bluuebunny/crossref_metadata_2025 huggingface dataset:
Maximizing Age-0 Spot Export from a South Carolina Estuary: An Evaluation of Coastal Impoundment Management Alternatives via Structured Decision Making
Authors: Robinson Kelly F. , Jennings Cecil A.
Published: July 2012

Estuaries are among the most productive of all ecosystems and provide critical nursery habitat for many young-of-the-year (age-0) marine fish. Along the South Carolina coast, former rice field impoundments in some estuarine areas are now managed to provide habitat for waterfowl. Marine fish that enter these structures during water level manipulation become trapped and suffer high mortality rates. Because these fish cannot emigrate back to coastal waters to complete their life cycles, these impoundments appear to act as sinks for marine-transient species. Our goal was to identify which of a set of management options would maximize export of age-0 spot Leiostomus xanthurus from the Combahee River, South Carolina, to the coastal population. We used a structured decision-making approach to evaluate four decision alternatives: to maintain status quo, to close all impoundments while age-0 spot are most abundant in the river, to change the water level manipulation strategy to improve fish passage from impoundments, or to breach all impoundments. We also wanted to evaluate how impoundments and natural mortality influence the export of age-0 spot. The optimal management decision was to change the water level manipulation strategy to increase fish passage from the impoundments. Spot export was most sensitive to juvenile settlement in the estuary and natural mortality. The results of this model can be used adaptively for impoundment management along the Combahee River and can be modified for other estuarine areas or other fish species.

Received August 11, 2011; accepted February 11, 2012
Anomalous Ocean Conditions May Explain the Recent Extreme Variability in Fraser River Sockeye Salmon Production
Authors: Thomson Richard E. , Beamish Richard J. , Beacham Terry D. , Trudel Marc , Whitfield Paul H. , Hourston Roy A. S.
Published: July 2012

Record low returns of sockeye salmon Oncorhynchus nerka to the Fraser River in 2009 were followed by record high returns to the river in 2010, providing an unprecedented opportunity to examine links between oceanic factors and the survival of Pacific salmon stocks. The low returns in 2009 indicated poor early marine survival of juvenile sockeye salmon in 2007. The poor survival was likely due to low food levels arising from unfavorable wind and runoff conditions in the Strait of Georgia and the Queen Charlotte Sound–Hecate Strait region in the spring of 2007. Conversely, the high returns in 2010 were associated with a large smolt output from the Fraser River and good early marine survival in 2008. This enhanced survival was likely associated with adequate food levels arising from favorable oceanic conditions in the Strait of Georgia and the Queen Charlotte Sound–Hecate Strait region in the spring of 2008. We speculate that ocean factors during the subsequent marine years also affected brood year strength. Specifically, the back-to-back La Niña winters of 2007–2008 and 2008–2009 would have negatively influenced the survivability of the 2007 entry stocks, while the El Niño winter of 2009–2010 would have positively affected the survivability of the 2008 entry stocks. We conclude that poor early marine survival leads to low production. However, if large numbers of healthy fish survive the early marine entry, and if conditions during at least one of the two ocean winters in the Gulf of Alaska are favorable to stock survivability, then returns to the river can be high.

Received September 27, 2011; accepted February 29, 2012
Performance of a Full-Duplex Passive Integrated Transponder (PIT) Antenna System in Estuarine Channels
Authors: Bass Arthur L. , Giannico Guillermo R. , Brooks Gabriel T.
Published: July 2012

Passive integrated transponder (PIT) technology is rarely utilized in estuaries due to (1) saline water's attenuation of an antenna's electromagnetic field, (2) rapidly changing water properties and levels, and (3) the challenges of installing and maintaining antennas in silty, brackish conditions. We present methods for the construction and installation of antennas that can detect 12-mm full-duplex PIT tags in salinities up to 33‰. We evaluated their reading performance under variable water salinities, temperatures, and depths in the upper estuaries of three streams. We found that water depth, salinity, and temperature were all negatively correlated with antenna current, but that the relative importance of these variables varied depending upon aspects of the antenna deployment. Since our antennas held amperage levels adequate for maintenance of a complete electromagnetic field throughout all test conditions, we suggest that successful detection was more dependent upon the antenna system's coverage of the water column and the swimming path of fish through the antenna system than individual antenna performance. In addition to fish, this technology could be applied to studies of mammals, crustaceans, and particles transported through estuarine channels.

Received July 28, 2011; accepted February 19, 2012
The Synchronous Failure of Juvenile Pacific Salmon and Herring Production in the Strait of Georgia in 2007 and the Poor Return of Sockeye Salmon to the Fraser River in 2009
Authors: Beamish R. J. , Neville C. , Sweeting R. , Lange K.
Published: July 2012

Trawl studies from 1998 to 2009 indicated that juvenile Pacific salmon Oncorhynchus spp. and Pacific herring Clupea pallasii represented 98% of the fish in the surface waters of the Strait of Georgia during the day in the spring and early summer. Standardized catches of all juvenile Pacific salmon in the trawl surveys were lowest in 2007. Catches of young-of-the-year Pacific herring were also extremely low in 2007. Three years later, the 2007 year-class had the lowest recruitment to the fishery in recorded history. In 2007, juvenile coho salmon O. kisutch and Chinook salmon O. tshawytscha were small and had the lowest condition of the fish in all surveys as well as a high percentage of empty stomachs. The early marine survival of coho salmon in 2007 and the total survival in 2008 were exceptionally poor. Trawl catches of juvenile chum salmon O. keta in 2007 were the lowest of all surveys. Adult chum salmon from these juveniles that returned in 2010 had extremely poor survival. Juvenile sockeye salmon O. nerka that entered the Strait of Georgia in the spring of 2007 and returned to the Fraser River as adults in 2009 also had such exceptionally poor marine survival that a judicial inquiry was conducted to determine the causes. The synchronous poor growth, survival, or both of all of the major species in the surface waters of the Strait of Georgia in the spring of 2007 indicated that there was a common cause which we propose as poor food production. The causes of the high mortality likely represented a unique extreme in the variability of the factors that normally affect the survival of juvenile Pacific salmon and Pacific herring in the early marine period in the Strait of Georgia.

Received September 27, 2011; accepted March 8, 2012
Implications of Mark-Selective Fishing for Ocean Harvests and Escapements of Sacramento River Fall Chinook Salmon Populations
Authors: Pyper Brian J. , Cramer Steven P. , Ericksen Randolph P. , Sitts Richard M.
Published: July 2012

The need to protect imperiled salmon stocks along the Pacific coast of North America has led to an increasing use of mark-selective fisheries (MSFs) as a management strategy to reduce harvest mortality of wild salmon while allowing harvest of abundant hatchery salmon. However, MSFs remain untested in ocean fisheries for Chinook salmon Oncorhynchus tshawytscha off the coasts of California and Oregon, where hatchery fish have been estimated to compose the majority of Chinook salmon but where harvests have been restricted to protect several imperiled stocks. We developed a quantitative framework based on conventional cohort models to examine how aggregate ocean harvest and in-river escapement of Sacramento River fall-run Chinook salmon, the numerically dominant stock in the region, would have differed under MSF scenarios compared with the historic, traditional fishery. At historic contact rates (fishing effort) for 1988–2007, we estimated that annual in-river escapement of natural-origin fish would have increased by 119% on average under MSF scenarios, while reductions in harvest would have been inversely proportional to the fraction of hatchery-origin fish. During the more recent period of constrained fishing (2001–2007), we estimated MSF outcomes for a range of plausible contact rates (40–60% of age-4 fish) and hatchery fractions (40–80% of Chinook salmon). The combination of these factors determined the magnitude of estimated harvest reductions or gains under MSFs, with total MSF harvest (2001–2007) ranging from 46% lower to 48% higher than historic harvest. Increases in total escapement of natural-origin fish (2001–2007) under MSFs ranged from 24% to 48% depending on the contact rate. Comparisons between the traditional fishery and simulated MSF outcomes were robust to a wide range of cohort parameter values, suggesting that our aggregate results provide useful insights into potential MSF outcomes and the effects of key uncertainties.

Received November 1, 2010; accepted December 19, 2011
Geographic Patterns of Fishes and Jellyfish in Puget Sound Surface Waters
Authors: Rice Casimir A. , Duda Jeffrey J. , Greene Correigh M. , Karr James R.
Published: July 2012

We explored patterns of small pelagic fish assemblages and biomass of gelatinous zooplankton (jellyfish) in surface waters across four oceanographic subbasins of greater Puget Sound. Our study is the first to collect data documenting biomass of small pelagic fishes and jellyfish throughout Puget Sound; sampling was conducted opportunistically as part of a juvenile salmon survey of daytime monthly surface trawls at 52 sites during May–August 2003. Biomass composition differed spatially and temporally, but spatial differences were more distinct. Fish dominated in the two northern basins of Puget Sound, whereas jellyfish dominated in the two southern basins. Absolute and relative abundance of jellyfish, hatchery Chinook salmon Oncorhynchus tshawytscha, and chum salmon O. keta decreased with increasing latitude, whereas the absolute and relative abundance of most fish species and the average fish species richness increased with latitude. The abiotic factors with the strongest relationship to biomass composition were latitude, water clarity, and sampling date. Further study is needed to understand the spatial and temporal heterogeneity in the taxonomic composition we observed in Puget Sound surface waters, especially as they relate to natural and anthropogenic influences.

Received March 24, 2010; accepted December 23, 2011
Rational argument, rational inference
Authors: Hahn Ulrike , Harris Adam J.L. , Oaksford Mike
Published: July 2012

Reasoning researchers within cognitive psychology have spent decades examining the extent to which human inference measures up to normative standards. Work here has been dominated by logic, but logic has little to say about most everyday, informal arguments. Empirical work on argumentation within psychology and education has studied the development and improvement of argumentation skills, but has been theoretically limited to broad structural characteristics. Using the catalogue of informal reasoning fallacies established over the centuries within the realms of philosophy, Hahn and Oaksford ( 2007a ) recently demonstrated how Bayesian probability can provide a normative standard by which to evaluate quantitatively the strength of a wide range of everyday arguments. This broadens greatly the potential scope of reasoning research beyond the rather narrow set of logical and inductive arguments that have been studied; it also provides a framework for the normative assessment of argument content that has been lacking in argumentation research. The Bayesian framework enables both qualitative and quantitative experimental predictions about what arguments people should consider to be weak and strong, against which people's actual judgements can be compared. This allows the different traditions of reasoning and argumentation research to be brought together both theoretically and in empirical research.
Precision manufacturing for clinical-quality regenerative medicines
Authors: Williams David J. , Thomas Robert J. , Hourd Paul C. , Chandra Amit , Ratcliffe Elizabeth , Liu Yang , Rayment Erin A. , Archer J. Richard
Published: July 2012

Innovations in engineering applied to healthcare make a significant difference to people's lives. Market growth is guaranteed by demographics. Regulation and requirements for good manufacturing practice—extreme levels of repeatability and reliability—demand high-precision process and measurement solutions. Emerging technologies using living biological materials add complexity. This paper presents some results of work demonstrating the precision automated manufacture of living materials, particularly the expansion of populations of human stem cells for therapeutic use as regenerative medicines. The paper also describes quality engineering techniques for precision process design and improvement, and identifies the requirements for manufacturing technology and measurement systems evolution for such therapies.
Precision engineering: an evolutionary perspective
Authors: Evans Chris J.
Published: July 2012

Precision engineering is a relatively new name for a technology with roots going back over a thousand years; those roots span astronomy, metrology, fundamental standards, manufacturing and money-making (literally). Throughout that history, precision engineers have created links across disparate disciplines to generate innovative responses to society's needs and wants. This review combines historical and technological perspectives to illuminate precision engineering's current character and directions. It first provides us a working definition of precision engineering and then reviews the subject's roots. Examples will be given showing the contributions of the technology to society, while simultaneously showing the creative tension between the technological convergence that spurs new directions and the vertical disintegration that optimizes manufacturing economics.
Lithography for enabling advances in integrated circuits and devices
Authors: Garner C. Michael
Published: July 2012

Because the transistor was fabricated in volume, lithography has enabled the increase in density of devices and integrated circuits. With the invention of the integrated circuit, lithography enabled the integration of higher densities of field-effect transistors through evolutionary applications of optical lithography. In 1994, the semiconductor industry determined that continuing the increase in density transistors was increasingly difficult and required coordinated development of lithography and process capabilities. It established the US National Technology Roadmap for Semiconductors and this was expanded in 1999 to the International Technology Roadmap for Semiconductors to align multiple industries to provide the complex capabilities to continue increasing the density of integrated circuits to nanometre scales. Since the 1960s, lithography has become increasingly complex with the evolution from contact printers, to steppers, pattern reduction technology at i-line, 248 nm and 193 nm wavelengths, which required dramatic improvements of mask-making technology, photolithography printing and alignment capabilities and photoresist capabilities. At the same time, pattern transfer has evolved from wet etching of features, to plasma etch and more complex etching capabilities to fabricate features that are currently 32 nm in high-volume production. To continue increasing the density of devices and interconnects, new pattern transfer technologies will be needed with options for the future including extreme ultraviolet lithography, imprint technology and directed self-assembly. While complementary metal oxide semiconductors will continue to be extended for many years, these advanced pattern transfer technologies may enable development of novel memory and logic technologies based on different physical phenomena in the future to enhance and extend information processing.
The engineering needed for particle physics
Authors: Myers Steve
Published: July 2012

Today's particle accelerators and detectors are among the most complicated and expensive scientific instruments ever built, and they exploit almost every aspect of today's cutting-edge engineering technologies. In many cases, accelerator needs have been the driving force behind these new technologies, necessity being the mother of invention. This paper gives an overview of some engineering requirements for the construction and operation of present-day accelerators and detectors.
Ultra-precision engineering in lithographic exposure equipment for the semiconductor industry
Authors: Schmidt Robert-H. Munnig
Published: July 2012

The developments in lithographic tools for the production of an integrated circuit (IC) are ruled by ‘Moore’s Law’:
the density of components on an IC doubles in about every two years
. The corresponding size reduction of the smallest detail in an IC entails several technological breakthroughs. The wafer scanner, the exposure system that defines those details, is the determining factor in these developments. This review deals with those aspects of the positioning systems inside these wafer scanners that enable the extension of Moore’s Law into the future. The design of these systems is increasingly difficult because of the accuracy levels in the sub-nanometre range coupled with motion velocities of several metres per second. In addition to the use of feedback control for the reduction of errors, high-precision model-based feed-forward control is required with an almost ideally reproducible motion-system behaviour and a strict limitation of random disturbing events. The full mastering of this behaviour even includes material drift on an atomic scale and is decisive for the future success of these machines.
Micro-machining
Authors: Brinksmeier Ekkard , Preuss Werner
Published: July 2012

Manipulating bulk material at the atomic level is considered to be the domain of physics, chemistry and nanotechnology. However, precision engineering, especially micro-machining, has become a powerful tool for controlling the surface properties and sub-surface integrity of the optical, electronic and mechanical functional parts in a regime where continuum mechanics is left behind and the quantum nature of matter comes into play. The surprising subtlety of micro-machining results from the extraordinary precision of tools, machines and controls expanding into the nanometre range—a hundred times more precise than the wavelength of light. In this paper, we will outline the development of precision engineering, highlight modern achievements of ultra-precision machining and discuss the necessity of a deeper physical understanding of micro-machining.
Precision engineering for future propulsion and power systems: a perspective from Rolls-Royce
Authors: Beale Sam
Published: July 2012

Rolls-Royce today is an increasingly global business, supplying integrated power systems to a wide variety of customers for use on land, at sea and in the air. Its reputation for ‘delivering excellence’ to these customers has been built largely on its gas turbine technology portfolio, and this reputation relies on the quality of the company's expertise in design, manufacture and delivery of services. This paper sets out to examine a number of examples, such as the high-pressure turbine blade, of the company's reliance on precision design and manufacture, highlighting how this precision contributes to customer satisfaction with its products. A number of measures the company is taking to accelerate its competitiveness in precision manufacture are highlighted, not least its extensive relationships with the academic research base. The paper finishes by looking briefly at the demands of the company's potential future product portfolio.
Precision surface measurement
Authors: Jiang X.
Published: July 2012

Surface size, geometry and texture are some of the most influential subjects in the fields of precision and ultra-precision engineering, defining the functional interface through which emerging products operate. Next-generation products demand super-smooth surfaces, freeform geometries or even deterministically introduced microstructures to provide functional performance. Technological progress using these surfaces types is possible only if the associated manufacturing processes are rigorously controlled and the surfaces are measurable. Metrology for advanced surfaces is not established. The current state of the art is challenged in respect to (i) surface characteristics, extremity of size, ultra precision, quality, geometric complexity, or combinations of these aspects, and (ii) measurement technology for the manufacturing environment, in particular, online, non-contact, high speed, ease of use, small footprint and robustness. This study addresses the challenges in this subject area and discusses some fundaments and principles derived from interdisciplinary research. The combination of these aspects is enabling the creation of manufacturing-environment-based measurement technology. This is expected to facilitate advanced surface manufacture over a wide range of sectors, including large science programmes and high-technology engineering.
Precision metrology
Authors: Jiang X. , Whitehouse D. J.
Published: July 2012

This article is a summary of the Satellite Meeting, which followed on from the Discussion Meeting at the Royal Society on ‘Ultra-precision engineering: from physics to manufacture’, held at the Kavli Royal Society International Centre, Chicheley Hall, Buckinghamshire, UK. The meeting was restricted to 18 invited experts in various aspects of precision metrology from academics from the UK and Sweden, Government Institutes from the UK and Germany and global aerospace industries. It examined and identified metrology problem areas that are, or may be, limiting future developments in precision engineering and, in particular, metrology. The Satellite Meeting was intended to produce a vision that will inspire academia and industry to address the solutions of those open-ended problems identified. The discussion covered three areas, namely the function of engineering parts, their measurement and their manufacture, as well as their interactions.
Pedobacter luteus sp. nov., isolated from soil
Authors: Oh Hyun-Woo , Kim Byung-Chun , Park Doo-Sang , Jeong Won-Jin , Kim Hyangmi , Lee Kang Hyun , Kim Sung Uk
Published: July 2012

Two strains of Gram-staining-negative, rod-shaped bacteria that were motile by gliding, N7d-4T and B4a-b5, were isolated during a study of culturable bacteria in soil cultivated with potatoes. These isolates grew at 15–37 °C and at pH 6.5–7.0. The major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0, iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The major polar lipids were phosphatidyl-N-methylethanolamine and phosphatidylethanolamine. The strains contained d-18 : 0 and d-19 : 0 sphingosines. The DNA G+C contents of strains N7d-4T and B4a-b5 were 48.5 and 46.9 mol% (HPLC), respectively. A phylogenetic analysis based on 16S rRNA gene sequences showed that strains N7d-4T and B4a-b5 were affiliated with

Pedobacter

species in the family

Sphingobacteriaceae

. Strains N7d-4T and B4a-b5 shared 99.9 % sequence similarity, and the most closely related

Pedobacter

type strains were

Pedobacter composti

TR6-06T (96.5 and 96.7 % sequence similarity, respectively),

P. oryzae

N7T (95.4 and 95.6 %) and

P. caeni

LMG 22862T (94.0 and 94.4 %). Phenotypic data and phylogenetic inference clearly distinguished the two isolates from other

Pedobacter

species. Based on these data, the isolates are considered to represent a novel species of the genus

Pedobacter

, for which the name Pedobacter luteus sp. nov. is proposed. The type strain is N7d-4T ( = KCTC 22699T  = DSM 22385T).
Lactobacillus kimchiensis sp. nov., isolated from a fermented food
Authors: Kim Jandi , Kim Joon Yong , Kim Min-Soo , Roh Seong Woon , Bae Jin-Woo
Published: July 2012

A novel bacterium was isolated from a traditional fermented food, kimchi. The morphology, physiology, biochemical properties and 16S rRNA gene sequence of strain L133T were studied. Strain L133T was Gram-reaction-positive, catalase-negative and homofermentative, with rod-shaped cells that formed cream colonies. Cells grew in the presence of 0–5 % (w/v) NaCl (optimum, 1–2 %), at pH 5.0–9.0 (optimum, pH 7.0–8.0) and at 15–37 °C (optimum, 25 °C). Comparative 16S rRNA gene and pheS sequence analysis of strain L133T indicated that the strain belonged to the genus

Lactobacillus

. The major fatty acids were identified as C18 : 1ω9c, C16 : 0 and C18 : 0, and the cell wall contained peptidoglycan of the l-Lys–d-Asp type. DNA–DNA relatedness values between strain L133T and related species were below 11±0.4 %. The DNA G+C content of strain L133T was 35.7 mol%. Analysis of 16S rRNA gene sequences, as well as physiological and biochemical tests, identified genotypic and phenotypic differences between strain L133T and other species of the genus

Lactobacillus

. Based on these analyses, strain L133T is proposed to be a novel species of the genus

Lactobacillus

, named Lactobacillus kimchiensis. The type strain is L133T ( = KACC 15533T = JCM 17702T = DSM 24716T).
Species reassignment of Geotrichum bryndzae, Geotrichum phurueaensis, Geotrichum silvicola and Geotrichum vulgare based on phylogenetic analyses and mating compatibility
Authors: Groenewald Marizeth , Coutinho Teresa , Smith Maudy Th. , van der Walt J. P.
Published: July 2012

The present classification of Galactomyces and its anamorph, Geotrichum, is based on various studies that used morphology, ecology, biochemistry, DNA–DNA reassociation comparisons and gene sequencing. In this study, the identities of strains of the Centraalbureau voor Schimmelcultures yeast culture collection, as well as seven strains from South Africa, were examined by analyses of the nucleotide divergence in the internal transcribed spacer regions of the nuclear rRNA gene (nrRNA) operon, the D1/D2 domains of the 26S rRNA gene and partial actin gene sequences as well as compatibility studies. The South African strains were assigned to species in the genus Galactomyces. The phylogenetic analyses and mating studies revealed that Geotrichum silvicola and Geotrichum bryndzae are synonyms of Galactomyces candidus and that Geotrichum vulgare is a synonym of Galactomyces pseudocandidus.
Salimesophilobacter vulgaris gen. nov., sp. nov., an anaerobic bacterium isolated from paper-mill wastewater
Authors: Zhang Yan-Zhou , Fang Ming-Xu , Zhang Wen-Wu , Li Tian-Tian , Wu Min , Zhu Xu-Fen
Published: July 2012

A novel anaerobic, heterotrophic bacterium, designated strain Zn2T, was isolated from the wastewater of a paper mill in Zhejiang, China. Cells were Gram-type-positive rods, 0.5–0.8 µm wide and 2–4 µm long, and were motile by a lateral flagellum. The ranges of temperature and pH for growth were 10–50 °C and pH 6.0–9.5. Optimal growth occurred at 35 °C and pH 7.3–7.5. The strain did not require NaCl for growth, but its inclusion in the medium improved growth (optimum concentration 6 %). Substrates utilized as sole carbon sources were peptone, tryptone, Casamino acids, d-xylose, salicin, glycerol, formate, acetate and propionate. The main products of carbohydrate fermentation were acetate, formate, propionate and lactate. Elemental sulfur, thiosulfate and Fe(III) were used as electron acceptors, but sulfate, sulfite, nitrate, nitrite and Mn(IV) were not. Growth was inhibited by the addition of 10 µg ampicillin, penicillin, tetracycline or chloramphenicol ml−1. iso-C15 : 0, C14 : 0, C16 : 0, C16 : 1
cis9 and C18 : 1
cis9 were the major fatty acids. Strain Zn2T did not contain any detectable menaquinones or ubiquinones. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, two unknown phospholipids and four unknown glycolipids. The genomic DNA G+C content was 37 mol%, as determined by HPLC. 16S rRNA gene sequence analysis revealed that strain Zn2T was a member of family

Clostridiaceae

, and was most closely related to the type strains of

Geosporobacter subterraneus

,

Thermotalea metallivorans

and

Caminicella sporogenes

, showing 91.2, 90.3 and 91.1 % sequence similarity, respectively. On the basis of its phenotypic and genotypic properties, strain Zn2T is suggested to represent a novel species of a new genus, for which the name Salimesophilobacter vulgaris gen. nov., sp. nov. is proposed. The type strain of Salimesophilobacter vulgaris is Zn2T ( = DSM 24770T  = JCM 17796T).
Massilia

yuzhufengensis sp. nov., isolated from an ice core
Authors: Shen Liang , Liu Yongqin , Wang Ninglian , Yao Tandong , Jiao Nianzhi , Liu Hongcan , Zhou Yuguang , Xu Baiqing , Liu Xiaobo
Published: July 2012

A Gram-negative, rod-shaped, aerobic, motile bacterium, strain Y1243-1T, was isolated from an ice core drilled from Yuzhufeng Glacier, Tibetan Plateau, China. Cells had polar flagella. The novel strain shared 94.7–97.6 % 16S rRNA gene sequence similarity with the type strains of species of the genus

Massilia

. The novel isolate is thus classified in the genus

Massilia

. The major fatty acids of strain Y1243-1T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) (43.98 %), C16 : 0 (27.86 %), C10 : 0 3-OH (7.10 %), C18 : 0 (6.95 %) and C18 : 1ω7c (5.01 %). The predominant isoprenoid quinone was Q-8. The DNA G+C content of strain Y1243-1T was 65.7 mol% (T
m). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. A number of phenotypic characteristics distinguished the novel isolate from the type strains of recognized

Massilia

species. Furthermore, in DNA–DNA hybridization tests, strain Y1243-1T shared 45 % relatedness with its closest phylogenetic relative,

Massilia consociata

CCUG 58010T. From the genotypic and phenotypic data, it is evident that strain Y1243-1T represents a novel species of the genus

Massilia

, for which the name

Massilia

yuzhufengensis sp. nov. is proposed. The type strain is Y1243-1T ( = KACC 16569T = CGMCC 1.12041T).
Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus sp. nov., isolated from marine environments
Authors: Jeong Sang Hyeon , Yang Sung-Hyun , Jin Hyun Mi , Kim Jeong Myeong , Kwon Kae Kyoung , Jeon Che Ok
Published: July 2012

Two novel Gram-stain-negative, chemoheterotrophic and strictly aerobic bacteria, strains GY2T and SPO729T, were isolated from a tidal flat at Gwangyang Bay in Korea and a marine sponge sample from the Pacific Ocean, respectively. The two strains were halotolerant, catalase- and oxidase-positive, and non-motile rods. Optimum temperature and pH for growth of both strains were observed to be 35 °C and pH 7.0–7.5, but optimum salinity for strain SPO729T [2–3 % (w/v)] was slightly higher than that for strain GY2T (1–2 %). The major cellular fatty acids of both strains were C16 : 0, iso-C15 : 0, iso-C17 : 0, iso-C17 : 1ω9c, C18 : 1ω7c, iso-C11 : 0 and iso-C11 : 0 3-OH. The genomic DNA G+C contents of strains GY2T and SPO729T were 55.1 and 57.9 mol%, respectively, and ubiquinone 8 (Q-8) was detected as the sole respiratory quinone from the two strains. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains GY2T and SPO729T formed tight phyletic lineages with members of the genus

Microbulbifer

. Strain GY2T was closely related to

Microbulbifer okinawensis

ABABA23T (98.2 %), strain SPO729T (98.0 %) and

Microbulbifer donghaiensis

CN85T (97.0 %); strain SPO729T was closely related to

M. okinawensis

ABABA23T (98.3 %) and

M. donghaiensis

CN85T (98.2 %). The DNA–DNA relatedness values of strain GY2T with

M. okinawensis

ABABA23T, strain SPO729T and

M. donghaiensis

CN85T were 40.0±2.1 %, 13.1±3.9 % and 16.2±5.8 %, respectively, whereas those of strain SPO729T with

M. okinawensis

ABABA23T and

M. donghaiensis

CN85T were 48.0±4.0 % and 34.6±9.3 %, respectively. On the basis of phenotypic and molecular features, it is concluded that the two strains GY2T and SPO729T represent two novel species of the genus

Microbulbifer

, for which the names Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus are proposed; the type strains are GY2T ( = KACC 16189T = JCM 17800T) and SPO729T ( = KCCM 42667T = JCM 14507T), respectively.
Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond
Authors: Snauwaert Isabel , Hoste Bart , De Bruyne Katrien , Peeters Karolien , De Vuyst Luc , Willems Anne , Vandamme Peter
Published: July 2012

Two lactic acid-producing, Gram-stain-positive rods were isolated from a microbial mat actively growing in the littoral zone of an Antarctic lake (Forlidas Pond) in the Pensacola mountains and studied using a polyphasic taxonomic approach. The isolates were examined by phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of pheS, rpoA and atpA, and biochemical and genotypic characteristics. One strain, designated LMG 26641, belonged to

Carnobacterium alterfunditum

and the other strain, designated LMG 26642T, could be assigned to a novel species, with

Carnobacterium funditum

DSM 5970T as its closest phylogenetic neighbour (99.2 % 16S rRNA gene sequence similarity). Carnobacterium iners sp. nov. could be distinguished biochemically from other members of the genus

Carnobacterium

by the lack of acid production from carbohydrates. DNA–DNA relatedness confirmed that strain LMG 26642T represented a novel species, for which we propose the name Carnobacterium iners sp. nov. (type strain is LMG 26642T  = CCUG 62000T).
Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus

Sphingopyxis

in the genus Sphingorhabdus gen. nov.
Authors: Jogler Mareike , Chen Hong , Simon Julia , Rohde Manfred , Busse Hans-Jürgen , Klenk Hans-Peter , Tindall Brian J. , Overmann Jörg
Published: July 2012

A previously undescribed aerobic, non-sporulating bacterium, strain G1A_585T, was isolated from an oligotrophic freshwater lake in Bavaria, Germany. The rod-shaped cells were Gram-stain-negative and non-motile. Based on 16S rRNA gene sequence similarity, strain G1A_585T was a member of the family

Sphingomonadaceae

and shared <95.2 % similarity with type strains of all members of the most closely related genus,

Sphingopyxis

. Phyogenetically, the isolate shared a root with strains of three marine species,

Sphingopyxis flavimaris

DSM 16223T,

Sphingopyxis marina

DSM 22363T and

Sphingopyxis litoris

DSM 22379T. The polar lipids of strain G1A_585T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipids, three glycolipids and one unknown lipid. Ubiquinone-10 was the dominant quinone (93.1 %) and ubiquinone-9 (6.5 %) was also detected. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 38.2 %); C16 : 1ω7c (33.6 %) and C14 : 0 2-OH (17.8 %). The major polyamine was spermidine and traces of 1,3-diaminopropane, putrescine and spermine were also detected. The DNA G+C content of strain G1A_585T was 55.7 mol% and the isolate was oxidase- and catalase-positive. Based on the phylogenetic relationship, the low DNA G+C content compared with most other members of the genus

Sphingopyxis

and the presence of signature nucleotides in the 16S rRNA gene sequence, a novel species in a new genus and species, Sphingorhabdus planktonica gen. nov., sp. nov., is proposed; the type strain of Sphingorhabdus planktonica is G1A_585T ( = DSM 25081T  = LMG 26646T). Because

Sphingopyxis flavimaris

DSM 16223T,

Sphingopyxis marina

DSM 22363T and

Sphingopyxis litoris

DSM 22379T form a phylogenetic group together with strain G1A_585T that is clearly separated from all other known

Sphingopyxis

strains and share signature nucleotides, these three

Sphingopyxis

strains are reclassified as members of the proposed novel genus Sphingorhabdus: Sphingorhabdus flavimaris comb. nov. (type strain SW-151T = DSM 16223T = KCTC 12232T), Sphingorhabdus marina comb. nov. (type strain FR1087T = DSM 22363T = IMSNU 14132T = KCTC 12763T = JCM 14161T) and Sphingorhabdus litoris comb. nov. (type strain FR1093T = DSM 22379T = IMSNU 14133T = KCTC 12764T = JCM 14162T).
Rudaeicoccus suwonensis gen. nov., sp. nov., an actinobacterium isolated from the epidermal tissue of a root of a Phalaenopsis orchid
Authors: Kim Soo-Jin , Jang Yun-Hee , Ahn Jae-Hyung , Weon Hang-Yeon , Schumann Peter , Chun Se-Chul , Kwon Soon-Wo , Kim Wan-Gyu
Published: July 2012

A bacterial strain, designated HOR6-4T, was isolated from the epidermal tissue of a root of a Phalaenopsis orchid. Strain HOR6-4T was characterized using a polyphasic approach. The cells were aerobic, Gram-stain-positive, non-motile coccoids. Phylogenetic analysis of its 16S rRNA gene sequence revealed a clear affiliation with the family

Dermacoccaceae

. Strain HOR6-4T showed relatively low 16S rRNA gene sequence similarity (below 95.9 %) to type strains of species with validly published names, showing the highest sequence similarities to the type strains of

Flexivirga alba

(95.8 %) and

Yimella lutea

(95.5 %). The DNA G+C content of strain HOR6-4T was 64.7 mol%. Strain HOR6-4T had anteiso-C17 : 0 (19.3 %), 10-methyl C18 : 0 (tuberculostearic acid; 13.5 %) and 10-methyl C17 : 0 (11.7 %) as the major fatty acids and contained MK-8(H4) and MK-8(H6) as the predominant quinones. Polar lipids were diphosphatidylglycerol, phosphatidylinositol, three aminophospholipids, two phospholipids and an aminolipid. The peptidoglycan type was A4α, with an l-Lys–l-Thr–d-Glu interpeptide bridge with a glycine residue bound to the alpha-carboxyl group of d-Glu in position 2 of the peptide subunit. Mycolic acids were not present. On the basis of comparative analysis of phenotypic and phylogenetic traits, strain HOR6-4T is considered to represent a novel species in a new genus in the family

Dermacoccaceae

, for which the name Rudaeicoccus suwonensis gen. nov., sp. nov. is proposed. The type strain of Rudaeicoccus suwonensis is HOR6-4T ( = KACC 12637T  = DSM 19560T).
Mucilaginibacter jinjuensis sp. nov., with xylan-degrading activity
Authors: Khan Haji , Chung Eu Jin , Kang Dong Young , Jeon Che Ok , Chung Young Ryun
Published: July 2012

A Gram-negative, rod-shaped, pale-orange-pigmented bacterial strain with xylan-degrading activity designated YC7004T was isolated from a rotten-wood sample collected at Jinju, Korea, and its taxonomic position was investigated by using a polyphasic approach. The strain grew optimally on R2A medium at 30 °C and at pH 6. The major isoprenoid quinone was MK7 and major fatty acids were summed feature 3, iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH, iso-C17 : 1ω9c and C16 : 1ω5c. The G+C content of the genomic DNA was 40.0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the strain belongs to the genus

Mucilaginibacter

in the family

Sphingobacteriaceae

. The most closely related species were

Mucilaginibacter daejeonensis

(95.5 %),

Mucilaginibacter frigoritolerans

(94.6 %) and

Mucilaginibacter mallensis

(94.0 %). Based on the phylogenetic and chemotaxonomic data analyses, strain YC7004T represents a novel species of the genus

Mucilaginibacter

with the proposed name of Mucilaginibacter jinjuensis sp. nov. The type strain is YC7004T ( = KACC 16571T = NBRC 108856T).
E2F7, a novel target, is up-regulated by p53 and mediates DNA damage-dependent transcriptional repression
Authors: Carvajal Luis A. , Hamard Pierre-Jacques , Tonnessen Crystal , Manfredi James J.
Published: July 2012

The p53 tumor suppressor protein is a transcription factor that exerts its effects on the cell cycle via regulation of gene expression. Although the mechanism of p53-dependent transcriptional activation has been well-studied, the molecular basis for p53-mediated repression has been elusive. The E2F family of transcription factors has been implicated in regulation of cell cycle-related genes, with E2F6, E2F7, and E2F8 playing key roles in repression. In response to cellular DNA damage, E2F7, but not E2F6 or E2F8, is up-regulated in a p53-dependent manner, with p53 being sufficient to increase expression of E2F7. Indeed, p53 occupies the promoter of the E2F7 gene after genotoxic stress, consistent with E2F7 being a novel p53 target. Ablation of E2F7 expression abrogates p53-dependent repression of a subset of its targets, including E2F1 and DHFR, in response to DNA damage. Furthermore, E2F7 occupancy of the E2F1 and DHFR promoters is detected, and expression of E2F7 is sufficient to inhibit cell proliferation. Taken together, these results show that p53-dependent transcriptional up-regulation of its target, E2F7, leads to repression of relevant gene expression. In turn, this E2F7-dependent mechanism contributes to p53-dependent cell cycle arrest in response to DNA damage.
Control of viral latency in neurons by axonal mTOR signaling and the 4E-BP translation repressor
Authors: Kobayashi Mariko , Wilson Angus C. , Chao Moses V. , Mohr Ian
Published: July 2012

Latent herpes simplex virus-1 (HSV1) genomes in peripheral nerve ganglia periodically reactivate, initiating a gene expression program required for productive replication. Whether molecular cues detected by axons can be relayed to cell bodies and harnessed to regulate latent genome expression in neuronal nuclei is unknown. Using a neuron culture model, we found that inhibiting mTOR, depleting its regulatory subunit raptor, or inducing hypoxia all trigger reactivation. While persistent mTORC1 activation suppressed reactivation, a mutant 4E-BP (eIF4E-binding protein) translational repressor unresponsive to mTORC1 stimulated reactivation. Finally, inhibiting mTOR in axons induced reactivation. Thus, local changes in axonal mTOR signaling that control translation regulate latent HSV1 genomes in a spatially segregated compartment.
Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain
Authors: Licatalosi Donny D. , Yano Masato , Fak John J. , Mele Aldo , Grabinski Sarah E. , Zhang Chaolin , Darnell Robert B.
Published: July 2012

Two polypyrimidine tract RNA-binding proteins (PTBs), one near-ubiquitously expressed (Ptbp1) and another highly tissue-restricted (Ptbp2), regulate RNA in interrelated but incompletely understood ways. Ptbp1, a splicing regulator, is replaced in the brain and differentiated neuronal cell lines by Ptbp2. To define the roles of Ptbp2 in the nervous system, we generated two independent Ptbp2-null strains, unexpectedly revealing that Ptbp2 is expressed in neuronal progenitors and is essential for postnatal survival. A HITS-CLIP (high-throughput sequencing cross-linking immunoprecipitation)-generated map of reproducible Ptbp2–RNA interactions in the developing mouse neocortex, combined with results from splicing-sensitive microarrays, demonstrated that the major action of Ptbp2 is to inhibit adult-specific alternative exons by binding pyrimidine-rich sequences upstream of and/or within them. These regulated exons are present in mRNAs encoding proteins associated with control of cell fate, proliferation, and the actin cytoskeleton, suggesting a role for Ptbp2 in neurogenesis. Indeed, neuronal progenitors in the Ptbp2-null brain exhibited an aberrant polarity and were associated with regions of premature neurogenesis and reduced progenitor pools. Thus, Ptbp2 inhibition of a discrete set of adult neuronal exons underlies early brain development prior to neuronal differentiation and is essential for postnatal survival.
The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence
Authors: Aksoy Ozlem , Chicas Agustin , Zeng Tianying , Zhao Zhen , McCurrach Mila , Wang Xiaowo , Lowe Scott W.
Published: July 2012

Oncogene-induced senescence is an anti-proliferative stress response program that acts as a fail-safe mechanism to limit oncogenic transformation and is regulated by the retinoblastoma protein (RB) and p53 tumor suppressor pathways. We identify the atypical E2F family member E2F7 as the only E2F transcription factor potently up-regulated during oncogene-induced senescence, a setting where it acts in response to p53 as a direct transcriptional target. Once induced, E2F7 binds and represses a series of E2F target genes and cooperates with RB to efficiently promote cell cycle arrest and limit oncogenic transformation. Disruption of RB triggers a further increase in E2F7, which induces a second cell cycle checkpoint that prevents unconstrained cell division despite aberrant DNA replication. Mechanistically, E2F7 compensates for the loss of RB in repressing mitotic E2F target genes. Together, our results identify a causal role for E2F7 in cellular senescence and uncover a novel link between the RB and p53 pathways.
No simpler than mammals: axon and dendrite regeneration in Drosophila: Figure 1.
Authors: Nawabi Homaira , Zukor Katherine , He Zhigang
Published: July 2012

Despite important progress made in understanding the mechanisms of axon regeneration, how a neuron responds to an injury and makes a regenerative decision remains unclear. In this issue of Genes & Development, Song and colleagues (pp. 1612–1625) investigate axonal and dendritic regeneration in the Drosophila peripheral nervous system (PNS). With some mechanisms shared with mammals, this study reveals surprisingly complicated regenerative responses in terms of cell type, developmental stage, and mechanism specificity. With forward genetic potential, such invertebrates should be powerful in dissecting the cellular and molecular control of neuronal repair.
Signalling mechanisms of the leukocyte integrin αMβ2: Current and future perspectives
Authors: Lim Jenson , Hotchin Neil A
Published: July 2012

Integrins are a family of heterodimeric cell adhesion receptors expressed on most cells and are involved in many cellular functions including phagocytosis, a process by which professional phagocytes recognise, bind and internalise foreign materials larger than 0.5 µm in diameter. An example of a phagocytic integrin receptor is αMβ2, and this review seeks to provide fresh insights into the current knowledge of this subject. Key areas that this review will emphasise include, the classical understanding of bi‐directional signalling to and from αMβ2 (aka inside‐out and outside‐in signalling, respectively). For inside‐out signalling, we will review the involvement of the small GTPase, Rap1, FERM‐containing proteins such as talin and kindlin‐3, some of the kinases, and the GEF, cytohesin‐1 and vasodilator‐stimulated phosphoprotein (VASP). We also summarise studies into outside‐in signalling, focussing on the roles of RhoA and RhoG, and activation of Rac1 through the complex comprising TIAM, 14‐3‐3 and β2. We will also consider non‐classical signalling processes, which include integrin clustering and membrane ruffling. Through this review, we hope to highlight the importance of αMβ2 signalling mechanisms and their relevance to other integrin‐mediated events.
First record of the deep‐water whalefish Cetichthys indagator (Actinopterygii: Cetomimidae) in the North Atlantic Ocean
Authors: Vieira R. P. , Christiansen B. , Christiansen S. , Gonçalves J. M. S.
Published: July 2012

The whalefish Cetichthys indagator is reported for the first time in the North Atlantic Ocean. This record increases to five the number of specimens ever caught and represents the northernmost occurrence of this species in the northern hemisphere.