecular Characteristics ◽

Rt Pcr ◽

Edible Fungus ◽

Qpcr Analysis ◽

Disease Diagnostics ◽

Wild Strains

A new partitivirus named Lentinula edodes partitivirus 1 (LePV1) was isolated from a diseased L. edodes strain with severe degeneration of the mycelium and imperfect browning in bag cultures. The nucleotide sequences of LePV1 dsRNA-1 and dsRNA-2 were determined; they were 2,382 bp and 2,245 bp in length, and each contained a single ORF encoding RNA-dependent RNA polymerase (RdRp) and coat protein (CP), respectively. The purified virus preparation contained isometric particles 34 nm in diameter encapsidating these dsRNAs. Phylogenetic analyses showed LePV1 to be a new member of Betapartitivirus, with the RdRp sequence most closely related to Grapevine partitivirus. RT-PCR analysis showed that 27 of the 56 Chinese L. edodes core collection strains carry LePV1, with the virus being more common in wild strains than cultivated strains. In addition, qPCR analysis suggested that coinfection with L. edodes mycovirus HKB (LeV-HKB) could increase replication of the RdRp gene of LePV1. This study may be essential for the development of more accurate disease diagnostics and the formulation of control strategies for viral diseases in L. edodes.

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Evolutionary History of Cucumber Mosaic Virus Deduced by Phylogenetic Analyses

Journal of Virology ◽

10.1128/jvi.76.7.3382-3387.2002 ◽

2002 ◽

Vol 76 (7) ◽

pp. 3382-3387 ◽

Cited By ~ 155

Author(s):

Marilyn J. Roossinck

Keyword(s):

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

Virus Isolate ◽

Phylogenetic Analyses ◽

Open Reading Frames ◽

Broad Host Range ◽

Nontranslated Region ◽

History Of ◽

Evolutionary Success ◽

Reading Frames

ABSTRACT Cucumber mosaic virus (CMV) is an RNA plant virus with a tripartite genome and an extremely broad host range. Previous evolutionary analyses with the coat protein (CP) and 5′ nontranslated region (NTR) of RNA 3 suggested subdivision of the virus into three groups, subgroups IA, IB, and II. In this study 15 strains of CMV whose nucleotide sequences have been determined were used for a complete phylogenetic analysis of the virus. The trees estimated for open reading frames (ORFs) located on the different RNAs were not congruent and did not completely support the subgrouping indicated by the CP ORF, indicating that different RNAs had independent evolutionary histories. This is consistent with a reassortment mechanism playing an important role in the evolution of the virus. The evolutionary trees of the 1a and 3a ORFs were more compact and displayed more branching than did those of the 2a and CP ORFs. This may reflect more rigid host-interactive constraints exerted on the 1a and 3a ORFs. In addition, analysis of the 3′ NTR that is conserved among all RNAs indicated that evolutionary constraints on this region are specific to the RNA component rather than the virus isolate. This indicates that functions other than replication are encoded in the 3′ NTR. Reassortment may have led to the genetic diversity found among CMV strains and contributed to its enormous evolutionary success.

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The New Human Babesia sp. FR1 Is a European Member of the Babesia sp. MO1 Clade

Pathogens ◽

10.3390/pathogens10111433 ◽

2021 ◽

Vol 10 (11) ◽

pp. 1433

Author(s):

Claire Bonsergent ◽

Marie-Charlotte de Carné ◽

Nathalie de la Cotte ◽

François Moussel ◽

Véronique Perronne ◽

...

Keyword(s):

Roe Deer ◽

Phylogenetic Analyses ◽

18S Rrna Gene ◽

Natural Host ◽

Etiological Agent ◽

Rrna Gene ◽

Separate Species ◽

Apical Membrane Antigen 1 ◽

Babesia Divergens

In Europe, Babesia divergens is responsible for most of the severe cases of human babesiosis. In the present study, we describe a case of babesiosis in a splenectomized patient in France and report a detailed molecular characterization of the etiological agent, named Babesia sp. FR1, as well as of closely related Babesia divergens, Babesia capreoli and Babesia sp. MO1-like parasites. The analysis of the conserved 18S rRNA gene was supplemented with the analysis of more discriminant markers involved in the red blood cell invasion process: rap-1a (rhoptry-associated-protein 1) and ama-1 (apical-membrane-antigen 1). The rap-1a and ama-1 phylogenetic analyses were congruent, placing Babesia sp. FR1, the new European etiological agent, in the American cluster of Babesia sp. MO1-like parasites. Based on two additional markers, our analysis confirms the clear separation of B. divergens and B. capreoli. Babesia sp. MO1-like parasites should also be considered as a separate species, with the rabbit as its natural host, differing from those of B. divergens (cattle) and B. capreoli (roe deer). The natural host of Babesia sp. FR1 remains to be discovered.

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Micromorphological, anatomical and molecular study of Hedera species (Araliaceae) in Iran

Acta Biologica Szegediensis ◽

10.14232/abs.2019.2.91-101 ◽

2020 ◽

Vol 63 (2) ◽

pp. 91-101

Author(s):

Elham Amini ◽

Fatemeh Nasrollahi ◽

Ali Sattarian ◽

Mahboobeh Haji Moradkhani ◽

Sohrab Boozarpour ◽

...

Keyword(s):

North Africa ◽

Phylogenetic Analyses ◽

Molecular Study ◽

Molecular Characteristics ◽

Nrdna Its ◽

Anticlinal Wall ◽

Data Set ◽

Phylogenetic Methods ◽

Extant Species ◽

Qualitative Characters

Hedera, with 12 extant species, is a genus of evergreen climbers native to Europe, north Africa, and south Asia. In this study, the micromorphological, anatomical structure and molecular evidences of 11 populations from two species of Hedera (H. helix and H. pastuchovii) have been considered to evaluate the relationships in Hedera. In total, seven quantitative and qualitative characters of pollen were selected and measured. Based on this study, the anticlinal wall and surface sculpturing of seed support for separation of two species of Hedera. Micromorphology of epidermis illustrated two types of epidermal cells: puzzle-shaped and polygonal cells. Using nuclear (nrDNA ITS) marker, we reconstructed phylogenetic relationships within two species of Hedera. This data set was analyzed by phylogenetic methods including Bayesian inference, maximum likelihood, and maximum parsimony. In phylogenetic analyses, all members of two species formed a well-supported clade (PP = 1; ML/BS = 100/100) and divided into two major clades (A and B). Neighbor Net diagram demonstrated separation of the studied populations. The results showed that these taxa differ in taxonomically important micromorphological, anatomical and molecular characteristics and these data provide reliable evidence for separation of these two species.

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Highly Divergent Genes for Methanopterin-Linked C1 Transfer Reactions in Lake Washington, Assessed via Metagenomic Analysis and mRNA Detection

Applied and Environmental Microbiology ◽

10.1128/aem.71.12.8846-8854.2005 ◽

2005 ◽

Vol 71 (12) ◽

pp. 8846-8854 ◽

Cited By ~ 15

Author(s):

Marina G. Kalyuzhnaya ◽

Sarah Bowerman ◽

Olivier Nercessian ◽

Mary E. Lidstrom ◽

Ludmila Chistoserdova

Keyword(s):

Phylogenetic Diversity ◽

Potential Role ◽

Phylogenetic Analyses ◽

Transfer Reactions ◽

Microb Ecol ◽

Mrna Detection ◽

Lake Washington ◽

History Of ◽

Metagenomic Approach ◽

Specific Mrna

ABSTRACT The origins and the evolutionary history of tetrahydromethanopterin-linked C1 transfer reactions that are part of two environmentally important biotransformations, methylotrophy and methanogenesis, are still not well understood. In previous studies, we have expanded the known phylogenetic diversity of these reactions by identifying genes highly diverging from the ones associated with cultivated Proteobacteria, Planctomycetes, or Archaea (M. G. Kalyuzhnaya, M. E. Lidstrom, and L. Chistoserdova, Microb. Ecol. 48:463-472, 2004; M. G. Kalyuzhnaya, O. Nercessian, M. E. Lidstrom, and L. Chistoserdova, Environ. Microbiol. 7:1269-1274, 2005). Here we used a metagenomic approach to demonstrate that these divergent genes are present with high abundance in the microbial community inhabiting Lake Washington sediment. We also gained preliminary insights into the genomic composition of the organisms possessing these genes by sequencing genomic fragments from three uncultured microbes possessing the genes of interest. Phylogenetic analyses suggested that, although distantly related to each other, these organisms deeply diverge from known Bacteria and Archaea, with more relation to the former, suggesting their affiliation with a new bacterial phylum. We also demonstrate, via specific mRNA detection, that these divergent genes are expressed in the environment, pointing toward their potential role in local carbon cycling.

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Diversity of formyltetrahydrofolate synthetase genes in the rumens of roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed different diets

Canadian Journal of Microbiology ◽

10.1139/cjm-2016-0424 ◽

2017 ◽

Vol 63 (1) ◽

pp. 11-19 ◽

Cited By ~ 1

Author(s):

Zhipeng Li ◽

Gemma Henderson ◽

Yahan Yang ◽

Guangyu Li

Keyword(s):

Corn Stover ◽

Sika Deer ◽

Roe Deer ◽

Alternative Pathway ◽

Phylogenetic Analyses ◽

Cervus Nippon ◽

Amino Acid Sequences ◽

Corn Silage ◽

Formyltetrahydrofolate Synthetase ◽

Capreolus Pygargus

Reductive acetogenesis by homoacetogens represents an alternative pathway to methanogenesis to remove metabolic hydrogen during rumen fermentation. In this study, we investigated the occurrence of homoacetogen in the rumens of pasture-fed roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed either oak-leaf-based (tannin-rich, 100 mg/kg dried matter), corn-stover-based, or corn-silage-based diets, by using formyltetrahydrofolate synthetase (FTHFS) gene sequences as a marker. The diversity and richness of FTHFS sequences was lowest in animals fed oak leaf, indicating that tannin-containing plants may affect rumen homoacetogen diversity. FTHFS amino acid sequences in the rumen of roe deer significantly differed from those of sika deer. The phylogenetic analyses showed that 44.8% of sequences in pasture-fed roe deer, and 72.1%, 81.1%, and 37.5% of sequences in sika deer fed oak-leaf-, corn-stover-, and corn-silage-based diets, respectively, may represent novel bacteria that have not yet been cultured. These results demonstrate that the rumens of roe deer and sika deer harbor potentially novel homoacetogens and that diet may influence homoacetogen community structure.

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Phosphates of the Streltsovsky ore field of South-Eastern Transbaikalia (Part 3)

Transbaikal State University Journal ◽

10.21209/2227-9245-2021-27-4-20-31 ◽

2021 ◽

Vol 27 (4) ◽

pp. 20-31

Author(s):

Yu. Pavlenko ◽

Keyword(s):

High Reliability ◽

Late Mesozoic ◽

South Eastern ◽

Eastern Transbaikalia ◽

Genetic Features ◽

Phosphate Mineralization ◽

Strategic Goals ◽

Evaluation Stage ◽

The Subject ◽

Object Of Study

The conclusions’ reliability of geologists who created the largest uranium ore base in the country on the territory of the Streltsovsky ore field (SOF) in the South-Eastern Transbaikalia, about the belonging of spatially isolated phosphate mineralization and powerful industrial mineralization to a final stage of Late Mesozoic tectonomagmatitic activation, is clarified. The relevance of the research lies in the need to study the geological materials at the SOF and the surrounding area to assess the prospects for involving in the exploitation of phosphate mineralization developed on the flanks of uranium deposits developed under the state program of the TOP. The object of study is the “blind” Argunskoye and Zherlovoye deposits and their western flanks on the surface, and the subject is the phosphate mineralization developed in the block of terrigenous-carbonate rocks. The purpose of the research is to clarify the time and features of the formation of phosphates, and the task is to assess the industrial significance of phosphate mineralization for decision-making. The methodology of scientific research is based on the interpretation of geological facts given in the literature and stock materials, use of concepts, terms, creation of hypotheses and their consequences, consistency of the comparison of which with the established facts determines the relatively high reliability of geological results. The author has used a descriptive method that takes into account a system of interrelated consistent positions, and a method of theoretical modeling, which raises the strategic goals of nature cognition to a higher scientific level. The results of the research are presented in three articles (parts). In the second part, phosphates of the region and SOF are characterized. It is established that the Talan manifestation of apatites belongs to the phosphate sorption-biogenic metalliferous formation of the Precambrian metamorphic rocks complex and combines the promising second and third most important industrial types of deposits. It is recommended to perform geological exploration at the evaluation stage and to test the electrothermal method for producing fused phosphate-magnesium fertilizers. In the third part, the known types of phosphogenesis and the genetic features of their manifestation in PSA are considered. Attention is drawn to the advantage of the recommended electrothermal method for processing apatite-carbonate and apatite-silicate rocks of the Talan manifestation

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Exposure to emissions from Mount Etna (Sicily, Italy) and incidence of thyroid cancer: a geographic analysis

Scientific Reports ◽

10.1038/s41598-020-77027-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Paolo Boffetta ◽

Lorenzo Memeo ◽

Dario Giuffrida ◽

Margherita Ferrante ◽

Salvatore Sciacca

Keyword(s):

Regression Analysis ◽

Thyroid Cancer ◽

Potential Role ◽

Incidence Rates ◽

Mount Etna ◽

Sensitivity Analyses ◽

Molecular Characteristics ◽

Special Focus ◽

Northeastern Sicily

AbstractAn increased incidence of thyroid cancer has been reported in the area close to Mount Etna, the largest volcano in Europe located in Northeastern Sicily. We tested the hypothesis that exposure to the emissions from the volcano is associated with thyroid cancer in 186 municipalities from three provinces surrounding the volcano (1.9 million inhabitants). We measured the angle between the bearing of the municipalities and each direction, with special focus on South-East, the prevalent direction of the plume, and conducted a regression analysis on 2003–2016 incidence rates of thyroid cancer, adjusting for distance from Mount Etna, population size, and income. A 10-degree increase in the angle with South-East was associated with a decrease in thyroid cancer rates in the whole population (− 0.67 cases/100,000, p = 0.002) and in women (− 1.54/100,000, p < 0.001), and were robust to several sensitivity analyses. Similar results were obtained for East-South-East direction. These results support the hypothesis of a potential role of exposure to the plume from Mount Etna in determining the high rates of thyroid cancer. The results need to be confirmed in analytical studies, in which information of exposure to chemicals originating from the volcano, as well as other possible causes, should be carefully measured, molecular characteristics of the tumors and taken into account.

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