Common Errors in Ecological Data Sharing

Objectives: (1) to identify common errors in data organization and metadata completeness that would preclude a “reader” from being able to interpret and re-use the data for a new purpose; and (2) to develop a set of best practices derived from these common errors that would guide researchers in creating more usable data products that could be readily shared, interpreted, and used. Methods: We used directed qualitative content analysis to assess and categorize data and metadata errors identified by peer reviewers of data papers published in the Ecological Society of America’s (ESA) Ecological Archives. Descriptive statistics provided the relative frequency of the errors identified during the peer review process. Results: There were seven overarching error categories: Collection & Organization, Assure, Description, Preserve, Discover, Integrate, and Analyze/Visualize. These categories represent errors researchers regularly make at each stage of the Data Life Cycle. Collection & Organization and Description errors were some of the most common errors, both of which occurred in over 90% of the papers. Conclusions: Publishing data for sharing and reuse is error prone, and each stage of the Data Life Cycle presents opportunities for mistakes. The most common errors occurred when the researcher did not provide adequate metadata to enable others to interpret and potentially re-use the data. Fortunately, there are ways to minimize these mistakes through carefully recording all details about study context, data collection, QA/ QC, and analytical procedures from the beginning of a research project and then including this descriptive information in the metadata

Implications of cellobiohydrolase glycosylation for use in biomass conversion

The cellulase producing ascomycete, Trichoderma reesei (Hypocrea jecorina), is known to secrete a range of enzymes important for ethanol production from lignocellulosic biomass. It is also widely used for the commercial scale production of industrial enzymes because of its ability to produce high titers of heterologous proteins. During the secretion process, a number of post-translational events can occur, however, that impact protein function and stability. Another ascomycete, Aspergillus niger var. awamori, is also known to produce large quantities of heterologous proteins for industry. In this study, T. reesei Cel7A, a cellobiohydrolase, was expressed in A. niger var. awamori and subjected to detailed biophysical characterization. The purified recombinant enzyme contains six times the amount of N-linked glycan than the enzyme purified from a commercial T. reesei enzyme preparation. The activities of the two enzyme forms were compared using bacterial (microcrystalline) and phosphoric acid swollen (amorphous) cellulose as substrates. This comparison suggested that the increased level of N-glycosylation of the recombinant Cel7A (rCel7A) resulted in reduced activity and increased non-productive binding on cellulose. When treated with the N-glycosidase PNGaseF, the molecular weight of the recombinant enzyme approached that of the commercial enzyme and the activity on cellulose was improved

Pulse Jet Mixer Overblow Testing for Assessment of Loadings During Multiple Overblows

The U.S. Department of Energy (DOE) Office of River Protection’s Waste Treatment Plant (WTP) is being designed and built to pretreat and then vitrify a large portion of the wastes in Hanford’s 177 underground waste storage tanks. The WTP consists of three primary facilities: pretreatment, low-activity waste (LAW) vitrification, and high-level waste (HLW) vitrification. The pretreatment facility will receive waste feed from the Hanford tank farms and separate it into 1) a high-volume, low-activity liquid stream stripped of most solids and radionuclides and 2) a much smaller volume of HLW slurry containing most of the solids and most of the radioactivity. Many of the vessels in the pretreatment facility will contain pulse jet mixers (PJMs) that will provide some or all of the mixing in the vessels. This technology was selected for use in so-called “black cell” regions of the WTP, where maintenance capability will not be available for the operating life of the WTP. PJM technology was selected for use in these regions because it has no moving mechanical parts that require maintenance. The vessels with the most concentrated slurries will also be mixed with air spargers and/or steady jets in addition to the mixing provided by the PJMs. This report contains the results of single and multiple PJM overblow tests conducted in a large, ~13 ft-diameter × 15-ft-tall tank located in the high bay of the Pacific Northwest National Laboratory (PNNL) 336 Building test facility. These single and multiple PJM overblow tests were conducted using water and a clay simulant to bound the lower and upper rheological properties of the waste streams anticipated to be processed in the WTP. Hydrodynamic pressures were measured at a number of locations in the test vessel using an array of nine pressure sensors and four hydrophones. These measurements were made under normal and limiting vessel operating conditions (i.e., maximum PJM fluid emptying velocity, maximum and minimum vessel contents for PJM operation, and maximum and minimum rheological properties). Test data collected from the PJM overblow tests were provided to Bechtel National, Inc. (BNI) for assessing hydrostatic, dynamic, and acoustic pressure loadings on in-tank structures during 1) single overblows; 2) multiple overlapping overblows of two to four PJMs; 3) simultaneous overblows of pairs of PJMs

The Tao of open science for ecology

The field of ecology is poised to take advantage of emerging technologies that facilitate the gathering, analyzing, and sharing of data, methods, and results. The concept of transparency at all stages of the research process, coupled with free and open access to data, code, and papers, constitutes “open science.” Despite the many benefits of an open approach to science, a number of barriers to entry exist that may prevent researchers from embracing openness in their own work. Here we describe several key shifts in mindset that underpin the transition to more open science. These shifts in mindset include thinking about data stewardship rather than data ownership, embracing transparency throughout the data life‐cycle and project duration, and accepting critique in public. Though foreign and perhaps frightening at first, these changes in thinking stand to benefit the field of ecology by fostering collegiality and broadening access to data and findings. We present an overview of tools and best practices that can enable these shifts in mindset at each stage of the research process, including tools to support data management planning and reproducible analyses, strategies for soliciting constructive feedback throughout the research process, and methods of broadening access to final research products

Support for maternal manipulation of developmental nutrition in a facultatively eusocial bee, Megalopta genalis (Halictidae)

Developmental maternal effects are a potentially important source of phenotypic variation, but they can be difficult to distinguish from other environmental factors. This is an important distinction within the context of social evolution, because if variation in offspring helping behavior is due to maternal manipulation, social selection may act on maternal phenotypes, as well as those of offspring. Factors correlated with social castes have been linked to variation in developmental nutrition, which might provide opportunity for females to manipulate the social behavior of their offspring. Megalopta genalis is a mass-provisioning facultatively eusocial sweat bee for which production of males and females in social and solitary nests is concurrent and asynchronous. Female offspring may become either gynes (reproductive dispersers) or workers (non-reproductive helpers). We predicted that if maternal manipulation plays a role in M. genalis caste determination, investment in daughters should vary more than for sons. The mass and protein content of pollen stores provided to female offspring varied significantly more than those of males, but volume and sugar content did not. Sugar content varied more among female eggs in social nests than in solitary nests. Provisions were larger, with higher nutrient content, for female eggs and in social nests. Adult females and males show different patterns of allometry, and their investment ratio ranged from 1.23 to 1.69. Adult body weight varied more for females than males, possibly reflecting increased variation in maternal investment in female offspring. These differences are consistent with a role for maternal manipulation in the social plasticity observed in M. genalis

Mixed plastics waste valorization through tandem chemical oxidation and biological funneling

115 p.-4 fig.-45 fig. supl.-14 tab supl.Mixed plastics waste represents an abundant and largely untapped feedstock for the production of valuable products. The chemical diversity and complexity of thesematerials, however, present major barriers to realizing this opportunity. In this work, we show that metal-catalyzed autoxidation depolymerizes comingled polymers into a mixture of oxygenated small molecules that are advantaged substrates for biological conversion. We engineer a robust soil bacterium, Pseudomonas putida, to funnel these oxygenated compounds into a single exemplary chemical product, either b-ketoadipate or polyhydroxyalkanoates. This hybrid process establishes a strategy for the selective conversion of mixed plastics waste into useful chemical products.Funding was provided by the US Department of Energy, Office of Energy Efficiency and Renewable Energy, Advanced Manufacturing Office (AMO), and Bioenergy Technologies Office (BETO). This work was performed as part of the BOTTLE Consortium and was supported by AMO and BETO under contract no. DE-AC36- 08GO28308 with the National Renewable Energy Laboratory (NREL),operated by the Alliance for Sustainable Energy, LLC. The BOTTLE Consortium includes members from MIT, funded under contract no. DE-AC36-08GO28308 with NREL. Contributions by S.S.S. were supported by the US Department of Energy, Office of Basic Energy Sciences, under award no. DEFG02-05ER15690.Peer reviewe

Eleven Quick Tips for Finding Research Data

Over the past decades, science has experienced rapid growth in the volume of data available for research—from a relative paucity of data in many areas to what has been recently described as a data deluge [‎1]. Data volumes have increased exponentially across all fields of science and human endeavour, including data from sky, earth, and ocean observatories; social media such as Facebook and Twitter; wearable health-monitoring devices; gene sequences and protein structures; and climate simulations [‎2]. This brings opportunities to enable more research, especially cross-disciplinary research that could not be done before. However, it also introduces challenges in managing, describing, and making data findable, accessible, interoperable, and reusable by researchers [‎3]. When this vast amount and variety of data is made available, finding relevant data to meet a research need is increasingly a challenge. In the past, when data were relatively sparse, researchers discovered existing data by searching literature, attending conferences, and asking colleagues. In today’s data-rich environment, with accompanying advances in computational and networking technologies, researchers increasingly conduct web searches to find research data. The success of such searches varies greatly and depends to a large degree on the expertise of the person looking for data, the tools used, and, partially, on luck. This article offers the following 11 quick tips that researchers can follow to more effectively and precisely discover data that meet their specific needs

The activities of Cel7A and rCel7A catylitic domains are compared on two cellulose substrates at 38°C

The extents of BC cellulose hydrolysis (panel A) is compared to the hydrolysis of PASC (panel B). The respective levels of bound enzyme are shown in panels C and D.<p><b>Copyright information:</b></p><p>Taken from "Implications of cellobiohydrolase glycosylation for use in biomass conversion"</p><p>http://www.biotechnologyforbiofuels.com/content/1/1/10</p><p>Biotechnology for Biofuels 2008;1():10-10.</p><p>Published online 1 May 2008</p><p>PMCID:PMC2427024.</p><p></p

Reconstructed molecular masses of the linker peptide CBM fragment of A) Cel7A and B) rCelA

<p><b>Copyright information:</b></p><p>Taken from "Implications of cellobiohydrolase glycosylation for use in biomass conversion"</p><p>http://www.biotechnologyforbiofuels.com/content/1/1/10</p><p>Biotechnology for Biofuels 2008;1():10-10.</p><p>Published online 1 May 2008</p><p>PMCID:PMC2427024.</p><p></p