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C-DEBI Newsletter – November 1, 2016
This newsletter is also accessible via our website.



Message from the Director:

Please join me in welcoming Gwen Noda as C-DEBI Diversity Director who in her few weeks at USC, has dived into leading our diversity efforts to serve our students, postdocs, faculty, and other participants at USC and across the nation. Ms. Noda is a Los Angeles native who earned her B.S. in Marine Biology and M.A. in Biology both from UCLA with a research focus on benthic aquatic invertebrates. She brings an extensive background in informal education in the field and classroom to support and grow our education and outreach programs, e.g., as former Co-Director of the Center for Ocean Sciences Education Excellence COSEE-West and coordinator of the FLOW Citizen Science Monitoring Program at Bolsa Chica Wetlands and State Beach for Amigos de Bolsa Chica among others. 
 
We are also excited by a recent Nature Communications paper proposing a new bacterial phyla classification that highlights several C-DEBI persons of interest!  “Edwardsbacteria”, “Wallbacteria”, and “Nealsonbacteria” nod to our former Director Katrina Edwards, current External Advisory Board member Judy Wall, and colleague and grant recipient Ken Nealson. For details see the Banfield lab paper Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.
 
Cheers,

Jan Amend
C-DEBI Director


 

Publications


Frontiers in Microbiology
Assessing Marine Microbial Induced Corrosion at Santa Catalina Island, California
Gustavo A. Ramírez*, Colleen L. Hoffman, Michael D. Lee, Ryan A. Lesniewski, Roman A. Barco*, Arkadiy Garber, Brandy M. Toner, Charles G. Wheat*, Katrina J. Edwards* and Beth N. Orcutt*
*C-DEBI Contribution 336


High iron and eutrophic conditions are reported as environmental factors leading to accelerated low-water corrosion, an enhanced form of near-shore microbial induced corrosion. To explore this hypothesis, we deployed flow-through colonization systems in laboratory-based aquarium tanks under a continuous flow of surface seawater from Santa Catalina Island, CA, USA, for periods of 2 and 6 months. Substrates consisted of mild steel – a major constituent of maritime infrastructure – and the naturally occurring iron sulfide mineral pyrite. Four conditions were tested: free-venting “high-flux” conditions; a “stagnant” condition; an “active” flow-through condition with seawater slowly pumped over the substrates; and an “enrichment” condition where the slow pumping of seawater was supplemented with nutrient rich medium. Electron microscopy analyses of the 2-month high flux incubations document coating of substrates with “twisted stalks,” resembling iron oxyhydroxide bioprecipitates made by marine neutrophilic Fe-oxidizing bacteria (FeOB). Six-month incubations exhibit increased biofilm and substrate corrosion in the active flow and nutrient enriched conditions relative to the stagnant condition. A scarcity of twisted stalks was observed for all 6 month slow-flow conditions compared to the high-flux condition, which may be attributable to oxygen concentrations in the slow-flux conditions being prohibitively low for sustained growth of stalk-producing bacteria. All substrates developed microbial communities reflective of the original seawater input, as based on 16S rRNA gene sequencing. Deltaproteobacteria sequences increased in relative abundance in the active flow and nutrient enrichment conditions, whereas Gammaproteobacteria sequences were relatively more abundant in the stagnant condition. These results indicate that (i) high-flux incubations with higher oxygen availability favor the development of biofilms with twisted stalks resembling those of marine neutrophilic FeOB and (ii) long-term nutrient stimulation results in substrate corrosion and biofilms with different bacterial community composition and structure relative to stagnant and non-nutritionally enhanced incubations. Similar microbial succession scenarios, involving increases in nutritional input leading to the proliferation of anaerobic iron and sulfur-cycling guilds, may occur at the nearby Port of Los Angeles and cause potential damage to maritime port infrastructure.


Frontiers in Microbiology
Physiological Ecology of Microorganisms in Subglacial Lake Whillans
Trista J. Vick-Majors, Andrew C. Mitchell, Amanda M. Achberger, Brent C. Christner, John E. Dore, Alexander B. Michaud*, Jill A. Mikucki, Alicia M. Purcell, Mark L. Skidmore, John C. Priscu and The WISSARD Science Team
*C-DEBI Contribution 337


Subglacial microbial habitats are widespread in glaciated regions of our planet. Some of these environments have been isolated from the atmosphere and from sunlight for many thousands of years. Consequently, ecosystem processes must rely on energy gained from the oxidation of inorganic substrates or detrital organic matter. Subglacial Lake Whillans (SLW) is one of more than 400 subglacial lakes known to exist under the Antarctic ice sheet; however, little is known about microbial physiology and energetics in these systems. When it was sampled through its 800 m thick ice cover in 2013, the SLW water column was shallow (~2 m deep), oxygenated, and possessed sufficient concentrations of C, N, and P substrates to support microbial growth. Here, we use a combination of physiological assays and models to assess the energetics of microbial life in SLW. In general, SLW microorganisms grew slowly in this energy-limited environment. Heterotrophic cellular carbon turnover times, calculated from 3H-thymidine and 3H-leucine incorporation rates, were long (60 to 500 days) while cellular doubling times averaged 196 days. Inferred growth rates (average ~0.006 d−1) obtained from the same incubations were at least an order of magnitude lower than those measured in Antarctic surface lakes and oligotrophic areas of the ocean. Low growth efficiency (8%) indicated that heterotrophic populations in SLW partition a majority of their carbon demand to cellular maintenance rather than growth. Chemoautotrophic CO2-fixation exceeded heterotrophic organic C-demand by a factor of ~1.5. Aerobic respiratory activity associated with heterotrophic and chemoautotrophic metabolism surpassed the estimated supply of oxygen to SLW, implying that microbial activity could deplete the oxygenated waters, resulting in anoxia. We used thermodynamic calculations to examine the biogeochemical and energetic consequences of environmentally imposed switching between aerobic and anaerobic metabolisms in the SLW water column. Heterotrophic metabolisms utilizing acetate and formate as electron donors yielded less energy than chemolithotrophic metabolisms when calculated in terms of energy density, which supports experimental results that showed chemoautotrophic activity in excess of heterotrophic activity. The microbial communities of subglacial lake ecosystems provide important natural laboratories to study the physiological and biogeochemical behavior of microorganisms inhabiting cold, dark environments.




Proposal Calls


C-DEBI: Call for Research Project and Postdoctoral Fellowship Proposals
C-DEBI invites proposals for 1-year research projects (in the anticipated range of $50,000-$80,000) and 1-2 year graduate student and postdoctoral fellowships that will significantly advance C-DEBI's central research agenda: to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales. C-DEBI's research agenda balances exploration-based discovery, hypothesis testing, data integration and synthesis, and systems-based modeling. C-DEBI research support is provided to “expeditions of opportunity”, and we’ve created a webpage listing potential options for participation. We welcome you to provide information about other expeditions of opportunity to share with the C-DEBI community! Help us further our mission to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields. This request for proposals is open to all interested researchers at US institutions able to receive NSF funding as a subaward. Proposal deadline: December 1, 2016.

IODP-USSSP: Special Call for Applications for Expedition 371
The International Ocean Discovery Program (IODP) is seeking scientists with expertise in sedimentology, Cenozoic calcareous nannofossil biostratigraphy, and Cenozoic radiolarian biostratigraphy to sail on Expedition 371 Tasman Frontier Subduction Initiation and Paleogene Climate aboard the JOIDES Resolution. The deadline to apply to this special call is November 7, 2016.

NSF: Divison of Molecular and Cellular Biosciences: Investigator-initiatied research projects (MCB) Program Solicitation
The Division of Molecular and Cellular Biosciences (MCB) supports quantitative, predictive, and theory-driven fundamental research and related activities designed to promote understanding of complex living systems at the molecular, subcellular, and cellular levels. MCB is soliciting proposals for hypothesis-driven and discovery research and related activities in four core clusters: Molecular Biophysics, Cellular Dynamics and Function, Genetic Mechanisms and Systems and Synthetic Biology. MCB gives high priority to research projects that use theory, methods, and technologies from physical sciences, mathematics, computational sciences, and engineering to address major biological questions.  Research supported by MCB uses a range of experimental approaches--including in vivo, in vitro and in silico strategies--and a broad spectrum of model and non-model organisms, especially microbes and plants. Typical research supported by MCB integrates theory and experimentation. Projects that address the emerging areas of multi-scale integration, molecular and cellular evolution, quantitative prediction of phenome from genomic information, and development of methods and resources are particularly welcome. Highest funding priority is given to applications that have outstanding intellectual merit and strong broader impacts. Proposals that include research motivated by relevance to human health or address the molecular basis of human diseases and treatment are not appropriate for the Division and will be returned without review. Full proposal deadline: November 15, 2016.

NSF: Division of Environmental Biology (core programs) (DEB) Program Solicitation
The Division of Environmental Biology (DEB) supports fundamental research on populations, species, communities, and ecosystems. Scientific emphases range across many evolutionary and ecological patterns and processes at all spatial and temporal scales. Areas of research include biodiversity, phylogenetic systematics, molecular evolution, life history evolution, natural selection, ecology, biogeography, ecosystem structure, function and services, conservation biology, global change, and biogeochemical cycles. Research on organismal origins, functions, relationships, interactions, and evolutionary history may incorporate field, laboratory, or collection-based approaches; observational or manipulative experiments; synthesis activities; as well as theoretical approaches involving analytical, statistical, or computational modeling. Preliminary proposal due date: January 23, 2017.

NSF: Long Term Research in Environmental Biology (LTREB) Program Solicitation
The Long Term Research in Environmental Biology (LTREB) Program supports the generation of extended time series of data to address important questions in evolutionary biology, ecology, and ecosystem science. Research areas include, but are not limited to, the effects of natural selection or other evolutionary processes on populations, communities, or ecosystems; the effects of interspecific interactions that vary over time and space; population or community dynamics for organisms that have extended life spans and long turnover times; feedbacks between ecological and evolutionary processes; pools of materials such as nutrients in soils that turn over at intermediate to longer time scales; and external forcing functions such as climatic cycles that operate over long return intervals. The Program intends to support decadal projects. Funding for an initial, 5-year period requires submission of a preliminary proposal and, if invited, submission of a full proposal that includes a 15-page project description. Proposals for the second five years of support (renewal proposals) are limited to a ten-page project description and do not require a preliminary proposal. Preliminary proposal due date: January 23, 2017.

NSF: Dear Colleague Letter (DCL): Provision of Shallow Advanced Piston Coring Capabilities on JOIDES Resolution to the U.S. Research Community: "JR100"
The Division of Ocean Sciences (OCE) of the National Science Foundation (NSF) is providing up to four weeks each year of access to the drill ship JOIDES Resolution for U.S. researchers to use the Advanced Piston Coring (APC) system to collect cores up to sub-bottom depths of 100 meters to address research on multiple aspects of geology and geophysics of the ocean basins. This program, referred to as “JR100”, will not be part of the JOIDES Resolution’s participation in the International Ocean Discovery Program (IODP), and will be funded, managed, and implemented separately from the IODP. Proposals for JR100 coring cruises will be accepted by relevant science programs following announcement of the JOIDES Resolution FY2019 schedule after the May 2017 JOIDES Resolution Facility Board meeting. Prospective PIs are strongly encouraged to consult with a Program Officer to determine the applicable program proposal submission guidelines and deadlines.

NSF: Call for expressions of interest regarding provision of marine seismic capabilities to the U.S. research community
Please submit written responses by November 11, 2016.

NSF: Integrated Earth Systems (IES) Program Solicitaiton
Full proposal deadline: November 14, 2016.

Gulf of Mexico Research Initiative: Request for Proposals VI
Letter of Intent Deadline: November 14, 2016.

DCO: Deep Energy Community, Third Call for Proposals
Application deadline: November 20, 2016.

IODP-USSSP: Proposals for Pre-Drilling Activities and Workshops
The U.S. Science Support Program (USSSP) accepts proposals on a rolling basis for pre-drilling activities and semi-annually for workshops (next submission deadline December 1, 2016), related to the International Ocean Discovery Program (IODP).

IODP-USSSP: Schlanger Ocean Drilling Fellowships
The submission deadline is December 2, 2016.

NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.

 


Education & Outreach


C-DEBI: Call for Education and Outreach Project Proposals
C-DEBI invites proposals to support education and outreach projects, with a budget of up to $50,000 and a project duration of 1 year. The C-DEBI Education & Outreach Grants Program will fund the development of educational opportunities and materials that are pertinent to deep biosphere research in the subseafloor environment in support of our education and outreach goal to create distinctive, targeted education programs and promote increased public awareness about life below the seafloor. Help us further our mission to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields. Proposal deadline: December 1, 2016.

U.S. Department of Homeland Security: HS-STEM Summer Internship Program
The U.S. Department of Homeland Security (DHS) Science and Technology Directorate Office of University Programs sponsors a 10-week summer internship program for undergraduate and graduate students majoring in homeland security related science, technology, engineering and mathematics (HS-STEM) disciplines. The program provides students with quality research experiences at federal research facilities located across the country and allows students the opportunity to establish connections with DHS professionals. It is open to students in a broad spectrum of HS-STEM Disciplines and DHS mission-relevant Research Areas. Undergraduate students receive a $6,000 stipend plus travel expenses. Graduate students receive a $7,000 stipend plus travel expenses. Application deadline: December 7, 2016.

IODP-USSSP: Onboard Outreach Program
The current deadline to apply is November 2, 2016.

NSF: Improving Undergraduate STEM Education: Education and Human Resources, Program Solicitation
Exploration and Design Tier for Engaged Student Learning & Institution and Community Transformation proposal deadline: November 2, 2016.

The Hydrographic Society Of America: Student Scholarships
Application deadlines: November 15, 2016.

The Data Incubator: 8-week fellowship
Application deadline: November 17, 2016.

NSF: ADVANCE: Increasing the Participation and Advancement of Women in Academic Science and Engineering Careers (ADVANCE) Program Solicitation
Letter of intent due date: December 14, 2016.


 

Meetings & Activities


Spotlight: Early career C-DEBI scientists learn to navigate the ocean with the National Deep Submergence Facility
In early August 2016, 24 early career scientists set sail from Woods Hole, Massachusetts on research cruise AT-36 to the northwest Atlantic continental slope. There, more than a kilometer beneath the water’s surface, new methane seeps and coral habitat had recently been discovered, and the multidisciplinary team of scientists was eager to conduct a more thorough investigation.The primary aim of the expedition was to train young researchers (and potential future users) on the operational realities and scientific capabilities of National Deep Submergence Facility (NDSF) assets. With this in mind, the Research Vessel Atlantis was filled to the brim with an impressive technical arsenal. The human occupied submersible Alvin shared deck space with the autonomous underwater vehicle Sentry and a number of more standard oceanographic tools; daily plans sought to leverage these complementary capabilities in support of an integrated scientific program. Among the scientific team were several members of the C-DEBI community, including Roman Barco, Anne Dekas, Colleen Hoffman, Sean Jungbluth, and Katrina Twing.

2016 AGU Fall Meeting: Deep Biosphere-related Sessions

Missing a session of interest? Let us know!

C-DEBI: Introduction to Bioinformatics Workshop, December 10-11, 2016
C-DEBI will be running our second “Introduction to Bioinformatics Workshop” in December of this year, tentatively at Stanford University. Location and dates are planned to precede with the American Geophysical Union Annual Meeting 2016 in San Francisco, CA. For those interested in the workshop but are unsure if it will be informative OR are interested but cannot attend, a digital version of the workshop exists as part of a collaboration between C-DEBI and ECOGEO. All information can be found here: https://www.earthcube.org/group/ecogeo/omicsvm. This resource includes a link to download the virtual environment used in this previous iteration of the workshop, videos of the corresponding presentations, and links to protocol.io that follow along with the videos. The upcoming C-DEBI workshop will include some modifications and updates. RSVP by November 4, 2016: space is limited and a hotel needs to be booked soon! Contact instructor Ben Tully directly.

SIO: Participate in a Science Verification Cruise (SVC) abord the R/V Sally Ride
Scripps Institution of Oceanography invites scientists from the US oceanographic community to participate in Science Verification Cruises (SVCs) aboard the Ocean Class research vessel Sally Ride beginning in the fall of 2016. The goal of SVCs is to exercise the ship, the crew, and all scientific systems to verify satisfactory operations, and to characterize the capabilities of each system. Our SVC operations are intended to be complementary to SVCs aboard Neil Armstrong, in order to evaluate the Ocean Class vessels (AGOR 27 & 28) collectively. To be successful, this process needs participation by experienced researchers who can use their knowledge of shipboard scientific operations to evaluate, comment on, and improve the capabilities of Sally Ride. Science verification cruises will be conducted offshore southern California, lasting five to seven days each. We currently have availability in October 2016 and early January 2017. We anticipate additional opportunities in 2017, contingent on ship scheduling. We are seeking broad expressions of interest and scientific foci to inform our early planning. Funds are available to support the travel and logistical expenses of participants. Ship time will be supported by the Office of Naval Research.

ISSM 2017: Conference Announcement
The International Society of Subsurface Microbiology (ISSM) is pleased to invite delegates to attend ISSM 2017. This conference is the tenth in a series of international conferences devoted to providing a better understanding of the ecology, microbial community composition and function, and biogeochemistry of the earth’s subsurface environments. The Conference is being held in Rotorua, New Zealand, from 6-10 November 2017. Rotorua is a stunning location with a wide range of environments - physical, cultural and social, to discover and explore. The conference promises to be an unforgettable event that will bring together a wide range of international delegates from all around the globe. The conference will span 5 days, including a day of excursions, and over this period conference delegates will hear from leading experts in subsurface microbiology and discuss cutting edge developments in this area. Abstract submissions open December 15, 2016.

IODP Workshop: Demystifying the IODP Proposal Process for Early Career Scientists, January 23-25, 2017, Austin, Texas
The application deadline is November 11, 2016.

IODP-USSSP: ECORD Accepting Applications for Facility Board
Application deadline: December 2, 2016.




Employment


University of Pennsylvania: Two Graduate Research Assistant Positions
The Department of Earth and Environmental Science and the Center for Energy Research at the University of Pennsylvania seek graduate students interested in any of the following research areas: geomicrobiology, ecology, microbe-microbe and microbe-mineral interactions, biogeochemistry, ecophysiology and bioenergetics. Potential projects include: i) Microbial remediation of asbestos- This project provides the opportunity to interrogate microbe-mineral interactions in human-disposed minerals. 
ii) Bioenergetic principles of energy metabolism- This project will focus on the ecophysiology of hydrogenotrophic methanogenesis and/or Fe(III) reduction from marine geothermal environments. 
iii) Taxonomic classification- Isolation and characterization of novel chemosynthetic microorganisms from anoxic environments. 
The prospective students will be expected to work at the interface between geology, chemistry, and biology. If interested in learning more about this opportunity please contact Ileana Pérez- Rodríguez at: perezrod@usc.edu.

Research Corporation of the University of Hawai’i: Marine Research Associate III
Participates in oceanographic research cruises. Works at sea to perform and supervise data collection as designated by Hawai‘i Ocean Time-Series (HOT) protocols. Plans, leads, and supervises cruise activities as Watch Leader as assigned, and decides on modifications as circumstances warrant. Works with scientific staff and Electronics Technician in acquisition, processing, and analysis of physical oceanographic data, including data from a conductivity/temperature/depth/oxygen device (CTD), a thermosalinograph, an Acoustic Doppler Current Profiler (ADCP), and various moored instruments. Participates in preparation and loading/unloading of instruments and gear for oceanographic research expeditions. Trains volunteers and students. Works directly with Principal Investigator (PI) and Marine Research Associate V (MRA V) on quality control, report writing, and data analysis/interpretation of results. Contributes original writings and graphics to data reports and other publications. Performs high accuracy measurement and analysis of salinity from water samples, with an Autosalinometer following protocols and within allowable error. Oversees quality control of salinity measurements in accordance with standards set by HOT project. Trains personnel on use of the salinometer. Works with the Electronics Engineer/Technician to calibrate and troubleshoot various marine instruments. Assists with maintaining and developing web content for project websites. Application deadline: November 4, 2016.

University of Minnesota: 3 Tenure-Track Faculty Positions in Microbiology
The College of Biological Sciences at the University of Minnesota announces a cluster hire in microbial biology that will recruit three tenure-track assistant professors in the new Department of Plant and Microbial Biology. We seek outstanding microbiologists who utilize various approaches (including physiology, molecular biology, computation, diversity, cell biology, genetics, biochemistry, ecology and/or evolution) to understand microorganisms in fundamental, environmental and/or applied contexts. We encourage applicants working in the following research areas: Archaeal Microbiology, Environmental Metagenomics, Eukaryotic Microbiology, Industrial Microbiology, Microbial Cellular Biology. Applications are due November 15, 2016.

SIO: Faculty Position in Biological Oceanography/Marine Ecology
Scripps Institution of Oceanography (SIO) at the University of California San Diego seeks an outstanding candidate with interests in marine ecosystem, population, or organismal response to global change, with strong preference for a sea-going scientist. Research areas of interest could include but are not limited to experimental pelagic ecology, pelagic or benthic deep-sea biology, population and evolutionary genetics, fisheries oceanography, biogeochemistry, or marine physiology and biochemistry. The successful candidate will have the opportunity to interact with large scale interdisciplinary SIO field research programs, including the California Current Ecosystem-LTER, the California Cooperative Oceanic Fisheries Investigations (CalCOFI), and others. The candidate will develop a vigorous extramurally-supported research program, be committed to active teaching and mentoring of graduate students, and will teach in the new marine biology undergraduate major. Our strong preference is for hiring at the level of Assistant Professor, but appointments at the Associate level will be considered. Application deadline: November 20, 2016.

SIO: Faculty Position in Marine Geophysics
SIO invites applications for a tenure-track faculty position in marine geophysics. SIO seeks candidates whose research interest is in using geophysical methods to study any region of the Earth beneath the sea, including its geological history, structure (thermal, seismic, electrical, magnetic, or petrological), past and current movements, fluid behavior, tectonics, volcanology, seismic history and processes, or mineral resources. This includes the development of methods and instruments to study any of these topics. Application deadline: November 20, 2016.

CIW: Geophysical Laboratory Postdoctoral Fellowships
The Geophysical Laboratory of the Carnegie Institution of Washington invites applications for postdoctoral fellowships. The Geophysical Laboratory emphasizes interdisciplinary experimental and theoretical research in fields ranging from geoscience, microbiology, chemistry, to physics. The Laboratory supports world-class facilities in high-pressure research; organic, stable isotope and biogeochemistry; mineral physics and petrology; and astrobiology. Carnegie Postdoctoral Fellowships are awarded once a year. The deadline for submitting an application is November 30, 2016 and the position begins the following summer or autumn.

Smithsonian: Research Geologist (Biomineralogy)
Application deadline: November 11, 2016.

LDEO: Postdoctoral Fellowships in the Earth and Environmental Sciences
The deadline for applications is November 14, 2016.

Rice University: Wiess Post-Doctoral Research Fellowship, Department of Earth Science
Application deadline: November 15, 2016.

University of California, Santa Cruz: Two Tenure-Track Faculty Positions in the Earth and Planetary Sciences Department
(1) Fresh Water. Next review date: November 23, 2016. (2) Global Biogeochemistry. December 1, 2016.

ExxonMobil: Member of Technical Staff - Microbiology

The Ohio State University: Assistant Professor in Earth Sciences

University of Southern Mississippi: Postdoctoral Research Position in Marine Microbial Ecology
Review of applicants will begin immediately and proceed until the position is filled.






Don’t forget to email me with any items you'd like to share in future newsletters! We will also broadcast this information on our social media outlets, Twitter and Facebook. You are what makes our deep biosphere community!

 
Best, 
 
Matt
 
-- 
Matthew Janicak
Data Manager
Center for Dark Energy Biosphere Investigations (C-DEBI)
University of Southern California
janicak@usc.edu
3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371
Phone: 708-691-9563, Fax: 213-740-2437

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