bluuebunny/crossref_metadata_2025_split huggingface dataset:
ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy
Authors: Vimont Noémie , Quah Fu Xiang , Guillaume-Schöpfer David , Roudier François , Dirlewanger Elisabeth , Wigge Philip A. , Wenden Bénédicte , Cortijo Sandra 
Published: May 2018

ABSTRACTChromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors, and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-box 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.
The in situ structures of mono-, di-, and tri-nucleosomes in human heterochromatin
Authors: Cai Shujun , Böck Désirée , Pilhofer Martin , Gan Lu 
Published: May 2018

AbstractThein situ3-D organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography (cryo-ET) to determine thein situstructures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.
Deciphering the targets of retroviral protease inhibitors in Plasmodium berghei
Authors: Machuki Noah , Mogire Reagan , Ndung’u Loise , Mwitari Peter , Kimani Francis , Matoke-Muhia Damaris , Kiboi Daniel , Magoma Gabriel 
Published: May 2018

AbstractRetroviral protease inhibitors (RPIs) such as lopinavir (LP) and saquinavir (SQ) are active against Plasmodium parasites. However, the exact molecular target(s) for these RPIs in the Plasmodium parasites remains poorly understood. We hypothesised that LP and SQ suppress parasite growth through inhibition of aspartyl proteases. Using reverse genetics approach, we embarked on separately generating knockout (KO) parasite lines lacking Plasmepsin 4 (PM4), PM7, PM8, or DNA damage-inducible protein 1 (Ddi1) in the rodent malaria parasite Plasmodium berghei ANKA. We then tested the suppressive profiles of the LP/Ritonavir (LP/RT) and SQ/RT as well as antimalarials; Amodiaquine (AQ) and Piperaquine (PQ) against the KO parasites in the standard 4-day suppressive test. The Ddi1 gene proved refractory to deletion suggesting that the gene is essential for the growth of the asexual blood stage parasites. Our results revealed that deletion of PM4 significantly reduces normal parasite growth rate phenotype (P = 0.003). Unlike PM4_KO parasites which were less susceptible to LP and SQ (P = 0.036, P = 0.030), the suppressive profiles for PM7_KO and PM8_KO parasites were comparable to those for the WT parasites. This finding suggests a potential role of PM4 in the LP and SQ action. On further analysis, modelling and molecular docking studies revealed that both LP and SQ displayed high binding affinities (-6.3 kcal/mol to -10.3 kcal/mol) towards the Plasmodium aspartyl proteases. We concluded that PM4 plays a vital role in assuring asexual stage parasite fitness and might be mediating LP and SQ action. The essential nature of the Ddi1 gene warrants further studies to evaluate its role in the parasite asexual blood stage growth as well as a possible target for the RPIs.Author summaryThe antiretroviral drugs (ARVs) such as LP or SQ that inhibit viral proteases reduce the rate of multiplication of the malaria parasites. The mode of action of these drugs against the parasites is however poorly understood. The proteases are among the enzymes that play essential roles in Plasmodium parasites. We sought to investigate the possible mode of action of these drugs by generating mutant parasites lacking specific aspartyl proteases namely PM4, PM7, PM8 or Ddi1 and then evaluate the susceptibility of the mutants to LP and SQ. We successfully generated parasites lacking either PM4, PM7 or PM8 but Ddi1 gene was refractory to deletion. From our data, we demonstrate that, unlike PM7 and PM8, the PM4 and Ddi1 are essential enzymes for asexual blood stage parasite fitness and survival and that the PM4 might be a target for the viral protease inhibitors in reducing parasite growth and multiplication. Further experiments using molecular docking tools show that LP or SQ have a high binding affinity for the Plasmodium aspartyl proteases.
Statistical Investigations of Protein Residue Direct Couplings
Authors: Neuwald Andrew F. , Altschul Stephen F. 
Published: May 2018

AbstractProtein Direct Coupling Analysis (DCA), which predicts residue-residue contacts based on covarying positions within a multiple sequence alignment, has been remarkably effective. This suggests that there is more to learn from sequence correlations than is generally assumed, and calls for deeper investigations into DCA and perhaps into other types of correlations. Here we describe an approach that enables such investigations by measuring, as an estimated p-value, the statistical significance of the association between residue-residue covariance and structural interactions, either internal or homodimeric. Its application to thirty protein superfamilies confirms that DCA scores correlate with 3D pairwise contacts with very high significance. This method also permits quantitative assessment of the relative performance of alternative DCA methods, and of the degree to which they detect direct versus indirect couplings. We illustrate its use to assess, for a given protein, the biological relevance of alternative conformational states, to investigate the possible mechanistic implications of differences between these states, and to characterize subtle aspects of direct couplings. Our analysis indicates that direct pairwise correlations may be largely distinct from correlated patterns associated with functional specialization, and that the joint analysis of both types of correlations can yield greater power. Our approach might be applied effectively to assessing multiple alignment quality, eliminating the need for benchmark alignments. Data, programs, and source code are freely available at http://evaldca.igs.umaryland.edu.Author SummaryThe success of Direct Coupling Analysis (DCA) for protein structure prediction suggests that multiple sequence alignments implicitly contain more structural information than had previously been realized, and prompts deeper investigations of the sequence correlations uncovered by either DCA or other approaches. To aid such investigations and thereby broaden the utility of and improve DCA, we describe an approach that measures the statistical significance of the association between DCA and either 3D structure or correlated patterns associated with functional specialization. This approach can be used to obtain better input alignments, and to evaluate the relative performance of DCA methods, their ability to distinguish direct from indirect couplings, and the potential biological relevance and mechanistic implications of alternative conformations and homodimeric interactions.
Detection of cellular microRNAs with programmable DNA nanoswitches
Authors: Chandrasekaran Arun Richard , MacIsaac Molly , Dey Paromita , Levchenko Oksana , Zhou Lifeng , Andres Madeline , Dey Bijan K. , Halvorsen Ken 
Published: May 2018

AbstractMicroRNAs are short non-coding regulatory RNAs that are increasingly used as disease biomarkers. Detection of microRNAs can be arduous and expensive, and often requires amplification, labeling, or radioactive probes. Here we report a single-step, non-enzymatic detection assay using conformationally responsive DNA nanoswitches. Termed miRacles (microRNAactivatedconditionallooping ofengineeredswitches), our assay has sub-attomole sensitivity and single-nucleotide specificity using an agarose gel electrophoresis readout. We detect cellular microRNAs from nanogram-scale RNA extracts of differentiating muscle cells, and demonstrate multiplexed detection of several microRNAs from one biological sample. We demonstrate one-hour detection without expensive equipment or reagents, making this assay a compelling alternative to qPCR and Northern blotting.Significance statementDetection of microRNAs play a key role in biological research and medical diagnostics, and current detection methods are expensive and require sophisticated processes. We presentmicroRNAactivatedconditionallooping ofengineeredswitches (miRacles), a mix-and-read strategy that is based on conformational changes of DNA nanoswitches upon binding a target microRNA. MiRacles has a sensitivity of ∼4 copies/cell and specificity of a single nucleotide, and can be performed in one hour at a fraction of the cost of traditional microRNA detection techniques. Our method can also be multiplexed to detect multiple microRNAs from one biological sample. The minimalistic miRacles assay has immediate application in biomedical research and longer term potential as a clinical tool.
Properties of cell signaling pathways and gene expression systems operating far from steady-state
Authors: Di Bella Juan Pablo , Colman-Lerner Alejandro , Ventura Alejandra C. 
Published: May 2018

AbstractLigand-receptor systems, covalent modification cycles, and transcriptional networks are basic units of signaling systems and their steady-state properties are well understood. However, the behavior of such systems before steady-state is poorly characterized. Here, we analyzed the properties of the input-output curves for each of these systems as they approach steady-state. In ligand-receptor systems, the EC50(concentration of the ligand that occupies 50% of the receptors) is higher before the system reaches steady-state. Based on this behavior, we have previously defined PRESS (for pre-equilibrium sensing and signaling), a general “systems level” mechanism cells may use to overcome input saturation. Originally, we showed that, given a step stimulation, PRESS operates when the kinetics of ligand-receptor binding are slower than the downstream signaling steps. Now, we show that, provided the input increases slowly, it is not essential for the ligand binding reaction itself to be slow. In addition, we demonstrate that covalent modification cycles and gene expression systems may also operate in PRESS mode. Thus, nearly all biochemical processes may operate in PRESS mode, suggesting that this mechanism may be ubiquitous in cell signaling systems.
Genetic, biochemical, and molecular characterization ofMethanosarcina barkerimutants lacking three distinct classes of hydrogenase
Authors: Mand Thomas D. , Kulkarni Gargi , Metcalf William W. 
Published: May 2018

ABSTRACTThe methanogenic archaeonMethanosarcina barkeriencodes three distinct types of hydrogenase, whose functions vary depending on the growth substrate. These include the F420-dependent (Frh), methanophenazine-dependent (Vht), and ferredoxin-dependent (Ech) hydrogenases. To investigate their physiological roles, we characterized a series of mutants lacking each hydrogenase in various combinations. Mutants lacking Frh, Vht, or Ech in any combination failed to grow on H2/CO2, whereas only Vht and Ech were essential for growth on acetate. In contrast, a mutant lacking all three grew on methanol with a final growth yield similar to wild-type, produced methane and CO2in the expected 3:1 ratio, but had aca.33% slower growth rate. Thus, hydrogenases play a significant, but non-essential, role during growth on this substrate. As previously observed, mutants lacking Ech fail to grow on methanol/H2unless supplemented with biosynthetic precursors. Interestingly, this phenotype was abolished in the Δech/Δfrhand Δech/Δfrh/Δvhtmutants, consistent with the idea that hydrogenases inhibit methanol oxidation in the presence of H2, which prevents production of reducing equivalents needed for biosynthesis. Quantification of methane and CO2produced from methanol by resting cell suspensions of various mutants supports this conclusion. Based on global transcriptional profiles, none of the hydrogenases are upregulated to compensate for loss of the others. However, transcript levels of the F420 dehydrogenase operon were significantly higher in all strains lackingfrh, suggesting a mechanism to sense the redox state of F420. The roles of the hydrogenases in energy conservation during growth with each methanogenic pathway are discussed.
Exploring the archaeome: detection of archaeal signatures in the human body
Authors: Pausan Manuela R. , Csorba Cintia , Singer Georg , Till Holger , Schöpf Veronika , Santigli Elisabeth , Klug Barbara , Högenauer Christoph , Blohs Marcus , Moissl-Eichinger Christine 
Published: May 2018

AbstractDue to their fundamentally different biology, archaea are consistently overlooked in conventional microbiome surveys. Using amplicon sequencing, we evaluated methodological set-ups to detect archaea in samples from five different body sites: respiratory tract (nose), digestive tract (mouth, appendix, and stool) and skin. With the optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in currently used, so-called “universal” approach) to 81 RSVs in a representative sample set. In order to assess the archaeome diversity, a specific archaea-targeting methodology is required, for which we propose a standard procedure. This methodology might not only prove useful for analyzing the human archaeome in more detail but could also be used for other holobionts’ samples.
Protein Gradients on the Nucleoid Position the Carbon-fixing Organelles of Cyanobacteria
Authors: MacCready Joshua S. , Hakim Pusparanee , Young Eric J. , Hu Longhua , Liu Jian , Osteryoung Katherine W. , Vecchiarelli Anthony G. , Ducat Daniel C. 
Published: May 2018

In BriefWe describe a novel positioning system that utilizes the cyanobacterial nucleoid to segregate, transport and equidistantly position the carbon-fixation machinery (carboxysomes).SummaryCarboxysomes are protein-based bacterial organelles that encapsulate a key enzyme of the Calvin-Benson-Bassham cycle. Previous work has implicated a ParA-like protein (hereafter McdA) as important for spatially organizing carboxysomes along the longitudinal axis of the model cyanobacterium Synechococcus elongatus PCC 7942. Yet, how self-organization of McdA emerges and contributes to carboxysome positioning is unknown. Here, we show that a small protein, termed McdB, localizes to carboxysomes through interactions with carboxysome shell proteins to drive emergent oscillatory patterning of McdA on the nucleoid. Our results demonstrate that McdB directly interacts to stimulate McdA ATPase activity, and indicate that carboxysome-dependent McdA depletion zone formation on the nucleoid is required for directed motion of carboxysomes towards increased concentrations of McdA. We propose that McdA and McdB are a new class of self-organizing proteins that follow a Brownian-ratchet mechanism, challenging the cytoskeletal model of organelle transport, for equidistant positioning of carboxysomes in cyanobacteria. These results have broader implications for understanding spatial organization of protein mega-complexes and organelles in bacteria more broadly.
Different states of priority recruit different neural codes in visual working memory
Authors: Yu Qing , Postle Bradley R. 
Published: May 2018

AbstractWe tracked the neural representation of the orientation and the location of stimuli held in working memory at different levels of priority (“attended” and “unattended” memory items -- AMI and UMI), using multivariate inverted encoding models of human fMRI. Although representation of the orientation of the AMI and of the UMI could be reconstructed in several brain regions, including in early visual and parietal regions, the identity of the UMI was actively represented in early visual cortex in a distinct “reversed” code, suggesting this region as a site of the focus of attention to nonspatial stimulus information. The location of stimuli was also broadly represented, although only in parietal cortex was the location of the UMI represented in a reversed code. Our results suggest that a common recoding operation may be engaged, across stimulus dimensions and brain areas, to retain information in working memory while outside the focus of attention.
The inhibition of automatic imitation: a meta-analysis and synthesis of fMRI studies
Authors: Darda Kohinoor M. , Ramsey Richard 
Published: May 2018

AbstractHumans copy other people without their conscious awareness, a behaviour known as automatic imitation. Although automatic imitation forms a key part of daily social interactions, we do not copy other people indiscriminately. Instead, we control imitative tendencies by prioritising some actions and inhibiting others. To date, neuroimaging studies investigating the control of automatic imitation have produced inconsistent findings. Some studies suggest that imitation control relies on a domain-specific neural circuit related to social cognition (the theory-of-mind network). In contrast, other studies show engagement of a domain-general neural circuit that is engaged during a diverse range of cognitive control tasks (the multiple demand network). Given the inconsistency of prior findings, in the current paper we avoided problems associated with interpreting individual studies by performing a meta-analysis. To do so, we used a multi-level kernel density analysis to quantitatively identify consistent patterns of activation across functional magnetic resonance imaging studies investigating the control of imitation. Our results show clear and consistent evidence across studies that the control of automatic imitation is guided by brain regions in the multiple demand network including dorsolateral frontoparietal cortex. In contrast, there was only limited evidence that regions in the theory of mind network were engaged. Indeed, medial prefrontal cortex showed no consistent engagement and right temporoparietal junction engagement may reflect spatial rather than imitative control. As such, the current meta-analysis reinforces the role of domain-general control mechanisms and provides limited evidence in support of the role of domain-specific processes in regulating imitative tendencies. Consequently, neurocognitive models of imitation need updating to place more emphasis on domain-general control mechanisms, as well as to consider more complex organisational structures of control, which may involve contributions from multiple cognitive systems.
Industrial relations in Poland
Authors: Czarzasty Jan , Mrozowicki Adam 
Published: May 2018

Purpose
The purpose of this paper is to examine the interrelations between the evolution of industrial relations (IR) and IR research in Poland in the historical context. Two questions are put forward: How was the evolution of the IR system in Poland influenced by the re-constitution of a particular model of the capitalism and the strategies and struggle of IR actors? How were the ways of approaching and theorizing IR influenced by the aforementioned evolution?

Design/methodology/approach
The paper draws upon academic literature, secondary data on actors and processes of IR as well as four expert interviews with the representatives of the first generation of IR scholars in Poland.

Findings
The paper suggests that the development of the IR system and the related scholarship can be divided into three phases: the pre-1989 period characterised by the lack of autonomous interests representation and rather limited IR research; the early development of the post-1989 IR system marked by the debates on the integrative role of IR as peacekeeping mechanism in the period of deep economic and political changes (1989-2004); the post-EU accession consolidation of the IR system characterised by the weakness of the IR actors vis-à-vis the state and increasing neo-etatist tendencies.

Originality/value
This paper contributes to the ongoing debate on the relationships between the emergent models of Eastern European capitalism and the evolution of IR systems. It critically analyses the state of the discussion on the IR field Poland emphasising the relevance of political-economic factors as well as the ideology of “social peace” for both the evolution of the IR system in the country and the state of the IR debate.
Integrating affect, cognition, and culture in Hispanic financial planning
Authors: Weisfeld-Spolter Suri , Sussan Fiona , Rippé Cindy , Gould Stephen 
Published: May 2018

Purpose
Debt is at a peak and consumers purport needing help with financial planning. To better understand the antecedents of financial planning behavior, the purpose of this paper is to examine the importance of cultural values in financial decision making within the context of Hispanic American consumers. A new conceptual model is proposed to integrate affect (cultural value) and cognition (financial knowledge) in financial planning.

Design/methodology/approach
To uncover respondents’ views on cultural values, financial knowledge, financial attitude, and financial planning behavior, an online survey hosted on a business school’s website was distributed to members of two Hispanic Chambers of Commerce. The survey consisted of five parts, and took each respondent an average of 15 minutes to complete. The final data set has 158 observations.

Findings
Results analyzed using structural equation modeling confirmed the hypotheses that financial knowledge, attitude, and perceived control simultaneously influence Hispanic consumers’ intentions to purchase financial planning products or services. More interestingly, these results confirm that multiple different routes coexist in the decision-making process, especially within the Hispanic financial planning context.

Originality/value
Key contributions of this paper include the conceptualization of cultural value as an antecedent to Hispanic financial behavior; detailing the different routes to financial decision making for US Hispanic consumers; and informing financial service managers on marketing strategies toward Hispanic consumers.