bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explorative Randomized Phase II Clinical Study of the Efficacy and Safety of Finafloxacin versus Ciprofloxacin for Treatment of Complicated Urinary Tract Infections
Authors: Wagenlehner F. , Nowicki M. , Bentley C. , Lückermann M. , Wohlert S. , Fischer C. , Vente A. , Naber K. , Dalhoff A. 
Published: January 2018

ABSTRACT
The broad-spectrum C-8-cyano-fluoroquinolone finafloxacin displays enhanced activity under acidic conditions. This phase II clinical study compared the efficacies and safeties of finafloxacin and ciprofloxacin in patients with complicated urinary tract infection and/or pyelonephritis. A 5-day regimen with 800 mg finafloxacin once a day (q.d.) (FINA05) had results similar to those of a 10-day regimen with 800 mg finafloxacin q.d. (FINA10). Combined microbiological and clinical responses at the test-of-cure (TOC) visit were 70% for FINA05, 68% for FINA10, and 57% for a 10-day ciprofloxacin regimen (CIPRO10) in 193 patients (64 for FINA05, 68 for FINA10, and 61 for CIPRO10) of the microbiological intent-to-treat (mITT) population. Additionally, the clinical effects of ciprofloxacin on patients with an acidic urine pH (80% of patients) were reduced, whereas the effects of finafloxacin were unchanged. Finafloxacin was safe and well tolerated. Overall, 43.4% of the patients in the FINA05 group, 42.7% in the FINA10 group, and 54.2% in the CIPRO10 group experienced mostly mild and treatment-emergent but unrelated adverse events. A short-course regimen of 5 days of finafloxacin resulted in high eradication and improved clinical outcome rates compared to those for treatment with ciprofloxacin for 10 days. In contrast to those of ciprofloxacin, the clinical effects of finafloxacin were not reduced by acidic urine pH. Hospitalized adults were randomized 1:1:1 to finafloxacin treatment (800 mg q.d.) for either 5 or 10 days or to ciprofloxacin treatment (400 mg/500 mg b.i.d.) for 10 days with an optional switch from intravenous (i.v.) to oral administration at day 3. The primary endpoint was the combined microbiological and clinical response at the TOC visit in the microbiological intent-to-treat population. (This study has been registered at ClinicalTrials.gov under identifier NCT01928433.)
Development of an Efficient Genome Editing Tool in Bacillus licheniformis Using CRISPR-Cas9 Nickase
Authors: Li Kaifeng , Cai Dongbo , Wang Zhangqian , He Zhili , Chen Shouwen 
Published: January 2018

ABSTRACTBacillusstrains are important industrial bacteria that can produce various biochemical products. However, low transformation efficiencies and a lack of effective genome editing tools have hindered its widespread application. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 techniques have been utilized in many organisms as genome editing tools because of their high efficiency and easy manipulation. In this study, an efficient genome editing method was developed forBacillus licheniformisusing a CRISPR-Cas9 nickase integrated into the genome ofB. licheniformisDW2 with overexpression driven by the P43 promoter. TheyvmCgene was deleted using the CRISPR-Cas9n technique with homology arms of 1.0 kb as a representative example, and an efficiency of 100% was achieved. In addition, two genes were simultaneously disrupted with an efficiency of 11.6%, and the large DNA fragmentbacABC(42.7 kb) was deleted with an efficiency of 79.0%. Furthermore, the heterologous reporter geneaprN, which codes for nattokinase inBacillus subtilis, was inserted into the chromosome ofB. licheniformiswith an efficiency of 76.5%. The activity of nattokinase in the DWc9nΔ7/pP43SNT-SsacCstrain reached 59.7 fibrinolytic units (FU)/ml, which was 25.7% higher than that of DWc9n/pP43SNT-SsacC. Finally, the engineered strain DWc9nΔ7 (ΔeprΔwprAΔmprΔaprEΔvprΔbprAΔbacABC), with multiple disrupted genes, was constructed using the CRISPR-Cas9n technique. Taken together, we have developed an efficient genome editing tool based on CRISPR-Cas9n inB. licheniformis. This tool could be applied to strain improvement for future research.IMPORTANCEAs important industrial bacteria,Bacillusstrains have attracted significant attention due to their production of biological products. However, genetic manipulation of these bacteria is difficult. The CRISPR-Cas9 system has been applied to genome editing in some bacteria, and CRISPR-Cas9n was proven to be an efficient and precise tool in previous reports. The significance of our research is the development of an efficient, more precise, and systematic genome editing method for single-gene deletion, multiple-gene disruption, large DNA fragment deletion, and single-gene integration inBacillus licheniformisvia Cas9 nickase. We also applied this method to the genetic engineering of the host strain for protein expression.
Pseudomonas aeruginosa Biofilm Antibiotic Resistance GenendvBExpression Requires the RpoS Stationary-Phase Sigma Factor
Authors: Hall Clayton W. , Hinz Aaron J. , Gagnon Luke B.-P. , Zhang Li , Nadeau Jean-Paul , Copeland Sarah , Saha Bratati , Mah Thien-Fah 
Published: January 2018

ABSTRACTChronic, biofilm-based bacterial infections are exceptionally difficult to eradicate due to the high degree of antibiotic recalcitrance exhibited by cells in biofilm communities. In the opportunistic pathogenPseudomonas aeruginosa, biofilm recalcitrance is multifactorial and arises in part from the preferential expression of resistance genes in biofilms compared to exponential-phase planktonic cells. One such mechanism involvesndvB, which we have previously shown to be expressed specifically in biofilms. In this study, we investigated the regulatory basis of this lifestyle-specific expression by developing an unstable green fluorescent protein (GFP) transcriptional reporter to observe the expression pattern ofndvB. We found that in addition to its expression in biofilms,ndvBwas upregulated in planktonic cells as they enter stationary phase. The transcription ofndvBin both growth phases was shown to be dependent on the stationary-phase sigma factor RpoS, and mutation of a putative RpoS binding site in thendvBpromoter abolished the activity of the promoter in stationary-phase cells. Overall, we have expanded our understanding of the temporal expression ofndvBinP. aeruginosaand have uncovered a regulatory basis for its growth phase-dependent expression.IMPORTANCEBacterial biofilms are more resistant to antibiotics than free-living planktonic cells, and understanding the mechanistic basis of this resistance can inform treatments of biofilm-based infections. In addition to chemical and structural barriers that can inhibit antibiotic entry, the upregulation of specific genes in biofilms contributes to the resistance. We investigated this biofilm-specific gene induction by examining expression patterns ofndvB, a gene involved in biofilm resistance of the opportunistic pathogenPseudomonas aeruginosa. We characterizedndvBexpression in planktonic and biofilm growth conditions with an unstable green fluorescent protein (GFP) reporter and found that the expression ofndvBin biofilms is dependent on the stationary-phase sigma factor RpoS. Overall, our results support the physiological similarity between biofilms and stationary-phase cells and suggest that the induction of some stationary-phase genes in biofilms may contribute to their increased antibiotic resistance.
Complete Genome Sequence of
Escherichia coli
Bacteriophage PGT2
Authors: Golomidova Alla K. , Kulikov Eugene E. , Kudryavtseva Anna V. , Letarov Andrey V. 
Published: January 2018

ABSTRACT

Bacteriophage PGT2 was isolated from horse feces by using an uncharacterized
Escherichia coli
strain, 7s, isolated from the same sample as the host. Bacteriophage PGT2 and a related phage, phiKT, which was previously isolated from the same source, are likely to represent a new genus within the
Autographivirinae
subfamily of the
Podoviridae
family of viruses.
Complete Genome Sequence of the African Green Monkey Simian Foamy Virus Serotype 3 Strain FV2014 (SFVcae_FV2014)
Authors: Nandakumar Subhiksha , Bae Eunhae H. , Khan Arifa S. 
Published: January 2018

ABSTRACT

The full-length sequence of simian foamy virus serotype 3 (SFV-3) strain FV2014, an African green monkey (
Chlorocebus aethiops
) isolate, was obtained using high-throughput sequencing. SFVcae_FV2014 consisted of 13,127 bp and had a genomic organization similar to those of other SFVs but was distinct from SFV strain LK3, isolated from the same monkey species.
Complete Genome Sequence of
Sphingorhabdus
sp. YGSMI21, Exhibiting High Enantioselective Epoxide Hydrolase Activity
Authors: Kim Hae-Seon , Cha Sun Ho , Suk Ho Young , Park Nyun-Ho , Woo Jung-Hee 
Published: January 2018

ABSTRACT

Sphingorhabdus
sp. YGSMI21 is a novel strain exhibiting high enantioselective hydrolysis activity for styrene oxide. Here, we present its complete genome sequence, consisting of one circular chromosome (3.86 Mb) and one plasmid (0.196 Mb).
An AlgU-Regulated Antisense Transcript Encoded within the Pseudomonas syringae
fleQ
Gene Has a Positive Effect on Motility
Authors: Markel Eric , Dalenberg Hollie , Monteil Caroline L. , Vinatzer Boris A. , Swingle Bryan 
Published: January 2018

ABSTRACT

Production of bacterial flagella is controlled by a multitiered regulatory system that coordinates the expression of 40 to 50 subunits and ordered assembly of these elaborate structures. Flagellar expression is environmentally controlled, presumably to optimize the benefits and liabilities of having these organelles on cell growth and survival. We recently reported a global survey of AlgU-dependent regulation and binding in
Pseudomonas syringae
pv. tomato DC3000 that included evidence for strong downregulation of many flagellar and chemotaxis motility genes. Here, we returned to those data to look for other AlgU-dependent influences on the flagellar regulatory network. We identified an AlgU-dependent antisense transcript expressed from within the
fleQ
gene, the master regulator of flagellar biosynthesis in
Pseudomonas
. We tested whether expression of this antisense RNA influenced bacterial behavior and found that it reduces AlgU-dependent downregulation of motility. Importantly, this antisense expression influenced motility only under conditions in which AlgU was expressed. Comparative sequence analysis of the locus containing the antisense transcript's AlgU-dependent promoter in over 300
Pseudomonas
genomes revealed sequence conservation in most strains that encode AlgU. This suggests that the antisense transcript plays an important role that is conserved across most of the genus
Pseudomonas
.

IMPORTANCE
Pseudomonas syringae
is a globally distributed host-specific bacterial pathogen that causes disease in a wide-range of plants. An elaborate gene expression regulation network controls flagellum production, which is important for proper flagellum assembly and a key aspect of certain lifestyle transitions.
P. syringae
pv. tomato DC3000 uses flagellum-powered motility in the early stages of host colonization and adopts a sessile lifestyle after entering plant tissues, but the regulation of this transition is not understood. Our work demonstrates a link between regulation of motility and global transcriptional control that facilitates bacterial growth and disease in plants. Additionally, sequence comparisons suggest that this regulation mechanism is conserved in most members of the genus
Pseudomonas
.
An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment
Authors: Fenstermacher Katherine J. , Achuthan Vasudevan , Schneider Thomas D. , DeStefano Jeffrey J. 
Published: January 2018

ABSTRACT

DNA polymerases (DNAPs) recognize 3′ recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to
Taq
and Klenow polymerases were identified using a modified systematic evolution of ligands by exponential enrichment (SELEX) approach. Two
Taq
-specific primers that bound ∼10 (Taq1) and over 100 (Taq2) times more stably than controls to
Taq
were identified. TaqI contained 8 nucleotides (5′-CACTAAAG-3′) that matched the phage T3 RNAP “core” promoter. Both primers dramatically outcompeted primers with similar binding thermodynamics in PCRs. Similarly, exonuclease
−
Klenow polymerase also selected a high-affinity primer that contained a related core promoter sequence from phage T7 RNAP (5′-ACTATAG-3′). For both
Taq
and Klenow, even small modifications to the sequence resulted in large losses in binding affinity, suggesting that binding was highly sequence specific. The results are discussed in the context of possible effects on multiprimer (multiplex) PCR assays, molecular information theory, and the evolution of RNAPs and DNAPs.

IMPORTANCE
This work further demonstrates that primer-dependent DNA polymerases can have strong sequence biases leading to dramatically tighter binding to specific sequences. These may be related to biological function or be a consequence of the structural architecture of the enzyme. New sequence specificity for
Taq
and Klenow polymerases were uncovered, and among them were sequences that contained the core promoter elements from T3 and T7 phage RNA polymerase promoters. This suggests the intriguing possibility that phage RNA polymerases exploited intrinsic binding affinities of ancestral DNA polymerases to develop their promoters. Conversely, DNA polymerases could have evolved from related RNA polymerases and retained the intrinsic binding preference despite there being no clear function for such a preference in DNA biology.
Viperin Restricts Zika Virus and Tick-Borne Encephalitis Virus Replication by Targeting NS3 for Proteasomal Degradation
Authors: Panayiotou Christakis , Lindqvist Richard , Kurhade Chaitanya , Vonderstein Kirstin , Pasto Jenny , Edlund Karin , Upadhyay Arunkumar S. , Överby Anna K. 
Published: January 2018

ABSTRACT

Flaviviruses are arthropod-borne viruses that constitute a major global health problem, with millions of human infections annually. Their pathogenesis ranges from mild illness to severe manifestations such as hemorrhagic fever and fatal encephalitis. Type I interferons (IFNs) are induced in response to viral infection and stimulate the expression of interferon-stimulated genes (ISGs), including that encoding viperin (virus-inhibitory protein, endoplasmic reticulum associated, IFN inducible), which shows antiviral activity against a broad spectrum of viruses, including several flaviviruses. Here we describe a novel antiviral mechanism employed by viperin against two prominent flaviviruses, tick-borne encephalitis virus (TBEV) and Zika virus (ZIKV). Viperin was found to interact and colocalize with the structural proteins premembrane (prM) and envelope (E) of TBEV, as well as with nonstructural (NS) proteins NS2A, NS2B, and NS3. Interestingly, viperin expression reduced the NS3 protein level, and the stability of the other interacting viral proteins, but only in the presence of NS3. We also found that although viperin interacted with NS3 of mosquito-borne flaviviruses (ZIKV, Japanese encephalitis virus, and yellow fever virus), only ZIKV was sensitive to the antiviral effect of viperin. This sensitivity correlated with viperin's ability to induce proteasome-dependent degradation of NS3. ZIKV and TBEV replication was rescued completely when NS3 was overexpressed, suggesting that the viral NS3 is the specific target of viperin. In summary, we present here a novel antiviral mechanism of viperin that is selective for specific viruses in the genus
Flavivirus
, affording the possible availability of new drug targets that can be used for therapeutic intervention.

IMPORTANCE
Flaviviruses are a group of enveloped RNA viruses that cause severe diseases in humans and animals worldwide, but no antiviral treatment is yet available. Viperin, a host protein produced in response to infection, effectively restricts the replication of several flaviviruses, but the exact molecular mechanisms have not been elucidated. Here we have identified a novel mechanism employed by viperin to inhibit the replication of two flaviviruses: tick-borne encephalitis virus (TBEV) and Zika virus (ZIKV). Viperin induced selective degradation via the proteasome of TBEV and ZIKV nonstructural 3 (NS3) protein, which is involved in several steps of the viral life cycle. Furthermore, viperin also reduced the stability of several other viral proteins in a NS3-dependent manner, suggesting a central role of NS3 in viperin's antiflavivirus activity. Taking the results together, our work shows important similarities and differences among the members of the genus
Flavivirus
and could lead to the possibility of therapeutic intervention.
Porcine Mx1 Protein Inhibits Classical Swine Fever Virus Replication by Targeting Nonstructural Protein NS5B
Authors: Zhou Jing , Chen Jing , Zhang Xiao-Min , Gao Zhi-Can , Liu Chun-Chun , Zhang Yun-Na , Hou Jin-Xiu , Li Zhao-Yao , Kan Lin , Li Wen-Liang , Zhou Bin 
Published: January 2018

ABSTRACT

Mx proteins are interferon (IFN)-induced GTPases that have broad antiviral activity against a wide range of RNA and DNA viruses; they belong to the dynamin superfamily of large GTPases. In this study, we confirmed the anti-classical swine fever virus (CSFV) activity of porcine Mx1
in vitro
and showed that porcine Mx2 (poMx2), human MxA (huMxA), and mouse Mx1 (mmMx1) also have anti-CSFV activity
in vitro
. Small interfering RNA (siRNA) experiments revealed that depletion of endogenous poMx1 or poMx2 enhanced CSFV replication, suggesting that porcine Mx proteins are responsible for the antiviral activity of interferon alpha (IFN-α) against CSFV infection. Confocal microscopy, immunoprecipitation, glutathione
S
-transferase (GST) pulldown, and bimolecular fluorescence complementation (BiFC) demonstrated that poMx1 associated with NS5B, the RNA-dependent RNA polymerase (RdRp) of CSFV. We used mutations in the poMx1 protein to elucidate the mechanism of their anti-CSFV activity and found that mutants that disrupted the association with NS5B lost all anti-CSV activity. Moreover, an RdRp activity assay further revealed that poMx1 undermined the RdRp activities of NS5B. Together, these results indicate that porcine Mx proteins exert their antiviral activity against CSFV by interacting with NS5B.

IMPORTANCE
Our previous studies have shown that porcine Mx1 (poMx1) inhibits classical swine fever virus (CSFV) replication
in vitro
and
in vivo
, but the molecular mechanism of action remains largely unknown. In this study, we dissect the molecular mechanism of porcine Mx1 and Mx2 against CSFV
in vitro
. Our results show that poMx1 associates with NS5B, the RNA-dependent RNA polymerase of CSFV, resulting in the reduction of CSFV replication. Moreover, the mutants of poMx1 further elucidate the mechanism of their anti-CSFV activities.
Identifying externally derived sulfur in conduit-type Cu–platinum-group element deposits: The importance of multiple sulfur isotope studies
Authors: Shahabi Far Maryam , Samson Iain M. , Gagnon Joel E. , Good David J. , Linnen Robert L. , Layne Graham D. , Wing Boswell A. 
Published: January 2018

Abstract
The Marathon conduit-type Cu–platinum-group element (PGE) deposit occurs within the Proterozoic Coldwell alkaline complex, Ontario, Canada, and comprises three zones of mineralization that occur at varying distances from the contact with Archean country rocks. Multiple sulfur isotope studies (δ34S, Δ33S, Δ36S) of sulfides from the Marathon deposit show that Δ33S and Δ36S measurements, as well as the relationship between them, are critical in demonstrating crustal S contamination. This is particularly significant for magmatic Cu-PGE deposits in contact with Archean country rocks where the δ34S of sulfides are within the range of typical mantle values (0‰ ± 2‰), as is the case at the Marathon deposit. Although the δ34S values of sulfides from the Marathon deposit did not reflect any evidence of crustal S assimilation, the Δ33S range (−0.91‰ to 0.00‰), and a negative correlation between Δ33S and Δ36S, indicate that S was derived from both the mantle and Archean supracrustal rocks. Given that the country rocks contain insignificant amounts of sulfide, crustal S assimilation must have occurred at depth, prior to magma emplacement. The magnitude of the Δ33S anomaly decreases with increasing distance from the basal contact, suggesting either that S contamination was greatest in the mineralized zone that occurred in close proximity to the contact or that crustal S signatures have been diluted in the mineralized zones further from the contact.
Immiscible shoshonitic and Fe-P-oxide melts preserved in unconsolidated tephra at El Laco volcano, Chile
Authors: Mungall J.E. , Long K. , Brenan J.M. , Smythe D. , Naslund H.R. 
Published: January 2018

Abstract
The origins of apparently magmatic Fe-P-O deposits like those of the El Laco volcanic complex, Chile, with masses on the order of 1 Gt remain contentious. Previous attention has been focused largely on the high–tonnage massive magnetite bodies that form the economic mineral deposits. Extensive occurrences of unconsolidated granular Fe–P–oxide materials or their apparent metamorphic equivalents have received relatively little attention. Here we report textures and compositions of unconsolidated Fe–P–oxide materials from Laco Sur, El Laco. Unconsolidated tephra at El Laco is dominated by hematite along with subsidiary Fe–phosphates, monazite, and silica. A porous hematite bomb contains menisci of two coexisting materials. One is hydrous shoshonitic glass with perlitic texture, and the other comprises fine-grained intergrowths of Fe–P–REE (rare earth element) oxides having the bulk composition of the eutectic in the system FePO4–Fe2O3 with minor S, Cl, and other components. We show by experiment that very similar compositions would have coexisted as immiscible silicate and oxide liquids at 900 °C and 1 GPa in the presence of carbonic vapor, magnetite, and quartz; both will also form anhydrous liquids at 1080 °C and 101 kPa. We infer the former existence of a phosphatic Fe-oxide magma rich in volatiles that underwent explosive degassing and consequent rapid compositional undercooling to produce the observed assemblage of Fe-oxide tephra containing small amounts of Fe–P–REE phosphates and silicate glass.