scholarly journals Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile

2020 ◽  
Vol 8 (7) ◽  
pp. 1077
Author(s):  
Yoanna Eissler ◽  
Cristina Dorador ◽  
Brandon Kieft ◽  
Verónica Molina ◽  
Martha Hengst
Keyword(s):  
Taxonomic Diversity ◽  
Extreme Environment ◽  
Lytic Enzymes ◽  
The Andes ◽  
The Family ◽  
Genes Encoding ◽  
Active Viral Replication ◽  
Chilean Altiplano ◽  
Flow Filtration ◽  
Viral Sequences

Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment.

scholarly journals Potential Role of Phospholipases in Virulence and Fungal Pathogenesis

2000 ◽  
Vol 13 (1) ◽  
pp. 122-143 ◽  
Author(s):  
Mahmoud A. Ghannoum
Keyword(s):  
Virulence Factor ◽  
Cell Damage ◽  
Pathogenic Fungi ◽  
Microbial Pathogens ◽  
Immunogold Electron Microscopy ◽  
Lytic Enzymes ◽  
Fungal Virulence ◽  
Phospholipase B ◽  
Genes Encoding

SUMMARY Microbial pathogens use a number of genetic strategies to invade the host and cause infection. These common themes are found throughout microbial systems. Secretion of enzymes, such as phospholipase, has been proposed as one of these themes that are used by bacteria, parasites, and pathogenic fungi. The role of extracellular phospholipase as a potential virulence factor in pathogenic fungi, including Candida albicans, Cryptococcus neoformans, and Aspergillus, has gained credence recently. In this review, data implicating phospholipase as a virulence factor in C. albicans, Candida glabrata, C. neoformans, and A. fumigatus are presented. A detailed description of the molecular and biochemical approaches used to more definitively delineate the role of phospholipase in the virulence of C. albicans is also covered. These approaches resulted in cloning of three genes encoding candidal phospholipases (caPLP1, caPLB2, and PLD). By using targeted gene disruption, C. albicans null mutants that failed to secrete phospholipase B, encoded by caPLB1, were constructed. When these isogenic strain pairs were tested in two clinically relevant murine models of candidiasis, deletion of caPLB1 was shown to lead to attenuation of candidal virulence. Importantly, immunogold electron microscopy studies showed that C. albicans secretes this enzyme during the infectious process. These data indicate that phospholipase B is essential for candidal virulence. Although the mechanism(s) through which phospholipase modulates fungal virulence is still under investigations, early data suggest that direct host cell damage and lysis are the main mechanisms contributing to fungal virulence. Since the importance of phospholipases in fungal virulence is already known, the next challenge will be to utilize these lytic enzymes as therapeutic and diagnostic targets.

A Family of Genes Clustered at the Triplo-lethal Locus of Drosophila melanogaster Has an Unusual Evolutionary History and Significant Synteny With Anopheles gambiae

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 613-621 ◽  
Author(s):  
Douglas R Dorer ◽  
Jamie A Rudnick ◽  
Etsuko N Moriyama ◽  
Alan C Christensen
Keyword(s):  
Phylogenetic Analysis ◽  
Drosophila Melanogaster ◽  
Anopheles Gambiae ◽  
Evolutionary History ◽  
Codon Bias ◽  
Good Target ◽  
The Family ◽  
Genes Encoding ◽  
And Function ◽  
Gambiae Genome

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

scholarly journals Regulation of Major Cellulosomal Endoglucanases of Clostridium thermocellum Differs from That of a Prominent Cellulosomal Xylanase

2005 ◽  
Vol 187 (7) ◽  
pp. 2261-2266 ◽  
Author(s):  
Tali W. Dror ◽  
Adi Rolider ◽  
Edward A. Bayer ◽  
Raphael Lamed ◽  
Yuval Shoham
Keyword(s):  
Growth Rate ◽  
Clostridium Thermocellum ◽  
Transcript Level ◽  
Clear Correlation ◽  
Transcript Levels ◽  
Batch Cultures ◽  
Processive Endoglucanase ◽  
The Family ◽  
Genes Encoding ◽  
Family 10 Xylanase

ABSTRACT The expression of scaffoldin-anchoring genes and one of the major processive endoglucanases (CelS) from the cellulosome of Clostridium thermocellum has been shown to be dependent on the growth rate. For the present work, we studied the gene regulation of selected cellulosomal endoglucanases and a major xylanase in order to examine the previously observed substrate-linked alterations in cellulosome composition. For this purpose, the transcript levels of genes encoding endoglucanases CelB, CelG, and CelD and the family 10 xylanase XynC were determined in batch cultures, grown on either cellobiose or cellulose, and in carbon-limited continuous cultures at different dilution rates. Under all conditions tested, the transcript levels of celB and celG were at least 10-fold higher than that of celD. Like the major processive endoglucanase CelS, the transcript levels of these endoglucanase genes were also dependent on the growth rate. Thus, at a rate of 0.04 h−1, the levels of celB, celG, and celD were threefold higher than those obtained in cultures grown at maximal rates (0.35 h−1) on cellobiose. In contrast, no clear correlation was observed between the transcript level of xynC and the growth rate—the levels remained relatively high, fluctuating between 30 and 50 transcripts per cell. The results suggest that the regulation of C. thermocellum endoglucanases is similar to that of the processive endoglucanase celS but differs from that of a major cellulosomal xylanase in that expression of the latter enzyme is independent of the growth rate.

scholarly journals Independent infections of porcine deltacoronavirus among Haitian children

Nature ◽  
2021 ◽  
Author(s):  
John A. Lednicky ◽  
Massimiliano S. Tagliamonte ◽  
Sarah K. White ◽  
Maha A. Elbadry ◽  
Md. Mahbubul Alam ◽  
...  
Keyword(s):  
Febrile Illness ◽  
Cell Receptor ◽  
Receptor Binding Domain ◽  
Mutational Signature ◽  
Host Cell Receptor ◽  
The Family ◽  
Genes Encoding ◽  
Animal Contact ◽  
Human Infections ◽  
Animal Reservoirs

AbstractCoronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, the emergence of coronavirus in our species has been associated with zoonotic transmissions from animal reservoirs1,2, underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae, human infections reported so far have been limited to alphacoronaviruses and betacoronaviruses3–5. Here we identify porcine deltacoronavirus strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the genes encoding Nsp15 and the spike glycoprotein. In particular, structural analysis predicts that one of the changes in the spike S1 subunit, which contains the receptor-binding domain, may affect the flexibility of the protein and its binding to the host cell receptor. Our findings highlight the potential for evolutionary change and adaptation leading to human infections by coronaviruses outside of the previously recognized human-associated coronavirus groups, particularly in settings where there may be close human–animal contact.

sry h-1, a new Drosophila melanogaster multifingered protein gene showing maternal and zygotic expression

1988 ◽  
Vol 8 (10) ◽  
pp. 4459-4468
Author(s):  
A Vincent ◽  
J Kejzlarovà-Lepesant ◽  
L Segalat ◽  
C Yanicostas ◽  
J A Lepesant
Keyword(s):  
Dna Sequences ◽  
Subsequent Development ◽  
Initiation Site ◽  
Protein Product ◽  
Protein Coding ◽  
Finger Protein ◽  
Early Embryos ◽  
The Family ◽  
Genes Encoding ◽  
Internal Initiation

Low-stringency hybridization of the Drosophila serendipity (sry) finger-coding sequences revealed copies of homologous DNA sequences in the genomes of members of the family Drosophilidae and higher vertebrates. sry h-1, a new Drosophila finger protein-coding gene isolated on the basis of this homology, encodes a 3.2-kilobase (kb) mRNA accumulating in eggs and abundant in early embryos. The predicted sry h-1 protein product, starting at an internal initiation site of translation, is a 868-amino-acid basic polypeptide containing eight TFIIIA-like fingers encoded by three separate exons. Links separating individual fingers in the sry h-1 protein are variable in length and sequence, in contrast with the invariant H/C link found in most multi-fingered proteins. The similarity of the developmental pattern of transcription of sry h-1 with that of several other Drosophila finger protein genes suggests the existence of a complex set of such genes encoding an information which is, at least partly, maternally provided to the embryo and required for activation of gene transcription in early embryos or maintenance of gene activity during subsequent development.

scholarly journals Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nojood A. Aalismail ◽  
David K. Ngugi ◽  
Rubén Díaz-Rúa ◽  
Intikhab Alam ◽  
Michael Cusack ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Sequences ◽  
Biofilm Formation ◽  
Atmospheric Transport ◽  
Taxonomic Diversity ◽  
Functional Metagenomics ◽  
Genetic Traits ◽  
Gene Catalogue ◽  
Range Transport ◽  
Genes Encoding

Abstract Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene Catalogue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 106 predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.

scholarly journals Taxonomic diversity of cockroach assemblages (Blattaria, Insecta) of the Aptian Crato Formation (Cretaceous, NE Brazil)

2016 ◽  
Vol 67 (5) ◽  
pp. 433-450 ◽  
Author(s):  
Shih-Wei Lee
Keyword(s):  
Lower Cretaceous ◽  
Taxonomic Diversity ◽  
Northeast Brazil ◽  
Taxonomic Richness ◽  
The Family ◽  
Endemic Genera

AbstractA comprehensive revision of 981 specimens of fossil cockroaches from the Lower Cretaceous laminated limestones of the Crato Formation of Northeast Brazil shows that they belong to eleven taxa, includingPiniblattella limai,P. magnasp. n.,Perlucipecta santanensis.sp. n.,Raptoblatta waddingtonae;Ocelloblattula santanensissp. n.,Elisama brevis(=E. americana, syn.n.),E. hindwingniisp. n.,Ponopterix axelrodi(=P. maximasyn.n.),Umenopterix burkhardicomb. n., andCratovitisma oldreadi(Umenocoleidae = Cratovitismidae syn.n. = Ponopterixidae syn.n.). The family Ectobiidae is numerically most abundant in the assemblage of cockroaches of the Crato Formation (83 % of cockroaches), followed by Blattulidae (13 %) and Umenocoleidae (4 %). 79.2 % of specimens are complete and fully articulated. Members of the family Alienopteridae are probably also present. Representatives of a relatively common Mesozoic superfamily Caloblattinoidea are missing. With the exception of the endemic generaCratovitismaandRaptoblattaand the exclusively Gondwanan genusOcelloblattula, all other genera were cosmopolitan. Taxonomic richness of cockroaches of the Crato Formation is thus rather low, and consists of geologically long-ranging and geographically-widespread genera, genera restricted to Gondwana, and short-ranging endemic genera found in the Crato Formation only.

New Ordovician marine macroalgae from North America, with observations onButhograptus,Callithamnopsis, andChaetocladus

2018 ◽  
Vol 93 (2) ◽  
pp. 197-214 ◽  
Author(s):  
Steven T. LoDuca
Keyword(s):  
Taxonomic Diversity ◽  
Microscopic Investigation ◽  
Electron Microscopic Investigation ◽  
Marine Macroalgae ◽  
Electron Microscopic ◽  
Green Algal ◽  
Extant Species ◽  
The Family ◽  
New Occurrences ◽  
Northern Michigan

AbstractOrdovician material from the Platteville Formation (Sandbian) of southern Wisconsin and Big Hill Formation (Katian) of northern Michigan is described that provides novel information about the phylogenetic affinity, taxonomic diversity, and stratigraphic range of the nonbiomineralized taxaButhograptus,Callithamnopsis, andChaetocladus. Two new species ofButhograptus, a previously monotypic genus, are erected on the basis of the Platteville Formation material,Buthograptus gundersonin. sp. andB.meyerin. sp., and new occurrences ofB.laxusare recorded from several localities and two distinct stratigraphic levels within this unit. On the basis of scanning electron microscopic investigation of the material and the fact that each of the threeButhograptusspecies has a close counterpart in the frond morphology of an extant species ofCaulerpa,Buthograptusis interpreted as a member of the green algal order Bryopsidales. New specimens from the Platteville Formation assigned toCallithamnopsisreveal new morphological details for the type species,C.fruticosa(Hall, 1865), aspects of which indicate that the genus belongs to the family Triploporellaceae rather than Seletonellaceae within the green algal order Dasycladales, andChaetocladusmaterial from the Big Hill Formation includes specimens that are formally assigned toChaetocladus dubius(Spencer, 1884), a species of dasycladalean alga known previously only from the mid-Silurian of Ontario.

Novel Data on the Taxonomic Diversity, Distribution, and Host Plants of Leafmining Moths of the Family Gracillariidae (Lepidoptera) in Siberia, Based on DNA Barcoding

2019 ◽  
Vol 99 (6) ◽  
pp. 796-819 ◽  
Author(s):  
N. I. Kirichenko ◽  
P. Triberti ◽  
E. N. Akulov ◽  
M. G. Ponomarenko ◽  
C. Lopez-Vaamonde
Keyword(s):  
Dna Barcoding ◽  
Host Plants ◽  
Taxonomic Diversity ◽  
The Family

scholarly journals Novel viruses detected in bats in the Republic of Korea

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sook-Young Lee ◽  
Chul-Un Chung ◽  
Jun Soo Park ◽  
Jae-Ku Oem
Keyword(s):  
Genetic Relationships ◽  
Rt Pcr ◽  
Entire Genome ◽  
Rotavirus A ◽  
Zoonotic Viruses ◽  
Feces Sample ◽  
The Family ◽  
The Republic ◽  
Viral Sequences ◽  
Generation Sequencing

AbstractBats are natural reservoirs for potential zoonotic viruses. In this study, next-generation sequencing was performed to obtain entire genome sequences of picornavirus from a picornavirus-positive bat feces sample (16BF77) and to explore novel viruses in a pooled bat sample (16BP) from samples collected in South Korea, 2016. Fourteen mammalian viral sequences were identified from 16BF77 and 29 from 16BP, and verified by RT-PCR. The most abundant virus in 16BF77 was picornavirus. Highly variable picornavirus sequences encoding 3Dpol were classified into genera Kobuvirus, Shanbavirus, and an unassigned group within the family Picornaviridae. Amino acid differences between these partial 3Dpol sequences were ≥ 65.7%. Results showed that one bat was co-infected by picornaviruses of more than two genera. Retrovirus, coronavirus, and rotavirus A sequences also were found in the BP sample. The retrovirus and coronavirus genomes were identified in nine and eight bats, respectively. Korean bat retroviruses and coronavirus demonstrated strong genetic relationships with a Chinese bat retrovirus (RfRV) and coronavirus (HKU5-1), respectively. A co-infection was identified in one bat with a retrovirus and a coronavirus. Our results indicate that Korean bats were multiply infected by several mammal viruses.

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