bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity
Authors: Adriaenssens Evelien M. , Cowan Don A. 
Published: May 2014

ABSTRACT

Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the bacterial and eukaryotic kingdoms, largely due to the absence of any universal phylogenetic marker. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for data sets of specific virus groups. Genes that have been used include those encoding structural proteins, such as portal protein, major capsid protein, and tail sheath protein, auxiliary metabolism genes, such as
psbA
,
psbB
, and
phoH
, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal, and seasonal variations and diversity in a wide range of habitats.
Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo
Authors: Waite David W. , Eason Daryl K. , Taylor Michael W. 
Published: May 2014

ABSTRACT
The critically endangered New Zealand parrot, the kakapo, is subject to an intensive management regime aiming to maintain bird health and boost population size. Newly hatched kakapo chicks are subjected to human intervention and are frequently placed in captivity throughout their formative months. Hand rearing greatly reduces mortality among juveniles, but the potential long-term impact on the kakapo gut microbiota is uncertain. To track development of the kakapo gut microbiota, fecal samples from healthy, prefledged juvenile kakapos, as well as from unrelated adults, were analyzed by using 16S rRNA gene amplicon pyrosequencing. Following the original sampling, juvenile kakapos underwent a period of captivity, so further sampling during and after captivity aimed to elucidate the impact of captivity on the juvenile gut microbiota. Variation in the fecal microbiota over a year was also investigated, with resampling of the original juvenile population. Amplicon pyrosequencing revealed a juvenile fecal microbiota enriched with particular lactic acid bacteria compared to the microbiota of adults, although the overall community structure did not differ significantly among kakapos of different ages. The abundance of key operational taxonomic units (OTUs) was correlated with antibiotic treatment and captivity, although the importance of these factors could not be proven unequivocally within the bounds of this study. Finally, the microbial community structure of juvenile and adult kakapos changed over time, reinforcing the need for continual monitoring of the microbiota as part of regular health screening.
The Key to Acetate: Metabolic Fluxes of Acetic Acid Bacteria under Cocoa Pulp Fermentation-Simulating Conditions
Authors: Adler Philipp , Frey Lasse Jannis , Berger Antje , Bolten Christoph Josef , Hansen Carl Erik , Wittmann Christoph 
Published: May 2014

ABSTRACTAcetic acid bacteria (AAB) play an important role during cocoa fermentation, as their main product, acetate, is a major driver for the development of the desired cocoa flavors. Here, we investigated the specialized metabolism of these bacteria under cocoa pulp fermentation-simulating conditions. A carefully designed combination of parallel13C isotope labeling experiments allowed the elucidation of intracellular fluxes in the complex environment of cocoa pulp, when lactate and ethanol were included as primary substrates among undefined ingredients. We demonstrate that AAB exhibit a functionally separated metabolism during coconsumption of two-carbon and three-carbon substrates. Acetate is almost exclusively derived from ethanol, while lactate serves for the formation of acetoin and biomass building blocks. Although this is suboptimal for cellular energetics, this allows maximized growth and conversion rates. The functional separation results from a lack of phosphoenolpyruvate carboxykinase and malic enzymes, typically present in bacteria to interconnect metabolism. In fact, gluconeogenesis is driven by pyruvate phosphate dikinase. Consequently, a balanced ratio of lactate and ethanol is important for the optimum performance of AAB. As lactate and ethanol are individually supplied by lactic acid bacteria and yeasts during the initial phase of cocoa fermentation, respectively, this underlines the importance of a well-balanced microbial consortium for a successful fermentation process. Indeed, AAB performed the best and produced the largest amounts of acetate in mixed culture experiments when lactic acid bacteria and yeasts were both present.
Novel Microarray Design for Molecular Serotyping of Shiga Toxin-Producing Escherichia coli Strains Isolated from Fresh Produce
Authors: Lacher David W. , Gangiredla Jayanthi , Jackson Scott A. , Elkins Christopher A. , Feng Peter C. H. 
Published: May 2014

ABSTRACT

Serotyping
Escherichia coli
is a cumbersome and complex procedure due to the existence of large numbers of O- and H-antigen types. It can also be unreliable, as many Shiga toxin-producing
E. coli
(STEC) strains isolated from fresh produce cannot be typed by serology or have only partial serotypes. The FDA
E. coli
identification (FDA-ECID) microarray, designed for characterizing pathogenic
E. coli
, contains a molecular serotyping component, which was evaluated here for its efficacy. Analysis of a panel of 75 reference
E. coli
strains showed that the array correctly identified the O and H types in 97% and 98% of the strains, respectively. Comparative analysis of 73 produce STEC strains showed that serology and the array identified 37% and 50% of the O types, respectively, and that the array was able to identify 16 strains that could not be O serotyped. Furthermore, the array identified the H types of 97% of the produce STEC strains compared to 65% by serology, including six strains that were mistyped by serology. These results show that the array is an effective alternative to serology in serotyping environmental
E. coli
isolates.
A Function of SmeDEF, the Major Quinolone Resistance Determinant of Stenotrophomonas maltophilia, Is the Colonization of Plant Roots
Authors: García-León Guillermo , Hernández Alvaro , Hernando-Amado Sara , Alavi Peyman , Berg Gabriele , Martínez José Luis 
Published: May 2014

ABSTRACT

Quinolones are synthetic antibiotics, and the main cause of resistance to these antimicrobials is mutation of the genes encoding their targets. However, in contrast to the case for other organisms, such mutations have not been found in quinolone-resistant
Stenotrophomonas maltophilia
isolates, in which overproduction of the SmeDEF efflux pump is a major cause of quinolone resistance. SmeDEF is chromosomally encoded and highly conserved in all studied
S. maltophilia
strains; it is an ancient element that evolved over millions of years in this species. It thus seems unlikely that its main function would be resistance to quinolones, a family of synthetic antibiotics not present in natural environments until the last few decades. Expression of SmeDEF is tightly controlled by the transcriptional repressor SmeT. Our work shows that plant-produced flavonoids can bind to SmeT, releasing it from
smeDEF
and
smeT
operators. Antibiotics extruded by SmeDEF do not impede the binding of SmeT to DNA. The fact that plant-produced flavonoids specifically induce
smeDEF
expression indicates that they are
bona fide
effectors regulating expression of this resistance determinant. Expression of efflux pumps is usually downregulated unless their activity is needed. Since
smeDEF
expression is triggered by plant-produced flavonoids, we reasoned that this efflux pump may have a role in the colonization of plants by
S. maltophilia
. Our results showed that, indeed, deletion of
smeE
impairs
S. maltophilia
colonization of plant roots. Altogether, our results indicate that quinolone resistance is a recent function of SmeDEF and that colonization of plant roots is likely one original function of this efflux pump.
Cellulolytic Streptomyces Strains Associated with Herbivorous Insects Share a Phylogenetically Linked Capacity To Degrade Lignocellulose
Authors: Book Adam J. , Lewin Gina R. , McDonald Bradon R. , Takasuka Taichi E. , Doering Drew T. , Adams Aaron S. , Blodgett Joshua A. V. , Clardy Jon , Raffa Kenneth F. , Fox Brian G. , Currie Cameron R. 
Published: May 2014

ABSTRACT

Actinobacteria in the genus
Streptomyces
are critical players in microbial communities that decompose complex carbohydrates in the soil, and these bacteria have recently been implicated in the deconstruction of plant polysaccharides for some herbivorous insects. Despite the importance of
Streptomyces
to carbon cycling, the extent of their plant biomass-degrading ability remains largely unknown. In this study, we compared four strains of
Streptomyces
isolated from insect herbivores that attack pine trees: DpondAA-B6 (SDPB6) from the mountain pine beetle, SPB74 from the southern pine beetle, and SirexAA-E (SACTE) and SirexAA-G from the woodwasp,
Sirex noctilio
. Biochemical analysis of secreted enzymes demonstrated that only two of these strains, SACTE and SDPB6, were efficient at degrading plant biomass. Genomic analyses indicated that SACTE and SDPB6 are closely related and that they share similar compositions of carbohydrate-active enzymes. Genome-wide proteomic and transcriptomic analyses revealed that the major exocellulases (GH6 and GH48), lytic polysaccharide monooxygenases (AA10), and mannanases (GH5) were conserved and secreted by both organisms, while the secreted endocellulases (GH5 and GH9 versus GH9 and GH12) were from diverged enzyme families. Together, these data identify two phylogenetically related insect-associated
Streptomyces
strains with high biomass-degrading activity and characterize key enzymatic similarities and differences used by these organisms to deconstruct plant biomass.
Expression of a Toll Signaling Regulator Serpin in a Mycoinsecticide for Increased Virulence
Authors: Yang Linzhi , Keyhani Nemat O. , Tang Guirong , Tian Chuang , Lu Ruipeng , Wang Xin , Pei Yan , Fan Yanhua 
Published: May 2014

ABSTRACT

Serpins are ubiquitously distributed serine protease inhibitors that covalently bind to target proteases to exert their activities. Serpins regulate a wide range of activities, particularly those in which protease-mediated cascades are active. The
Drosophila melanogaster
serpin Spn43Ac negatively controls the Toll pathway that is activated in response to fungal infection. The entomopathogenic fungus
Beauveria bassiana
offers an environmentally friendly alternative to chemical pesticides for insect control. However, the use of mycoinsecticides remains limited in part due to issues of efficacy (low virulence) and the recalcitrance of the targets (due to strong immune responses). Since Spn43Ac acts to inhibit Toll-mediated activation of defense responses, we explored the feasibility of a new strategy to engineer entomopathogenic fungi with increased virulence by expression of Spn43Ac in the fungus. Compared to the 50% lethal dose (LD
50
) for the wild-type parent, the LD
50
of
B. bassiana
expressing Spn43Ac (strain Bb::S43Ac-1) was reduced ∼3-fold, and the median lethal time against the greater wax moth (
Galleria mellonella
) was decreased by ∼24%, with the more rapid proliferation of hyphal bodies being seen in the host hemolymph.
In vitro
and
in vivo
assays showed inhibition of phenoloxidase (PO) activation in the presence of Spn43Ac, with Spn43Ac-mediated suppression of activation by chymotrypsin, trypsin, laminarin, and lipopolysaccharide occurring in the following order: chymotrypsin and trypsin > laminarin > lipopolysaccharide. Expression of Spn43Ac had no effect on the activity of the endogenous
B. bassiana
-derived cuticle-degrading protease (CDEP-1). These results expand our understanding of Spn43Ac function and confirm that suppression of insect immune system defenses represents a feasible approach to engineering entomopathogenic fungi for greater efficacy.
High-Precision Fitting Measurements of the Kinetics of Size Changes during Germination of Individual Bacillus Spores
Authors: Liang Jintao , Zhang Pengfei , Setlow Peter , Li Yong-Qing 
Published: May 2014

ABSTRACT

High-precision measurements of size changes of individual bacterial spores based on ellipse fitting to bright-field images recorded with a digital camera were employed to monitor the germination of
Bacillus
spores with a precision of ∼5 nm. To characterize the germination of individual spores, we recorded bright-field and phase-contrast images and found that the timing of changes in their normalized intensities coincided, so the bright-field images can be used to characterize spore size and refractility changes during germination. The major conclusions from this work were as follows. (i) The sizes of germinating
B. cereus
spores were nearly unchanged until
T
release
, the time of the completion of CaDPA (a 1:1 chelate of Ca
2+
and dipicolinic acid [DPA]) release after addition of nutrient germinants. (ii) The minor axis of germinating
B. cereus
spores rapidly increased by ∼50 nm in a few seconds right after
T
release
, while the major axis was slightly decreased or unchanged. Both the minor and major axes remained unchanged for a further 30 to 45 s and then increased by 100 to 200 nm by
T
lys
, the time of completion of cortex lysis. (iii) Individual spores in a population showed significant heterogeneity in the timing of germination events, such as
T
release
and
T
lys
, but also variation in size changes during germination. (iv)
Bacillus subtilis
wild-type spores,
B. subtilis
spores lacking the cortex-lytic enzyme CwlJ, and wild-type
Bacillus megaterium
spores showed similar kinetics of size changes during nutrient germination. The size increases in germinating spores probably result from uptake of water and cortex lysis after completion of CaDPA release.
Atmospheric N Deposition Increases Bacterial Laccase-Like Multicopper Oxidases: Implications for Organic Matter Decay
Authors: Freedman Zachary , Zak Donald R. 
Published: May 2014

ABSTRACTAnthropogenic release of biologically available nitrogen (N) has increased dramatically over the last 150 years, which can alter the processes controlling carbon (C) storage in terrestrial ecosystems. In a northern hardwood forest ecosystem located in Michigan in the United States, nearly 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This change occurred concomitantly with compositional changes inBasidiomycetefungi and inActinobacteria, as well as the downregulation of fungal lignocelluloytic genes. Recently, laccase-like multicopper oxidases (LMCOs) have been discovered among bacteria which can oxidize β-O-4 linkages in phenolic compounds (e.g., lignin and humic compounds), resulting in the production of dissolved organic carbon (DOC). Here, we examined how nearly 2 decades of experimental N deposition has affected the abundance and composition of saprotrophic bacteria possessing LMCO genes. In our experiment, LMCO genes were more abundant in the forest floor under experimental N deposition whereas the abundances of bacteria and fungi were unchanged. Experimental N deposition also led to less-diverse, significantly altered bacterial and LMCO gene assemblages, with taxa implicated in organic matter decay (i.e.,Actinobacteria,Proteobacteria) accounting for the majority of compositional changes. These results suggest that experimental N deposition favors bacteria in the forest floor that harbor the LMCO gene and represents a plausible mechanism by which anthropogenic N deposition has reduced decomposition, increased soil C storage, and accelerated phenolic DOC production in our field experiment. Our observations suggest that future rates of atmospheric N deposition could fundamentally alter the physiological potential of soil microbial communities.
Response of a Rice Paddy Soil Methanogen to Syntrophic Growth as Revealed by Transcriptional Analyses
Authors: Liu Pengfei , Yang Yanxiang , Lü Zhe , Lu Yahai 
Published: May 2014

ABSTRACT

Members of
Methanocellales
are widespread in paddy field soils and play the key role in methane production. These methanogens feature largely in these organisms' adaptation to low H
2
and syntrophic growth with anaerobic fatty acid oxidizers. The adaptive mechanisms, however, remain unknown. In the present study, we determined the transcripts of 21 genes involved in the key steps of methanogenesis and acetate assimilation of
Methanocella conradii
HZ254, a strain recently isolated from paddy field soil.
M. conradii
was grown in monoculture and syntrophically with
Pelotomaculum thermopropionicum
(a propionate syntroph) or
Syntrophothermus lipocalidus
(a butyrate syntroph). Comparison of the relative transcript abundances showed that three hydrogenase-encoding genes and all methanogenesis-related genes tested were upregulated in cocultures relative to monoculture. The genes encoding formylmethanofuran dehydrogenase (Fwd), heterodisulfide reductase (Hdr), and the membrane-bound energy-converting hydrogenase (Ech) were the most upregulated among the evaluated genes. The expression of the formate dehydrogenase (Fdh)-encoding gene also was significantly upregulated. In contrast, an acetate assimilation gene was downregulated in cocultures. The genes coding for Fwd, Hdr, and the D subunit of F
420
-nonreducing hydrogenase (Mvh) form a large predicted transcription unit; therefore, the Mvh/Hdr/Fwd complex, capable of mediating the electron bifurcation and connecting the first and last steps of methanogenesis, was predicted to be formed in
M. conradii
. We propose that
Methanocella
methanogens cope with low H
2
and syntrophic growth by (i) stabilizing the Mvh/Hdr/Fwd complex and (ii) activating formate-dependent methanogenesis.
Aminopeptidase N1 (EtAPN1), an M1 Metalloprotease of the Apicomplexan Parasite Eimeria tenella, Participates in Parasite Development
Authors: Gras Simon , Byzia Anna , Gilbert Florence B. , McGowan Sheena , Drag Marcin , Silvestre Anne , Niepceron Alisson , Lecaille Fabien , Lalmanach Gilles , Brossier Fabien 
Published: May 2014

ABSTRACT

Aminopeptidases N are metalloproteases of the M1 family that have been reported in numerous apicomplexan parasites, including
Plasmodium
,
Toxoplasma
,
Cryptosporidium
, and
Eimeria
. While investigating the potency of aminopeptidases as therapeutic targets against coccidiosis, one of the most important avian diseases caused by the genus
Eimeria
, we identified and characterized
Eimeria tenella
aminopeptidase N1 (EtAPN1). Its inhibition by bestatin and amastatin, as well as its reactivation by divalent ions, is typical of zinc-dependent metalloproteases. EtAPN1 shared a similar sequence, three-dimensional structure, and substrate specificity and similar kinetic parameters with A-M1 from
Plasmodium falciparum
(PfA-M1), a validated target in the treatment of malaria. EtAPN1 is synthesized as a 120-kDa precursor and cleaved into 96-, 68-, and 38-kDa forms during sporulation. Further, immunolocalization assays revealed that, similar to PfA-M1, EtAPN1 is present during the intracellular life cycle stages in both the parasite cytoplasm and the parasite nucleus. The present results support the hypothesis of a conserved role between the two aminopeptidases, and we suggest that EtAPN1 might be a valuable target for anticoccidiosis drugs.
Trypanosoma brucei Translation Initiation Factor Homolog EIF4E6 Forms a Tripartite Cytosolic Complex with EIF4G5 and a Capping Enzyme Homolog
Authors: Freire Eden R. , Malvezzi Amaranta M. , Vashisht Ajay A. , Zuberek Joanna , Saada Edwin A. , Langousis Gerasimos , Nascimento Janaína D. F. , Moura Danielle , Darzynkiewicz Edward , Hill Kent , de Melo Neto Osvaldo P. , Wohlschlegel James A. , Sturm Nancy R. , Campbell David A. 
Published: May 2014

ABSTRACT

Trypanosomes lack the transcriptional control characteristic of the majority of eukaryotes that is mediated by gene-specific promoters in a one-gene–one-promoter arrangement. Rather, their genomes are transcribed in large polycistrons with no obvious functional linkage. Posttranscriptional regulation of gene expression must thus play a larger role in these organisms. The eIF4E homolog TbEIF4E6 binds mRNA cap analogs
in vitro
and is part of a complex
in vivo
that may fulfill such a role. Knockdown of TbEIF4E6 tagged with protein A-tobacco etch virus protease cleavage site-protein C to approximately 15% of the normal expression level resulted in viable cells that displayed a set of phenotypes linked to detachment of the flagellum from the length of the cell body, if not outright flagellum loss. While these cells appeared and behaved as normal under stationary liquid culture conditions, standard centrifugation resulted in a marked increase in flagellar detachment. Furthermore, the ability of TbEIF4E6-depleted cells to engage in social motility was reduced. The TbEIF4E6 protein forms a cytosolic complex containing a triad of proteins, including the eIF4G homolog TbEIF4G5 and a hypothetical protein of 70.3 kDa, referred to as TbG5-IP. The TbG5-IP analysis revealed two domains with predicted secondary structures conserved in mRNA capping enzymes: nucleoside triphosphate hydrolase and guanylyltransferase. These complex members have the potential for RNA interaction, either via the 5′ cap structure for TbEIF4E6 and TbG5-IP or through RNA-binding domains in TbEIF4G5. The associated proteins provide a signpost for future studies to determine how this complex affects capped RNA molecules.
Dynamics of Expression and Maturation of the Type III Secretion System of Enteropathogenic Escherichia coli
Authors: Yerushalmi Gal , Litvak Yael , Gur-Arie Lihi , Rosenshine Ilan 
Published: May 2014

ABSTRACT

Enteropathogenic
Escherichia coli
(EPEC) is a major cause of food poisoning, leading to significant morbidity and mortality. EPEC virulence is dependent on a type III secretion system (T3SS), a molecular syringe employed by EPEC to inject effector proteins into host cells. The injected effector proteins subvert host cellular functions to the benefit of the infecting bacteria. The T3SS and related genes reside in several operons clustered in the locus of enterocyte effacement (LEE). We carried out simultaneous analysis of the expression dynamics of all the LEE promoters and the rate of maturation of the T3SS. The results showed that expression of the
LEE1
operon is activated immediately upon shifting the culture to inducing conditions, while expression of other LEE promoters is activated only ∼70 min postinduction. Parallel analysis showed that the T3SS becomes functional around 100 min postinduction. The T3SS core proteins EscS, EscT, EscU, and EscR are predicted to be involved in the first step of T3SS assembly and are therefore included among the
LEE1
genes. However, interfering with the temporal regulation of EscS, EscT, EscU, and EscR expression has only a marginal effect on the rate of the T3SS assembly. This study provides a comprehensive description of the transcription dynamics of all the LEE genes and correlates it to that of T3SS biogenesis.