bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ice‐binding proteins confer freezing tolerance in transgenic Arabidopsis thaliana
Authors: Bredow Melissa , Vanderbeld Barbara , Walker Virginia K. 
Published: June 2016

SummaryLolium perenne is a freeze‐tolerant perennial ryegrass capable of withstanding temperatures below −13 °C. Ice‐binding proteins (IBPs) presumably help prevent damage associated with freezing by restricting the growth of ice crystals in the apoplast. We have investigated the expression, localization and in planta freezing protection capabilities of two L. perenne IBP isoforms, LpIRI2 and LpIRI3, as well as a processed IBP (LpAFP). One of these isoforms, LpIRI2, lacks a conventional signal peptide and was assumed to be a pseudogene. Nevertheless, both LpIRI2 and LpIRI3 transcripts were up‐regulated following cold acclimation. LpIRI2 also demonstrated ice‐binding activity when produced recombinantly in Escherichia coli. Both the LpIRI3 and LpIRI2 isoforms appeared to accumulate in the apoplast of transgenic Arabidopsis thaliana plants. In contrast, the fully processed isoform, LpAFP, remained intracellular. Transgenic plants expressing either LpIRI2 or LpIRI3 showed reduced ion leakage (12%–39%) after low‐temperature treatments, and significantly improved freezing survival, while transgenic LpAFP‐expressing lines did not confer substantial subzero protection. Freeze protection was further enhanced by with the introduction of more than one IBP isoform; ion leakage was reduced 26%–35% and 10% of plants survived temperatures as low as −8 °C. Our results demonstrate that apoplastic expression of multiple L. perenne IBP isoforms shows promise for providing protection to crops susceptible to freeze‐induced damage.
Variation in pathotypes and virulence of Plasmodiophora brassicae populations in Germany
Authors: Zamani‐Noor N. 
Published: June 2016

Between 2012 and 2015, 49 new clubroot‐infested fields were identified in 12 German federal states. Clubroot disease incidence varied within these fields from 22% to 92%. Field information revealed that in 85% of fields, oilseed rape was grown in rotation once every 2 or 3 years. Frequency of OSR in the rotation was significantly correlated with the incidence and prevalence of clubroot disease. The disease was detected in fields with soil pH ranging from 5.1 to 8.3, and a significant negative correlation was found between soil pH and the disease incidence of infested fields. Furthermore, more cases of disease and severe incidences were observed in sandy loam and loamy sand as compared with other soil types. Pathotype classification of the 49 Plasmodiophora brassicae populations was conducted on two differential sets, the European Clubroot Differential set and the set of Somé (1996). Additionally, the degree of virulence of the collected isolates was analysed on the clubroot‐resistant oilseed rape cv. Mendel. The results showed variation in pathotype distribution in different regions in Germany. The majority of isolates according to Somé were pathotypes 1 and 3, respectively, with pathotypes 2 and 5 in the minority. Detailed classification according to Buczacki showed the dominance of 16/31/31, 16/14/30 and 16/14/31 populations among 20 distinct virulence patterns of collected isolates. From all populations tested for virulence on cv. Mendel, 15 isolates were found to be moderately or highly virulent. These virulent populations were not restricted to a small geographical area in the country.
Monitoring fungi in ecological restorations of coastal Indiana, U.S.A.
Authors: Avis Peter G. , Gaswick Wyatt C. , Tonkovich Gayle S. , Leacock Patrick R. 
Published: June 2016

AbstractMonitoring of ecological restorations has rarely focused on fungi. In this study, we conduct a first‐ever monitoring of macrofungi in ecological restorations of coastal Indiana (U.S.A.) and present an approach and considerations that can be followed elsewhere. Forty‐two sites were surveyed over a 2‐year period for the presence of saprotrophic, mycorrhizal, and parasitic macrofungi. Sites included those considered to be restoration, prerestoration, or reference and were in wooded, semiwooded, or grassland habitats. With 1,103 observations, 277 species of fungi were identified. Most fungi were found in wooded habitats though some were in grassland restorations. Invasive plant cover negatively impacted fungal species richness. Monitored sites were compared to a set of reference sites using two different similarity indices (overlap and Jaccard), as well as the ratios of different fungal functional guilds, revealing that choice of index can impact how restorations are perceived to match targets. Last, we present a novel, tractable, and conservative way to assess and rank sites by the functional trait guilds of fungi. We show that such an approach can provide important additional information about the success of restorations such that functional guild ratios could be used as an indicator of restoration progress early‐on while functional values are better used in later phases.
Automated Geocoding of Textual Documents: A Survey of Current Approaches
Authors: Melo Fernando , Martins Bruno 
Published: June 2016

AbstractThis survey article describes previous research addressing text‐based document geocoding, i.e. the task of predicting the geospatial coordinates of latitude and longitude, that best correspond to an entire document, based on its textual contents. We describe (1) early document geocoding systems that use heuristics over place names mentioned in the text (e.g. names of cities and states), (2) probabilistic language modeling approaches, where generative models are built for different regions in the world (usually considering a discretization based on a rectangular grid) from the words occurring in a set of georeferenced training documents, which are then used to predict per‐region probabilities for previously unseen test documents, (3) combinations of different models and heuristics, including clustering procedures, feature selection approaches, and/or language models built from different sources, and (4) recent approaches based on discriminative classification models.
Extraocular muscle dysinnervation disorder resembling Duane retraction syndrome in a 9‐month‐old French Bulldog
Authors: Mari Lorenzo , Blacklock Benjamin T. , Stavinohova Renata , De Risio Luisa 
Published: June 2016

AbstractA 9‐month‐old French Bulldog was presented with a chronic history of lateral strabismus and intermittent third eyelid protrusion in the left eye. The neuro‐ophthalmological examination revealed mild ptosis of the left upper eyelid, mild lateral strabismus, and external ophthalmoparesis of the left eye. Retraction and ventral deviation of the left eye globe with protrusion of the third eyelid and elevation of the upper eyelid were elicited on attempted voluntary adduction of the left eye. Hematology, serum biochemistry, serology for infectious diseases, magnetic resonance of the head, and cerebrospinal fluid analysis did not reveal significant abnormalities. Forced duction test did not show signs of mechanical restriction in ocular motility. A suspected congenital cranial dysinnervation disorder resembling Duane retraction syndrome in humans was diagnosed based on the typical clinical signs and exclusion of structural abnormalities. The clinical signs remained stable for 9 months until the time of writing this report.
A tool set to allow rapid screening of dog families with PRA for association with candidate genes
Authors: Winkler Paige A. , Davis Jennifer A. , Petersen‐Jones Simon M. , Venta Patrick J. , Bartoe Joshua T. 
Published: June 2016

AbstractObjectiveTo develop a method to rapidly screen candidate genes for association with recessively inherited progressive retinal atrophy (PRA) in pedigrees of dog in which a causative mutation has not been identified.Animal studiedThirteen PRA‐affected dogs were used in this study.ProceduresTwo microsatellite markers (MS) were designed flanking 45 candidate genes. MS markers were analyzed for heterozygosity and allelic richness. Two dog breeds, in which the causative mutation has been identified (Entlebucher Sennenhunds [ES] and PDE6A‐mutant dogs [PDE6A]), were used to validate the MS marker panel. One breed in which the causative mutation is currently unknown (Old English Sheepdog [OES]) was investigated in this study utilizing the MS panel.ResultsMarker heterozygosity excluded 38 of 45 and 41 of 45 candidate genes (ES and PDE6A, respectively) with each true culprit gene remaining on the list of nonexcluded candidate genes. Additionally, 41 of 45 genes were excluded for OES.ConclusionsThis tool set was used quickly and efficiently to narrow down 45 candidate genes for recessively inherited PRA in two types of dogs with known mutations and one type of dog with an unknown mutation.
Presence and Persistence of Viable, Clinically Relevant Legionella pneumophila Bacteria in Garden Soil in the Netherlands
Authors: van Heijnsbergen E. , van Deursen A. , Bouwknegt M. , Bruin J. P. , de Roda Husman A. M. , Schalk J. A. C. 
Published: June 2016

ABSTRACT

Garden soils were investigated as reservoirs and potential sources of pathogenic
Legionella
bacteria.
Legionella
bacteria were detected in 22 of 177 garden soil samples (12%) by amoebal coculture. Of these 22
Legionella
-positive soil samples, seven contained
Legionella pneumophila
. Several other species were found, including the pathogenic
Legionella longbeachae
(4 gardens) and
Legionella sainthelensi
(9 gardens). The
L. pneumophila
isolates comprised 15 different sequence types (STs), and eight of these STs were previously isolated from patients according to the European Working Group for
Legionella
Infections (EWGLI) database. Six gardens that were found to be positive for
L. pneumophila
were resampled after several months, and in three gardens,
L. pneumophila
was again isolated. One of these gardens was resampled four times throughout the year and was found to be positive for
L. pneumophila
on all occasions.

IMPORTANCE
Tracking the source of infection for sporadic cases of Legionnaires' disease (LD) has proven to be hard.
L. pneumophila
ST47, the sequence type that is most frequently isolated from LD patients in the Netherlands, is rarely found in potential environmental sources. As
L. pneumophila
ST47 was previously isolated from a garden soil sample during an outbreak investigation, garden soils were investigated as reservoirs and potential sources of pathogenic
Legionella
bacteria. The detection of viable, clinically relevant
Legionella
strains indicates that garden soil is a potential source of
Legionella
bacteria, and future research should assess the public health implication of the presence of
L. pneumophila
in garden soil.
Activating Intrinsic Carbohydrate-Active Enzymes of the Smut Fungus Ustilago maydis for the Degradation of Plant Cell Wall Components
Authors: Geiser Elena , Reindl Michèle , Blank Lars M. , Feldbrügge Michael , Wierckx Nick , Schipper Kerstin 
Published: June 2016

ABSTRACT

The microbial conversion of plant biomass to valuable products in a consolidated bioprocess could greatly increase the ecologic and economic impact of a biorefinery. Current strategies for hydrolyzing plant material mostly rely on the external application of carbohydrate-active enzymes (CAZymes). Alternatively, production organisms can be engineered to secrete CAZymes to reduce the reliance on externally added enzymes. Plant-pathogenic fungi have a vast repertoire of hydrolytic enzymes to sustain their lifestyle, but expression of the corresponding genes is usually highly regulated and restricted to the pathogenic phase. Here, we present a new strategy in using the biotrophic smut fungus
Ustilago maydis
for the degradation of plant cell wall components by activating its intrinsic enzyme potential during axenic growth. This fungal model organism is fully equipped with hydrolytic enzymes, and moreover, it naturally produces value-added substances, such as organic acids and biosurfactants. To achieve the deregulated expression of hydrolytic enzymes during the industrially relevant yeast-like growth in axenic culture, the native promoters of the respective genes were replaced by constitutively active synthetic promoters. This led to an enhanced conversion of xylan, cellobiose, and carboxymethyl cellulose to fermentable sugars. Moreover, a combination of strains with activated endoglucanase and β-glucanase increased the release of glucose from carboxymethyl cellulose and regenerated amorphous cellulose, suggesting that mixed cultivations could be a means for degrading more complex substrates in the future. In summary, this proof of principle demonstrates the potential applicability of activating the expression of native CAZymes from phytopathogens in a biocatalytic process.

IMPORTANCE
This study describes basic experiments that aim at the degradation of plant cell wall components by the smut fungus
Ustilago maydis
. As a plant pathogen, this fungus contains a set of lignocellulose-degrading enzymes that may be suited for biomass degradation. However, its hydrolytic enzymes are specifically expressed only during plant infection. Here, we provide the proof of principle that these intrinsic enzymes can be synthetically activated during the industrially relevant yeast-like growth. The fungus is known to naturally synthesize valuable compounds, such as itaconate or glycolipids. Therefore, it could be suited for use in a consolidated bioprocess in which more complex and natural substrates are simultaneously converted to fermentable sugars and to value-added compounds in the future.
Listeria monocytogenes DNA Glycosylase AdlP Affects Flagellar Motility, Biofilm Formation, Virulence, and Stress Responses
Authors: Zhang Ting , Bae Dongryeoul , Wang Chinling 
Published: June 2016

ABSTRACT

The temperature-dependent alteration of flagellar motility gene expression is critical for the foodborne pathogen
Listeria monocytogenes
to respond to a changing environment. In this study, a genetic determinant,
L. monocytogenes
f2365_0220
(
lmof2365_0220
), encoding a putative protein that is structurally similar to the
Bacillus cereus
alkyl base DNA glycosylase (AlkD), was identified. This determinant was involved in the transcriptional repression of flagellar motility genes and was named
adlP
(encoding an
A
lk
D
-
l
ike
p
rotein [AdlP]). Deletion of
adlP
activated the expression of flagellar motility genes at 37°C and disrupted the temperature-dependent inhibition of
L. monocytogenes
motility. The
adlP
null strains demonstrated decreased survival in murine macrophage-like RAW264.7 cells and less virulence in mice. Furthermore, the deletion of
adlP
significantly decreased biofilm formation and impaired the survival of bacteria under several stress conditions, including the presence of a DNA alkylation compound (methyl methanesulfonate), an oxidative agent (H
2
O
2
), and aminoglycoside antibiotics. Our findings strongly suggest that
adlP
may encode a bifunctional protein that transcriptionally represses the expression of flagellar motility genes and influences stress responses through its DNA glycosylase activity.

IMPORTANCE
We discovered a novel protein that we named
A
lk
D
-
l
ike
p
rotein (AdlP). This protein affected flagellar motility, biofilm formation, and virulence. Our data suggest that AdlP may be a bifunctional protein that represses flagellar motility genes and influences stress responses through its DNA glycosylase activity.
Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers
Authors: Perez Maëva , Juniper S. Kim 
Published: June 2016

ABSTRACT

The symbiotic relationship between vestimentiferan tubeworms and their intracellular chemosynthetic bacteria is one of the more noteworthy examples of adaptation to deep-sea hydrothermal vent environments. The tubeworm symbionts have never been cultured in the laboratory. Nucleotide sequences from the small subunit rRNA gene suggest that the intracellular symbionts of the eastern Pacific vent tubeworms
Oasisia alvinae
,
Riftia pachyptila
,
Tevnia jerichonana
, and
Ridgeia piscesae
belong to the same phylotype of gammaproteobacteria, “
Candidatus
Endoriftia persephone.” Comparisons of symbiont genomes between the East Pacific Rise tubeworms
R. pachyptila
and
T. jerichonana
confirmed that these two hosts share the same symbionts. Two
Ridgeia
symbiont genomes were assembled from trophosome metagenomes from worms collected from the Juan de Fuca Ridge (one and five individuals, respectively). We compared these assemblies to those of the sequenced
Riftia
and
Tevnia
symbionts. Pangenome composition, genome-wide comparisons of the nucleotide sequences, and pairwise comparisons of 2,313 orthologous genes indicated that “
Ca
. Endoriftia persephone” symbionts are structured on large geographical scales but also on smaller scales and possibly through host specificity.

IMPORTANCE
Remarkably, the intracellular symbionts of four to six species of eastern Pacific vent tubeworms all belong to the same phylotype of gammaproteobacteria, “
Candidatus
Endoriftia persephone.” Understanding the structure, dynamism, and interconnectivity of “
Ca
. Endoriftia persephone” populations is important to advancing our knowledge of the ecology and evolution of their host worms, which are often keystone species in vent communities. In this paper, we present the first genomes for symbionts associated with the species
R. piscesae
, from the Juan de Fuca Ridge. We then combine these genomes with published symbiont genomes from the East Pacific Rise tubeworms
R. pachyptila
and
T. jerichonana
to develop a portrait of the “
Ca
. Endoriftia persephone” pangenome and an initial outline of symbiont population structure in the different host species. Our study is the first to apply genome-wide comparisons of “
Ca
. Endoriftia persephone” assemblies in the context of population genetics and molecular evolution.
Effects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate on Nitrification and Nitrifiers in Two Contrasting Agricultural Soils
Authors: Shi Xiuzhen , Hu Hang-Wei , Müller Christoph , He Ji-Zheng , Chen Deli , Suter Helen Charlotte 
Published: June 2016

ABSTRACT

The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is a powerful tool that can be used to promote nitrogen (N) use efficiency and reduce N losses from agricultural systems by slowing nitrification. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in nitrification and N
2
O production; however, their responses to DMPP amendment and the microbial mechanisms underlying the variable efficiencies of DMPP across different soils remain largely unknown. Here we compared the impacts of DMPP on nitrification and the dynamics of ammonia oxidizers between an acidic pasture soil and an alkaline vegetable soil using a
15
N tracing and
13
CO
2
-DNA–stable-isotope probing (SIP) technique. The results showed that DMPP significantly inhibited nitrification and N
2
O production in the vegetable soil only, and the transient inhibition was coupled with a significant decrease in AOB abundance. No significant effects on the community structure of ammonia oxidizers or the abundances of total bacteria and denitrifiers were observed in either soil. The
15
N tracing experiment revealed that autotrophic nitrification was the predominant form of nitrification in both soils. The
13
CO
2
-DNA–SIP results indicated the involvement of AOB in active nitrification in both soils, but DMPP inhibited the assimilation of
13
CO
2
into AOB only in the vegetable soil. Our findings provide evidence that DMPP could effectively inhibit nitrification through impeding the abundance and metabolic activity of AOB in the alkaline vegetable soil but not in the acidic pasture soil, possibly due to the low AOB abundance or the adsorption of DMPP by organic matter.

IMPORTANCE
The combination of the
15
N tracing model and
13
CO
2
-DNA–SIP technique provides important evidence that the nitrification inhibitor DMPP could effectively inhibit nitrification and nitrous oxide emission in an alkaline soil through influencing the abundance and metabolic activity of AOB. In contrast, DMPP amendment has no significant effect on nitrification or nitrifiers in an acidic soil, potentially owing to the low abundance of AOB and the possible adsorption of DMPP by organic matter. Our findings have direct implications for improved agricultural practices through utilizing the nitrification inhibitor DMPP in appropriate situations, and they emphasize the importance of microbial communities to the efficacy of DMPP.
The
blp
Locus of Streptococcus pneumoniae Plays a Limited Role in the Selection of Strains That Can Cocolonize the Human Nasopharynx
Authors: Valente Carina , Dawid Suzanne , Pinto Francisco R. , Hinds Jason , Simões Alexandra S. , Gould Katherine A. , Mendes Luís A. , de Lencastre Hermínia , Sá-Leão Raquel 
Published: June 2016

ABSTRACT

Nasopharyngeal colonization is important for
Streptococcus pneumoniae
evolution, providing the opportunity for horizontal gene transfer when multiple strains co-occur. Although colonization with more than one strain of pneumococcus is common, the factors that influence the ability of strains to coexist are not known. A highly variable
blp
(bacteriocin-like peptide) locus has been identified in all sequenced strains of
S. pneumoniae
. This locus controls the regulation and secretion of bacteriocins, small peptides that target other bacteria. In this study, we analyzed a series of cocolonizing isolates to evaluate the impact of the
blp
locus on human colonization to determine whether competitive phenotypes of bacteriocin secretion restrict cocolonization. We identified a collection of 135 nasopharyngeal samples cocolonized with two or more strains, totaling 285 isolates. The
blp
locus of all strains was characterized genetically with regard to pheromone type, bacteriocin/immunity content, and potential for locus functionality. Inhibitory phenotypes of bacteriocin secretion and locus activity were assessed through overlay assays. Isolates from single colonizations (
n
= 298) were characterized for comparison. Cocolonizing strains had a high diversity of
blp
cassettes; approximately one-third displayed an inhibitory phenotype
in vitro
. Despite
in vitro
evidence of competition, pneumococci cocolonized the subjects independently of
blp
pheromone type (
P
= 0.577), bacteriocin/immunity content,
blp
locus activity (
P
= 0.798), and inhibitory phenotype (
P
= 0.716). In addition, no significant differences were observed when single and cocolonizing strains were compared. Despite clear evidence of
blp
-mediated competition in experimental models, the results of our study suggest that the
blp
locus plays a limited role in restricting pneumococcal cocolonization in humans.

IMPORTANCE
Nasopharyngeal colonization with
Streptococcus pneumoniae
(pneumococcus) is important for pneumococcal evolution, as the nasopharynx represents the major site for horizontal gene transfer when multiple strains co-occur, a phenomenon known as cocolonization. Understanding how pneumococcal strains interact within the competitive environment of the nasopharynx is of chief importance in the context of pneumococcal ecology. In this study, we used an unbiased collection of naturally co-occurring pneumococcal strains and showed that a biological process frequently used by bacteria for competition—bacteriocin production—is not decisive in the coexistence of pneumococci in the host, in contrast to what has been shown in experimental models.