bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multimerization of Homo sapiens TRPA1 ion channel cytoplasmic domains
Authors: Martinez Gilbert Q. , Gordon Sharona E. 
Published: November 2018

AbstractThe transient receptor potential Ankyrin-1 (TRPA1) ion channel is modulated by myriad noxious stimuli that interact with multiple regions of the channel, including cysteine-reactive natural extracts from onion and garlic which modify residues in the cytoplasmic domains. The way in which TRPA1 cytoplasmic domain modification is coupled to opening of the ion-conducting pore has yet to be elucidated. The cryo-EM structure of TRPA1 revealed a tetrameric C-terminal coiled-coil surrounded by N-terminal ankyrin repeat domains (ARDs), an architecture shared with the canonical transient receptor potential (TRPC) ion channel family. Similarly, structures of the TRP melastatin (TRPM) ion channel family also showed a C-terminal coiled-coil surrounded by N-terminal cytoplasmic domains. This conserved architecture may indicate a common gating mechanism by which modification of cytoplasmic domains can transduce conformational changes to open the ion-conducting pore. We developed an in vitro system in which N-terminal ARDs and C-terminal coiled-coil domains can be expressed in bacteria and maintain the ability to interact. We tested three gating regulators: temperature; the polyphosphate compound IP6; and the covalent modifier allyl isothiocyanate to determine whether they alter N-and C-terminal interactions. We found that none of the modifiers tested abolished ARD-coiled-coil interactions, though there was a significant reduction at 37°C. We found that coiled-coils tetramerize in a concentration dependent manner, with monomers and trimers observed at lower concentrations. Our system provides a method for examining the mechanism of oligomerization of TRPA1 cytoplasmic domains as well as a system to study the transmission of conformational changes resulting from covalent modification.
BMN 250, a fusion of lysosomal alpha-N-acetylglucosaminidase with IGF2, exhibits different patterns of cellular uptake into critical cell types of Sanfilippo syndrome B disease pathogenesis
Authors: Yogalingam Gouri , Luu Amanda R , Prill Heather , Lo Melanie J. , Yip Bryan , Holtzinger John , Christianson Terri , Aoyagi-Scharber Mika , Lawrence Roger , Crawford Brett E. , LeBowitz Jonathan H. 
Published: November 2018

ABSTRACTSanfilippo syndrome type B (Sanfilippo B; Mucopolysaccharidosis type IIIB) occurs due to genetic deficiency of lysosomal alpha-N-acetylglucosaminidase (NAGLU) and subsequent lysosomal accumulation of heparan sulfate (HS), which coincides with devastating neurodegenerative disease. Because NAGLU expressed in Chinese hamster ovary cells is not mannose-6-phosphorylated, we developed an insulin-like growth factor 2 (IGF2)-tagged NAGLU molecule (BMN 250; tralesinidase alfa) that binds avidly to the IGF2 / cation-independent mannose 6-phosphate receptor (CI-MPR) for glycosylation independent lysosomal targeting. BMN 250 is currently being developed as an investigational enzyme replacement therapy for Sanfilippo B. Here we distinguish two cellular uptake mechanisms by which BMN 250 is targeted to lysosomes. In normal rodent-derived neurons and astrocytes, the majority of BMN250 uptake over 24 hours reaches saturation, which can be competitively inhibited with IGF2, suggestive of CI-MPR-mediated uptake. Kuptake, defined as the concentration of enzyme at half-maximal uptake, is 5 nM and 3 nM in neurons and astrocytes, with a maximal uptake capacity (Vmax) corresponding to 764 nmol/hr/mg and 5380 nmol/hr/mg, respectively. Similar to neurons and astrocytes, BMN 250 uptake in Sanfilippo B patient fibroblasts is predominantly CI-MPR-mediated, resulting in augmentation of NAGLU activity with doses of enzyme that fall well below the Kuptake (5 nM), which are sufficient to prevent HS accumulation. In contrast, uptake of the untagged recombinant human NAGLU (rhNAGLU) enzyme in neurons, astrocytes and fibroblasts is negligible at the same doses tested. In microglia, receptor-independent uptake, defined as enzyme uptake resistant to competition with excess IGF2, results in appreciable lysosomal delivery of BMN 250 and rhNAGLU (Vmax=12,336 nmol/hr/mg and 5469 nmol/hr/mg, respectively). These results suggest that while receptor-independent mechanisms exist for lysosomal targeting of rhNAGLU in microglia, BMN 250, by its IGF2 tag moiety, confers increased CI-MPR-mediated lysosomal targeting to neurons and astrocytes, two additional critical cell types of Sanfilippo B disease pathogenesis.
Heterogeneity of Incipient Atrophy Patterns in Parkinson’s Disease
Authors: Maia Pedro D. , Pandya Sneha , Torok Justin , Gupta Ajay , Zeighami Yashar , Raj Ashish 
Published: November 2018

AbstractParkinson’s Disease (PD) is a the second most common neurodegenerative disorder after Alzheimer’s disease and is characterized by cell death in the amygdala and in substructures of the basal ganglia such as the substantia nigra. Since neuronal loss in PD leads to measurable atrophy patterns in the brain, there is clinical value in understanding where exactly the pathology emerges in each patient and how incipient atrophy relates to the future spread of disease. A recent seed-inference algorithm combining an established network-diffusion model with an L1-penalized optimization routine led to new insights regarding the non-stereotypical origins of Alzheimer’s pathologies across individual subjects. Here, we leverage the same technique to PD patients, demonstrating that the high variability in their atrophy patterns also translates into heterogeneous seed locations. Our individualized seeds are significantly more predictive of future atrophy than a single seed placed at the substantia nigra or the amygdala. We also found a clear distinction in seeding patterns between two PD subgroups – one characterized by predominant involvement of brainstem and ventral nuclei, and the other by more widespread frontal and striatal cortices. This might be indicative of two distinct etiological mechanisms operative in PD. Ultimately, our methods demonstrate that the early stages of the disease may exhibit incipient atrophy patterns that are more complex and variable than generally appreciated.
Maximizing the quality of NMR automatic metabolite profiling by a machine learning based prediction of signal parameters
Authors: Cañueto Daniel , Navarro Miriam , Bulló Mónica , Correig Xavier , Cañellas Nicolau 
Published: November 2018

AbstractThe quality of automatic metabolite profiling in NMR datasets in complex matrices can be compromised by the multiple sources of variability in the samples. These sources cause uncertainty in the metabolite signal parameters and the presence of multiple low-intensity signals. Lineshape fitting approaches might produce suboptimal resolutions or distort the fitted signals to adapt them to the complex spectrum lineshape. As a result, tools tend to restrict their use to specific matrices and strict protocols to reduce this uncertainty. However, the analysis and modelling of the signal parameters collected during a first profiling iteration can further reduce the uncertainty by the generation of narrow and accurate predictions of the expected signal parameters. In this study, we show that, thanks to the predictions generated, better profiling quality indicators can be outputted and the performance of automatic profiling can be maximized. Thanks to the ability of our workflow to learn and model the sample properties, restrictions in the matrix or protocol and limitations of lineshape fitting approaches can be overcome.
A structure-based approach towards identification of inhibitory fragments for eleven-nineteen-leukemia protein (ENL) YEATS domain
Authors: Heidenreich David , Moustakim Moses , Schmidt Jurema , Merk Daniel , Brennan Paul E. , Fedorov Oleg , Chaikuad Apirat , Knapp Stefan 
Published: November 2018

ABSTRACTLysine acetylation is an epigenetic mark that is principally recognized by bromodomains and recently structurally diverse YEATS domains also emerged as readers of lysine acetyl/acylations. Here we present a crystallography-based strategy and the discovery of fragments binding to the ENL YEATS domain, a potential drug target. Crystal structures combined with synthetic efforts led to the identification of a sub-micromolar binder, providing first starting points for the development of chemical probes for this reader domain family.
Consensus sequence design as a general strategy to create hyperstable, biologically active proteins
Authors: Sternke Matt , Tripp Katherine W. , Barrick Doug 
Published: November 2018

AbstractConsensus sequence design offers a promising strategy for designing proteins of high stability while retaining biological activity since it draws upon an evolutionary history in which residues important for both stability and function are likely to be conserved. Although there have been several reports of successful consensus design of individual targets, it is unclear from these anecdotal studies how often this approach succeeds, and how often it fails. Here, we attempt to assess generality by designing consensus sequences for a set of six protein families with a range of chain-lengths, structures, and activities. We characterize the resulting consensus proteins for stability, structure, and biological activities in an unbiased way. We find that all six consensus proteins adopt cooperatively folded structures in solution. Strikingly, four out of six of these consensus proteins show increased thermodynamic stability over naturally-occurring homologues. Each consensus protein tested for function maintained at least partial biological activity. Though peptide binding affinity by a consensus-designed SH3 is rather low, Kmvalues for consensus enzymes are similar to values from extant homologues. Though consensus enzymes are slower than extant homologues at low temperature, they are faster than some thermophilic enzymes at high temperature. An analysis of sequence properties shows consensus proteins to be enriched in charged residues, and rarified in uncharged polar residues. Sequence differences between consensus and extant homologues are predominantly located at weakly conserved surface residues, highlighting the importance of these residues in the success of the consensus strategy.Significance StatementA major goal of protein design is to create proteins that have high stability and biological activity. Drawing on evolutionary information encoded within extant protein sequences, consensus sequence design has produced several successes in achieving this goal. Here we explore the generality with which consensus design can be used to enhance protein stability and maintain biological activity. By designing and characterizing consensus sequences for six unrelated protein families, we find that consensus design shows high success rates in creating well-folded, hyperstable proteins that retain biological activities. Remarkably, many of these consensus proteins show higher stabilities than naturally-occurring sequences of their respective protein families. Our study highlights the utility of consensus sequence design and informs the mechanisms by which it works.
Systems-level properties of EGFR/Ras/ERK signalling amplify local signals to generate gene expression plasticity
Authors: Davies Alexander E. , Gillies Taryn E. , Siebert Stefan , Pargett Michael , Tobin Savannah J. , Ram Abhineet R. , Juliano Celina , Quon Gerald , Bissell Mina J. , Albeck John G. 
Published: November 2018

AbstractThe EGFR/Ras/ERK signalling pathway is a driver of cancer cell proliferation and metastasis in tumours that exhibit high cell-to-cell heterogeneity. While the signalling activity of this pathway is frequently amplified in tumours, it is not understood how the kinetic aspects of its activation in tumours differ from normal cellular signalling. Using live-cell reporters of ERK signalling in the breast cancer progression series HMT-3522, we found that ERK activity in invasive cells is similar in amplitude to isogenic non-malignant cells but is highly dynamic and more disordered, leading to more heterogeneous expression of ERK target genes. Our analysis reveals that this diversification arises from systems-level functions of the pathway, including intracellular amplification of amphiregulin-mediated paracrine signalling and differential kinetic filtering by genes including Fra-1, c-Myc, and Egr1. Our findings establish a mechanism for the generation of non-genetic tumour cell plasticity arising from the specific quantitative properties of a signal transduction pathway.
Prefrontal cortex creates novel navigation sequences from hippocampal place-cell replay with spatial reward propagation
Authors: Cazin Nicolas , Alonso Martin Llofriu , Chiodi Pablo Scleidorovich , Pelc Tatiana , Harland Bruce , Weitzenfeld Alfredo , Fellous Jean-Marc , Dominey Peter Ford 
Published: November 2018

AbstractAs rats learn to search for multiple sources of food or water in a complex environment, they generate increasingly efficient trajectories between reward sites, across multiple trials. This optimization capacity has been characterized in the Traveling Salesrat Problem (TSP) (de Jong et al (2011). Such spatial navigation capacity involves the replay of hippocampal place-cells during awake states, generating small sequences of spatially related place-cell activity that we call “snippets”. These snippets occur primarily during sharp-wave-ripple (SWR) events. Here we focus on the role of replay during the awake state, as the animal is learning across multiple trials. We hypothesize that snippet replay generates synthetic data that can substantially expand and restructure the experience available to make PFC learning more optimal. We developed a model of snippet generation that is modulated by reward, propagated in the forward and reverse directions. This implements a form of spatial credit assignment for reinforcement learning. We use a biologically motivated computational framework known as ‘reservoir computing’ to model PFC in sequence learning, in which large pools of prewired neural elements process information dynamically through reverberations. This PFC model is ideal to consolidate snippets into larger spatial sequences that may be later recalled by subsets of the original sequences. Our simulation experiments provide neurophysiological explanations for two pertinent observations related to navigation. Reward modulation allows the system to reject non-optimal segments of experienced trajectories, and reverse replay allows the system to “learn” trajectories that is has not physically experienced, both of which significantly contribute to the TSP behavior.Author SummaryAs rats search for multiple sources of food in a complex environment, they generate increasingly efficient trajectories between reward sites, across multiple trials, characterized in the Traveling Salesrat Problem (TSP). This likely involves the coordinated replay of place-cell “snippets” between successive trials. We hypothesize that “snippets” can be used by the prefrontal cortex (PFC) to implement a form of reward-modulated reinforcement learning. Our simulation experiments provide neurophysiological explanations for two pertinent observations related to navigation. Reward modulation allows the system to reject non-optimal segments of experienced trajectories, and reverse replay allows the system to “learn” trajectories that it has not physically experienced, both of which significantly contribute to the TSP behavior.
The distinct biochemical property enables thymidylate kinase as a drug target and participates in pyrimidine drug sensitivity inCandida albicans
Authors: Huang Chang-Yu , Chen Yee-Chun , Wu-Hsieh Betty A. , Fang Jim-Min , Chang Zee-Fen 
Published: November 2018

AbstractThe ability to overcome drug resistance in outbreaks ofCandida albicansinfection is an unmet need in health management. Here, we investigatedCDC8, which encodes thymidylate kinase (TMPK), as a potential drug target for the treatment ofC. albicansinfection. In this study, we found that the specific region spanning amino acids 106-123, namely, the Ca-loop ofC. albicansTMPK (CaTMPK) contributes to the hyperactivity of this enzyme compared to the human enzyme (hTMPK) and to the utilization of deoxyuridine monophosphate (dUMP)/ deoxy-5-Fluorouridine monophosphate (5-FdUMP) as a substrate. Notably, CaTMPK but not hTMPK enables dUTP/5-FdUTP-mediated DNA toxicity in yeast. CRISPR-mediated deletion of this Ca-loop inC. albicansdemonstrated the critical role of this Ca-loop in fungal growth and susceptibility to 5-Fluorouridine (5-FUrd). Moreover, pathogenic and drug-resistantC. albicansclones were similarly sensitive to 5-FUrd. Thus, this study not only identified a target site for the development of CaTMPK-selective drugs but also revealed 5-FUrd to be a potential drug for the treatment ofC. albicansinfection.Author summaryThe emergence of drug-resistantC. albicansstrains is a serious medical concern that may be addressed by targeting an essential fungal enzyme.CDC8encodes thymidylate kinase (TMPK), which is the key enzyme required for dTTP synthesis and is an essential gene for yeast growth. Therefore, the differences of TMPK between human andC. albicanscan be a potential drug targeting site. This study defines a specific Ca-loop unique to CaTMPK fromC. albicans, contributing to hyper-activity over human enzyme (hTMPK). CRSPR-edited deletion of this loop also suppressed the growth ofC. albicans. Moreover, we present evidence that this loop enables dUMP utilization by CaTMPK, but not hTMPK. CaTMPK is also capable of using 5-FdUMP as a substrate, which contributes to 5-FUrd-mediated toxicity. Importantly, we found that many drug resistant pathogenicC. albicansisolates from patients are sensitive to 5-FUrd, which has not been used as a drug against fungal infection.
Mitotic phosphorylation by Nek6 and Nek7 reduces microtubule affinity of EML4 to alter spindle dynamics and promote chromosome congression
Authors: Adib Rozita , Montgomery Jessica M. , Atherton Joseph , O’Regan Laura , Richards Mark W. , Straatman Kees R. , Roth Daniel , Straube Anne , Bayliss Richard , Moores Carolyn A. , Fry Andrew M. 
Published: November 2018

ABSTRACTEML4 is a microtubule-associated protein that promotes microtubule stability. We show here that EML4 is distributed as punctate foci along the microtubule lattice in interphase but exhibits reduced association with spindle microtubules in mitosis. Microtubule sedimentation and cryo-electron microscopy and 3D reconstruction reveal that EML4 binds via its basic N-terminal domain to the acidic C-terminal tails of α- and β-tubulin on the microtubule surface. The mitotic kinases Nek6 and Nek7 can phosphorylate EML4 N-terminal domain at S144 and S146 in vitro, and depletion of these kinases leads to increased EML4 binding to microtubules in mitosis. An S144A-S146A double mutant not only binds inappropriately to mitotic microtubules but also interferes with chromosome congression. Meanwhile, constitutive activation of Nek6 or Nek7 reduces EML4 association with interphase microtubules. Together, these data support a model in which Nek6 and Nek7-dependent phosphorylation promotes dissociation of EML4 from microtubules in mitosis thereby altering microtubule dynamics to enable chromosome congression.
Technology efficiency or allocation efficiency
Authors: Cai Hailong , Yan Tianyao 
Published: November 2018

Purpose
The emergence of mega-farms in middle-income countries like Brazil and Ukraine and the efforts to consolidate small farms into larger ones in China and elsewhere have suggested that new institutional arrangements and technology progress may increase the significant farm economies of size, and therefore challenging the classical inverse relationship (IR) between productivity and farm size. The purpose of this paper is to conduct a research to examine the existence of IR in China’s cereal production and further explore the possible mechanism.

Design/methodology/approach
Based on the panel data concerning farms from 31 provinces in China in 2009–2014, technology efficiency and allocation efficiency in cereal production were measured based on the Translog production function.

Findings
In China, an IR exists between wheat, rice and maize production after controlling the related variables. Further, the presence of this IR is due to allocation efficiency rather than technology efficiency. Results of technology efficiency show that there is no significant difference between different size groups; in other words, even the larger size groups enjoy a higher technology efficiency in rice production. Results of allocation efficiency demonstrate that, compared with the larger farms, smaller holders tend to invest more in factors which are beneficial in growing productivity. Hence, yields of small-size farms exceed those of large-size farms, which consequently leads to the IR.

Practical implications
The scale consolidation of cropland is harmless to the efficiency of factor utilization and, conversely, may contribute in improving the technology efficiency of specific crops (like rice). Based on the results of allocation efficiency estimation, the extent of misallocation in large scales is relatively less due to their less input of fertilizer and pesticide; thus, the size-improving policy of farmland may contribute to the ease of the non-point pollution in agriculture.

Originality/value
The existing discussions of the IR in the context of recent China mainly focus on the accurate verification of IRs. This paper steps forward from the perspective of technology efficiency and allocation efficiency and explores the exact resources of IR with up-to-date and representative data and hopes to find some new conclusions.
Farm size and use of inputs: explanations for the inverse productivity relationship
Authors: Cheng Shen , Zheng Zhihao , Henneberry Shida 
Published: November 2018

PurposeThe relationship between farm size and land productivity is a hotly debated issue in the study of agricultural economics and development economics. The purpose of this paper is to explore the causes leading to the inverse productivity relationship by examining the relationship between farm size and factor inputs.Design/methodology/approachWith a large panel data set of farm households in China during 2010–2011, this study uses the factor demand models to examine the relationship between farm size and per-mu labor and non-labor inputs while employing a stochastic frontier production function in determining the difference of labor efforts in farming operation across farm sizes. Moreover, the models for value-added margins and profits are used to further determine producer behavior of small-size farms.FindingsResults of this study show that, as compared to larger farms, smaller farms not only utilize more labor and non-labor inputs per mu, but also benefit from a higher labor effort. Moreover, smaller farms concentrate more on grain output and cash costs while focusing less on the family labor input costs in an effort to maximize value-added margins rather than profits. The higher yields on smaller farms are thus a result of the utilization of a relatively higher level of labor and non-labor inputs along with skilled-oriented precision farming technology. The inverse productivity relationship is explained by the behavior of small-size producers with employment constraints, leading to smaller farms generating a higher yield than larger farms.Originality/valueWhile Sen (1966), Feder (1985), Eswaran and Kotwal (1986) and others have theoretically derived the causal relationship between the incomplete factor markets, especially incomplete labor markets, and the inverse productivity, empirical studies to test the causal relationships are limited. In particular, a solid foundation based on an empirical analysis is lacking when it comes to explaining the inverse productivity in China. Results of this study are expected to have significant policy implications in terms of the understanding of small-size producer behavior and the associated mechanism underlying the inverse relationship between farm size and land productivity.