bluuebunny/crossref_metadata_2025_split huggingface dataset:
Obatoclax Inhibits Alphavirus Membrane Fusion by Neutralizing the Acidic Environment of Endocytic Compartments
Authors: Varghese Finny S. , Rausalu Kai , Hakanen Marika , Saul Sirle , Kümmerer Beate M. , Susi Petri , Merits Andres , Ahola Tero 
Published: December 2016

ABSTRACT

As new pathogenic viruses continue to emerge, it is paramount to have intervention strategies that target a common denominator in these pathogens. The fusion of viral and cellular membranes during viral entry is one such process that is used by many pathogenic viruses, including chikungunya virus, West Nile virus, and influenza virus. Obatoclax, a small-molecule antagonist of the Bcl-2 family of proteins, was previously determined to have activity against influenza A virus and also Sindbis virus. Here, we report it to be active against alphaviruses, like chikungunya virus (50% effective concentration [EC
50
] = 0.03 μM) and Semliki Forest virus (SFV; EC
50
= 0.11 μM). Obatoclax inhibited viral entry processes in an SFV temperature-sensitive mutant entry assay. A neutral red retention assay revealed that obatoclax induces the rapid neutralization of the acidic environment of endolysosomal vesicles and thereby most likely inhibits viral fusion. Characterization of escape mutants revealed that the L369I mutation in the SFV E1 fusion protein was sufficient to confer partial resistance against obatoclax. Other inhibitors that target the Bcl-2 family of antiapoptotic proteins inhibited neither viral entry nor endolysosomal acidification, suggesting that the antiviral mechanism of obatoclax does not depend on its anticancer targets. Obatoclax inhibited the growth of flaviviruses, like Zika virus, West Nile virus, and yellow fever virus, which require low pH for fusion, but not that of pH-independent picornaviruses, like coxsackievirus A9, echovirus 6, and echovirus 7. In conclusion, obatoclax is a novel inhibitor of endosomal acidification that prevents viral fusion and that could be pursued as a potential broad-spectrum antiviral candidate.
Alternative Protein Sources in the Diet Modulate Microbiota and Functionality in the Distal Intestine of Atlantic Salmon (Salmo salar)
Authors: Gajardo Karina , Jaramillo-Torres Alexander , Kortner Trond M. , Merrifield Daniel L. , Tinsley John , Bakke Anne Marie , Krogdahl Åshild 
Published: December 2016

ABSTRACT

The present study aimed to investigate whether alternative dietary protein sources modulate the microbial communities in the distal intestine (DI) of Atlantic salmon, and whether alterations in microbiota profiles are reflected in modifications in host intestinal function and health status. A 48-day feeding trial was conducted, in which groups of fish received one of five diets: a reference diet in which fishmeal (diet FM) was the only protein source and four experimental diets with commercially relevant compositions containing alternative ingredients as partial replacements of fishmeal, i.e., poultry meal (diet PM), a mix of soybean meal and wheat gluten (diet SBMWG), a mix of soy protein concentrate and poultry meal (diet SPCPM), and guar meal and wheat gluten (diet GMWG). Samples were taken of DI digesta and mucosa for microbial profiling using high-throughput sequencing and from DI whole tissue for immunohistochemistry and expression profiling of marker genes for gut health. Regardless of diet, there were significant differences between the microbial populations in the digesta and the mucosa in the salmon DI. Microbial richness was higher in the digesta than the mucosa. The digesta-associated bacterial communities were more affected by the diet than the mucosa-associated microbiota. Interestingly, both legume-based diets (SBMWG and GMWG) presented high relative abundance of lactic acid bacteria in addition to alteration in the expression of a salmon gene related to cell proliferation (
pcna
). It was, however, not possible to ascertain the cause-effect relationship between changes in bacterial communities and the host's intestinal responses to the diets.

IMPORTANCE
The intestine of cultivated Atlantic salmon shows symptoms of compromised function, which are most likely caused by imbalances related to the use of new feed ingredients. Intestinal microbiota profiling may become in the future a valuable endpoint measurement in order to assess fish intestinal health status and effects of diet. The present study aimed to gain information about whether alternative dietary protein sources modulate the microbial communities in the Atlantic salmon intestine and whether alterations in microbiota profiles are reflected in alterations in host intestinal function and health status. We demonstrate here that there are substantial differences between the intestinal digesta and mucosa in the presence and abundance of bacteria. The digesta-associated microbiota showed clear dependence on the diet composition, whereas mucosa-associated microbiota appeared to be less affected by diet composition. Most important, the study identified bacterial groups associated with diet-induced gut dysfunction that may be utilized as microbial markers of gut health status in fish.
Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities
Authors: Patin Nastassia V. , Schorn Michelle , Aguinaldo Kristen , Lincecum Tommie , Moore Bradley S. , Jensen Paul R. 
Published: December 2016

ABSTRACT

Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus
Salinispora
were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities.

IMPORTANCE
Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete
Salinispora arenicola
affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to
S. arenicola
extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.
The Sinorhizobium (Ensifer) fredii HH103 Nodulation Outer Protein NopI Is a Determinant for Efficient Nodulation of Soybean and Cowpea Plants
Authors: Jiménez-Guerrero Irene , Pérez-Montaño Francisco , Medina Carlos , Ollero Francisco Javier , López-Baena Francisco Javier 
Published: December 2016

ABSTRACT

The type III secretion system (T3SS) is a specialized secretion apparatus that is commonly used by many plant and animal pathogenic bacteria to deliver proteins, termed effectors, to the interior of the host cells. These effectors suppress host defenses and interfere with signal transduction pathways to promote infection. Some rhizobial strains possess a functional T3SS, which is involved in the suppression of host defense responses, host range determination, and symbiotic efficiency. The analysis of the genome of the broad-host-range rhizobial strain
Sinorhizobium fredii
HH103 identified eight genes that code for putative T3SS effectors. Three of these effectors, NopL, NopP, and NopI, are
Rhizobium
specific. In this work, we demonstrate that NopI, whose amino acid sequence shows a certain similarity with NopP, is secreted through the
S. fredii
HH103 T3SS in response to flavonoids. We also determined that NopL can be considered an effector since it is directly secreted to the interior of the host cell as demonstrated by adenylate cyclase assays. Finally, the symbiotic phenotype of single, double, and triple
nopI
,
nopL
, and
nopP
mutants in soybean and cowpea was assayed, showing that NopI plays an important role in determining the number of nodules formed in both legumes and that the absence of both NopL and NopP is highly detrimental for symbiosis.

IMPORTANCE
The paper is focused on three
Rhizobium
-specific T3SS effectors of
Sinorhizobium fredii
HH103, NopL, NopP, and NopI. We demonstrate that
S. fredii
HH103 is able to secrete through the T3SS in response to flavonoids the nodulation outer protein NopI. Additionally, we determined that NopL can be considered an effector since it is secreted to the interior of the host cell as demonstrated by adenylate cyclase assays. Finally, nodulation assays of soybean and cowpea indicated that NopI is important for the determination of the number of nodules formed and that the absence of both NopL and NopP negatively affected nodulation.
Erg4A and Erg4B Are Required for Conidiation and Azole Resistance via Regulation of Ergosterol Biosynthesis in Aspergillus fumigatus
Authors: Long Nanbiao , Xu Xiaoling , Zeng Qiuqiong , Sang Hong , Lu Ling 
Published: December 2016

ABSTRACT

Ergosterol, a fungus-specific sterol enriched in cell plasma membranes, is an effective antifungal drug target. However, current knowledge of the ergosterol biosynthesis process in the saprophytic human fungal pathogen
Aspergillus fumigatus
remains limited. In this study, we found that two endoplasmic reticulum-localized sterol C-24 reductases encoded by both
erg4A
and
erg4B
homologs are required to catalyze the reaction during the final step of ergosterol biosynthesis. Loss of one homolog of Erg4 induces the overexpression of the other one, accompanied by almost normal ergosterol synthesis and wild-type colony growth. However, double deletions of
erg4A
and
erg4B
completely block the last step of ergosterol synthesis, resulting in the accumulation of ergosta-5,7,22,24(28)-tetraenol, a precursor compound of ergosterol. Further studies indicate that
erg4A
and
erg4B
are required for conidiation but not for hyphal growth. Importantly, the Δ
erg4A
Δ
erg4B
mutant still demonstrates wild-type virulence in a compromised mouse model but displays remarkable increased susceptibility to antifungal azoles. Our data suggest that inhibitors of Erg4A and Erg4B may serve as effective candidates for adjunct antifungal agents with azoles.

IMPORTANCE
Knowledge of the ergosterol biosynthesis pathway in the human opportunistic pathogen
A. fumigatus
is useful for designing and finding new antifungal drugs. In this study, we demonstrated that the endoplasmic reticulum-localized sterol C-24 reductases Erg4A and Erg4B are required for conidiation via regulation of ergosterol biosynthesis. Moreover, inactivation of both Erg4A and Erg4B results in hypersensitivity to the clinical guideline-recommended antifungal drugs itraconazole and voriconazole. Therefore, our finding indicates that inhibition of Erg4A and Erg4B might be an effective approach for alleviating
A. fumigatus
infection.
A Rhizobiales-Specific Unipolar Polysaccharide Adhesin Contributes to Rhodopseudomonas palustris Biofilm Formation across Diverse Photoheterotrophic Conditions
Authors: Fritts Ryan K. , LaSarre Breah , Stoner Ari M. , Posto Amanda L. , McKinlay James B. 
Published: December 2016

ABSTRACT

Bacteria predominantly exist as members of surfaced-attached communities known as biofilms. Many bacterial species initiate biofilms and adhere to each other using cell surface adhesins. This is the case for numerous ecologically diverse
Alphaprotebacteria
, which use polar exopolysaccharide adhesins for cell-cell adhesion and surface attachment. Here, we show that
Rhodopseudomonas palustris
, a metabolically versatile member of the alphaproteobacterial order
Rhizobiales
, contains a functional unipolar polysaccharide (UPP) biosynthesis gene cluster. Deletion of genes predicted to be critical for UPP biosynthesis and export abolished UPP production. We also found that
R. palustris
uses UPP to mediate biofilm formation across diverse photoheterotrophic growth conditions, wherein light and organic substrates are used to support growth. However, UPP was less important for biofilm formation during photoautotrophy, where light and CO
2
support growth, and during aerobic respiration with organic compounds. Expanding our analysis beyond
R. palustris
, we examined the phylogenetic distribution and genomic organization of UPP gene clusters among
Rhizobiales
species that inhabit diverse niches. Our analysis suggests that UPP is a conserved ancestral trait of the
Rhizobiales
but that it has been independently lost multiple times during the evolution of this clade, twice coinciding with adaptation to intracellular lifestyles within animal hosts.

IMPORTANCE
Bacteria are ubiquitously found as surface-attached communities and cellular aggregates in nature. Here, we address how bacterial adhesion is coordinated in response to diverse environments using two complementary approaches. First, we examined how
Rhodopseudomonas palustris
, one of the most metabolically versatile organisms ever described, varies its adhesion to surfaces in response to different environmental conditions. We identified critical genes for the production of a unipolar polysaccharide (UPP) and showed that UPP is important for adhesion when light and organic substrates are used for growth. Looking beyond
R. palustris
, we performed the most comprehensive survey to date on the conservation of UPP biosynthesis genes among a group of closely related bacteria that occupy diverse niches. Our findings suggest that UPP is important for free-living and plant-associated lifestyles but dispensable for animal pathogens. Additionally, we propose guidelines for classifying the adhesins produced by various
Alphaprotebacteria
, facilitating future functional and comparative studies.
Detection of Salmonella enterica in Meat in Less than 5 Hours by a Low-Cost and Noncomplex Sample Preparation Method
Authors: Fachmann M. S. R. , Löfström C. , Hoorfar J. , Hansen F. , Christensen J. , Mansdal S. , Josefsen M. H. 
Published: December 2016

ABSTRACT

Salmonella
is recognized as one of the most important foodborne bacteria and has wide health and socioeconomic impacts worldwide. Fresh pork meat is one of the main sources of
Salmonella
, and efficient and fast methods for detection are therefore necessary. Current methods for
Salmonella
detection in fresh meat usually include >16 h of culture enrichment, in a few cases <12 h, thus requiring at least two working shifts. Here, we report a rapid (<5 h) and high-throughput method for screening of
Salmonella
in samples from fresh pork meat, consisting of a 3-h enrichment in standard buffered peptone water and a real-time PCR-compatible sample preparation method based on filtration, centrifugation, and enzymatic digestion, followed by fast-cycling real-time PCR detection. The method was validated in an unpaired comparative study against the Nordic Committee on Food Analysis (NMKL) reference culture method 187. Pork meat samples (
n
= 140) were either artificially contaminated with
Salmonella
at 0, 1 to 10, or 10 to 100 CFU/25 g of meat or naturally contaminated. Cohen's kappa for the degree of agreement between the rapid method and the reference was 0.64, and the relative accuracy, sensitivity, and specificity for the rapid method were 81.4, 95.1, and 97.9%, respectively. The 50% limit of detections (LOD
50
s) were 8.8 CFU/25 g for the rapid method and 7.7 CFU/25 g for the reference method. Implementation of this method will enable faster release of
Salmonella
low-risk meat, providing savings for meat producers, and it will help contribute to improved food safety.

IMPORTANCE
While the cost of analysis and hands-on time of the presented rapid method were comparable to those of reference culture methods, the fast product release by this method can provide the meat industry with a competitive advantage. Not only will the abattoirs save costs for work hours and cold storage, but consumers and retailers will also benefit from fresher meat with a longer shelf life. Furthermore, the presented sample preparation might be adjusted for application in the detection of other pathogenic bacteria in different sample types.
Complete Genome Sequence of Dehalococcoides mccartyi Strain WBC-2, Capable of Anaerobic Reductive Dechlorination of Vinyl Chloride
Authors: Molenda Olivia , Tang Shuiquan , Edwards Elizabeth A. 
Published: December 2016

ABSTRACT

Dehalococcoides mccartyi
strain WBC-2 dechlorinates carcinogen vinyl chloride to ethene in the West Branch Canal Creek (WBC-2) microbial consortium used for bioaugmentation. We assembled and closed the complete genome sequence of this prokaryote using metagenomic sequencing from an enrichment culture.
Complete Genome Sequence of
Lymantria dispar multiple nucleopolyhedrovirus
Isolated in Southwestern Poland
Authors: Krejmer-Rabalska Martyna , Rabalski Lukasz , Skrzecz Iwona , Szewczyk Boguslaw 
Published: December 2016

ABSTRACT

We report here the complete genomic sequence of Polish alphabaculovirus isolated from dead gypsy moth caterpillars. Its genome structure and G+C content indicate that it is a
Lymantria dispar multiple nucleopolyhedrovirus
(LdMNPV) strain which possesses the shortest sequence among eight other (similar to reference sequence AF081810) LdMNPV sequences available in GenBank; it is 159,729 bp long.
Metagenomics Analysis of Microorganisms in Freshwater Lakes of the Amazon Basin
Authors: Toyama Danyelle , Kishi Luciano Takeshi , Santos-Júnior Célio Dias , Soares-Costa Andrea , de Oliveira Tereza Cristina Souza , de Miranda Fernando Pellon , Henrique-Silva Flávio 
Published: December 2016

ABSTRACT
The Amazon Basin is the largest hydrographic basin on the planet, and the dynamics of its aquatic microorganisms strongly impact global biogeochemical cycles. However, it remains poorly studied. This metagenome project was performed to obtain a snapshot of prokaryotic microbiota from four important lakes in the Amazon Basin.
Streptococcus oralis Neuraminidase Modulates Adherence to Multiple Carbohydrates on Platelets
Authors: Singh Anirudh K. , Woodiga Shireen A. , Grau Margaret A. , King Samantha J. 
Published: December 2016

ABSTRACT

Adherence to host surfaces is often mediated by bacterial binding to surface carbohydrates. Although it is widely appreciated that some bacterial species express glycosidases, previous studies have not considered whether bacteria bind to multiple carbohydrates within host glycans as they are modified by bacterial glycosidases.
Streptococcus oralis
is a leading cause of subacute infective endocarditis. Binding to platelets is a critical step in disease; however, the mechanisms utilized by
S. oralis
remain largely undefined. Studies revealed that
S. oralis
, like
Streptococcus gordonii
and
Streptococcus sanguinis
, binds platelets via terminal sialic acid. However, unlike those organisms,
S. oralis
produces a neuraminidase, NanA, which cleaves terminal sialic acid. Further studies revealed that following NanA-dependent removal of terminal sialic acid,
S. oralis
bound exposed β-1,4-linked galactose. Adherence to both these carbohydrates required Fap1, the
S. oralis
member of the serine-rich repeat protein (SRRP) family of adhesins. Mutation of a conserved residue required for sialic acid binding by other SRRPs significantly reduced platelet binding, supporting the hypothesis that Fap1 binds this carbohydrate. The mechanism by which Fap1 contributes to β-1,4-linked galactose binding remains to be defined; however, binding may occur via additional domains of unknown function within the nonrepeat region, one of which shares some similarity with a carbohydrate binding module. This study is the first demonstration that an SRRP is required to bind β-1,4-linked galactose and the first time that one of these adhesins has been shown to be required for binding of multiple glycan receptors.
Collateral Damage: Detrimental Effect of Antibiotics on the Development of Protective Immune Memory
Authors: Benoun Joseph M. , Labuda Jasmine C. , McSorley Stephen J. 
Published: December 2016

ABSTRACTAntibiotic intervention is an effective treatment strategy for many bacterial infections and liberates bacterial antigens and stimulatory products that can induce an inflammatory response. Despite the opportunity for bacterial killing to enhance the development of adaptive immunity, patients treated successfully with antibiotics can suffer from reinfection. Studies in mouse models ofSalmonellaandChlamydiainfection also demonstrate that early antibiotic intervention reduces host protective immunity to subsequent infection. This heightened susceptibility to reinfection correlates with poor development of Th1 and antibody responses in antibiotic-treated mice but can be overcome by delayed antibiotic intervention, thus suggesting a requirement for sustained T cell stimulation for protection. Although the contribution of memory T cell subsets is imperfectly understood in both of these infection models, a protective role for noncirculating memory cells is suggested by recent studies. Together, these data propose a model where antibiotic treatment specifically interrupts tissue-resident memory T cell formation. Greater understanding of the mechanistic basis of this phenomenon might suggest therapeutic interventions to restore a protective memory response in antibiotic-treated patients, thus reducing the incidence of reinfection.
‘Not used to be worn as a Jewel’: The wearing of precious stones in early modern England – ornaments or medicine?
Authors: Blaen Tom 
Published: December 2016

Abstract

Precious stones played an important role in early modern medicine. These widespread medicinal objects could be administered in a variety of ways and, most importantly, by wearing. It is here that these medicinal jewels overlap with the famous desire of the gentry of the period to partake in opulent displays of gemstones on their person. This paper examines whether it is possible to tease apart these intersecting motivations for ornamenting the body with gemstones: was it for health or was it for beauty? The wearing of stones for cures is often found in printed material of sixteenth- and seventeenth-century Britain, including Nicholas Culpeper's famous
Pharmacopoeia
, but tracing records of actual medical use is complicated. Amulets and astrological sigils are an obvious source of jewellery worn for curative rather than primarily ornamental purposes, although these trod a perilous and blurred line between legitimate medicine and diabolic magic. The clearest examples are the wearing of stones with little or no aesthetic value (e.g. like the fabulous, to an extent fictional, toad-stone) which ultimately, it is argued, are of most use in determining the motivations for the wearing of medicinal stones.