bluuebunny/crossref_metadata_2025_split huggingface dataset:
Universal metabolic constraints on the thermal tolerance of marine phytoplankton
Authors: Barton Samuel , Jenkins James , Buckling Angus , Schaum C.-Elisa , Smirnoff Nicholas , Yvon-Durocher Gabriel 
Published: June 2018

AbstractMarine phytoplankton are responsible for over 45% of annual global net primary production. Ocean warming is expected to drive massive reorganisation of phytoplankton communities, resulting in pole-ward range shifts and sharp declines in species diversity, particularly in the tropics. The impacts of warming on phytoplankton species depend critically on their physiological sensitivity to temperature change, characterised by thermal tolerance curves. Local extinctions arise when temperatures exceed species’ thermal tolerance limits. The mechanisms that determine the characteristics of thermal tolerance curves (e.g. optimal and maximal temperatures) and their variability among the broad physiological diversity of marine phytoplankton are however poorly understood. Here we show that differences in the temperature responses of photosynthesis and respiration establish physiological trade-offs that constrain the thermal tolerance of 18 species of marine phytoplankton, spanning cyanobacteria as well as the red and green super-families. Across all species we found that rates of respiration were more sensitive to increasing temperature and typically had higher optimal temperatures than photosynthesis. Consequently, the fraction of photosynthetic energy available for allocation to growth (carbon-use efficiency) declined exponentially with rising temperatures with a sensitivity that was invariant among the 18 species. Furthermore, the optimal temperature of growth was generally lower than that of photosynthesis and as a result, supra-optimal declines in growth rate were associated with temperature ranges where the carbon-use efficiency exhibited accelerated declines. These highly conserved patterns demonstrate that the limits of thermal tolerance in marine phytoplankton are underpinned by common metabolic constraints linked to the differential temperature responses of photosynthesis and respiration.Significance StatementThe impacts of warming on marine phytoplankton depend on their sensitivity to rising temperatures, yet there is currently limited understanding of the mechanisms that limit thermal tolerance among the diversity of marine phytoplankton. Using a comparative study on the dominant, ecologically important lineages of marine phytoplankton – Bacillariophyceae, Dinophyceae, Cyanophyceae, Prasinophyceae, Prymnesiophyceae – we show that rates of respiration are consistently more sensitive to increasing temperature than photosynthesis. Consequently, the fraction of photosynthetic energy available for growth declines with rising temperatures with a sensitivity that is invariant among species. Our results suggest that declines in phytoplankton performance at high temperatures are driven by universal metabolic constrains linked to rising respiratory costs eventually exceeding the supply of reduced carbon from photosynthesis.
APC/CCdh1-mediated degradation of Cdh1 during meiosis inS. cerevisiae
Authors: Ostapenko Denis , Solomon Mark J. 
Published: June 2018

ABSTRACTThe Anaphase-Promoting Complex/Cyclosome (APC/C) is a ubiquitin ligase that promotes the ubiquitination and subsequent degradation of numerous cell cycle regulators during mitosis and in G1. Proteins are recruited to the APC/C by activator proteins such as Cdh1. During the cell cycle, Cdh1 is subject to precise regulation so that substrates are not degraded prematurely. We have explored the regulation of Cdh1 during the developmental transition into meiosis and sporulation in the budding yeastS. cerevisiae. Transition to sporulation medium triggers the degradation of Cdh1. Degradation requires that cells be of the a/a mating type and be starved for glucose, but they do not actually need to enter into the meiotic program. Degradation requires an intact SNF1 protein kinase complex (orthologous to the mammalian AMPK nutritional sensor), which is activated by the absence of glucose. Cdh1 degradation is mediated by the APC/C itself in a ‘trans’ mechanism in which one molecule of Cdh1 recruits a second molecule of Cdh1 to the APC/C for ubiquitination. However, Cdh1-Cdh1 recognition does not depend on the degradation motifs or binding sites involved in the recognition of typical APC/C substrates. We hypothesize that Cdh1 degradation is necessary for the preservation of cell cycle regulators and chromosome cohesion proteins between the reductional and equational meiotic divisions, which occur without the intervening Gap or S phases found in mitotic cell cycles.
FtsW is a peptidoglycan polymerase that is activated by its cognate penicillin-binding protein
Authors: Taguchi Atsushi , Welsh Michael A. , Marmont Lindsey S. , Lee Wonsik , Kahne Daniel , Bernhardt Thomas G. , Walker Suzanne 
Published: June 2018

AbstractThe peptidoglycan cell wall is essential for the survival and shape maintenance ofbacteria.1 For decades it was thought that only penicillin-binding proteins (PBPs) effected peptidoglycan synthesis. Recently, it was shown that RodA, a member of the Rod complex involved in side wall peptidoglycan synthesis, acts as a peptidoglycan polymerase.2–4 RodA is absent or dispensable in many bacteria that contain a cell wall; however, all of these bacteria have a RodA homologue, FtsW, which is a core member of the divisome complex that is essential for septal cell wall assembly.5,6 FtsW was previously proposed flip the peptidoglycan precursor Lipid II to the peripasm,7,8 but we report here that FtsW polymerizes Lipid II. We show that FtsW polymerase activity depends on the presence of the class B PBP (bPBP) that it recruits to the septum. We also demonstrate that the polymerase activity of FtsW is required for its function in vivo. Our findings establish FtsW as a peptidoglycan polymerase that works with its cognate bPBP to produce septal peptidoglycan during cell division.
Post-translational modifications drive protein stability to control the dynamic beer brewing proteome
Authors: Kerr Edward D. , Caboche Christopher H. , Schulz Benjamin L. 
Published: June 2018

AbstractMashing is a key step in beer brewing in which starch and proteins are solubilized from malted barley in a hot water extraction and digested to oligomaltose and free amino nitrogen. We used SWATH-MS to measure the abundance and site-specific modifications of proteins throughout a small-scale pale ale mash. Proteins extracted from the malt at low temperatures early in the mash decreased precipitously in abundance at higher temperatures late in the mash due to temperature/time-induced unfolding and aggregation. We validated these observations using experimental manipulation of time and temperature parameters in a micro-scale pale ale mash. Correlation analysis of temperature/time-dependent abundance showed that sequence and structure were the main features that controlled protein abundance profiles. Partial proteolysis by barley proteases was common early in the mash. The resulting proteolytically clipped proteins were particularly sensitive and were preferentially lost at high temperatures late in the mash, while intact proteins remained soluble. The beer brewing proteome is therefore driven by the interplay between protein solubilisation and proteolysis, which are in turn determined by barley variety, growth conditions, and brewing process parameters.
A computational protocol to characterize elusive Candidate Phyla Radiation bacteria in oral environments using metagenomic data
Authors: Meng Peiqi , Lu Chang , Lou Xinzhe , Zhang Qian , Jia Peizeng , Yan Zhimin , Lin Jiuxiang , Chen Feng 
Published: June 2018

AbstractSeveral studies have documented the diversity and potential pathogenic associations of organisms in the human oral cavity. Although much progress has been made in understanding the complex bacterial community inhabiting the human oral cavity, our understanding of some microorganisms is less resolved due to a variety of reasons. One such little-understood group is the candidate phyla radiation (CPR), which is a recently identified, but highly abundant group of ultrasmall bacteria with reduced genomes and unusual ribosomes. Here, we present a computational protocol for the detection of CPR organisms from metagenomic data. Our approach relies on a self-constructed dataset comprising published CPR genomic sequences as a filter to identify CPR sequences from metagenomic sequencing data. After assembly and functional prediction, the taxonomic affiliation of CPR contigs can be identified through phylogenetic analysis with publically available 16S rRNA gene and ribosomal proteins, in addition to sequence similarity analyses (e.g., average nucleotide identity calculations and contig mapping). Using this protocol, we reconstructed two draft genomes of organisms within the TM7 superphylum, that had genome sizes of 0.594 Mb and 0.678 Mb. Among the predicted functional genes of the constructed genomes, a high percentage were related to signal transduction, cell motility, and cell envelope biogenesis, which could contribute to cellular morphological changes in response to environmental cues.ImportanceCandidate phyla radiation (CPR) bacterial group is a recently identified, but highly diverse and abundant group of ultrasmall bacteria exhibiting reduced genomes and limited metabolic capacities. A number of studies have reported their potential pathogenic associations in multiple mucosal diseases including periodontitis, halitosis, and inflammatory bowel disease. However, CPR organisms are difficult to cultivate and are difficult to detect with PCR-based methods due to divergent genetic sequences. Thus, our understanding of CPR has lagged behind that of other bacterial component. Here, we used metagenomic approaches to overcome these previous barriers to CPR identification, and established a computational protocol for detection of CPR organisms from metagenomic samples. The protocol describe herein holds great promise for better understanding the potential biological functioning of CPR. Moreover, the pipeline could be applied to other organisms that are difficult to cultivate.
Performance Assessment of Variant Calling Pipelines using Human Whole Exome Sequencing and Simulated data
Authors: Kumaran Manojkumar , Subramanian Umadevi , Devarajan Bharanidharan 
Published: June 2018

AbstractThe whole exome sequencing (WES) is a time-consuming technology in the identification of clinical variants and it demands the accurate variant caller tools. The currently available tools compromise accuracy in predicting the specific types of variants. Thus, it is important to find out the possible combination of best aligner-variant caller tools for detecting SNVs and InDels separately. Moreover, many important aspects of InDel detection are not overlooked while comparing the performance of tools. One such aspect is the detection of InDels with respect to base pair length. To assess the performance of variant (especially InDels) caller in combination with different aligners, 20 automated pipelines were developed and evaluated using gold reference variant dataset (NA12878) from Genome in a Bottle (GiaB) consortium of human whole exome sequencing. Additionally, the simulated exome data from two human reference genome sequences (GRCh37 and GRCh38) were used to compare the performance of the pipelines. By analyzing various performance metrices, we observed that BWA and Novoalign aligners performed better with DeepVariant and SAMtools callers for detecting SNVs, and with DeepVariant and GATK for Indels. Altogether, DeepVariant with BWA and Novoalign performed best. Further, we showed that merging the top performing pipelines improved the accurate variant call set. Collectively, this study would help the investigators to effectively improve the sensitivity and accuracy in detecting specific variants.
Salmonellaeffectors SseK1 and SseK3 target death domain proteins in the TNF and TRAIL signaling pathways
Authors: Newson Joshua P M , Scott Nichollas E , Wah Chung Ivy Yeuk , Fok Lung Tania Wong , Giogha Cristina , Wang Nancy , Strugnell Richard A , Brown Nat F , Cygler Miroslaw , Pearson Jaclyn S , Hartland Elizabeth L 
Published: June 2018

AbstractStrains ofSalmonellautilise two distinct type three secretion systems to deliver effector proteins directly into host cells. TheSalmonellaeffectors SseK1 and SseK3 are arginine glycosyltransferases that modify mammalian death domain containing proteins with N-acetyl glucosamine (GlcNAc) when overexpressed ectopically or as recombinant protein fusions. Here, we combined Arg-GlcNAc glycopeptide immunoprecipitation and mass spectrometry to identify host proteins GlcNAcylated by endogenous levels of SseK1 and SseK3 duringSalmonellainfection. We observed that SseK1 modified the mammalian signaling protein TRADD, but not FADD as previously reported. Overexpression of SseK1 greatly broadened substrate specificity, while ectopic co-expression of SseK1 and TRADD increased the range of modified arginine residues within the death domain of TRADD. In contrast, endogenous levels of SseK3 resulted in modification of the death domains of receptors of the mammalian TNF superfamily, TNFR1 and TRAILR, at residues Arg376and Arg293respectively. Structural studies on SseK3 showed that the enzyme displays a classic GT-A glycosyltransferase fold and binds UDP-GlcNAc in a narrow and deep cleft with the GlcNAc facing the surface. Together our data suggests that Salmonellae carryingsseK1andsseK3employ the glycosyltransferase effectors to antagonise different components of death receptor signaling.
Development of a genetically encoded sensor for endogenous CaMKII activity
Authors: Ardestani Goli , West Megan , Maresca Thomas J. , Fissore Rafael A. , Stratton Margaret M. 
Published: June 2018

ABSTRACTCaMKII is a crucial oligomeric enzyme in neuronal and cardiac signaling, fertilization and immunity. Here, we report the construction of a novel, substrate-based, genetically-encoded sensor for CaMKII activity, FRESCA (FRET-basedSensor forCaMKIIActivity). Currently, there is one biosensor for CaMKII activity, Camui, which contains CaMKII. FRESCA allows us to measure all endogenous CaMKII variants, while Camui can track a single variant. Since there are ~40 CaMKII variants, using FRESCA to measure aggregate activity allows a fresh perspective on CaMKII activity. We show, using live-cell imaging, FRESCA response is concurrent with Ca2+rises in HEK293T cells and mouse eggs. In eggs, we stimulate oscillatory patterns of Ca2+and observe the differential responses of FRESCA and Camui. Our results implicate an important role for the variable linker region in CaMKII, which tunes its activation. FRESCA will be a transformative tool for studies in neurons, cardiomyocytes and other CaMKII-containing cells.
BindSpace: decoding transcription factor binding signals by large-scale joint embedding
Authors: Yuan Han , Kshirsagar Meghana , Zamparo Lee , Lu Yuheng , Leslie Christina S. 
Published: June 2018

AbstractDecoding transcription factor (TF) binding signals in genomic DNA is a fundamental problem. Here we present a prediction model called BindSpace that learns to embed DNA sequences and TF class/family labels into the same space. By training on binding data for hundreds of TFs and embedding over 1M DNA sequences, BindSpace achieves state-of-the-art multiclass binding prediction performance,in vitroandin vivo, and can distinguish signals of closely related TFs.
Innovation, firms’ performance and environmental turbulence: is there a moderator or mediator?
Authors: Turulja Lejla , Bajgoric Nijaz 
Published: June 2018

PurposeThe purpose of this paper is to draw on dynamic capability view and contingency theory to clarify the nature of the effect of environmental turbulence on the relationships between firm’s both product and process innovations and business performance.Design/methodology/approachThe authors developed and empirically tested two structural models using structural equation modeling approach. The first model deals with both product and process innovations as the mediators between environmental turbulence and business performance. The second model considers the moderating effect of environmental turbulence between innovation and business performance.FindingsThe findings show that environmental turbulence does not moderate the relationship between innovation and business performance. The authors have found a clear role of environmental turbulence in boosting innovation rather than moderating the relationship between innovation and performance.Research limitations/implicationsThe data set is a cross-section of heterogeneous firms regarding the industry.Practical implicationsManagers should be aware of the importance of the innovation for the environmental turbulence and dynamism counteracting. The results imply a negative influence of environmental turbulence on business performance. However, with the innovation in the equation, this influence can be positive, because it boosts firms to innovate and though to achieve better business performance.Originality/valueIt contributes the management and innovation research and practice through offering insights into the role of environmental turbulence in product innovation, process innovation as well as organizational business performance through comprehensive analysis of mediation and moderation effects between the observed constructs.
Orchestration of innovation networks in collaborative settings
Authors: Milwood Pauline A. , Roehl Wesley S. 
Published: June 2018

Purpose
Few papers address innovation activities among tourism entities. The purpose of this paper is to elucidate the extent to which the theoretical framework of network orchestration can explain the system of relations underlying roles and behaviors of tourism actors in collaborative innovation settings.

Design/methodology/approach
Using interview data collected from destination management organizations and their destination partners within two polar-sampled North American destinations, this study identifies relationships which underlie the behaviors of tourism and hospitality actors engaged in collaborative innovative activities. To understand these relationships, this study abductively imposes the emergent theoretical framework of network orchestration and offers practical implications for conducting successful innovation among tourism collaborators.

Findings
First, orchestration of knowledge mobility processes in collaborative innovation settings is associated with trust, perceived fairness and the search for experts within the network. Second, orchestration of innovation appropriability processes is associated with forging shared ownership and knowledge exchange with “dissimilar” partners. Third, orchestration of network stability processes is associated with enhancing the reputation of influential actors within the tourism destination, and shared visioning of future innovation outcomes.

Originality/value
This paper contributes to the collaborative innovation landscape by testing the emerging theoretical framework of network orchestration and proposing practical implications for hospitality and tourism actors engaged in innovative activities. The research further demonstrates the value of abductive reasoning for elucidating theory from interview evidence and proposes a model for future studies on collaborative innovation networks.
Perception of ethical climate and turnover intention among nursing staff: does organizational cynicism mediate?
Authors: Munir Yasin , Ghafoor Muhammad Mudasar , Rasli Amran M.D. 
Published: June 2018

PurposeThe purpose of this paper is to explore the mediating effect of organizational cynicism between the relationship of perception of ethical climate and turnover intention among nurses working in public sector hospitals.Design/methodology/approachA quantitative approach was utilized and 870 questionnaires were distributed to collect data from nursing staff working in Punjab region of Pakistan by using non-probability multistage sampling technique. A total of 711 questionnaires were returned out of which 668 questionnaires were scrutinized. Additionally, confirmatory factor analysis and structural equation modeling were applied to analyze the data.FindingsThe results revealed a full mediating effect of organizational cynicism between the relationship of perception of ethical climate and turnover intention.Research limitations/implicationsThe current study has adopted a multistage non-probability sampling technique to collect data because the management of hospitals restricted researcher access to personal information about the nurses. Therefore, at the first stage, the researcher used convenience sampling and at the second stage, the researcher utilized quota sampling to collect the data. Moreover, the findings of the current study are based on cross-sectional data because of the limited time and resources.Practical implicationsThe current study fosters the ongoing debate in organizational studies related to cynicism and it is noteworthy for the nursing managers to understand the significant factors which directly or indirectly affect the nursing attitude.Originality/valueThe current study explored the mediating role of organizational cynicism between perception of ethical climate and turnover intention in nursing profession to fill the research gap.
Building pharmaceutical relationship marketing and social media impact
Authors: Enyinda Chris I. , Ogbuehi Alphonso O. , Mbah Chris H. 
Published: June 2018

Purpose
The purpose of this paper is to identify key social medial channels which pharmaceutical firms need to consider when desiring to understand consumer behavior, build, maintain and proactively manage relationships. Also, it proposes the application of analytic hierarchy process (AHP) sensitivity analysis algorithm to test the stability or robustness of the priority ranking. Specifically, this paper leverages performance sensitivity analysis to evaluate how small changes (perturbation) in the major objectives of the pharmaceutical relationship marketing (PRM) tactics within the social media environment will influence the ranking of the alternative course of actions.

Design/methodology/approach
This paper used AHP-based questionnaire survey to evaluate the relative importance of factors accounting for PRM and the impact of social media channels. The major objectives and the alternative strategies used were from literature reviewed. Interviews with senior managers were insightful and helpful in the wording, content and format of the questionnaire.

Findings
Customer engagement is the most important PRM tactic, followed by communication and trust. The performance sensitivity analysis carried out on the PRM tactics showed that the ranking associated with social media channel options remained robust or insensitive to small perturbations.

Research limitations/implications
The data procured for this paper were based on one focal pharmaceutical firm. Convincing the same to grant an interview and late responding to the questionnaire was a great challenge.

Practical implications
Social media impact on pharmaceutical marketing relationship is important for pharmaceutical marketers. PRM bodes well with the social media environment. Pharmaceutical industry can build and maintain relationships with consumers through social media. Firms that leverage social media to enhance their PRM tactics will be viewed favorably in terms of trust, transparency, openness and honesty. The results provide pharmaceutical marketing managers with insightful and valuable information with respect to the role or social media impact on the PRM. The AHP model, objectives and their relative importance provide valuable information for managers on how to monitor the values that matters to customers the most.

Originality/value
This paper is one of the very few on the PRM and perhaps the first that examines social impact leveraging the AHP model. In addition, this paper contributes to the relationship marketing literature by leveraging a multi-criteria decision-making algorithm to prioritize the most important factors accounting for the PRM strategies.