scholarly journals Erratum to: Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans

2021 ◽  
Vol 13 (8) ◽  
Author(s):  
Arturo González-Robles ◽  
Mónica González-Lázaro ◽  
Anel Edith Lagunes-Guillén ◽  
Maritza Omaña-Molina ◽  
Luis Fernando Lares-Jiménez ◽  
...  
Keyword(s):  
Morphological Data ◽  
Comparative Genomic ◽  
Free Living

scholarly journals Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans

2020 ◽  
Vol 12 (10) ◽  
pp. 1734-1750
Author(s):  
Arturo González-Robles ◽  
Mónica González-Lázaro ◽  
Anel Edith Lagunes-Guillén ◽  
Maritza Omaña-Molina ◽  
Luis Fernando Lares-Jiménez ◽  
...  
Keyword(s):  
Protein Import ◽  
Acanthamoeba Castellanii ◽  
Morphological Data ◽  
Comparative Genomic ◽  
Reaction Products ◽  
Free Living ◽  
Transmission Electron ◽  
Complete Set ◽  
Taxonomic Groups ◽  
Naegleria Lovaniensis

Abstract Peroxisomes perform various metabolic processes that are primarily related to the elimination of reactive oxygen species and oxidative lipid metabolism. These organelles are present in all major eukaryotic lineages, nevertheless, information regarding the presence of peroxisomes in opportunistic parasitic protozoa is scarce and in many cases it is still unknown whether these organisms have peroxisomes at all. Here, we performed ultrastructural, cytochemical, and bioinformatic studies to investigate the presence of peroxisomes in three genera of free-living amoebae from two different taxonomic groups that are known to cause fatal infections in humans. By transmission electron microscopy, round structures with a granular content limited by a single membrane were observed in Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba polyphaga, Acanthamoeba royreba, Balamuthia mandrillaris (Amoebozoa), and Naegleria fowleri (Heterolobosea). Further confirmation for the presence of peroxisomes was obtained by treating trophozoites in situ with diaminobenzidine and hydrogen peroxide, which showed positive reaction products for the presence of catalase. We then performed comparative genomic analyses to identify predicted peroxin homologues in these organisms. Our results demonstrate that a complete set of peroxins—which are essential for peroxisome biogenesis, proliferation, and protein import—are present in all of these amoebae. Likewise, our in silico analyses allowed us to identify a complete set of peroxins in Naegleria lovaniensis and three novel peroxin homologues in Naegleria gruberi. Thus, our results indicate that peroxisomes are present in these three genera of free-living amoebae and that they have a similar peroxin complement despite belonging to different evolutionary lineages.

scholarly journals The Motility Symbiont of the Termite Gut Flagellate Caduceia versatilis Is a Member of the “Synergistes” Group

2007 ◽  
Vol 73 (19) ◽  
pp. 6270-6276 ◽  
Author(s):  
Yuichi Hongoh ◽  
Tomoyuki Sato ◽  
Michael F. Dolan ◽  
Satoko Noda ◽  
Sadaharu Ui ◽  
...  
Keyword(s):  
Morphological Data ◽  
Termite Species ◽  
Entire Surface ◽  
Free Living ◽  
Sequence Identity ◽  
Novel Genus And Species ◽  
Host Cell Surface ◽  
The One ◽  
Specific Cluster

ABSTRACT The flagellate Caduceia versatilis in the gut of the termite Cryptotermes cavifrons reportedly propels itself not by its own flagella but solely by the flagella of ectosymbiotic bacteria. Previous microscopic observations have revealed that the motility symbionts are flagellated rods partially embedded in the host cell surface and that, together with a fusiform type of ectosymbiotic bacteria without flagella, they cover almost the entire surface. To identify these ectosymbionts, we conducted 16S rRNA clone analyses of bacteria physically associated with the Caduceia cells. Two phylotypes were found to predominate in the clone library and were phylogenetically affiliated with the “Synergistes” phylum and the order Bacteroidales in the Bacteroidetes phylum. Probes specifically targeting 16S rRNAs of the respective phylotypes were designed, and fluorescence in situ hybridization (FISH) was performed. As a result, the “Synergistes” phylotype was identified as the motility symbiont; the Bacteroidales phylotype was the fusiform ectobiont. The “Synergistes” phylotype was a member of a cluster comprising exclusively uncultured clones from the guts of various termite species. Interestingly, four other phylotypes in this cluster, including the one sharing 95% sequence identity with the motility symbiont, were identified as nonectosymbiotic, or free-living, gut bacteria by FISH. We thus suggest that the motility ectosymbiont has evolved from a free-living gut bacterium within this termite-specific cluster. Based on these molecular and previous morphological data, we here propose a novel genus and species, “Candidatus Tammella caduceiae,” for this unique motility ectosymbiont of Caducaia versatilis.

scholarly journals Molecular and Morphological Data Support the Existence of a Sexual Cycle in Species of the Genus Paracoccidioides

2012 ◽  
Vol 12 (3) ◽  
pp. 380-389 ◽  
Author(s):  
Marcus de Melo Teixeira ◽  
Raquel Cordeiro Theodoro ◽  
Lorena da Silveira Derengowski ◽  
André Moraes Nicola ◽  
Eduardo Bagagli ◽  
...  
Keyword(s):  
Paracoccidioides Brasiliensis ◽  
Sexual Cycle ◽  
Morphological Data ◽  
Comparative Genomic ◽  
Mating Types ◽  
Isolated Populations ◽  
Dimorphic Fungi ◽  
Filamentous Form ◽  
Content Type

ABSTRACTThe genusParacoccidioidesincludes the thermodimorphic speciesParacoccidioides brasiliensisandP. lutzii, both of which are etiologic agents of paracoccidioidomycosis, a systemic mycosis that affects humans in Latin America. Despite the common occurrence of a sexual stage among closely related fungi, this has not been observed withParacoccidioidesspecies, which have thus been considered asexual. Molecular evolutionary studies revealed recombination events within isolated populations of the genusParacoccidioides, suggesting the possible existence of a sexual cycle. Comparative genomic analysis of all dimorphic fungi andSaccharomyces cerevisiaedemonstrated the presence of conserved genes involved in sexual reproduction, including those encoding mating regulators such as MAT, pheromone receptors, pheromone-processing enzymes, and mating signaling regulators. The expression of sex-related genes in the yeast and mycelial phases of bothParacoccidioidesspecies was also detected by real-time PCR, with nearly all of these genes being expressed preferentially in the filamentous form of the pathogens. In addition, the expression of sex-related genes was responsive to the putative presence of pheromone in the supernatants obtained from previous cocultures of strains of two different mating types.In vitrocrossing of isolates of different mating types, discriminated by phylogenetic analysis of the α-box (MAT1-1) and the high-mobility-group (HMG) domain (MAT1-2), led to the identification of the formation of young ascocarps with constricted coiled hyphae related to the initial stage of mating. These genomic and morphological analyses strongly support the existence of a sexual cycle in species of the genusParacoccidioides.

scholarly journals Rhabditophanes diutinus a parthenogenetic clade IV nematode with dauer larvae

2020 ◽  
Vol 16 (12) ◽  
pp. e1009113
Author(s):  
Alex Dulovic ◽  
Tess Renahan ◽  
Waltraud Röseler ◽  
Christian Rödelsperger ◽  
Ann M. Rose ◽  
...  
Keyword(s):  
Life Cycle ◽  
Expression Patterns ◽  
Parasitic Nematodes ◽  
Comparative Genomic ◽  
Phylogenetic Distance ◽  
Life Stages ◽  
Model Species ◽  
Free Living ◽  
Infective Larvae ◽  
Dauer Larvae

Comparative studies using non-parasitic model species such as Caenorhabditis elegans, have been very helpful in investigating the basic biology and evolution of parasitic nematodes. However, as phylogenetic distance increases, these comparisons become more difficult, particularly when outside of the nematode clade to which C. elegans belongs (V). One of the reasons C. elegans has nevertheless been used for these comparisons, is that closely related well characterized free-living species that can serve as models for parasites of interest are frequently not available. The Clade IV parasitic nematodes Strongyloides are of great research interest due to their life cycle and other unique biological features, as well as their medical and veterinary importance. Rhabditophanes, a closely related free-living genus, forms part of the Strongyloidoidea nematode superfamily. Rhabditophanes diutinus (= R. sp. KR3021) was included in the recent comparative genomic analysis of the Strongyloididae, providing some insight into the genomic nature of parasitism. However, very little is known about this species, limiting its usefulness as a research model. Here we provide a species description, name the species as R. diutinus and investigate its life cycle and subsequently gene expression in multiple life stages. We identified two previously unreported starvation induced life stages: dauer larvae and arrested J2 (J2A) larvae. The dauer larvae are morphologically similar to and are the same developmental stage as dauers in C. elegans and infective larvae in Strongyloides. As in C. elegans and Strongyloides, dauer formation is inhibited by treatment with dafachronic acid, indicating some genetic control mechanisms are conserved. Similarly, the expression patterns of putative dauer/infective larva control genes resemble each other, in particular between R. diutinus and Strongyloides spp. These findings illustrate and increase the usefulness of R. diutinus as a non-parasitic, easy to work with model species for the Strongyloididae for studying the evolution of parasitism as well as many aspects of the biology of Strongyloides spp, in particular the formation of infective larvae.

scholarly journals Plasmids encode niche-specific traits in Lactobacillaceae

2020 ◽  
Author(s):  
Dimple Davray ◽  
Dipti Deo ◽  
Ram Kulkarni
Keyword(s):  
Metal Ion ◽  
Gc Content ◽  
Major Facilitator Superfamily ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Fermented Foods ◽  
Probiotic Properties ◽  
Free Living ◽  
Content Type ◽  
Living Species

Species belonging to the family Lactobacillaceae are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species have been individually reported to harbour plasmids that encode important genes. In this study, we performed comparative genomic analysis of publicly available data for 512 plasmids from 282 strains represented by 51 species of this family and correlated the genomic features of plasmids with the ecological niches in which these species are found. Two-thirds of the species had at least one plasmid-harbouring strain. Plasmid abundance and GC content were significantly lower in vertebrate-adapted species as compared to nomadic and free-living species. Hierarchical clustering highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the vertebrate-adapted species. EggNOG-assisted functional annotation revealed that genes associated with transposition, conjugation, DNA repair and recombination, exopolysaccharide production, metal ion transport, toxin–antitoxin system, and stress tolerance were significantly enriched on the plasmids of the nomadic and in some cases nomadic and free-living species. On the other hand, genes related to anaerobic metabolism, ABC transporters and the major facilitator superfamily were overrepresented on the plasmids of the vertebrate-adapted species. These genomic signatures correlate with the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of vertebrate-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to their respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria.

scholarly journals Plasmids encode niche-specific traits in Lactobacillaceae

2020 ◽  
Author(s):  
Dimple Davray ◽  
Dipti Deo ◽  
Ram Kulkarni
Keyword(s):  
Gc Content ◽  
Nucleotide Sequences ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Fermented Foods ◽  
Probiotic Properties ◽  
Genome Sequences ◽  
Free Living ◽  
Wide Range ◽  
Living Species

AbstractThe species of family Lactobacillaceae are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species have been individually reported to harbor plasmids that encode important genes. In this study, we performed comparative genomic analysis of the publically available data of 512 plasmids from 282 strains represented by 51 species of this family and correlated the genomic features of plasmids with the ecological niches in which these species are found. Two-third of the species had at least one plasmid-harboring strain. Plasmid abundance and GC content were significantly lower in the vertebrate-adapted species as compared to the nomadic and free-living species. Hierarchical clustering (HCL) highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the vertebrate-adapted species. EggNOG assisted functional annotation revealed that genes associated with transposition, conjugation, DNA repair and recombination, exopolysaccharide production, metal ion transport, toxin-antitoxin system, and stress tolerance were significantly enriched on the plasmids of the nomadic and in some cases nomadic and free-living species. On the other hand, genes related to anaerobic metabolism, ABC transporters, and major facilitator superfamily were found to be overrepresented on the plasmids of the vertebrate-adapted species. These genomic signatures are correlated to the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of the vertebrate-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to the respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria.Impact statementThe bacteria of the family Lactobacillaceae are present in the wide range of habitats and play an important role in human health, fermented foods and chemical industries. A few studies have demonstrated the presence of plasmids in the individual strains of Lactobacillaceae species encoding various traits. Extensive data of genome sequences of the lactobacilli are becoming available; however, no comprehensive analysis of the plasmid-encoded genes and determining their biological relevance across lactobacilli has been undertaken at a larger scale. In this study, we explored the genomic content of 512 plasmids of Lactobacillaceae species and correlated it to the three types of these species according to their ecological niches – vertebrate-adapted, free-living and nomadic. Comparatively lower plasmid abundance and GC content in the vertebrate-adapted species could be correlated to the presence of these species in the nutrient-rich environment. The genomic content of the plasmids was consistent with the respective lifestyle adopted by lactobacilli suggesting that the plasmids might enhance the niche-specific fitness of the strains. The plethora of important genes present on the plasmids can also make them a highly useful tool in improving the probiotic, technological and food-related properties of lactobacilli.Data summaryNucleotide sequences of plasmids of Lactobacillus strains for which complete genome sequences were available were retrieved from the NCBI genome [https://www.ncbi.nlm.nih.gov/genome] and PATRIC 3.5.41 databases on 31st March 2019. The dataset includes 512 nucleotide sequences of plasmids of 282 strains belonging to genus Lactobacillus before its reclassification into several genera (1). Details of the plasmids have been given in Table S1.

scholarly journals Trophic Specialization Results in Genomic Reduction in Free-Living MarineIdiomarinaBacteria

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Qi-Long Qin ◽  
Yi Li ◽  
Lin-Lin Sun ◽  
Zhi-Bin Wang ◽  
Shi Wang ◽  
...  
Keyword(s):  
Genome Size ◽  
Bacterial Genome ◽  
Substrate Utilization ◽  
Comparative Genomic ◽  
Metabolic Efficiency ◽  
Trophic Specialization ◽  
Free Living ◽  
Carbohydrate Utilization ◽  
New Hypothesis ◽  
Living Bacteria

ABSTRACTThe streamlining hypothesis is generally used to explain the genomic reduction events related to the small genome size of free-living bacteria like marine bacteria SAR11. However, our current understanding of the correlation between bacterial genome size and environmental adaptation relies on too few species. It is still unclear whether there are other paths leading to genomic reduction in free-living bacteria. The genome size of marine free-living bacteria of the genusIdiomarinabelonging to the orderAlteromonadales(Gammaproteobacteria) is much smaller than the size of related genomes from bacteria in the same order. Comparative genomic and physiological analyses showed that the genomic reduction pattern in this genus is different from that of the classical SAR11 lineage. Genomic reduction reconstruction and substrate utilization profile showed thatIdiomarinaspp. lost a large number of genes related to carbohydrate utilization, and instead they specialized on using proteinaceous resources. Here we propose a new hypothesis to explain genomic reduction in this genus; we propose that trophic specialization increasing the metabolic efficiency for using one kind of substrate but reducing the substrate utilization spectrum could result in bacterial genomic reduction, which would be not uncommon in nature. This hypothesis was further tested in another free-living genus,Kangiella, which also shows dramatic genomic reduction. These findings highlight that trophic specialization is potentially an important path leading to genomic reduction in some marine free-living bacteria, which is distinct from the classical lineages like SAR11.IMPORTANCEThe streamlining hypothesis is usually used to explain the genomic reduction events in free-living bacteria like SAR11. However, we find that the genomic reduction phenomenon in the bacterial genusIdiomarinais different from that in SAR11. Therefore, we propose a new hypothesis to explain genomic reduction in this genus based on trophic specialization that could result in genomic reduction, which would be not uncommon in nature. Not only can the trophic specialization hypothesis explain the genomic reduction in the genusIdiomarina, but it also sheds new light on our understanding of the genomic reduction processes in other free-living bacterial lineages.

scholarly journals The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria

2020 ◽  
Author(s):  
Rebecca Ansorge ◽  
Stefano Romano ◽  
Lizbeth Sayavedra ◽  
Maxim Rubin-Blum ◽  
Harald Gruber-Vodicka ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Hydrothermal Vents ◽  
Driving Forces ◽  
Genetic Material ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Free Living ◽  
Bacterial Populations ◽  
Genomic Studies ◽  
Sulfur Oxidizing

AbstractSulfur-oxidizing Thioglobaceae, often referred to as SUP05 and Arctic96BD clades, are widespread and common to hydrothermal vents and oxygen minimum zones. They impact global biogeochemical cycles and exhibit a variety of host-associated and free-living lifestyles. The evolutionary driving forces that led to the versatility, adoption of multiple lifestyles and global success of this family are largely unknown. Here, we perform an in-depth comparative genomic analysis using all available and newly generated Thioglobaceae genomes. Gene content variation was common, throughout taxonomic ranks and lifestyles. We uncovered a pool of variable genes within most Thioglobaceae populations in single environmental samples and we referred to this as the ‘hidden pangenome’. The ‘hidden pangenome’ is often overlooked in comparative genomic studies and our results indicate a much higher intra-specific diversity within environmental bacterial populations than previously thought. Our results show that core-community functions are different from species core genomes suggesting that core functions across populations are divided among the intra-specific members within a population. Defense mechanisms against foreign DNA and phages were enriched in symbiotic lineages, indicating an increased exchange of genetic material in symbioses. Our study suggests that genomic plasticity and frequent exchange of genetic material drives the global success of this family by increasing its evolvability in a heterogeneous environment.

scholarly journals Energy Expenditure during Free Flight in Trained and Free-Living Eurasian Kestrels (Falco Tinnunculus)

The Auk ◽  
1987 ◽  
Vol 104 (4) ◽  
pp. 603-616 ◽  
Author(s):  
Dirkjan Masman ◽  
Marcel Klaassen
Keyword(s):  
Energy Expenditure ◽  
Body Mass ◽  
Morphological Data ◽  
Energy Budgets ◽  
Published Data ◽  
Falco Tinnunculus ◽  
Free Living ◽  
Avian Flight ◽  
Flight Costs ◽  
Directional Flight

Abstract During directional flight trained Eurasian Kestrels (Falco tinnunculus) in the laboratory expended 13.8 W. Free-living birds expended 14.6 W during nonsoaring flight that included both directional flight and wind hovering. The former value was obtained by combining food balance and indirect calorimetry techniques, the latter by doubly labeled water (Dz18O). Because the energy-expenditure rates are so similar for directional flight alone and for wind hovering and directional flight combined, we argue that the value for either mode of kestrel flight may be used to analyze time-energy budgets. We predicted avian flight costs (et) from an equation based on published data on flight costs in 14 species (body mass 3.8-1,000 g): where M is body mass (g), bw is wing span (cm), and Sw is wing area (cm2). Inclusion of the morphological data with body mass significantly improved the prediction of flight cost [r2 = 0.84 vs. r2 = 0.75 without bw and sw, Fc (2,18) = 5.34, P < 0.05]. Received 8 May 1986, accepted 29 November 1986.

Scanning electron microscopy of freeze-fractured prescapular lymph node of caprine

1984 ◽  
Vol 42 ◽  
pp. 244-245
Author(s):  
O. Faroon ◽  
F. Al-Bagdadi ◽  
T. G. Snider ◽  
C. Titkemeyer
Keyword(s):  
Lymph Node ◽  
Lymph Nodes ◽  
Lymphatic System ◽  
Three Dimensional ◽  
Meat Products ◽  
The Body ◽  
Morphological Data ◽  
The World ◽  
Cellular Constituent ◽  
Scanning Electron

The lymphatic system is very important in the immunological activities of the body. Clinicians confirm the diagnosis of infectious diseases by palpating the involved cutaneous lymph node for changes in size, heat, and consistency. Clinical pathologists diagnose systemic diseases through biopsies of superficial lymph nodes. In many parts of the world the goat is considered as an important source of milk and meat products.The lymphatic system has been studied extensively. These studies lack precise information on the natural morphology of the lymph nodes and their vascular and cellular constituent. This is due to using improper technique for such studies. A few studies used the SEM, conducted by cutting the lymph node with a blade. The morphological data collected by this method are artificial and do not reflect the normal three dimensional surface of the examined area of the lymph node. SEM has been used to study the lymph vessels and lymph nodes of different animals. No information on the cutaneous lymph nodes of the goat has ever been collected using the scanning electron microscope.

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