bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Binary Mixture of Helicoverpa armigera Single Nucleopolyhedrovirus Genotypic Variants Has Improved Insecticidal Characteristics for Control of Cotton Bollworms
Authors: Arrizubieta Maite , Simón Oihane , Williams Trevor , Caballero Primitivo
Published: April 2015

The genotypic diversity of two Spanish isolates ofHelicoverpa armigerasingle nucleopolyhedrovirus (HearSNPV) was evaluated with the aim of identifying mixtures of genotypes with improved insecticidal characteristics for control of the cotton bollworm. Two genotypic variants, HearSP1A and HearSP1B, were clonedin vitrofrom the most pathogenic wild-type isolate of the Iberian Peninsula, HearSNPV-SP1 (HearSP1-wt). Similarly, six genotypic variants (HearLB1 to -6) were obtained by endpoint dilution from larvae collected from cotton crops in southern Spain that died from virus disease during laboratory rearing. Variants differed significantly in their insecticidal properties, pathogenicity, speed of kill, and occlusion body (OB) production (OBs/larva). HearSP1B was ∼3-fold more pathogenic than HearSP1-wt and the other variants. HearLB1, HearLB2, HeaLB5, and HearLB6 were the fastest-killing variants. Moreover, although highly virulent, HearLB1, HearLB4, and HearLB5 produced more OBs/larva than did the other variants. The co-occluded HearSP1B:LB6 mixture at a 1:1 proportion was 1.7- to 2.8-fold more pathogenic than any single variant and other mixtures tested and also killed larvae as fast as the most virulent genotypes. Serial passage resulted in modified proportions of the component variants of the HearSP1B:LB6 co-occluded mixture, suggesting that transmissibility could be further improved by this process. We conclude that the improved insecticidal phenotype of the HearSP1B:LB6 co-occluded mixture underlines the utility of the genotypic variant dissection and reassociation approach for the development of effective virus-based insecticides.
Development and Application of a Blastocystis Subtype-Specific PCR Assay Reveals that Mixed-Subtype Infections Are Common in a Healthy Human Population
Authors: Scanlan Pauline D. , Stensvold Christen Rune , Cotter Paul D.
Published: April 2015

The human gut is host to a diversity of microorganisms, including the single-celled microbial eukaryote
Blastocystis.
Research has shown that most carriers host a single
Blastocystis
subtype (ST), which is unusual given the considerable within-host species diversity observed for other microbial genera in this ecosystem. However, our limited knowledge of both the incidence and biological significance of
Blastocystis
diversity within hosts (i.e., so-called mixed infections) is likely due to problems with existing methodologies. Here, we developed and applied
Blastocystis
ST-specific PCRs for the investigation of the most common subtypes of
Blastocystis
(ST1 to ST4) to a healthy human cohort (
n
= 50). We detected mixed infections in 22% of the cases, all of which had been identified as single-ST infections in a previous study using state-of-the-art methods. Our results show that certain STs occur predominantly as either single (ST3 and 4) or mixed (ST1) infections, which may reflect
inter alia
transient colonization patterns and/or cooperative or competitive interactions between different STs. Comparative analyses with other primers that have been used extensively for ST-specific analysis found them unsuitable for detection of mixed- and, in some cases, single-ST infections. Collectively, our data shed new light on the diversity of
Blastocystis
within and between human hosts. Moreover, the development of these PCR assays will facilitate future work on the molecular epidemiology and significance of mixed infections in groups of interest, including health and disease cohorts, and also help identify sources of
Blastocystis
transmission to humans, including identifying potential animal and environmental reservoirs.
The Impact of Gamma Radiation on Sediment Microbial Processes
Authors: Brown Ashley R. , Boothman Christopher , Pimblott Simon M. , Lloyd Jonathan R.
Published: April 2015

Microbial communities have the potential to control the biogeochemical fate of some radionuclides in contaminated land scenarios or in the vicinity of a geological repository for radioactive waste. However, there have been few studies of ionizing radiation effects on microbial communities in sediment systems. Here, acetate and lactate amended sediment microcosms irradiated with gamma radiation at 0.5 or 30 Gy h
−1
for 8 weeks all displayed NO
3
−
and Fe(III) reduction, although the rate of Fe(III) reduction was decreased in 30-Gy h
−1
treatments. These systems were dominated by fermentation processes. Pyrosequencing indicated that the 30-Gy h
−1
treatment resulted in a community dominated by two Clostridial species. In systems containing no added electron donor, irradiation at either dose rate did not restrict NO
3
−
, Fe(III), or SO
4
2−
reduction. Rather, Fe(III) reduction was stimulated in the 0.5-Gy h
−1
-treated systems. In irradiated systems, there was a relative increase in the proportion of bacteria capable of Fe(III) reduction, with
Geothrix fermentans
and
Geobacter
sp. identified in the 0.5-Gy h
−1
and 30-Gy h
−1
treatments, respectively. These results indicate that biogeochemical processes will likely not be restricted by dose rates in such environments, and electron accepting processes may even be stimulated by radiation.
Two-Component-System Histidine Kinases Involved in Growth of Listeria monocytogenes EGD-e at Low Temperatures
Authors: Pöntinen Anna , Markkula Annukka , Lindström Miia , Korkeala Hannu
Published: April 2015

Two-component systems (TCSs) aid bacteria in adapting to a wide variety of stress conditions. While the role of TCS response regulators in the cold tolerance of the psychrotrophic foodborne pathogen
Listeria monocytogenes
has been demonstrated previously, no comprehensive studies showing the role of TCS histidine kinases of
L. monocytogenes
at low temperature have been performed. We compared the expression levels of each histidine kinase-encoding gene of
L. monocytogenes
EGD-e in logarithmic growth phase at 3°C and 37°C, as well as the expression levels 30 min, 3 h, and 7 h after cold shock at 5°C and preceding cold shock (at 37°C). We constructed a deletion mutation in each TCS histidine kinase gene, monitored the growth of the EGD-e wild-type and mutant strains at 3°C and 37°C, and measured the minimum growth temperature of each strain. Two genes,
yycG
and
lisK
, proved significant in regard to induced relative expression levels under cold conditions and cold-sensitive mutant phenotypes. Moreover, the Δ
resE
mutant showed a lower growth rate than that of wild-type EGD-e at 3°C. Eleven other genes showed upregulated gene expression but revealed no cold-sensitive phenotypes. The results show that the histidine kinases encoded by
yycG
and
lisK
are important for the growth and adaptation of
L. monocytogenes
EGD-e at low temperature.
Interactions between Human Norovirus Surrogates and Acanthamoeba spp
Authors: Hsueh Tun-Yun , Gibson Kristen E.
Published: April 2015

Human noroviruses (HuNoVs) are the most common cause of food-borne disease outbreaks, as well as virus-related waterborne disease outbreaks in the United States. Here, we hypothesize that common free-living amoebae (FLA)—ubiquitous in the environment, known to interact with pathogens, and frequently isolated from water and fresh produce—could potentially act as reservoirs of HuNoV and facilitate the environmental transmission of HuNoVs. To investigate FLA as reservoirs for HuNoV, the interactions between two
Acanthamoeba
species,
A. castellanii
and
A. polyphaga
, as well as two HuNoV surrogates, murine norovirus type 1 (MNV-1) and feline calicivirus (FCV), were evaluated. The results showed that after 1 h of amoeba-virus incubation at 25°C, 490 and 337 PFU of MNV-1/ml were recovered from
A. castellanii
and
A. polyphaga
, respectively, while only few or no FCVs were detected. In addition, prolonged interaction of MNV-1 with amoebae was investigated for a period of 8 days, and MNV-1 was demonstrated to remain stable at around 200 PFU/ml from day 2 to day 8 after virus inoculation in
A. castellanii
. Moreover, after a complete amoeba life cycle (i.e., encystment and excystment), infectious viruses could still be detected. To determine the location of virus associated with amoebae, immunofluorescence experiments were performed and showed MNV-1 transitioning from the amoeba surface to inside the amoeba over a 24-h period. These results are significant to the understanding of how HuNoVs may interact with other microorganisms in the environment in order to aid in its persistence and survival, as well as potential transmission in water and to vulnerable food products such as fresh produce.
σ
54
-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111
Authors: Lardi Martina , Aguilar Claudio , Pedrioli Alessandro , Omasits Ulrich , Suppiger Angela , Cárcamo-Oyarce Gerardo , Schmid Nadine , Ahrens Christian H. , Eberl Leo , Pessi Gabriella
Published: April 2015

Members of the genus
Burkholderia
are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen
Burkholderia cenocepacia
H111 to nitrogen limitation at the transcript and protein expression levels. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins, and the two-component regulatory system NtrBC,
B. cenocepacia
H111 also upregulated polyhydroxybutyrate (PHB) accumulation and exopolysaccharide (EPS) production in response to nitrogen shortage. A search for consensus sequences in promoter regions of nitrogen-responsive genes identified a σ
54
consensus sequence. The mapping of the σ
54
regulon as well as the characterization of a σ
54
mutant suggests an important role of σ
54
not only in control of nitrogen metabolism but also in the virulence of this organism.
Enhancing the Detection of Giardia duodenalis Cysts in Foods by Inertial Microfluidic Separation
Authors: Ganz Kyle R. , Clime Liviu , Farber Jeffrey M. , Corneau Nathalie , Veres Teodor , Dixon Brent R.
Published: April 2015

The sensitivity and specificity of current
Giardia
cyst detection methods for foods are largely determined by the effectiveness of the elution, separation, and concentration methods used. The aim of these methods is to produce a final suspension with an adequate concentration of
Giardia
cysts for detection and a low concentration of interfering food debris. In the present study, a microfluidic device, which makes use of inertial separation, was designed and fabricated for the separation of
Giardia
cysts. A cyclical pumping platform and protocol was developed to concentrate 10-ml suspensions down to less than 1 ml. Tests involving
Giardia duodenalis
cysts and 1.90-μm microbeads in pure suspensions demonstrated the specificity of the microfluidic chip for cysts over smaller nonspecific particles. As the suspension cycled through the chip, a large number of beads were removed (70%) and the majority of the cysts were concentrated (82%). Subsequently, the microfluidic inertial separation chip was integrated into a method for the detection of
G. duodenalis
cysts from lettuce samples. The method greatly reduced the concentration of background debris in the final suspensions (10-fold reduction) in comparison to that obtained by a conventional method. The method also recovered an average of 68.4% of cysts from 25-g lettuce samples and had a limit of detection (LOD) of 38 cysts. While the recovery of cysts by inertial separation was slightly lower, and the LOD slightly higher, than with the conventional method, the sample analysis time was greatly reduced, as there were far fewer background food particles interfering with the detection of cysts by immunofluorescence microscopy.
Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types
Authors: Reavy Brian , Swanson Maud M. , Cock Peter J. A. , Dawson Lorna , Freitag Thomas E. , Singh Brajesh K. , Torrance Lesley , Mushegian Arcady R. , Taliansky Michael
Published: April 2015

The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family
Microviridae
(icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of
Microviridae
major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily
Gokushovirinae
, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family
Circoviridae
in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the
Circoviridae
showed that they are a novel clade of
Circoviridae
-related CRESS-DNA viruses distinct from known
Circoviridae
genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors.
Evaluation of Lactococcus lactis Isolates from Nondairy Sources with Potential Dairy Applications Reveals Extensive Phenotype-Genotype Disparity and Implications for a Revised Species
Authors: Cavanagh Daniel , Casey Aidan , Altermann Eric , Cotter Paul D. , Fitzgerald Gerald F. , McAuliffe Olivia
Published: April 2015

Lactococcus lactis
is predominantly associated with dairy fermentations, but evidence suggests that the domesticated organism originated from a plant niche.
L. lactis
possesses an unusual taxonomic structure whereby strain phenotypes and genotypes often do not correlate, which in turn has led to confusion in
L. lactis
classification. A bank of
L. lactis
strains was isolated from various nondairy niches (grass, vegetables, and bovine rumen) and was further characterized on the basis of key technological traits, including growth in milk and key enzyme activities. Phenotypic analysis revealed all strains from nondairy sources to possess an
L. lactis
subsp.
lactis
phenotype (
lactis
phenotype); however, seven of these strains possessed an
L. lactis
subsp.
cremoris
genotype (
cremoris
genotype), determined by two separate PCR assays. Multilocus sequence typing (MLST) showed that strains with
lactis
and
cremoris
genotypes clustered together regardless of habitat, but it highlighted the increased diversity that exists among “wild” strains. Calculation of average nucleotide identity (ANI) and tetranucleotide frequency correlation coefficients (TETRA), using the JSpecies software tool, revealed that
L. lactis
subsp.
cremoris
and
L. lactis
subsp.
lactis
differ in ANI values by ∼14%, below the threshold set for species circumscription. Further analysis of strain TIFN3 and strains from nonindustrial backgrounds revealed TETRA values of <0.99 in addition to ANI values of <95%, implicating that these two groups are separate species. These findings suggest the requirement for a revision of
L. lactis
taxonomy.
Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress
Authors: Jenkins Claire , Dallman Timothy J. , Launders Naomi , Willis Caroline , Byrne Lisa , Jorgensen Frieda , Eppinger Mark , Adak Goutam K. , Aird Heather , Elviss Nicola , Grant Kathie A. , Morgan Dilys , McLauchlin Jim
Published: April 2015

An increase in the number of cases of Shiga toxin-producing
Escherichia coli
(STEC) O157 phage type 2 (PT2) in England in September 2013 was epidemiologically linked to watercress consumption. Whole-genome sequencing (WGS) identified a phylogenetically related cluster of 22 cases (outbreak 1). The isolates comprising this cluster were not closely related to any other United Kingdom strain in the Public Health England WGS database, suggesting a possible imported source. A second outbreak of STEC O157 PT2 (outbreak 2) was identified epidemiologically following the detection of outbreak 1. Isolates associated with outbreak 2 were phylogenetically distinct from those in outbreak 1. Epidemiologically unrelated isolates on the same branch as the outbreak 2 cluster included those from human cases in England with domestically acquired infection and United Kingdom domestic cattle. Environmental sampling using PCR resulted in the isolation of STEC O157 PT2 from irrigation water at one implicated watercress farm, and WGS showed this isolate belonged to the same phylogenetic cluster as outbreak 2 isolates. Cattle were in close proximity to the watercress bed and were potentially the source of the second outbreak. Transfer of STEC from the field to the watercress bed may have occurred through wildlife entering the watercress farm or via runoff water. During this complex outbreak investigation, epidemiological studies, comprehensive testing of environmental samples, and the use of novel molecular methods proved invaluable in demonstrating that two simultaneous outbreaks of STEC O157 PT2 were both linked to the consumption of watercress but were associated with different sources of contamination.
Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water
Authors: Islam M. Shahinoor , Zhang Yanyan , McPhedran Kerry N. , Liu Yang , Gamal El-Din Mohamed
Published: April 2015

The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum
Proteobacteria
was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of
Alpha
- and
Gammaproteobacteria
sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely,
Burkholderiales
,
Pseudomonadales
,
Bdellovibrionales
, and
Sphingomonadales
, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>10
9
gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O
3
/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds.
Eaf1 Links the NuA4 Histone Acetyltransferase Complex to Htz1 Incorporation and Regulation of Purine Biosynthesis
Authors: Cheng Xue , Auger Andréanne , Altaf Mohammed , Drouin Simon , Paquet Eric , Utley Rhea T. , Robert François , Côté Jacques
Published: April 2015

Proper modulation of promoter chromatin architecture is crucial for gene regulation in order to precisely and efficiently orchestrate various cellular activities. Previous studies have identified the stimulatory effect of the histone-modifying complex NuA4 on the incorporation of the histone variant H2A.Z (Htz1) at the
PHO5
promoter (A. Auger, L. Galarneau, M. Altaf, A. Nourani, Y. Doyon, R. T. Utley, D. Cronier, S. Allard, and J. Côté, Mol Cell Biol 28:2257–2270, 2008,
http://dx.doi.org/10.1128/MCB.01755-07
).
In vitro
studies with a reconstituted system also indicated an intriguing cross talk between NuA4 and the H2A.Z-loading complex, SWR-C (M. Altaf, A. Auger, J. Monnet-Saksouk, J. Brodeur, S. Piquet, M. Cramet, N. Bouchard, N. Lacoste, R. T. Utley, L. Gaudreau, J. Côté, J Biol Chem 285:15966–15977, 2010,
http://dx.doi.org/10.1074/jbc.M110.117069
). In this work, we investigated the role of the NuA4 scaffold subunit Eaf1 in global gene expression and genome-wide incorporation of Htz1. We found that loss of Eaf1 affects Htz1 levels mostly at the promoters that are normally highly enriched in the histone variant. Analysis of
eaf1
mutant cells by expression array unveiled a relationship between NuA4 and the gene network implicated in the purine biosynthesis pathway, as
EAF1
deletion cripples induction of several
ADE
genes. NuA4 directly interacts with Bas1 activation domain, a key transcription factor of adenine genes. Chromatin immunoprecipitation (ChIP) experiments demonstrate that nucleosomes on the inactive
ADE17
promoter are acetylated already by NuA4 and enriched in Htz1. Upon derepression, these poised nucleosomes respond rapidly to activate
ADE
gene expression in a mechanism likely reminiscent of the
PHO5
promoter, leading to nucleosome disassembly. These detailed molecular events depict a specific case of cross talk between NuA4-dependent acetylation and incorporation of histone variant Htz1, presetting the chromatin structure over
ADE
promoters for subsequent chromatin remodeling and activated transcription.
Aspergillus nidulans Ambient pH Signaling Does Not Require Endocytosis
Authors: Lucena-Agell Daniel , Galindo Antonio , Arst Herbert N. , Peñalva Miguel A.
Published: April 2015

Aspergillus nidulans
(Pal) ambient pH signaling takes place in cortical structures containing components of the ESCRT pathway, which are hijacked by the alkaline pH-activated, ubiquitin-modified version of the arrestin-like protein PalF and taken to the plasma membrane. There, ESCRTs scaffold the assembly of dedicated Pal proteins acting downstream. The molecular details of this pathway, which results in the two-step proteolytic processing of the transcription factor PacC, have received considerable attention due to the key role that it plays in fungal pathogenicity. While current evidence strongly indicates that the pH signaling role of ESCRT complexes is limited to plasma membrane-associated structures where PacC proteolysis would take place, the localization of the PalB protease, which almost certainly catalyzes the first and only pH-regulated proteolytic step, had not been investigated. In view of ESCRT participation, this formally leaves open the possibility that PalB activation requires endocytic internalization. As endocytosis is essential for hyphal growth, nonlethal endocytic mutations are predicted to cause an incomplete block. We used a SynA internalization assay to measure the extent to which any given mutation prevents endocytosis. We show that none of the tested mutations impairing endocytosis to different degrees, including
slaB1
, conditionally causing a complete block, have any effect on the activation of the pathway. We further show that PalB, like PalA and PalC, localizes to cortical structures in an alkaline pH-dependent manner. Therefore, signaling through the Pal pathway does not involve endocytosis.
Diversification of Paralogous α-Isopropylmalate Synthases by Modulation of Feedback Control and Hetero-Oligomerization in Saccharomyces cerevisiae
Authors: López Geovani , Quezada Héctor , Duhne Mariana , González James , Lezama Mijail , El-Hafidi Mohammed , Colón Maritrini , Martínez de la Escalera Ximena , Flores-Villegas Mirelle Citlali , Scazzocchio Claudio , DeLuna Alexander , González Alicia
Published: April 2015

Production of α-isopropylmalate (α-IPM) is critical for leucine biosynthesis and for the global control of metabolism. The budding yeast
Saccharomyces cerevisiae
has two paralogous genes,
LEU4
and
LEU9
, that encode α-IPM synthase (α-IPMS) isozymes. Little is known about the biochemical differences between these two α-IPMS isoenzymes. Here, we show that the Leu4 homodimer is a leucine-sensitive isoform, while the Leu9 homodimer is resistant to such feedback inhibition. The
leu4
Δ mutant, which expresses only the feedback-resistant Leu9 homodimer, grows slowly with either glucose or ethanol and accumulates elevated pools of leucine; this phenotype is alleviated by the addition of leucine. Transformation of the
leu4
Δ mutant with a centromeric plasmid carrying
LEU4
restored the wild-type phenotype. Bimolecular fluorescent complementation analysis showed that Leu4-Leu9 heterodimeric isozymes are formed
in vivo
. Purification and kinetic analysis showed that the hetero-oligomeric isozyme has a distinct leucine sensitivity behavior. Determination of α-IPMS activity in ethanol-grown cultures showed that α-IPM biosynthesis and growth under these respiratory conditions depend on the feedback-sensitive Leu4 homodimer. We conclude that retention and further diversification of two yeast α-IPMSs have resulted in a specific regulatory system that controls the leucine–α-IPM biosynthetic pathway by selective feedback sensitivity of homomeric and heterodimeric isoforms.
Cryptococcus Strains with Different Pathogenic Potentials Have Diverse Protein Secretomes
Authors: Campbell Leona T. , Simonin Anna R. , Chen Cuilan , Ferdous Jannatul , Padula Matthew P. , Harry Elizabeth , Hofer Markus , Campbell Iain L. , Carter Dee A.
Published: April 2015

Secreted proteins are the frontline between the host and pathogen. In mammalian hosts, secreted proteins enable invasive infection and can modulate the host immune response. Cryptococcosis, caused by pathogenic
Cryptococcus
species, begins when inhaled infectious propagules establish to produce pulmonary infection, which, if not resolved, can disseminate to the central nervous system to cause meningoencephalitis. Strains of
Cryptococcus
species differ in their capacity to cause disease, and the mechanisms underlying this are not well understood. To investigate the role of secreted proteins in disease, we determined the secretome for three genome strains of
Cryptococcus
species, including a hypovirulent and a hypervirulent strain of
C. gattii
and a virulent strain of
C. neoformans
. Sixty-seven unique proteins were identified, with different numbers and types of proteins secreted by each strain. The secretomes of the virulent strains were largely limited to proteolytic and hydrolytic enzymes, while the hypovirulent strain had a diverse secretome, including non-conventionally secreted canonical cytosolic and immunogenic proteins that have been implicated in virulence. The hypovirulent strain cannot establish pulmonary infection in a mouse model, but strains of this genotype have caused human meningitis. To directly test brain infection, we used intracranial inoculation and found that the hypovirulent strain was substantially more invasive than its hypervirulent counterpart. We suggest that immunogenic proteins secreted by this strain invoke a host response that limits pulmonary infection but that there can be invasive growth and damage if infection reaches the brain. Given their known role in virulence, it is possible that non-conventionally secreted proteins mediate this process.
Draft Genome Sequence of Bioactive-Compound-Producing Cyanobacterium Tolypothrix campylonemoides Strain VB511288
Authors: Das Subhadeep , Singh Deeksha , Madduluri Madhavi , Chandrababunaidu Mathu Malar , Gupta Akash , Adhikary Siba Prasad , Tripathy Sucheta
Published: April 2015

We report here the draft genome sequence of Tolypothrix campylonemoides VB511288, isolated from building facades in Santiniketan, India. The members of this genus produce several compounds of commercial importance. The draft assembly is 10,627,177 bases in 135 scaffolds, and it contains 7,886 protein-coding genes, 994 pseudogenes, 18 rRNA genes, and 76 tRNA genes.
Genome Sequence of Magnetospirillum magnetotacticum Strain MS-1
Authors: Smalley Matthew D. , Marinov Georgi K. , Bertani L. Elizabeth , DeSalvo Gilberto
Published: April 2015

Here, we report the genome sequence of
Magnetospirillum magnetotacticum
strain MS-1, which consists of of 36 contigs and 4,136 protein-coding genes.
Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment
Authors: Pereira Jamile Queiroz , Ambrosini Adriana , Sant’Anna Fernando Hayashi , Tadra-Sfeir Michele , Faoro Helisson , Pedrosa Fábio Oliveira , Souza Emanuel Maltempi , Brandelli Adriano , Passaglia Luciane M. P.
Published: April 2015

Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments.
Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields
Authors: de Souza Rocheli , Sant’Anna Fernando Hayashi , Ambrosini Adriana , Tadra-Sfeir Michele , Faoro Helisson , Pedrosa Fabio Oliveira , Souza Emanuel Maltempi , Passaglia Luciane M. P.
Published: April 2015

Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences.
Transcriptional Analysis of the MrpJ Network: Modulation of Diverse Virulence-Associated Genes and Direct Regulation of
mrp
Fimbrial and
flhDC
Flagellar Operons in Proteus mirabilis
Authors: Bode Nadine J. , Debnath Irina , Kuan Lisa , Schulfer Anjelique , Ty Maureen , Pearson Melanie M.
Published: April 2015

The enteric bacterium
Proteus mirabilis
is associated with a significant number of catheter-associated urinary tract infections (UTIs). Strict regulation of the antagonistic processes of adhesion and motility, mediated by fimbriae and flagella, respectively, is essential for disease progression. Previously, the transcriptional regulator MrpJ, which is encoded by the
mrp
fimbrial operon, has been shown to repress both swimming and swarming motility. Here we show that MrpJ affects an array of cellular processes beyond adherence and motility. Microarray analysis found that expression of
mrpJ
mimicking levels observed during UTIs leads to differential expression of 217 genes related to, among other functions, bacterial virulence, type VI secretion, and metabolism. We probed the molecular mechanism of transcriptional regulation by MrpJ using transcriptional reporters and chromatin immunoprecipitation (ChIP). Binding of MrpJ to two virulence-associated target gene promoters, the promoters of the flagellar master regulator
flhDC
and
mrp
itself, appears to be affected by the condensation state of the native chromosome, although both targets share a direct MrpJ binding site proximal to the transcriptional start. Furthermore, an
mrpJ
deletion mutant colonized the bladders of mice at significantly lower levels in a transurethral model of infection. Additionally, we observed that
mrpJ
is widely conserved in a collection of recent clinical isolates. Altogether, these findings support a role of MrpJ as a global regulator of
P. mirabilis
virulence.
Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii
Authors: Gallagher Larry A. , Ramage Elizabeth , Weiss Eli J. , Radey Matthew , Hayden Hillary S. , Held Kiara G. , Huse Holly K. , Zurawski Daniel V. , Brittnacher Mitchell J. , Manoil Colin
Published: April 2015

Acinetobacter baumannii
is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources for
A. baumannii
strain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that make
A. baumannii
a formidable public health threat.

IMPORTANCE
Acinetobacter baumannii
is one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate of
A. baumannii
that is highly virulent and representative of current outbreak strains.
Biosynthesis of the Common Polysaccharide Antigen of Pseudomonas aeruginosa PAO1: Characterization and Role of GDP-
d
-Rhamnose:GlcNAc/GalNAc-Diphosphate-Lipid α1,3-
d
-Rhamnosyltransferase WbpZ
Authors: Wang Shuo , Hao Youai , Lam Joseph S. , Vlahakis Jason Z. , Szarek Walter A. , Vinnikova Anna , Veselovsky Vladimir V. , Brockhausen Inka
Published: April 2015

The opportunistic pathogen
Pseudomonas aeruginosa
produces two major cell surface lipopolysaccharides, characterized by distinct O antigens, called common polysaccharide antigen (CPA) and O-specific antigen (OSA). CPA contains a polymer of
d
-rhamnose (
d
-Rha) in α1-2 and α1-3 linkages. Three putative glycosyltransferase genes,
wbpX
,
wbpY
, and
wbpZ
, are part of the CPA biosynthesis cluster. To characterize the enzymatic function of the
wbpZ
gene product, we chemically synthesized the donor substrate GDP-
d
-Rha and enzymatically synthesized GDP-
d
-[
3
H]Rha. Using nuclear magnetic resonance (NMR) spectroscopy, we showed that WbpZ transferred one
d
-Rha residue from GDP-
d
-Rha in α1-3 linkage to both GlcNAc- and GalNAc-diphosphate-lipid acceptor substrates. WbpZ is also capable of transferring
d
-mannose (
d
-Man) to these acceptors. Therefore, WbpZ has a relaxed specificity with respect to both acceptor and donor substrates. The diphosphate group of the acceptor, however, is required for activity. WbpZ does not require divalent metal ion for activity and exhibits an unusually high pH optimum of 9. WbpZ from PAO1 is therefore a GDP-
d
-Rha:GlcNAc/GalNAc-diphosphate-lipid α1,3-
d
-rhamnosyltransferase that has significant activity of GDP-
d
-Man:GlcNAc/GalNAc-diphosphate-lipid α1,3-
d
-mannosyltransferase. We used site-directed mutagenesis to replace the Asp residues of the two DXD motifs with Ala. Neither of the mutant constructs of
wbpZ
(D172A or D254A) could be used to rescue CPA biosynthesis in the Δ
wbpZ
knockout mutant in a complementation assay. This suggested that D172 and D254 are essential for WbpZ function. This work is the first detailed characterization study of a
d
-Rha-transferase and a critical step in the development of CPA synthesis inhibitors.

IMPORTANCE
This is the first characterization of a
d
-rhamnosyltransferase and shows that it is essential in
Pseudomonas aeruginosa
for the synthesis of the common polysaccharide antigen.
BAREFOOT AND SHOD CONDITIONS: HOW TO RECONCILE THEM FOR PLANTAR PRESSURE ANALYSIS IN THE OXFORD FOOT MODEL
Authors: JAITMAN A. D. , EVANS N. D. , CHAPPELL M. J.
Published: April 2015

The foot plays an important role as it is the only connection that the human body has with the floor when walking, running, etc. The two main techniques commonly used to study the lower limb in biomechanics are gait analysis and plantar pressure measurements. However, they require different settings: One requires barefoot experimentation and the other requires the subject to be shod. The method proposed in this paper attempts to solve this problem by designing shoes that can mimic both conditions. This allows the analysis of both approaches simultaneously and therefore provides valuable inputs for the development of a well validated model of the foot.
DIFFUSION MRI-BASED FIBER TRACKING IN HEALTHY AND BRAIN INJURY PATIENTS: A COMPARISON OF DIFFERENT SOFTWARE TOOLS
Authors: LUCCONI GIULIA , ROMEO CHIARA , BONETTI ROBERTO , CENNI PATRIZIA , SCRITTORI NICOLETTA
Published: April 2015

In this work, we compared different DTI-based fibertracking software using deterministic and probabilistic approaches. DTI brain images of 35 healthy and five brain-injury patients were acquired with Philips Achieva 1.5 T scanner using an EPI-SE DTI sequence with 16 diffusion directions. Images were analyzed with Philips FiberTrack module, DTI-Studio and FSL. We studied corticospinal tract and corpus callosum, considering different termination criteria for the fibertracking algorithm. Group studies were performed to create a database of healthy patients. Results of FSL fibertracking with 1 or 2 fibers per voxel were no statistically different. T-tests between Philips and DTI-Studio led to p-values > 0.01 for corticospinal tract and < 0.01 for corpus callosum. FSL analysis led to higher ADC and lower FA values, with significative differences with the other software. In brain injury patients we measured different fibers orientation, reduced FA and increased ADC around the lesion. In conclusion, although DTI fibertracking is a promising non-invasive preoperative imaging tool, the outcome is strongly influenced by the algorithm used and the parameters chosen for the seed generation and fiber propagation.
Heat Transfer and Pressure Drop Characteristics of Plain Fin-and-Tube Heat Exchangers Having 5.0 mm Tubes Under Dehumidifying Condition
Authors: Kim Nae-Hyun
Published: April 2015

In this study, wet surface pressure drop and heat transfer characteristics of plain finned heat exchangers having 5.0 mm diameter (5.3 mm after tube expansion) tubes were investigated. Nine samples having different fin pitches (1.1 to 1.3 mm) and tube rows (1 to 3 rows) were tested. The fin pitch had a negligible effect on j and f factors. Both j and f factors decreased as the number of tube row increased. When compared the j and f factors of the samples having 5.3 mm diameter tubes with those of 7.3 mm diameter tubes, 5.3 mm samples yielded higher j factors and lower f factors. The j/f ratios of 5.3 mm samples are larger than those of 7.3 mm samples which implies that 5.3 mm geometry is more beneficial than 7.3 mm geometry.
ATP Synthase
Authors: Junge Wolfgang , Nelson Nathan
Published: April 2015

Oxygenic photosynthesis is the principal converter of sunlight into chemical energy. Cyanobacteria and plants provide aerobic life with oxygen, food, fuel, fibers, and platform chemicals. Four multisubunit membrane proteins are involved: photosystem I (PSI), photosystem II (PSII), cytochrome b6f (cyt b6f), and ATP synthase (FOF1). ATP synthase is likewise a key enzyme of cell respiration. Over three billion years, the basic machinery of oxygenic photosynthesis and respiration has been perfected to minimize wasteful reactions. The proton-driven ATP synthase is embedded in a proton tight-coupling membrane. It is composed of two rotary motors/generators, FOand F1, which do not slip against each other. The proton-driven FOand the ATP-synthesizing F1are coupled via elastic torque transmission. Elastic transmission decouples the two motors in kinetic detail but keeps them perfectly coupled in thermodynamic equilibrium and (time-averaged) under steady turnover. Elastic transmission enables operation with different gear ratios in different organisms.
Magic Angle Spinning NMR of Proteins: High-Frequency Dynamic Nuclear Polarization and 1H Detection
Authors: Su Yongchao , Andreas Loren , Griffin Robert G.
Published: April 2015

Magic angle spinning (MAS) NMR studies of amyloid and membrane proteins and large macromolecular complexes are an important new approach to structural biology. However, the applicability of these experiments, which are based on 13C- and 15N-detected spectra, would be enhanced if the sensitivity were improved. Here we discuss two advances that address this problem: high-frequency dynamic nuclear polarization (DNP) and 1H-detected MAS techniques. DNP is a sensitivity enhancement technique that transfers the high polarization of exogenous unpaired electrons to nuclear spins via microwave irradiation of electron–nuclear transitions. DNP boosts NMR signal intensities by factors of 102 to 103, thereby overcoming NMR's inherent low sensitivity. Alternatively, it permits structural investigations at the nanomolar scale. In addition, 1H detection is feasible primarily because of the development of MAS rotors that spin at frequencies of 40 to 60 kHz or higher and the preparation of extensively 2H-labeled proteins.
Neurodegenerative Diseases: Expanding the Prion Concept
Authors: Walker Lary C. , Jucker Mathias
Published: April 2015

The prion paradigm has emerged as a unifying molecular principle for the pathogenesis of many age-related neurodegenerative diseases. This paradigm holds that a fundamental cause of specific disorders is the misfolding and seeded aggregation of certain proteins. The concept arose from the discovery that devastating brain diseases called spongiform encephalopathies are transmissible to new hosts by agents consisting solely of a misfolded protein, now known as the prion protein. Accordingly, “prion” was defined as a “proteinaceous infectious particle.” As the concept has expanded to include other diseases, many of which are not infectious by any conventional definition, the designation of prions as infectious agents has become problematic. We propose to define prions as “proteinaceous nucleating particles” to highlight the molecular action of the agents, lessen unwarranted apprehension about the transmissibility of noninfectious proteopathies, and promote the wider acceptance of this revolutionary paradigm by the biomedical community.
Neurological Aspects of Human Glycosylation Disorders
Authors: Freeze Hudson H. , Eklund Erik A. , Ng Bobby G. , Patterson Marc C.
Published: April 2015

This review presents principles of glycosylation, describes the relevant glycosylation pathways and their related disorders, and highlights some of the neurological aspects and issues that continue to challenge researchers. More than 100 rare human genetic disorders that result from deficiencies in the different glycosylation pathways are known today. Most of these disorders impact the central and/or peripheral nervous systems. Patients typically have developmental delays/intellectual disabilities, hypotonia, seizures, neuropathy, and metabolic abnormalities in multiple organ systems. Among these disorders there is great clinical diversity because all cell types differentially glycosylate proteins and lipids. The patients have hundreds of misglycosylated products, which afflict a myriad of processes, including cell signaling, cell-cell interaction, and cell migration. This vast complexity in glycan composition and function, along with the limited availability of analytic tools, has impeded the identification of key glycosylated molecules that cause pathologies. To date, few critical target proteins have been pinpointed.
Visual Guidance in Control of Grasping
Authors: Janssen Peter , Scherberger Hansjörg
Published: April 2015

Humans and other primates possess a unique capacity to grasp and manipulate objects skillfully, a facility pervasive in everyday life that has undoubtedly contributed to the success of our species. When we reach and grasp an object, various cortical areas in the parietal and frontal lobes work together effortlessly to analyze object shape and position, transform this visual information into useful motor commands, and implement these motor representations to preshape the hand before contact with the object is made. In recent years, a growing number of studies have investigated the neural circuits underlying object grasping in both the visual and motor systems of the macaque monkey. The accumulated knowledge not only helps researchers understand how object grasping is implemented in the primate brain but may also contribute to the development of novel neural interfaces and neuroprosthetics.
The Genetics of Neuropsychiatric Diseases: Looking In and Beyond the Exome
Authors: Heinzen Erin L. , Neale Benjamin M. , Traynelis Stephen F. , Allen Andrew S. , Goldstein David B.
Published: April 2015

Next-generation sequencing, which allows genome-wide detection of rare and de novo mutations, is transforming neuropsychiatric disease genetics through identifying on an unprecedented scale genes and protein-coding mutations that confer risk. Although understanding how regulatory variants influence risk remains a challenge, we are likely transitioning into a phase of neuropsychiatric disease genetics in which the rate-limiting step may no longer be gene discovery. Instead, the future will concentrate more on the biological and clinical translation of the torrent of specific risk mutations identified through next-generation sequencing. Here, we review the recent progress that resulted specifically from exome sequencing and emphasize the need for rigorous statistical evaluation of the expanding data sets, as well as expanded functional analysis of implicated proteins and mutations. Then, we introduce some of the expected opportunities and challenges investigators face when moving beyond the exome. Finally, we briefly highlight the challenge of deriving translational benefit from the progress in genetics.
Systems Pharmacology Links GPCRs with Retinal Degenerative Disorders
Authors: Chen Yu , Palczewski Krzysztof
Published: April 2015

In most biological systems, second messengers and their key regulatory and effector proteins form links between multiple cellular signaling pathways. Such signaling nodes can integrate the deleterious effects of genetic aberrations, environmental stressors, or both in complex diseases, leading to cell death by various mechanisms. Here we present a systems (network) pharmacology approach that, together with transcriptomics analyses, was used to identify different G protein–coupled receptors that experimentally protected against cellular stress and death caused by linked signaling mechanisms. We describe the application of this concept to degenerative and diabetic retinopathies in appropriate mouse models as an example. Systems pharmacology also provides an attractive framework for devising strategies to combat complex diseases by using (repurposing) US Food and Drug Administration–approved pharmacological agents.