bluuebunny/crossref_metadata_2025 huggingface dataset:
Community structure and the behavior of transnational sustainability governors: Toward a multi‐relational approach
Authors: Fransen Luc , Schalk Jelmer , Auld Graeme
Published: January 2018

Hundreds of transnational private governance organizations (TPGOs) have emerged in recent decades to govern social and environmental conditions of production using voluntary standards. A debate persists over whether the ties among different TPGOs and other organizations create a professional community that affects the behavior of TPGOs. To help resolve this debate, we analyze multiple ties among agriculture TPGOs to offer a more robust exploration of community structures and their potential effects for three forms of TPGO behavior – coordination, collaboration, and isomorphism. Our aggregate measure of ties reveals a thin community dominated by older TPGOs and TPGOs advancing a broad notion of sustainability that were created by Solidaridad, the World Wildlife Fund, and/or Unilever. The clearest community structures are built from ties that exhibit the potential for not actual collaboration, coordination, and isomorphism. Thus, while there exists convergence toward an emergent TPGO‐community, obstacles remain to more intense behavioral effects for TPGOs.
Generation of red drum(Sciaenops ocellatus)hematology Reference Intervals with a focus on identified outliers
Authors: Harr Kendal E. , Deak Kristina , Murawski Steven A. , Reavill Drury R. , Takeshita Ryan A.
Published: January 2018

Background

TheDeepwater Horizon(DWH) oil spill in 2010 released millions of barrels of crude oil into the northern Gulf of Mexico, exposing numerous species of animals to the toxic components of oil. A comprehensive assessment of morbidity and mortality caused byDWHoil exposure was undertaken by theDWHNatural Resource Damage Trustees to characterize ecosystem damages.

Objectives

This study aimed to characterize normal hematologicRIs in red drum fish with blood cell descriptions, and to demonstrate the importance of identifying and removing outliers when generatingRI.

Methods

Two years after the oil spill, 57 adult, red drum fish of mixed sexes were caught along the eastern Louisiana coastline. Eight different sites were chosen to catch the fish; 6 sites were contaminated with oil, and 2 sites were not contaminated at the time of the oil spill. HematologicRIs were generated from heparinized whole blood samples of healthy red drum as determined by gross examination and histopathologic examination. Two methods were used to detect hematologic effects likely caused by oil contamination.

Results

Red drumPCVs (RI 42–62%) were higher than previously reported in cold water and bottom‐dwelling fish species, while absoluteWBCcounts (RI 2.9–8.7  × 109/L) were comparable toWBCcounts previously reported in other fish species with heterophil and lymphocyte absolute concentrations frequently being equivalent. Anemic animals (PCV<42%) were only identified in oil‐contaminated sites.

Conclusion

RIs in many wild fish species are lacking, and therefore, this study provides valuable baseline data on healthy red drum fish. The outliers assessed usingASVCP RIguidelines can provide valuable clinical information regarding individuals in population health assessments, which may be more sensitive for the detection of abnormalities than for population statistics comparing the mean. The importance of removing outliers and rerunningRIstatistics is highlighted by this field example.
Carbon dioxide emission and its regulation at land–water interface downstream of a point source at Ganga River (India)
Authors: Jaiswal Deepa , Siddiqui Ekabal , Verma Kavita , Pandey Jitendra
Published: January 2018

The streams and rivers are considered hotspots of CO2 exchange; and representative direct CO2 emission measurements are essential for a correct regional estimate. We measured CO2 emission flux at 15 sites at land–water interface downstream of a point source during low flow for three consecutive months for the year 2017. The general range of CO2 efflux observed here was close to the results of regional studies, although values near the point source were disproportionately high (>350 mg/m2/h). CO2 emission flux showed strong dependence on total organic carbon (TOC; R2 = 0.96; P < 0.001),
(R2 = 0.88; P < 0.001), soluble reactive‐P (SRP; R2 = 0.91; P < 0.001) and microbial activity measured in terms of fluorescein diacetate activity (FDAase; R2 = 0.92; P < 0.001) and substrate induced respiration (SIR; R2 = 0.96; P < 0.001). Because point source‐associated interfaces provide heterogeneous habitats, our study suggests the need for large scale monitoring of CO2 emission at land–water interface of major rivers for more correctly presenting the regional scale CO2 budget.
Linking species traits to agroecosystem services: a functional analysis of weed communities
Authors: Bàrberi P , Bocci G , Carlesi S , Armengot L , Blanco‐Moreno J M , Sans F X
Published: January 2018

There is a growing interest in the use of functional approaches for the study of weed assemblages, to disentangle underlying processes determining their composition and dynamics. Functional approaches are based on the assumption that weed community composition and dynamics can be best explained by a set of species traits expressing their response to agricultural disturbance. This knowledge should help develop more sustainable, ecologically based weed management systems. Trait‐based data required for this kind of analysis are available from various sources, but most of them either cover mainly non‐weedy species or, in the case of weed‐focussed trait databases, they cover a limited number of species. In this work, we present a trait database for 240 weed species common throughout Europe, including not only response traits but also effect traits, that is linked to selected agroecosystem services and disservices. A case study is presented where our weed trait database is used in conjunction with appropriate statistical analysis to highlight the distribution of weed functional groups in soyabean crop communities from an experiment including different tillage and weed management systems. Finally, we discuss the strengths, weaknesses, opportunities and threats of this functional approach. By highlighting the links between weed species and agroecosystem (dis)services, this approach could be a useful resource for scientists, farm managers and policymakers.
Continuous Blending for Processes
Authors: Ulvila Ed
Published: January 2018

The purpose of continuous blending is to be able to feed downstream processing equipment without interruption which helps assure a continuous flow of product out of the processing plant to the consumer shelves. Over the years a couple of different continuous blending methods have been employed with slight variations. Most successful systems employ batching or in-line continuous systems that are based on volumetric flow or mass flow of ingredients.

Paper published with permission.
Manufacturing Execution System = “Empowerment”
Authors: Ricker Jim
Published: January 2018

Today’s e-Commerce systems are applying pressure on the manufacturing industry. Shorter lead times, smaller production runs, just-in-time inventory and build-to-order are all manufacturing operations’ nightmares. Worse, with ERP, CRM, APS and SCM, each application provides significant content but it is very difficult to make them all work together. The Manufacturing Execution System is the glue that turns all the pieces of the puzzle into one solid solution. Manufacturing Execution System accomplishes this by becoming the source of real-time production/fulfillment data and the central data source.

Manufacturing Execution System applications effectively fall into the following areas:

_ Enterprise system integration

_ Production tracking w/genealogy

_ Real-time Inventory Management

_ Manufacturing operations management

* (ERP - enterprise resource management, CRM - customer relationship management, APS - advanced planning and scheduling, SCM - supply chain management).

Paper published with permission.
Evaporator Automation
Authors: Milla Jose “Danny” , Bellarde Marcelo
Published: January 2018

TASTE evaporators were invented in the 1960’s in order to improve the flavor of concentrated orange juice. Most of the evaporators in service at this time were of the forced re-circulation type and the concentrated product was of inferior quality and had burned or cooked flavors. TASTE is an acronym for Temperature Accelerated Short Time Evaporator and its innovation was to reduce the temperature and amount of contact time that the juice spent in this thermally abusive environment.

In this paper, the authors would like to explore two different but complementary issues concerning evaporators. One discussion concerns streamlining the process and operation of evaporators in order to gain multiple benefits in a plant environment. The other is to discuss new control technologies, specifically “Advanced” or Model Predictive Control and its application to automated °Brix control.

Paper published with permission.
Flow and Heat Transfer Through Helix Tubular Coils Theory and Practice for Pasteurization and Sterilization and Potential for the Citrus Industry
Authors: Young Gary C. , Carlson Robert
Published: January 2018

Pathogens are becoming more important than they have in the past. This is due to many factors, including the critical segments of the population (young, elderly, pregnant women, and individuals without natural immunity) now make-up 25% of the population. Analytical techniques are refined so that illnesses and their sources can be identified. Obviously, in the past, many sick people either were not treated and it was not proven why they were sick, or, they passed away and their death was termed “due to natural causes.” Also, the types of organisms that cause food-borne diseases of one type or another have increased over the years. At one time, organisms such as E. coli were simply an indicator of unsanitary conditions or fecal material. Now small numbers of certain strains of E. coli can cause severe illnesses and death.

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Process Safety Management and Risk Management Program (PSM/RMP) Audits: Are You Prepared?
Authors: Ira Martha Mead
Published: January 2018

In June 1996, the Environmental Protection Agency (EPA) promulgated 40 CFR Part 68, Accidental Release Prevention Requirements: Risk Management Programs (RMP) Under Clean Air Act, Section 112 r (7), commonly called the RMP rule. Much of the RMP rule was already required by the Occupational Safety and Health Administration’s (OSHA) 29 CFR 1910.119 Process Safety Management of Highly Hazardous Chemicals (the PSM Standard), which had been issued four years earlier. Because both of these regulations include anhydrous ammonia at a threshold level of 10,000 lbs., many refrigerated warehousing and manufacturing facilities are subject to them. Since the two regulations have the same threshold quantity for ammonia, facilities that are subject to RMP are also subject to PSM. While the focus of the two regulations differs, there are many common requirements, as shown in Table 1, Comparison of Process Safety Management and Risk Management Program Requirements. Both rules require the development of extensive accident prevention programs, which include Process Hazard Analyses, operation and maintenance procedures, training, and emergency response plans. The RMP rule also requires Offsite Consequence Analyses and a Plan summary submittal to the EPA before a process starts up and at five-year intervals thereafter. The Program 3 Prevention Program required to satisfy RMP, is almost identical to a PSM program. Most subject facilities, therefore, use their PSM Program to serve as their RMP Prevention Program. In Florida, the Department of Community Affairs (DCA) took delegation of the RMP rule from the EPA and is the enforcing agency in this state. Since the summer of 2000, the DCA has been auditing RMP facilities for compliance with the rule, and their list of audit subjects has included several citrus manufacturing facilities. The DCA staff has been performing very thorough audits, looking closely at all of the RMP Prevention Program, or PSM Program, elements and evaluating their implementation status at each site. The DCA typically cites RMP Prevention Program deficiencies in the following areas: Mechanical Integrity, Standard Operating Procedures, Process Hazard Analysis, training records, incident investigation reporting, compliance audits, and emergency response planning. Although Florida does not have a State-OSHA program, the DCA is, effectively, serving in this function as they audit the PSM programs of refrigerated facilities throughout the state. Facility owners should therefore ensure that their PSM/RMP Prevention Programs are well developed and well implemented prior to a DCA audit.

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Use of 3-A Standards in the Juice Industry
Authors: Rugh Timothy R.
Published: January 2018

3-A Sanitary Standards, Inc. (3-A SSI) is a not-for-profit 501(c)(3) organization whose mission is to enhance product safety for consumers of food, beverages, and pharmaceutical products through the development and use of 3-A Sanitary Standards and 3-A Accepted Practices. This presentation is intended to introduce the significance of 3-A Standards and Accepted Practices for the dairy and food processing industries, describe the formation and role of the new 3-A SSI, and present the benefits of expanding the use of 3-A Standards into new industries, such as the juice industry, for the mutual benefit of equipment fabricators, users, and regulatory professionals.

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World-Class Standards for Ammonia Refrigeration Systems
Authors: DeMarco Joseph N.
Published: January 2018

In spite of the fact that anhydrous ammonia is classified as a highly hazardous chemical, it continues to be the preferred refrigerant for industrial refrigeration users. Ammonia systems offer high-energy efficiency, low capital cost, and simplicity that other systems simply cannot match. This paper summarizes Tropicana’s approach to addressing possible safety concerns with their large refrigeration systems, by developing and implementing “World-Class” standards, and upgrading existing plant facilities. The largest single undertaking in this process was the building of a 14,000-ton compressor room in Bradenton, Florida, to replace a large and antiquated central machine room. This complex and difficult project required a thorough consideration of refrigeration design principles and serves as the major backdrop for the following discussion. It is hoped that others can learn from this juice processor’s experience in search of “World-Class” standards for safety, reliability, and efficiency of their refrigeration systems. Enhancing the safety of a plant’s ammonia systems should be a common goal for all processors in our industry.

Paper published with permission.
Integration of Statistical Process Control Data Into Control and Information Systems for Production Optimization and Regulatory Compliance
Authors: Fair Douglas C. , Redifer Jim
Published: January 2018

Data and Information from the plant floor is proliferating as more sophisticated machinery, instrumentation, and computer based devices are introduced into the manufacturing process. The use of Statistic Process Control to utilize this data goes beyond just measuring and analyzing product specific information. Food processing and manufacturing operations need to integrate real-time data and SPC data analysis into their operation in order to be a world-class manufacturer.

To facilitate these goals, an organization must have a vision for an automation and information infrastructure as well as a data strategy. This discussion will touch on a number of key points in formulating that vision, as well as some specific functionalities using data and SPC that one would want to achieve.

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Energy Savings and Opportunities in the Citrus Industry
Authors: Lewis Nathaniel , Thomas Charles
Published: January 2018

The following opportunities have significant potential to reduce the energy needs of a citrus plant. Each opportunity is identified with specific recommendations. The recent increases in fuel cost have renewed the interest and necessity to review the energy saving opportunities. Measures that were not economical a couple of years ago may now have respectable paybacks.

The opportunities are divided into the following topics:

• Boiler

• Feed Mill

• Refrigeration

• Evaporation

• Rates

Paper published with permission.
Machine Safety: Risk Assessment, Risk Reduction
Authors: Ladd Michael D.
Published: January 2018

Worker safety is an issue of major concern worldwide. Evidence to this fact is noted with recent efforts to harmonize US machine safety standards with that of the European Machinery Directive. Changes to the US standards have a dramatic affect on new equipment design. Additionally, older machinery that is still in use must now be upgraded to meet these new requirements. In other words, the end user must now follow the same standards as new equipment manufacturers.

Paper published with permission.
Energy Efficient Lighting Design Criteria: Cost-Effective Solutions in an Industrial Environment
Authors: Agraz Frank J. , Maneri John
Published: January 2018

The continual rising cost of energy, existing outdated lighting technology, and inefficient lighting designs have given property owners the opportunity to improve their facilities by retrofitting their existing luminaires with an energy efficient lighting system. A lighting retrofit uses the existing electrical infrastructure to replace, relocate, or convert existing luminaires with the latest generation of cost-effective components.

New lighting technology has emerged within the last 6 years that generates energy savings of 40% to 50% while maintaining existing light levels. These upgraded and field-tested solutions lower energy consumption, generate a healthy financial return on investment, and can improve both the quality and quantity of light in the task area.

As with any other solution, a cost-effective lighting system must be designed and engineered carefully to accommodate the needs of each work space. Simply installing a new lamp into an existing luminaire will not necessarily guarantee substantial energy savings or an improved lighting environment. In any space that uses electric lighting, the lighting designer must evaluate potential solutions for energy consumption, maintenance concerns, delivered light levels, hostile environments, and the overall economic impact of installing and long-term operation of the new system.

In this paper, the author will discuss energy efficient lighting design criteria and how a lighting designer properly engineers a retrofit project to deliver energy savings without sacrificing light levels. The discussion includes a summary of both traditional and emerging technologies, and the long-term impact on energy consumption, maintenance, return on investment, lighting quality, and delivered light levels.

Paper published with permission.
Update on Huanglongbing Progression and Current Research in Florida
Authors: Brlansky R. H.
Published: January 2018

Citrus Huanglongbing (HLB) or citrus greening disease has been in Florida since at least 2005 and has spread to all of the citrus producing regions. The Asian citrus psyllid (Diaphorina citri) is the insect that transmits the suspected causal bacterium which is tentatively named Candidatus Liberibacter asiaticus. Symptoms of the disease are first the yellow shoot (huanglongbing) and the development of the blotchy mottle symptom in the leaves. Mineral deficiency symptoms are often found on infected trees and may mimic normal deficiency symptoms. Fruit on infected trees may be small and lopsided and may abscise prematurely and therefore productivity is reduced. Tree decline eventually occurs. The suspected causal bacterium has not been obtained in pure culture and a polymerase chain reaction (PCR) test along with symptoms, is the only way to verify infected trees. All citrus cultivars appear susceptible. Current management strategies are chemical and biological control to reduced psyllid populations, inspections for infected trees and removal of infected trees to reduce the available pathogen inoculum. Current research on psyllid control, psyllid transmission, symptomology, detection, culturing the causal agent, development of new detection methods, alternative hosts of the psyllid and the causal agent, physiology of the disease, resistant or tolerant cultivar development and more is discussed. HLB is a major problem for citrus production and often limits commercial production.

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Future Trends in Ammonia Refrigeration Design
Authors: Welch Jeff
Published: January 2018

While many citrus processing plants already enjoy the excellent benefits of ammonia refrigerant, its continued use must be effective and safe. This paper explores the design and application trends that will shape the use and application of ammonia in central refrigeration systems in the future.

Paper published with permission.
Rheological Behavior of Citrus Pulp and its Application to Aseptic Processing
Authors: Levati Manuele
Published: January 2018

High-density citrus pulp is becoming increasingly popular in the beverage industry; however, its unique rheological behavior poses some challenges for its processing in heat exchangers, including high pressures resulting from its high viscosity and the difficulties producing an even mixture. The rheological behavior of 850 g/l citrus pulp has been studied at different temperatures between 20 °C and 80 °C and applied to computerized fluid dynamics (CFD) simulations of flow in circular pipes and annular heat exchangers in order to determine flow characteristics and solutions for pulp mixing.

Paper published with permission.
REVIEWS OF ACOUSTICAL PATENTS
Authors: Fulop Sean A. , Rice Lloyd
Published: January 2018

The purpose of these acoustical patent reviews is to provide enough information for a Journal reader to decide whether to seek more information from the patent itself. Any opinions expressed here are those of the reviewers as individuals and are not legal opinions. Printed copies of United States Patents may be ordered at $3.00 each from the Commissioner of Patents and Trademarks, Washington, DC 20231. Patents are available via the Internet at http:// www.uspto.gov .
Engineering precision biomaterials for personalized medicine
Authors: Aguado Brian A. , Grim Joseph C. , Rosales Adrianne M. , Watson-Capps Jana J. , Anseth Kristi S.
Published: January 2018

A unit operations approach for designing precision biomaterial-based medical devices may lead to more effective personalized therapies.
Antibiotic Resistance Plasmids Cointegrated into a Megaplasmid Harboring the
bla
OXA-427
Carbapenemase Gene
Authors: Desmet Stefanie , Nepal Suruchi , van Dijl Jan Maarten , Van Ranst Marc , Chlebowicz Monika A. , Rossen John W. , Van Houdt Jeroen K. J. , Maes Piet , Lagrou Katrien , Bathoorn Erik
Published: January 2018

OXA-427 is a new class D carbapenemase encountered in different species of
Enterobacteriaceae
in a Belgian hospital. To study the dispersal of this gene, we performed a comparative analysis of two plasmids containing the
bla
OXA-427
gene, isolated from a
Klebsiella pneumoniae
strain and an
Enterobacter cloacae
complex strain. The two IncA/C2 plasmids containing
bla
OXA-427
share the same backbone; in the
K. pneumoniae
strain, however, this plasmid is cointegrated into an IncFIb plasmid, forming a 321-kb megaplasmid with multiple multiresistance regions.
Intrapulmonary Pharmacokinetics of Lascufloxacin in Healthy Adult Volunteers
Authors: Furuie Hidetoshi , Tanioka Sayoko , Shimizu Keiko , Manita Shigeru , Nishimura Masaharu , Yoshida Hisao
Published: January 2018

This study was performed to investigate the intrapulmonary penetration of lascufloxacin in humans. Thirty healthy adult male Japanese subjects, allocated into five groups, received lascufloxacin in a single oral dose of 75 mg. Bronchoalveolar lavage and blood sampling were performed simultaneously in each subject at 1, 2, 4, 6, or 24 h after administration, and lascufloxacin concentrations in plasma, epithelial lining fluid, and alveolar macrophages were determined. Lascufloxacin was rapidly distributed to the epithelial lining fluid with a time to maximum drug concentration (
T
max
) of 1 h, which was identical to that in plasma. The maximum concentration of drug (
C
max
) values in plasma, epithelial lining fluid, and alveolar macrophages were 0.576, 12.3, and 21.8 μg/ml, respectively. The corresponding area under the concentration-time curve from 0 to 24 h (AUC
0–24
) values were 7.67, 123, and 325 μg · h/ml. The mean drug concentrations in the epithelial lining fluid and alveolar macrophages were much higher than those in plasma at all time points examined, and the average site-to-free plasma concentration ratios fell within the ranges of 57.5 to 86.4 and 71.0 to 217, respectively. Drug levels in epithelial lining fluid and alveolar macrophages exceeded the MIC
90
values for common respiratory pathogens. (This study was registered at JAPIC under registration number JapicCTI-142547.)
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

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

Bacillusstrains 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

Chronic, 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

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

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

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

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

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

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

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

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

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.