bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of woody fuel characteristics on fuel ignition and consumption: a case study from a eucalypt forest in south-west Western Australia
Authors: Hollis J. J. , McCaw W. L. , Cruz M. G.
Published: May 2018

Coarse woody debris (>0.6 cm in diameter) is an important component of the fuel complex in Australian eucalypt forests, influencing both fire behaviour, smoke production and post-fire ecological processes. We investigated how physical characteristics of woody fuel affected ignition and consumption during an experimental fire where the fuel complex characteristics, fire weather and fire behaviour varied within a narrow range. Decay status, bark condition, arrangement, suspension and extent of charring were classified for 2866 coarse woody fuel particles. We used generalised linear model (GLM) analysis to explain ignition success and the extent of consumption of individual particles, with a focus on larger diameter fuels (>7.5 cm in diameter), which comprised 83% of the woody fuel load and 94% of the woody fuel consumed during the flaming and smouldering stages of combustion. Ignition success was best explained by a model that included fuel arrangement (a surrogate of fuel proximity), suspension and decay status. The extent of fuel consumption was greater for pieces in advanced stages of decay, but suspension (inversely related) and arrangement (directly related) also affected the outcome. Forest management practices, previous fire history and other natural disturbances are likely to influence the distribution of pre-fire diameters and suspension classes that characterise large woody fuels at a site, and will therefore influence woody fuel consumption. This has practical implications for quantifying heat release and atmospheric emissions from fires burning in forests with different management histories.
Regulation of myeloid cell phagocytosis by LRRK2 via WAVE2 complex stabilization is altered in Parkinson’s disease
Authors: Kim Kwang Soo , Marcogliese Paul C. , Yang Jungwoo , Callaghan Steve M. , Resende Virginia , Abdel-Messih Elizabeth , Marras Connie , Visanji Naomi P. , Huang Jana , Schlossmacher Michael G. , Trinkle-Mulcahy Laura , Slack Ruth S. , Lang Anthony E. ,   Canadian Lrrk2 in Inflammation Team (CLINT), Park David S. , Brown Earl , Gibbings Derrick , Hayley Shawn , Park David , Philpott Dana C. , Rioux John D. , Schlossmacher Michael , Schurr Erwin
Published: May 2018

Significance

Determining the role for LRRK2, the most common Parkinson’s disease (PD) gene in neurons has been a challenge for the field. Combining interaction data from an unbiased screen in flies and a conserved physical relationship, we show that LRRK2 binds and phosphorylates the actin remodeling protein WAVE2 specifically in myeloid cells. Furthermore, we demonstrate that this relationship is important for WAVE2 stability and the dynamics of the phagocytic response. Finally, we provide evidence that in both mammalian cocultures, flies, and a murine model of PD that LRRK2s action on WAVE2 may be important for neuronal survival. This work supports the role for LRRK2 in immune-signaling and the role for the immune system in the pathogenesis and progression of PD.
Sequentially bridged graphene sheets with high strength, toughness, and electrical conductivity
Authors: Wan Sijie , Li Yuchen , Mu Jiuke , Aliev Ali E. , Fang Shaoli , Kotov Nicholas A. , Jiang Lei , Cheng Qunfeng , Baughman Ray H.
Published: May 2018

Significance

There is a continuing search for manufacturable sheets having high strength and toughness in all sheet directions for diverse applications, from airplanes to windmills. Cross-plied carbon fibers in a polymer resin requiring high-temperature cure presently provide the common solution. We demonstrate cross-linked graphene sheets that are manufacturable from graphene platelets, which are resin-free, processable at low temperature, contain less than 10 wt % additives, and provide high strength and record toughness in all in-plane directions. This advance results from successive use of π–π and covalent cross-linking agents. Simultaneous enhancement of strength, durability, and electrical conductivity are demonstrated. Spectroscopic measurements, including Raman studies of interplatelet stress transfer, elucidate the chemical nature and physical consequences of these dual cross-linking agents.
Approach to classify, separate, and enrich objects in groups using ensemble sorting
Authors: Turk-MacLeod Rebecca , Henson Alon , Rodriguez-Garcia Marc , Gibson Graham M. , Aragon Camarasa Gerardo , Caramelli Dario , Padgett Miles J. , Cronin Leroy
Published: May 2018

Significance

The sorting and separation of objects, from single cells, droplets, or macromolecules, to materials, is an important operation central to many scientific investigations. Indeed, it is central to the fabrication of machines and detection technologies; however, most methods focus on separating individual components which can be costly and time-consuming, and it is difficult to achieve high throughput at low error rates. Here, we propose a simple method applicable over a large size and material range to sort objects in groups or ensembles using a set of registers, which are themselves sorted again, and then re-sorted iteratively. The result is a lossless enrichment process that leads to a very high purity and can cope with errors and highly dynamic populations.
Insulin suppresses the production of fibroblast growth factor 23 (FGF23)
Authors: Bär Ludmilla , Feger Martina , Fajol Abul , Klotz Lars-Oliver , Zeng Shufei , Lang Florian , Hocher Berthold , Föller Michael
Published: May 2018

Significance

Fibroblast growth factor 23 (FGF23) regulates phosphate and vitamin D metabolism and induces left heart hypertrophy. The importance of FGF23 is supported by the consequences of FGF23 deficiency: FGF23-deficient mice have a significantly reduced life span and recapitulate human age-associated diseases. Moreover, FGF23 has gained attention as a potential disease biomarker due to its positive correlation with disease activity, progression, and outcome in chronic kidney disease or cardiovascular disorders. It is, however, not entirely clear whether FGF23 merely indicates disease or actively contributes to disease progression. Therefore, it is important to explore the regulation of FGF23 production, which is similarly incompletely understood. Our paper identifies fundamental insulin/IGF1-dependent PI3K/Akt/FOXO1 signaling as a key suppressor of FGF23 formation.
Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions
Authors: Edison John R. , Spencer Ryan K. , Butterfoss Glenn L. , Hudson Benjamin C. , Hochbaum Allon I. , Paravastu Anant K. , Zuckermann Ronald N. , Whitelam Stephen
Published: May 2018

Significance

Commonly observed secondary structures of proteins, such as

α

-helices and

β

-sheets, are built from a
trans-
amide backbone with residues sampling a single region of the Ramachandran plot. Here we report a secondary structure displayed by biomimetic peptoid polymers in which the backbone exhibits the
cis
conformation and alternating residues display rotational states of opposed (pseudo)chirality. This structure is linear and untwisted and enables strands to pack densely into extended bilayer nanosheets.
Effects of the hippopotamus on the chemistry and ecology of a changing watershed
Authors: Stears Keenan , McCauley Douglas J. , Finlay Jacques C. , Mpemba James , Warrington Ian T. , Mutayoba Benezeth M. , Power Mary E. , Dawson Todd E. , Brashares Justin S.
Published: May 2018

Significance

Hippopotami exert a strong influence on the biogeochemistry and ecology of freshwater ecosystems by excreting terrestrially derived organic matter into these systems. These impacts are likely to be strongly controlled by hydrology. In sub-Saharan Africa, anthropogenic water abstraction and climate change are significantly altering water cycles, often reducing dry-season flow. In this study, we report how hippopotami shape water chemistry and biodiversity patterns in a human-altered river. Importantly, we note that during recently prolonged low-flow periods the influence of the hippopotamus was greatly altered such that its nutrient contributions promoted eutrophication and affected biodiversity. These results highlight the extent to which human modification of environmental systems may unexpectedly alter the impacts of ecologically influential species at multiple scales.
The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast
Authors: Sharp Nathaniel P. , Sandell Linnea , James Christopher G. , Otto Sarah P.
Published: May 2018

Significance

Organisms vary in the number of genome copies per cell: ploidy. By altering how DNA is replicated and repaired, ploidy may determine the number and types of mutations that arise, affecting how evolution proceeds. We sequenced the genomes of >200 replicate lines of yeast (
Saccharomyces cerevisiae
) with one versus two genome copies (haploid versus diploid) after accumulation of thousands of new mutations. Haploids were more susceptible to single-nucleotide mutations, particularly for DNA replicated later in the cell cycle, whereas large changes to genome structure were more common in diploids. Haploid and diploid populations will therefore have access to distinct kinds of genetic variation, contributing to differences in their evolutionary potential.
Salicylic acid-independent role of NPR1 is required for protection from proteotoxic stress in the plant endoplasmic reticulum
Authors: Lai Ya-Shiuan , Renna Luciana , Yarema John , Ruberti Cristina , He Sheng Yang , Brandizzi Federica
Published: May 2018

Significance

The biosynthetic ability of the endoplasmic reticulum (ER) is essential to eukaryotic life. Disruption of such ability ignites ER stress, a potentially lethal condition. Known sensors perceive and respond to ER stress, but how their signaling is modulated is largely unknown, especially in plants. We demonstrate that the transcriptional cofactor NPR1, previously involved in salicylic acid (SA)-mediated immune defense, is translocated to the nucleus upon ER stress-induced reduction of the cytosolic redox potential, which is generally induced by SA. We also show that NPR1 interacts with the unfolded protein response (UPR) regulators bZIP28 and bZIP60 and suppresses the UPR independently from SA. This work identifies NPR1 as a critical modulator of the plant UPR and demonstrates convergence of signal decoding in ER stress and SA-mediated defense.
High-capacity rechargeable batteries based on deeply cyclable lithium metal anodes
Authors: Shi Qiuwei , Zhong Yiren , Wu Min , Wang Hongzhi , Wang Hailiang
Published: May 2018

Significance

Lithium metal is considered as the ultimate choice of anode for high-energy batteries, but the existing Li metal electrodes are usually limited to shallow cycling conditions (1 mAh cm
−2
) and thus inefficient utilization (<1%). We achieve Li metal electrodes deeply and stably cyclable to capacities >10 mAh cm
−2
, enabled by slow release of LiNO
3
into carbonate electrolyte and its subsequent decomposition to form a protective layer for reversible, dendrite-free, and highly dense Li metal deposition. Based on that, we demonstrate a Li-MoS
3
(in close-to-stoichiometric ratio) cell showing high areal and specific capacity and energy.
Effect of quartz-powder on the properties of conventional cementitious materials and geopolymers
Authors: Rashad Alaa M.
Published: May 2018

In the recent years, grinding technology has been brought a new product with prospective properties. If quartz sand is ground, a new product is obtained with superior properties than its original. The literature contains some studies focused on employing quartz powder (QP) in traditional cementitious materials and geopolymers as additives to obtain modified matrices. This article presents a brief of the past studies fixated on adding QP into different matrices. Fresh and hardened properties have been briefed.

This review was submitted as part of the 2018 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.
Numerical investigation of porous materials composites reinforced with natural fibers
Authors: Chikhi M , Metidji N , Mokhtari F , Merzouk N k
Published: May 2018

The present article tends to predict the effective thermal properties of porous biocomposites materials. The composites matrix consists on porous materials namely gypsum and the reinforcement is a natural fiber as date palm fibers. The numerical study is done using Comsol software resolving the heat transfer equation. The results are fitted with theoretical model and experimental results. The results of this study indicate that the porosity has an effect on the Effective thermal conductivity biocompoites.
Hypertension Induced Morphological and Physiological Changes in Cells of the Arterial Wall
Authors: Martinez-Quinones Patricia , McCarthy Cameron G , Watts Stephanie W , Klee Nicole S , Komic Amel , Calmasini Fabiano B , Priviero Fernanda , Warner Alexander , Chenghao Yu , Wenceslau Camilla F
Published: May 2018

Morphological and physiological changes in the vasculature have been described in the evolution and maintenance of hypertension. Hypertension-induced vascular dysfunction may present itself as a contributing, or consequential factor, to vascular remodeling caused by chronically elevated systemic arterial blood pressure. Changes in all vessel layers, from the endothelium to the perivascular adipose tissue (PVAT), have been described. This mini-review focuses on the current knowledge of the structure and function of the vessel layers, specifically muscular arteries: intima, media, adventitia, PVAT, and the cell types harbored within each vessel layer. The contributions of each cell type to vessel homeostasis and pathophysiological development of hypertension will be highlighted.
Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome
Authors: Cheng Lixin , Leung Kwong-Sak
Published: May 2018

Motivation

Moonlighting proteins are a class of proteins having multiple distinct functions, which play essential roles in a variety of cellular and enzymatic functioning systems. Although there have long been calls for computational algorithms for the identification of moonlighting proteins, research on approaches to identify moonlighting long non-coding RNAs (lncRNAs) has never been undertaken. Here, we introduce a novel methodology, MoonFinder, for the identification of moonlighting lncRNAs. MoonFinder is a statistical algorithm identifying moonlighting lncRNAs without a priori knowledge through the integration of protein interactome, RNA–protein interactions and functional annotation of proteins.

Results

We identify 155 moonlighting lncRNA candidates and uncover that they are a distinct class of lncRNAs characterized by specific sequence and cellular localization features. The non-coding genes that transcript moonlighting lncRNAs tend to have shorter but more exons and the moonlighting lncRNAs have a variable localization pattern with a high chance of residing in the cytoplasmic compartment in comparison to the other lncRNAs. Moreover, moonlighting lncRNAs and moonlighting proteins are rather mutually exclusive in terms of both their direct interactions and interacting partners. Our results also shed light on how the moonlighting candidates and their interacting proteins implicated in the formation and development of cancers and other diseases.

Availability and implementation

The code implementing MoonFinder is supplied as an R package in the supplementary material.

Supplementary information

Supplementary data are available at Bioinformatics online.
Discovery and Validation of Methylation Biomarkers for Ulcerative Colitis Associated Neoplasia
Authors: Beggs Andrew D , James Jonathan , Caldwell Germaine , Prout Toby , Dilworth Mark P , Taniere Phillipe , Iqbal Tariq , Morton Dion G , Matthews Glenn
Published: May 2018

Background and aims

Ulcerative colitis (UC) is associated with a higher background risk of dysplasia and/or neoplasia due to chronic inflammation. There exist few biomarkers for identification of patients with dysplasia, and targeted biopsies in this group of patients are inaccurate in reliably identifying dysplasia. We aimed to examine the epigenome of UC dysplasia and to identify and validate potential biomarkers

Methods

Colonic samples from patients with UC-associated dysplasia or neoplasia underwent epigenome-wide analysis on the Illumina 450K methylation array. Markers were validated by bisulphite pyrosequencing on a secondary validation cohort and accuracy calculated using logistic regression and receiver-operator curves.

Results

Twelve samples from 4 patients underwent methylation array analysis and 6 markers (GNG7, VAV3, KIF5C, PIK3R5, TUBB6, and ZNF583) were taken forward for secondary validation on a cohort of 71 colonic biopsy samples consisting of normal uninflamed mucosa from control patients, acute and chronic colitis, “field” mucosa in patients with dysplasia/neoplasia, dysplasia, and neoplasia. Methylation in the beta-tubulin TUBB6 correlated with the presence of dysplasia (P < 0.0001) and accurately discriminated between dysplasia and nondysplastic tissue, even in the apparently normal field mucosa downstream from dysplastic lesions (AUC 0.84, 95% CI 0.81–0.87).

Conclusions

Methylation in TUBB6 is a potential biomarker for UC- associated dysplasia. Further validation is needed and is ongoing as part of the ENDCAP-C study.
Quality over Quantity: Assessing the Impact of Frequent Public Interaction Compared to Problem-Solving Activities on Police Officer Job Satisfaction
Authors: Sytsma Victoria A , Piza Eric L
Published: May 2018

Research outside the field of policing has shown that job satisfaction predicts job performance. While policing research has demonstrated performing community-oriented policing (COP) activities generally improves police officer job satisfaction, the mechanism through which it occurs remains unclear. This study contributes to the community-policing literature through a survey of 178 police officers at the Toronto Police Service. The survey instrument measures the mechanism through which job satisfaction is impacted. Results indicate that primary response officers are more likely to be somewhat or very unsatisfied with their current job assignment compared with officers with a COP assignment—confirming what previous research has found. Further, those who interact with the public primarily for the purpose of engaging in problem-solving are more likely to be very satisfied with their current job assignment compared with those who do so primarily for the purpose of responding to calls for service. Engaging in problem-solving increases the odds of being very satisfied in one’s job assignment, and the combination of frequent contacts with the public and problem-solving is less important than problem-solving alone. The implications of the study findings for COP strategies are discussed.
Elucidating the potential of crude cell extracts for producing pyruvate from glucose
Authors: Garcia David C , Mohr Benjamin P , Dovgan Jakob T , Hurst Gregory B , Standaert Robert F , Doktycz Mitchel J
Published: May 2018

Living systems possess a rich biochemistry that can be harnessed through metabolic engineering to produce valuable therapeutics, fuels and fine chemicals. In spite of the tools created for this purpose, many organisms tend to be recalcitrant to modification or difficult to optimize. Crude cellular extracts, made by lysis of cells, possess much of the same biochemical capability, but in an easier to manipulate context. Metabolic engineering in crude extracts, or cell-free metabolic engineering, can harness these capabilities to feed heterologous pathways for metabolite production and serve as a platform for pathway optimization. However, the inherent biochemical potential of a crude extract remains ill-defined, and consequently, the use of such extracts can result in inefficient processes and unintended side products. Herein, we show that changes in cell growth conditions lead to changes in the enzymatic activity of crude cell extracts and result in different abilities to produce the central biochemical precursor pyruvate when fed glucose. Proteomic analyses coupled with metabolite measurements uncover the diverse biochemical capabilities of these different crude extract preparations and provide a framework for how analytical measurements can be used to inform and improve crude extract performance. Such informed developments can allow enrichment of crude extracts with pathways that promote or deplete particular metabolic processes and aid in the metabolic engineering of defined products.
Dynamics of ‘Candidatus Liberibacter asiaticus’ Colonization of New Growth of Citrus
Authors: Hilf Mark E. , Luo Weiqi
Published: May 2018

‘Candidatus Liberibacter asiaticus’ is a phloem-colonizing intracellular bacterial pathogen of citrus associated with the disease huanglongbing. A study of patterns of colonization and bacterial population growth in new growth of different citrus types was conducted by pruning infected citron, sweet orange, sour orange, mandarin, citrange, and Citrus macrophylla trees to force the growth of axillary and adventitious shoots. The first three leaves on newly emerged shoots were collected at 30, 60, and 90 days to assess colonization and population growth of ‘Ca. L. asiaticus’ using real time PCR (qPCR). Single trials were conducted with mandarin and citron, two trials each for citrange, sour orange and sweet orange, and four trials for C. macrophylla. In citron the proportion of colonized leaves increased significantly over time, with 67, 85, and 96% of leaves colonized at 30, 60, and 90 days, respectively. For the other citrus types, the exact proportion of colonized leaves differed, but colonization exceeded 60% in mandarin, sour orange, and citrange, and exceeded 80% at 30 days in two trials with sweet orange and three trials with C. macrophylla, but there was no significant increase in the proportion of colonized leaves at 60 and 90 days. Bacteria were readily detected by 30 days in new leaves of all citrus types. Differences in the growth of the bacterial population between citrus types and at different times of the year were noted, but common trends were apparent. In general, bacterial titers peaked at 60 days, except in leaves of C. macrophylla where bacterial titers peaked at 30 days. The early and consistently high proportion of leaf colonization observed for new growth of sweet orange during two trials and for C. macrophylla during three trials indicates a near synchronous colonization of new leaves by 30 days.
The Commission on Magnet® Recognition
Authors: Moran Janice W.
Published: May 2018

The American Nurses Credentialing Center (ANCC) Commission on Magnet® Recognition is a voluntary governing body that oversees the Magnet Recognition Program®. Commission members are appointed by the ANCC Board of Directors and are expert representatives from various sectors of the nursing community. In addition, 1 commission member represents public consumers.
Engaging Nurses in the Development and Implementation of a Professional Practice Model Through Nursing Salons
Authors: Hodge Margaret Blakeman , Campbell Patricia , Tobar Kelly
Published: May 2018

Developing creative ways to solicit nurse input into practice is a challenge for nurse executives. Engaging nurses through the use of nursing salons was seen as an innovative way to engage nurses. Feedback from nurses participating in salons informed development of a Professional Practice Model that reflects nursing practice at this large academic medical center and provided a voice to nursing.
Describing Nurse Leaders’ and Direct Care Nurses’ Perceptions of a Healthy Work Environment in Acute Care Settings, Part 2
Authors: Huddleston Penny , Gray Jennifer
Published: May 2018

BACKGROUND:

The American Association of Critical-Care Nurses (AACN) Healthy Work Environment Assessment Tool was developed as a simple screening tool to assess the characteristics of a healthy work environment (HWE) in critical care environments.

PURPOSES:

The purposes of these 2 qualitative research studies are to explore the nurse leaders’ and direct care nurses’ perceptions of the meaning of a HWE, to describe the nurse leaders’ and direct care nurses’ perceptions of a HWE, and to define the characteristics of a HWE in acute care settings.

METHODS:

Exploratory descriptive designs using focus groups and guided questions with tape-recorded interviews were used to define the characteristics of an HWE.

RESULTS:

The 6 original themes from AACN HWE standards and 2 new themes emerged as a result of the nurse leaders and direct care nurses defining the characteristics of a HWE, which included appropriate staffing, authentic leadership, effective decision making, meaningful recognition, skilled communication, true collaboration genuine teamwork, and physical and psychological safety. The qualitative statements from these 2 studies will be used in future studies to describe and develop HWE scales for nurse leaders and direct care nurses and to assess the psychometric properties of these new tools.
Nurses’ Perception of Shared Decision-Making Processes
Authors: Gerard Sally O. , Owens Deborah L. , Oliver Patricia
Published: May 2018

OBJECTIVE:

The aim of this study is to describe how measuring the perceived and desired decision-making capacity of nurses in a model of shared governance (SG) can be beneficial.

BACKGROUND:

Shared governance (SG) increases nurse’s control over professional practice. Engagement in SG can be impacted by how much decision-making power nurses desire. This concept related to decision making has been termed decisional involvement (DI). Few studies exist that examine the concept of DI.

METHODS:

Using the Decisional Involvement Scale, acute care nurses were sampled concerning desired and perceived decision making on 21 topics related to nursing practice.

RESULTS:

Analysis of the data identified different governance priorities for several areas. Of particular interest was that those nurses on SG councils for more than 5 years did not report higher satisfaction with decision involvement.

CONCLUSIONS:

A comprehensive evaluation of shared decision making was a valuable tool to establish a baseline of data and seek opportunities for improvement. A well-integrated model of SG requires continuous improvement and analysis to be sustained. Measuring and evaluating staff nurses desire to control varied aspects of DI can allow organizations to make focused efforts to strengthen SG.
Shelf–ocean exchange and hydrography west of the Antarctic Peninsula: a review
Authors: Moffat C. , Meredith M.
Published: May 2018

The West Antarctic Peninsula (WAP) is a highly productive marine ecosystem where extended periods of change have been observed in the form of glacier retreat, reduction of sea-ice cover and shifts in marine populations, among others. The physical environment on the shelf is known to be strongly influenced by the Antarctic Circumpolar Current flowing along the shelf slope and carrying warm, nutrient-rich water, by cold waters flooding into the northern Bransfield Strait from the Weddell Sea, by an extensive network of glaciers and ice shelves, and by strong seasonal to inter-annual variability in sea-ice formation and air–sea interactions, with significant modulation by climate modes like El Niño–Southern Oscillation and the Southern Annular Mode. However, significant gaps have remained in understanding the exchange processes between the open ocean and the shelf, the pathways and fate of oceanic water intrusions, the shelf heat and salt budgets, and the long-term evolution of the shelf properties and circulation. Here, we review how recent advances in long-term monitoring programmes, process studies and newly developed numerical models have helped bridge these gaps and set future research challenges for the WAP system.

This article is part of the theme issue ‘The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change’.
Impact of sea-ice melt on dimethyl sulfide (sulfoniopropionate) inventories in surface waters of Marguerite Bay, West Antarctic Peninsula
Authors: Stefels Jacqueline , van Leeuwe Maria A. , Jones Elizabeth M. , Meredith Michael P. , Venables Hugh J. , Webb Alison L. , Henley Sian F.
Published: May 2018

The Southern Ocean is a hotspot of the climate-relevant organic sulfur compound dimethyl sulfide (DMS). Spatial and temporal variability in DMS concentration is higher than in any other oceanic region, especially in the marginal ice zone. During a one-week expedition across the continental shelf of the West Antarctic Peninsula (WAP), from the shelf break into Marguerite Bay, in January 2015, spatial heterogeneity of DMS and its precursor dimethyl sulfoniopropionate (DMSP) was studied and linked with environmental conditions, including sea-ice melt events. Concentrations of sulfur compounds, particulate organic carbon (POC) and chlorophyll
a
in the surface waters varied by a factor of 5–6 over the entire transect. DMS and DMSP concentrations were an order of magnitude higher than currently inferred in climatologies for the WAP region. Particulate DMSP concentrations were correlated most strongly with POC and the abundance of haptophyte algae within the phytoplankton community, which, in turn, was linked with sea-ice melt. The strong sea-ice signal in the distribution of DMS(P) implies that DMS(P) production is likely to decrease with ongoing reductions in sea-ice cover along the WAP. This has implications for feedback processes on the region's climate system.

This article is part of the theme issue ‘The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change’.
A ‘shallow bathtub ring’ of local sedimentary iron input maintains the Palmer Deep biological hotspot on the West Antarctic Peninsula shelf
Authors: Sherrell Robert M. , Annett Amber L. , Fitzsimmons Jessica N. , Roccanova Vincent J. , Meredith Michael P.
Published: May 2018

Palmer Deep (PD) is one of several regional hotspots of biological productivity along the inner shelf of the West Antarctic Peninsula. The proximity of hotspots to shelf-crossing deep troughs has led to the ‘canyon hypothesis’, which proposes that circumpolar deep water flowing shoreward along the canyons is upwelled on the inner shelf, carrying nutrients including iron (Fe) to surface waters, maintaining phytoplankton blooms. We present here full-depth profiles of dissolved and particulate Fe and manganese (Mn) from eight stations around PD, sampled in January and early February of 2015 and 2016, allowing the first detailed evaluation of Fe sources to the area's euphotic zone. We show that upwelling of deep water does not control Fe flux to the surface; instead, shallow sediment-sourced Fe inputs are transported horizontally from surrounding coastlines, creating strong vertical gradients of dissolved Fe within the upper 100 m that supply this limiting nutrient to the local ecosystem. The supply of bioavailable Fe is, therefore, not significantly related to the canyon transport of deep water. Near shore time-series samples reveal that local glacial meltwater appears to be an important Mn source but, surprisingly, is not a large direct Fe input to this biological hotspot.

This article is part of the theme issue ‘The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change’.
Inter-decadal variability of phytoplankton biomass along the coastal West Antarctic Peninsula
Authors: Kim Hyewon , Ducklow Hugh W. , Abele Doris , Ruiz Barlett Eduardo M. , Buma Anita G. J. , Meredith Michael P. , Rozema Patrick D. , Schofield Oscar M. , Venables Hugh J. , Schloss Irene R.
Published: May 2018

The West Antarctic Peninsula (WAP) is a climatically sensitive region where periods of strong warming have caused significant changes in the marine ecosystem and food-web processes. Tight coupling between phytoplankton and higher trophic levels implies that the coastal WAP is a bottom-up controlled system, where changes in phytoplankton dynamics may largely impact other food-web components. Here, we analysed the inter-decadal time series of year-round chlorophyll-a(Chl) collected from three stations along the coastal WAP: Carlini Station at Potter Cove (PC) on King George Island, Palmer Station on Anvers Island and Rothera Station on Adelaide Island. There were trends towards increased phytoplankton biomass at Carlini Station (PC) and Palmer Station, while phytoplankton biomass declined significantly at Rothera Station over the studied period. The impacts of two relevant climate modes to the WAP, the El Niño-Southern Oscillation and the Southern Annular Mode, on winter and spring phytoplankton biomass appear to be different among the three sampling stations, suggesting an important role of local-scale forcing than large-scale forcing on phytoplankton dynamics at each station. The inter-annual variability of seasonal bloom progression derived from considering all three stations together captured ecologically meaningful, seasonally co-occurring bloom patterns which were primarily constrained by water-column stability strength. Our findings highlight a coupled link between phytoplankton and physical and climate dynamics along the coastal WAP, which may improve our understanding of overall WAP food-web responses to climate change and variability.

This article is part of the theme issue ‘The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change’.
Spring–summer net community production, new production, particle export and related water column biogeochemical processes in the marginal sea ice zone of the Western Antarctic Peninsula 2012–2014
Authors: Ducklow Hugh W. , Stukel Michael R. , Eveleth Rachel , Doney Scott C. , Jickells Tim , Schofield Oscar , Baker Alex R. , Brindle John , Chance Rosie , Cassar Nicolas
Published: May 2018

New production (New P, the rate of net primary production (NPP) supported by exogenously supplied limiting nutrients) and net community production (NCP, gross primary production not consumed by community respiration) are closely related but mechanistically distinct processes. They set the carbon balance in the upper ocean and define an upper limit for export from the system. The relationships, relative magnitudes and variability of New P (from
15
NO
3
–
uptake), O
2
 : argon-based NCP and sinking particle export (based on the
238
U : 
234
Th disequilibrium) are increasingly well documented but still not clearly understood. This is especially true in remote regions such as polar marginal ice zones. Here we present a 3-year dataset of simultaneous measurements made at approximately 50 stations along the Western Antarctic Peninsula (WAP) continental shelf in midsummer (January) 2012–2014. Net seasonal-scale changes in water column inventories (0–150 m) of nitrate and iodide were also estimated at the same stations. The average daily rates based on inventory changes exceeded the shorter-term rate measurements. A major uncertainty in the relative magnitude of the inventory estimates is specifying the start of the growing season following sea-ice retreat. New P and NCP(O
2
) did not differ significantly. New P and NCP(O
2
) were significantly greater than sinking particle export from thorium-234. We suggest this is a persistent and systematic imbalance and that other processes such as vertical mixing and advection of suspended particles are important export pathways.

This article is part of the theme issue ‘The marine system of the west Antarctic Peninsula: status and strategy for progress in a region of rapid change’.
Flow modification associated with reduced genetic health of a river-breeding frog,Rana boylii
Authors: Peek Ryan A. , O’Rourke Sean M. , Miller Michael R.
Published: May 2018

River regulation or flow modification—the hydrological alteration of flow by dams and diversions—has been implicated as a cause of fundamental change to downstream aquatic ecosystems. Flow modification changes the patterns and functionality of the natural flow regime, and has the potential to restrict population connectivity and gene flow in river-dependent organisms. Since population connectivity and the maintenance of genetic diversity are fundamental drivers of long-term persistence, understanding the extent flow modification impacts these critical attributes of genetic health is an important goal for long-term conservation. Foothill yellow-legged frogs (Rana boylii) were historically abundant throughout many western rivers but have declined since the onset of regulation. However, the extent to whichR. boyliipopulations in rivers with altered flow regimes are maintaining connectivity and genetic diversity is unknown. Here we use genetic methods to investigate the impacts of flow alteration onR. boyliito explore their potential for long-term persistence under continued flow modification. We foundR. boyliiin rivers with flow modification showed striking patterns of isolation and trajectories of genetic diversity loss relative to unregulated rivers. For example, flow modification explained the greatest amount of variance in population genetic differentiation compared with other covariates including geographic distance. Importantly, patterns of connectivity and genetic diversity loss were observed regardless of flow alteration level but were most prominent in locations with the greatest flow modification intensity. Although our results do not bode well for long-term persistence ofR. boyliipopulations under current flow regulation regimes, they do highlight the power of genetic monitoring for assessing population health in aquatic organisms.
Brief Freezing Steps Lead to Robust Immunofluorescence in Drosophila Larval Brains
Authors: Buckley Dominic , Thapa Ada , Nguyen Minh Q. , Blankinship Essence , Williamson Diana , Cloud Veronica , Mohan Ryan D.
Published: May 2018

Drosophila melanogaster possess complex neuronal networks regulating sophisticated behavioral outputs that aid in studying the molecular mechanisms of neuronal function and neurodegenerative disease. Immunofluorescence (IF) techniques provide a way to visualize the spatiotemporal organization of these networks, permitting observation of their development, functional location, remodeling, and eventually - degradation. However, general immunostaining techniques do not always result in sufficient antibody penetration through the brain, and techniques used to enhance permeability can compromise structural integrity. We have found that freezing larval brains facilitates permeability with no apparent loss of antibody specificity or structural integrity. To demonstrate the advantage of this freezing technique, we compared results to two commonly used permeation methods: Detergent alone (Basic) and proteolytic degradation (Collagenase) techniques.

Here we compare four different immunofluorescence techniques demonstrating that freezing Drosophila brains results in robust staining of small neurons in the larval brain without compromising structural integrity.
Automating multimodal microscopy with NanoJ-Fluidics
Authors: Almada Pedro , Pereira Pedro M. , Culley Siân , Caillol Ghislaine , Boroni-Rueda Fanny , Dix Christina L. , Laine Romain F. , Charras Guillaume , Baum Buzz , Leterrier Christophe , Henriques Ricardo
Published: May 2018

Fluorescence microscopy can reveal all aspects of cellular mechanisms, from molecular details to dynamics, thanks to approaches such as super-resolution and live-cell imaging. Each of its modalities requires specific sample preparation and imaging conditions to obtain high-quality, artefact-free images, ultimately providing complementary information. Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows involving multiple sample preparation steps. We present a robust fluidics approach to automate complex sequences of treatment, labelling and imaging of live and fixed cells. Our open-source NanoJ-Fluidics system is based on low-cost LEGO hardware controlled by ImageJ-based software and can be directly adapted to any microscope, providing easy-to-implement high-content, multimodal imaging with high reproducibility. We demonstrate its capacity to carry out complex sequences of experiments such as super-resolved live-to-fixed imaging to study actin dynamics; highly-multiplexed STORM and DNA-PAINT acquisitions of multiple targets; and event-driven fixation microscopy to study the role of adhesion contacts in mitosis.
Temperature response of Rubisco kinetics in Arabidopsis thaliana: thermal breakpoints and implications for reaction mechanisms
Authors: Boyd Ryan A. , Cavanagh Amanda P. , Kubien David S. , Cousins Asaph B.
Published: May 2018

Optimization of Rubisco kinetics could improve photosynthetic efficiency, ultimatly resulting in increased crop yield. However, imprecise knowledge of the reaction mechanism and the individual rate constants limit our ability to optimize the enzyme. Membrane inlet mass spectrometery (MIMS) may offer benefits over traditional methods for determining individual rate constants of the Rubisco reaction mechanism, as it can directly monitor concentration changes in CO2, O2, and their isotopologs during assays. However, a direct comparsion of MIMS to the traditional Radiolabel method of determining Rubisco kinetic parameters has not been made. Here, the temperature responses of Rubisco kinetic parameters from Arabidopsis thaliana were measured using the Radiolabel and MIMS methods. The two methods provided comparable parameters above 25 °C, but temperature responses deviated at low temperature as MIMS derived catalytic rates of carboxylation, oxygenation, and CO2/O2 specificity showed thermal breakpoints. Here we discuss the variability and uncertainty surrounding breakpoints in the Rubisco temperature response and relavance of individual rate constants of the reaction mechanisms to potential breakpoints.
Guppies prefer to follow large (robot) leaders irrespective of own size
Authors: Bierbach David , Mönck Hauke J. , Lukas Juliane , Habedank Marie , Romanczuk Pawel , Landgraf Tim , Krause Jens
Published: May 2018

Body size is often assumed to determine how successful an individual can lead others with larger individuals being more likely to lead than smaller ones. However, direct evidence for such a relation is scarce. Furthermore, even if larger individuals are more likely to lead, body size correlates often with specific behavioral patterns (e.g., swimming capacity) and it is thus unclear whether larger individuals are more often followed than smaller ones because they are larger or because they behave in a certain way. To control for behavioral differences among differentially-sized leaders, we used biomimetic robotic fish – Robofish – of different sizes. Robofish is accepted as a conspecific by live guppies (Poecilia reticulata) and provides standardized behaviors irrespective of its size. We specifically asked whether larger leaders are preferentially followed when behavior is controlled for and whether the preferences of followers depend on their own body size or their risk taking behavior (‘boldness’). We found that live guppies followed larger Robofish leaders closer than smaller ones and this pattern was independent of the followers’ own body size as well as risk-taking behavior. This is the first study that shows a ‘bigger is better’ pattern in leadership in shoaling fish that is fully independent of behavioral differences between differentially-sized leaders and followers’ own size and personality.
Inositol 1,4,5-trisphosphate receptor type2-independent Ca2+ release from the endoplasmic reticulum in astrocytes
Authors: Okubo Yohei , Kanemaru Kazunori , Suzuki Junji , Kobayashi Kenta , Hirose Kenzo , Iino Masamitsu
Published: May 2018

Accumulating evidence indicates that astrocytes are actively involved in the physiological and pathophysiological functions of the brain. Intracellular Ca2+ signaling, especially Ca2+ release from the endoplasmic reticulum (ER), is considered to be crucial for the regulation of astrocytic functions. Mice with genetic deletion of inositol 1,4,5-trisphosphate receptor type 2 (IP3R2) are reportedly devoid of astrocytic Ca2+ signaling, and thus widely used to explore the roles of Ca2+ signaling in astrocytic functions. While functional deficits in IP3R2-knockout (KO) mice have been found in some reports, no functional deficit was observed in others. Thus, there remains a controversy regarding the functional significance of astrocytic Ca2+ signaling. To address this controversy, we re-evaluated the assumption that Ca2+ release from the ER is abolished in IP3R2-KO astrocytes using a highly sensitive imaging technique. We expressed the ER luminal Ca2+ indicator G-CEPIA1er in cortical and hippocampal astrocytes to directly visualize spontaneous and stimulus-induced Ca2+ release from the ER. We found attenuated but significant Ca2+ release in response to application of norepinephrine to IP3R2-KO astrocytes. This IP3R2-independent Ca2+ release induced only minimal cytosolic Ca2+ transients but induced robust Ca2+ increases in mitochondria that are frequently in close contact with the ER. These results indicate that ER Ca2+ release is retained and is sufficient to increase the Ca2+ concentration in close proximity to the ER in IP3R2-KO astrocytes.
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia
Authors: Minuesa Gerard , Albanese Steven K. , Chow Arthur , Schurer Alexandra , Park Sun-Mi , Rotsides Christina Z. , Taggart James , Rizzi Andrea , Naden Levi N. , Chou Timothy , Gourkanti Saroj , Cappel Daniel , Passarelli Maria C. , Fairchild Lauren , Adura Carolina , Glickman J Fraser , Schulman Jessica , Famulare Christopher , Patel Minal , Eibl Joseph K. , Ross Gregory M. , Tan Derek , Leslie Christina , Beuming Thijs , Goldgur Yehuda , Chodera John D. , Kharas Michael G.
Published: May 2018

The MUSASHI family of RNA binding proteins (MSI1 and MSI2) contribute to a wide spectrum of cancers including acute myeloid leukemia. We found that the small molecule Ro 08–2750 (Ro) directly binds to MSI2 and competes for its RNA binding in biochemical assays. Ro treatment in mouse and human myeloid leukemia cells resulted in an increase in differentiation and apoptosis, inhibition of known MSI-targets, and a shared global gene expression signature similar to shRNA depletion of MSI2. Ro demonstrated in vivo inhibition of c-MYC and reduced disease burden in a murine AML leukemia model. Thus, we have identified a small molecule that targets MSI’s oncogenic activity. Our study provides a framework for targeting RNA binding proteins in cancer.