bluuebunny/crossref_metadata_2025 huggingface dataset:
Fungal effector Jsi1 hijacks plant JA/ET signaling through Topless
Authors: Darino Martin , Marques Joana , Chia Khong-Sam , Aleksza David , Soto Luz Mayela , Uhse Simon , Borg Michael , Betz Ruben , Bindics Janos , Zienkiewicz Krzysztof , Feussner Ivo , Petit-Houdenot Yohann , Djamei Armin
Published: November 2019

Ustilago maydis (U. maydis) is the causal agent of maize smut disease. During the colonization process, the fungus secretes effector proteins which suppress immune responses and redirect the host-metabolism in favor of the pathogen. Here we describe a novel strategy by which U. maydis induces plant jasmonate/ethylene (JA/ET) hormone signaling and thereby biotrophic susceptibility. The U. maydis effector Jasmonate/Ethylene signaling inducer 1 (Jsi1) possesses an ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif, DLNxxP, which interacts with the second WD40 domain of the conserved plant co-repressor family Topless/Topless related (TPL/TPR). Jsi1 interaction with TPL/TPRs leads to derepression of the ethylene response factor (ERF) branch of the JA/ET signaling pathway, supporting biotrophic susceptibility. Jsi1 likely activates the ERF branch by interfering with the binding of endogenous DLNxxP motif-containing ERF transcription factors to TPL/TPR proteins. The identification of effector proteins possessing a DLNxxP motif in different fungal species with biotrophic and hemibiotrophic lifestyles together with the validation of the interaction between such effectors from Magnaporthe oryzae (M. oryzae), Sporisorium scitamineum (S. scitamineum), and S. reilianum with TPL proteins indicates the convergent evolution of effectors for modulating the TPL/TPR co-repressor hub.
Expression, Purification, and Functional Reconstitution of19F-labeled Cytochrome b5 in Peptide Nanodiscs for NMR Studies
Authors: Bai Jia , Wang Jian , Ravula Thirupathi , Im Sang-Choul , Anantharamaiah G. M. , Waskell Lucy , Ramamoorthy Ayyalusamy
Published: November 2019

Microsomal cytochrome b5 (cytb5) is a membrane-bound protein capable of donating the second electron to cytochrome P450s (CYP P450s) in the CYP P450s monooxygenase reactions. Recent studies have demonstrated the importance of the transmembrane domain of cytb5 in the interaction with cytP450 by stabilizing its monomeric structure. While recent NMR studies have provided high-resolution insights into the structural interactions between the soluble domains of ~16-kDa cytb5 and ~57-kDa cytP450 in a membrane environment, there is need for studies to probe the residues in the transmembrane region as well as to obtain intermolecular distance constraints to better understand the very large size cytb5-cytP450 complex structure in a near native membrane environment. In this study, we report the expression, purification, functional reconstitution of19F-labeled full-length rabbit cytb5 in peptide based nanodiscs for structural studies using NMR spectroscopy. Size exclusion chromatography, dynamic light scattering, transmission electron microscopy, and NMR experiments show a stable reconstitution of cytb5 in 4F peptide-based lipid-nanodiscs. Our results demonstrate that the use of peptide-nanodiscs containing cytb519F-labeled with 5-fluorotryptophan (5FW) enables, for the first time, the detection of residues from the transmembrane domain in different lipid compositions by solution19F NMR experiments.19F NMR results revealing the interaction of the transmembrane domain of cytb5 with the full-length rabbit Cytochrome P450 2B4 (CYP2B4) are also presented. We expect the results presented in this study to be useful to devise approaches to probe the structure, dynamics and functional roles of transmembrane domains of a membrane protein, and also to measure intermolecular19F-19F distance constraints to determine the structural interactions between the transmembrane domains.
Evolutionary repair: changes in multiple functional modules allow meiotic cohesin to support mitosis
Authors: Hsieh Yu-Ying Phoebe , Makrantoni Vasso , Robertson Daniel , Marston Adèle L , Murray Andrew W
Published: November 2019

Different members of the same protein family often perform distinct cellular functions. How much are these differing functions due to changes in a protein’s biochemical activity versus changes in other proteins? We asked how the budding yeast,Saccharomyces cerevisiae,evolves when forced to use the meiosis-specific kleisin, Rec8, instead of the mitotic kleisin, Scc1, during the mitotic cell cycle. This perturbation impairs sister chromosome linkage and reduces reproductive fitness by 45%. We evolved 15 populations for 1750 generations, substantially increasing their fitness, and analyzed their genotypes and phenotypes. We found no mutations in Rec8, but many populations had mutations in the transcriptional mediator complex, cohesin-related genes, and cell cycle regulators that induce S phase. These mutations improve sister chromosome cohesion and slow genome replication in Rec8-expressing cells. We conclude that changes in known and novel partners allow proteins to improve their ability to perform new functions.
Gene Expression of Functionally-Related Genes Coevolves Across Fungal Species: Detecting Coevolution of Gene Expression Using Phylogenetic Comparative Methods
Authors: Cope Alexander L. , O’Meara Brian , Gilchrist Michael A.
Published: November 2019

Background

Researchers often measure changes in gene expression across conditions to better understand the shared functional roles and regulatory mechanisms of different genes. Analogous to this is comparing gene expression across species, which can improve our understanding of the evolutionary processes shaping the evolution of both individual genes and functional pathways. One area of interest is determining genes showing signals of coevolution, which can also indicate potential functional similarity, analogous to co-expression analysis often performed across conditions for a single species. However, as with any trait, comparing gene expression across species can be confounded by the non-independence of species due to shared ancestry, making standard hypothesis testing inappropriate.

Results

We compared RNA-Seq data across 18 fungal species using a multivariate Brownian Motion phylogenetic comparative method (PCM), which allowed us to quantify coevolution between protein pairs while directly accounting for the shared ancestry of the species. Our work indicates proteins which physically-interact show stronger signals of coevolution than randomly-generated pairs. Interactions with stronger empirical and computational evidence also showing stronger signals of coevolution. We examined the effects of number of protein interactions and gene expression levels on coevolution, finding both factors are overall poor predictors of the strength of coevolution between a protein pair. Simulations further demonstrate the potential issues of analyzing gene expression coevolution without accounting for shared ancestry in a standard hypothesis testing framework. Furthermore, our simulations indicate the use of a randomly-generated null distribution as a means of determining statistical significance for detecting coevolving genes with phylogenetically-uncorrected correlations, as has previously been done, is less accurate than PCMs, although is a significant improvement over standard hypothesis testing. These methods are further improved by using a phylogenetically-corrected correlation metric.

Conclusions

Our work highlights potential benefits of using PCMs to detect gene expression coevolution from high-throughput omics scale data. This framework can be built upon to investigate other evolutionary hypotheses, such as changes in transcription regulatory mechanisms across species.
Elucidating the regulation of glucose tolerance through the interaction between the reaction product and active site pocket residues of a β-glucosidase from Halothermothrix orenii
Authors: Sinha Sushant K , Das Shibashis , Konar Sukanya , Ghorai Pradip Kr. , Das Rahul , Datta Supratim
Published: November 2019

β-glucosidase catalyzes the hydrolysis of β-1,4 linkage between two glucose molecules in cello-oligosaccharides and is prone to inhibition by the reaction product glucose. Relieving the glucose inhibition of β-glucosidase is a significant challenge. Towards the goal of understanding how glucose interacts with β-glucosidase, we expressed in Escherichia coli, the Hore_15280 gene encoding a β-glucosidase in Halothermothrix orenii. Our results show that the enzyme is glucose tolerant, and its activity stimulated in the presence of up to 0.5 M glucose. NMR analyses show the unexpected interactions between glucose and the β-glucosidase at lower concentrations of glucose that however does not lead to enzyme inhibition. We identified non-conserved residues at the aglycone-binding and the gatekeeper site and show that increased hydrophobicity at the pocket entrance and a reduction in steric hindrances are critical towards enhanced substrate accessibility and significant improvement in activity. Analysis of structures and in combination with molecular dynamics simulations show that glucose increases the accessibility of the substrate by enhancing the structural flexibility of the active site pocket and may explain the stimulation in specific activity up to 0.5 M glucose. Such novel regulation of β-glucosidase activity by its reaction product may offer novel ways of engineering glucose tolerance.
Exhaustive reconstruction of the CRISPR locus inMycobacterium tuberculosiscomplex using short reads
Authors: Guyeux Christophe , Sola Christophe , Refrégier Guislaine
Published: November 2019

Spoligotyping, a graphical partial display of the CRISPR locus that can be producedin vitroorin silico, is an important tool for analyzing the diversity of givenMycobacterium tuberculosiscomplex (MTC) isolates. As other CRISPR loci, this locus is made up of an alternation between direct repeats and spacers, and flanked bycasgenes. Unveiling the genetic mechanisms of its evolution requires to have a fairly large amount of fully reconstructed loci among all MTC lineages.

In this article, we point out and resolve the problem of CRISPR reconstruction based on short read sequences. We first show that more than 1/3 of the currently assembled genomes available for this complex contain a CRISPR locus erroneously reconstructed, and errors can be very significant. Second, we present a new computational method allowing this locus to be reconstructed extensively and reliablyin silicousing short read sequencing runs. Third, using this method, we describe new structural characteristics of CRISPR locus by lineages. We show how both the classical experimentalin vitroapproach and the basicin silicospoligotyping provided by existing analytic tools miss a whole diversity of this locus in MTC, by not capturing duplications, spacer and direct repeats variants, and IS6110insertion locations. This description is extended in a second article that presents general rules for the evolution of the CRISPR locus in MTC.

This work opens new perspectives for a larger exploration of CRISPR loci diversity and of mechanisms involved in its evolution and its functionality.
Effects of surfaces and macromolecular crowding on bimolecular reaction rates
Authors: Andrews Steven S.
Published: November 2019

Biological cells are complex environments that are densely packed with macromolecules and subdivided by membranes, both of which affect the rates of chemical reactions. It is well known that crowding reduces the volume available to reactants, which increases reaction rates, and also inhibits reactant diffusion, which decreases reaction rates. This work investigates these effects quantitatively using analytical theory and particle-based simulations. A reaction rate equation based on only these two processes turned out to be inconsistent with simulation results. However, accounting for diffusion inhibition by the surfaces of nearby obstacles, which affects access to reactants, led to perfect agreement for reactions near impermeable planar membranes and improved agreement for reactions in crowded spaces. A separate model that quantified reactant occlusion by crowders, and extensions to a thermodynamic “cavity” model proposed by Berezhkovskii and Szabo (J. Phys. Chem. B 120:5998, 2016), were comparably successful. These results help elucidate reaction dynamics in confined spaces and improve prediction of in vivo reaction rates from in vitro ones.
Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates
Authors: Rossio Valentina , Paulo Joao A. , Chick Joel , Brasher Bradley , Gygi Steven P. , King Randall W.
Published: November 2019

Deubiquitylating enzymes (DUBs) counteract ubiquitylation to control stability or activity of substrates. Identification of DUB substrates is challenging because multiple DUBs act on the same substrates, thwarting genetic approaches. Here, we circumvented redundancy by broadly inhibiting DUBs inXenopusegg extract. DUB inhibition increases ubiquitylation of hundreds of proteins, depleting free ubiquitin without inducing widespread degradation. Restoring available ubiquitin led to proteasomal degradation of over thirty proteins, indicating that deubiquitylation is essential to maintain their stability. We confirmed their DUB-dependent stability with recombinant human proteins, demonstrating evolutionary conservation. We profiled the ability of DUBs to rescue protein stability, and found that USP7 has a unique ability to broadly antagonize proteasomal degradation. Together, we provide a comprehensive characterization of ubiquitin dynamics in theXenopussystem, identify new DUB substrates, and present a new approach to characterize physiological DUB specificity that overcomes challenges posed by DUB redundancy
Evaluation of Dose Fractionated Polymyxin B on Acute Kidney Injury: A Translational In Vivo Model
Authors: Liu Jiajun , Pais Gwendolyn M. , Avedissian Sean N. , Gilchrist Annette , Lee Andrew , Rhodes Nathaniel J. , Hauser Alan R. , Scheetz Marc H.
Published: November 2019

The polymyxins are last-line defense for highly resistant infections. Nephrotoxicity, however, is a dose-limiting factor. Yet, approaches to mitigate nephrotoxicity are poorly defined. This study aimed to investigate the impact of dose fractionated (once, twice and thrice daily) polymyxin B (PB) on acute kidney injury (AKI) in a pre-clinical model. Secondarily, we aimed to describe the pharmacokinetic (PK) profile of PB. Sprague-Dawley rats were assigned to experimental groups with different dosing intervals but constant total daily exposure (12 mg/kg/day into single, twice daily, and thrice daily doses) and controls received normal saline subcutaneously over 3 days. Blood and urine samples were collected, and kidneys were harvested at necropsy. A three-compartment model best described the data and Bayesian observed vs. predicted concentration demonstrated bias, imprecision, and R2 of 0.129 mg/L, 0.729 mg2/L2 and 0.652, respectively. PB exposure (i.e. AUC24h) were similar across treatment groups over time (p=0.87). As a representative, urinary KIM-1 were elevated on days 1 and 2 for experimental groups compared to controls, and thrice daily group experienced the most KIM-1 increase [mean increase (95% CI) day 1 from day −1, 4.44 (0.89, 8.00) ng/mL; p=0.018] as compared to control [mean increase (95% CI) day 1 from day −1, 0.03 (−0.42, 0.49) ng/mL; p=0.99]. Correspondingly, significant histopathological damage was observed with the same group (p=0.013) (controls as a referent). Our findings suggested that fractionating the PB dose thrice daily resulted in the most injury in a rat model.
Improvement of cryo-EM maps by density modification
Authors: Terwilliger Thomas C. , Ludtke Steven J. , Read Randy J. , Adams Paul D. , Afonine Pavel V.
Published: November 2019

A density modification procedure for improving maps produced by single-particle electron cryo-microscopy is presented. The theoretical basis of the method is identical to that of maximum-likelihood density modification, previously used to improve maps from macromolecular X-ray crystallography. Two key differences from applications in crystallography are that the errors in Fourier coefficients are largely in the phases in crystallography but in both phases and amplitudes in electron cryo-microscopy, and that half-maps with independent errors are available in electron cryo-microscopy. These differences lead to a distinct approach for combination of information from starting maps with information obtained in the density modification process. The applicability of density modification theory to electron cryo-microscopy was evaluated using half-maps for apoferritin at a resolution of 3.1 Å and a matched 1.8 Å reference map. Error estimates for the map obtained by density modification were found to closely agree with true errors as estimated by comparison with the reference map. The density modification procedure was applied to a set of 104 datasets where half-maps, a full map and a model all had been deposited. The procedure improved map-model correlation and increased the visibility of details in the maps. The procedure requires two unmasked half-maps and a sequence file or other source of information on the volume of the macromolecule that has been imaged.
Real time structural search of the Protein Data Bank
Authors: Guzenko Dmytro , Burley Stephen K. , Duarte Jose M.
Published: November 2019

Detection of protein structure similarity is a central challenge in structural bioinformatics. Comparisons are usually performed at the polypeptide chain level, however the functional form of a protein within the cell is often an oligomer. This fact, together with recent growth of oligomeric structures in the Protein Data Bank (PDB), demands more efficient approaches to oligomeric assembly alignment/retrieval. Traditional methods use atom level information, which can be complicated by the presence of topological permutations within a polypeptide chain and/or subunit rearrangements. These challenges can be overcome by comparing electron density volumes directly. But, brute force alignment of 3D data is a compute intensive search problem. We developed a 3D Zernike moment normalization procedure to orient electron density volumes and assess similarity with unprecedented speed. Similarity searching with this approach enables real-time retrieval of proteins/protein assemblies resembling a target, from PDB or user input, together with resulting alignments (http://shape.rcsb.org).

Author Summary

Protein structures possess wildly varied shapes, but patterns at different levels are frequently reused by nature. Finding and classifying these similarities is fundamental to understand evolution. Given the continued growth in the number of known protein structures in the Protein Data Bank, the task of comparing them to find the common patterns is becoming increasingly complicated. This is especially true when considering complete protein assemblies with several polypeptide chains, where the large sizes further complicate the issue. Here we present a novel method that can detect similarity between protein shapes and that works equally fast for any size of proteins or assemblies. The method looks at proteins as volumes of density distribution, departing from what is more usual in the field: similarity assessment based on atomic coordinates and chain connectivity. A volumetric function is amenable to be decomposed with a mathematical tool known as 3D Zernike polynomials, resulting in a compact description as vectors of Zernike moments. The tool was introduced in the 1990s, when it was suggested that the moments could be normalized to be invariant to rotations without losing information. Here we demonstrate that in fact this normalization is possible and that it offers a much more accurate method for assessing similarity between shapes, when compared to previous attempts.
Precise spatial spatial memory in local random networks
Authors: Natale Joseph L. , Hentschel H. George E. , Nemenman Ilya
Published: November 2019

Self-sustained, elevated neuronal activity persisting on time scales of ten seconds or longer is thought to be vital for aspects of working memory, including brain representations of real space. Continuous-attractor neural networks, one of the most well-known modeling frameworks for persistent activity, have been able to model crucial aspects of such spatial memory. These models tend to require highly structured or regular synaptic architectures. In contrast, we elaborate a geometrically-embedded model with a local but otherwise random connectivity profile which, combined with a global regulation of the mean firing rate, produces localized, finely spaced discrete attractors that effectively span a 2D manifold. We demonstrate how the set of attracting states can reliably encode a representation of the spatial locations at which the system receives external input, thereby accomplishing spatial memory via attractor dynamics without synaptic fine-tuning or regular structure. We measure the network’s storage capacity and find that the statistics of retrievable positions are also equivalent to a full tiling of the plane, something hitherto achievable only with (approximately) translationally invariant synapses, and which may be of interest in modeling such biological phenomena as visuospatial working memory in two dimensions.
TheLegionella pneumophilametaeffector Lpg2505 (SusF) regulates SidI-mediated translation inhibition and GDP-dependent glycosyltransferase activity
Authors: Joseph Ashley M. , Pohl Adrienne E. , Ball Theodore J. , Abram Troy G. , Johnson David K. , Geisbrecht Brian V. , Shames Stephanie R.
Published: November 2019

Legionella pneumophila, the etiological agent of Legionnaires Disease, employs an arsenal of hundreds of Dot/Icm-translocated effector proteins to facilitate replication within eukaryotic phagocytes. Several effectors, called metaeffectors, function regulate the activity of other Dot/Icm-translocated effectors during infection. The metaeffector Lpg2505 is essential forL. pneumophilaintracellular replication only when its cognate effector, SidI, is present. SidI is a cytotoxic effector that interacts with the host translation factor eEF1A and potently inhibits eukaryotic protein translation by an unknown mechanism. Here, we evaluated the impact of Lpg2505 on SidI-mediated phenotypes and investigated the mechanism of SidI function. We determined that Lpg2505 binds with nanomolar affinity to SidI and suppresses SidI-mediated inhibition of protein translation. SidI binding to eEF1A and SusF is not mutually exclusive and these proteins bind distinct regions of SidI. We also discovered that SidI possesses GDP-dependent glycosyltransferase activity and that this activity is regulated by Lpg2505. We have therefore renamed Lpg2505, SusF (suppressor ofSidI function). This work reveals novel enzymatic activity for SidI and provides insight into how intracellular replication ofL. pneumophilais regulated by a metaeffector.
Adult Muscle Stem Cell Self-Renewal Induced by Endurance Exercise is Mediated by Inhibition of Mitochondrial Oxygen Consumption
Authors: Abreu Phablo , Kowaltowski Alicia J.
Published: November 2019

Skeletal muscle stem cells (satellite cells) are well known to participate in regeneration and maintenance of the tissue over time. Studies have shown increases in the number of satellite cells after exercise, but their functional role in endurance training remains unexplored. Here, we found that injured muscles from endurance-exercised mice display improved regenerative capacity, demonstrated through higher densities of newly formed myofibers compared to controls, as well as lower inflammation and fibrosis. Enhanced myogenic function was accompanied by an increased fraction of satellite cells expressing self-renewal markers. Control satellite cells had morphologies suggestive of early differentiation, while endurance exercise enhanced myogenic colony formation. The beneficial effects of endurance exercise were associated with satellite cell metabolic reprogramming, including reduced mitochondrial respiration (O2consumption) under resting conditions (absence of muscle injury) and increased stemness. During proliferation or activated states (three days after injury), O2consumption was equal in control and exercised cells. Surprisingly, inhibition of mitochondrial O2consumption was sufficient to enhance muscle stem cell self-renewal characteristicsin vitro. Moreover, transplanted muscle satellite cells from exercised mice or cells with reduced mitochondrial respiration promoted a significant reduction in inflammation compared to controls. We propose that endurance exercise promotes self-renewal and inhibits differentiation in satellite cells, an effect promoted by metabolic reprogramming and respiratory inhibition, and which is associated with a more favorable muscular response to injury.
Advantages of acute brain slices prepared at physiological temperature in characterization of synaptic functions
Authors: Eguchi Kohgaku , Velicky Philipp , Hollergschwandtner Elena , Itakura Makoto , Fukazawa Yugo , Danzl Johann Georg , Shigemoto Ryuichi
Published: November 2019

Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability and higher detectability of long-term depression after motor learning compared with slices prepared at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions.
SparK: A Publication-quality NGS Visualization Tool
Authors: Kurtenbach Stefan , William Harbour J.
Published: November 2019

While there are sophisticated resources available for displaying NGS data, including the Integrative Genomics Viewer (IGV) and the UCSC genome browser, exporting regions and assembling figures for publication remains challenging. In particular, customizing track appearance and overlaying track replicates is a manual and time-consuming process. Here, we present SparK, a tool which auto-generates publication-ready, high-resolution, true vector graphic figures from any NGS-based tracks, including RNA-seq, ChIP-seq, and ATAC-seq. Novel functions of SparK include averaging of replicates, plotting standard deviation tracks, and highlighting significantly changed areas. SparK is written in Python 3, making it executable on any major OS platform. Using command line prompts to generate figures allows later changes to be made very easy. For instance, if the genomic region of the plot needs to be changed, or tracks need to be added or removed, the figure can easily be re-generated within seconds without the manual process of re-exporting and re-assembling everything. After plotting with SparK, changes to the output SVG vector graphic files are simple to make, including text, lines, and colors. SparK is publicly available on GitHub: https://github.com/harbourlab/SparK.
Unsupervised domain adaptation for the automated segmentation of neuroanatomy in MRI: a deep learning approach
Authors: Novosad Philip , Fonov Vladimir , Collins D. Louis
Published: November 2019

Neuroanatomical segmentation in T1-weighted magnetic resonance imaging of the brain is a prerequisite for quantitative morphological measurements, as well as an essential element in general pre-processing pipelines. While recent fully automated segmentation methods based on convolutional neural networks have shown great potential, these methods nonetheless suffer from severe performance degradation when there are mismatches between training (source) and testing (target) domains (e.g. due to different scanner acquisition protocols or due to anatomical differences in the respective populations under study). This work introduces a new method for unsupervised domain adaptation which improves performance in challenging cross-domain applications without requiring any additional annotations on the target domain. Using a previously validated state-of-the-art segmentation method based on a context-augmented convolutional neural network, we first demonstrate that networks with better domain generalizability can be trained using extensive data augmentation with label-preserving transformations which mimic differences between domains. Second, we incorporate unlabelled target domain samples into training using a self-ensembling approach, demonstrating further performance gains, and further diminishing the performance gap in comparison to fully-supervised training on the target domain.
A Mechanism for Beam-Induced Motion in Cryo-Electron Microscopy
Authors: Thorne Robert E.
Published: November 2019

Estimates of heat transfer rates during plunge cooling and patterns of ice observed in cryo-EM samples indicate that the grid bars cool much more slowly than do the support foil and sample near the middle of the grid openings. The resulting transient temperature differences generate transient tensile stresses in the support foil. Most of this foil stress develops while the sample is liquid and cooling toward its glass transition Tg, and so does not generate tensile sample stress. As the grid bars continue cooling toward the cryogen temperature and contracting, the tensile stress in the foil is released, placing the sample in compressive stress. Radiation-induced creep in the presence of this compressive stress should generate a doming of the sample in the foil openings, as is observed experimentally. Crude estimates of the magnitude of doming that may be generated by this mechanism are consistent with observation. Several approaches to reducing beam-induced motion are discussed.
GLP-1R is downregulated in beta cells of NOD mice and T1D patients
Authors: Recino Asha , Barkan Kerry , Schmidt-Christensen Anja , Nilsson Julia , Holmes Nick , Howie Duncan , Holmberg Dan , Larsson Pär , Flodström-Tullberg Malin , Laraia Luca , Spring David R , Hecksher-Sørensen Jacob , Cooke Anne , Ladds Graham , Wållberg Maja
Published: November 2019

Glucagon-like peptide 1 (GLP-1) is produced by L cells in the small intestine in response to ingested glucose and increases insulin release from pancreatic beta cells by activation of its cognate receptor (GLP-1R). Stimulation of this receptor also contributes to increased beta cell survival and regeneration. We have found that pancreatic beta cells from Non Obese Diabetic (NOD) mice express significantly lower levels of GLP-1R than C57BL/6 mice, leaving the NOD beta cells with an impaired response to GLP-1 stimulation. The lower expression appears to be caused by accelerated degradation of GLP-1R in the beta cells, a process that can be reversed by inhibiting trafficking to the lysosome. Importantly, our results appear to translate to the human disease since we also observed significantly lower expression of the GLP-1R in pancreatic islets from donors with type 1 diabetes. These results suggest that beta cell physiology may play a role in susceptibility to autoimmune inflammation.
Analysis of regulatory element evolution between human and mouse reveals a lack ofcis-transcompensation
Authors: Mattioli Kaia , Oliveros Winona , Gerhardinger Chiara , Andergassen Daniel , Maass Philipp G. , Rinn John L. , Melé Marta
Published: November 2019

Gene expression differences between species are driven by bothcisandtranseffects. Whereasciseffects are caused by genetic variants in close proximity to the target gene,transeffects are due to distal genetic variants that affect diffusible elements such as transcription factors. Previous studies have mostly assessed the impact ofcisandtranseffects at the gene level. However, howcisandtranseffects differentially impact regulatory elements such as enhancers and promoters remains poorly understood. Here, we used massively parallel reporter assays to directly measurecisandtranseffects between human and mouse embryonic stem cells at thousands of individual regulatory elements. Our approach revealed thatciseffects are widespread across regulatory elements, and the strongestciseffects are associated with the disruption of motifs recognized by strong transcriptional activators. Conversely, we found thattranseffects are rare but stronger in enhancers than promoters, and can be attributed to a subset of transcription factors that are differentially expressed between human and mouse. While previous studies have found extensive co-occurrence ofcisandtranseffects in opposite directions that stabilize gene expression throughout evolution, we find thatcis-transcompensation is uncommon within individual regulatory elements. Thus, our results are consistent with a model wherein compensatorycis-transeffects at the gene level are explained bycisandtranseffects that separately impact several regulatory elements rather thancis-transeffects that occur simultaneously within a single regulatory element. Together, these results indicate that studying the evolution of individual regulatory elements is pivotal to understand the tempo and mode of gene expression evolution.
Human origin and migration deciphered from a novel genomic footprints of mitochondrial sequences
Authors: Mahapatra Aritra , Mukherjee Jayanta
Published: November 2019

The origin of modern human and their migration across the world is one of the most debated topics for the decades. There exist two different hypotheses, recent African origin and multi-regional evolution, based on the genomic studies, haplogroups, archaeological records, cultural behaviors, palaeontology studies, etc. Various studies placed the modern humans in a phylogenetic tree to depict the relationships among them. The debate for determining those regions of Africa which witnessed the first origin of humans still exists. The conflicts between the results obtained from the molecular data and the archaeological and palaeontological reports still exist. We adopt a novel genomic feature derived from the whole mitochondrial sequence, and using a novel distance function the phylogenetic trees are constructed based on the feature which provide a new insight on human migration. We propose a new method to derive the bootstrap replica from the genome sequences by considering the genetic variance to demonstrate the robustness of the obtained trees. The results derived from the genomic feature are more consistent with the archaeological findings based on the time of origin of different communities. We find that west and central African communities are placed at the basal point with a very high bootstrap score. This study roughly estimates the existence of the archaic human at 800-900 kilo years ago and presence of human in Africa at 600-700 kilo years ago. This supports the presence of an ancestor in the west and central Africa much earlier than that of the fossils identified.
Trend and pattern of economic and financial crimes statutes in Nigeria
Authors: Aigbovo Osaretin
Published: November 2019

Purpose

The purpose of this paper is to examine the general direction and pattern of modern economic and financial crimes statutes in Nigeria.

Design/methodology/approach

This paper examines Nigerian economic and financial crime statues.

Findings

This paper identifies the trend and features, which are common to all the statutes irrespective of economic and financial crime covered by them.

Originality/value

This paper shows that although Nigerian economic and financial crimes statutes have evolved gradually from Military era Decrees, and target different aspects of economic and financial crimes, there are certain features, which are common to all of them.
Strengthening the role of lawyers and other professional advisers in addressing economic and financial crimes in Indonesia
Authors: Lukito Anastasia Suhartati
Published: November 2019

Purpose

This paper aims to explain the regulations in Indonesia that apply to lawyers and other professional advisers in terms of their obligations as reporting parties of suspicious financial transactions with respect to money laundering and other financial crimes. As lawyers and other professional advisers offer services to the business community in Indonesia, they are vulnerable to becoming parties to illegal business transactions. The results could lead to bribery, graft, tax crime and corruption in Indonesia.

Design/methodology/approach

This paper explores and analyzes the obligations of lawyers and other professional advisers under Indonesian law, with particular reference to their obligations as reporting parties in efforts to prevent economic crime within the country’s business community.

Findings

Lawyers and other professional advisers, as reporting parties, can be viewed as the gatekeepers that inhibit economic and financial crimes. Consequently, a new perspective is needed for all of the legal professions so that they can protect themselves from the risks of being targeted by nefarious clients/offenders. To strengthen the role of these advisers, it is recommended that both a code of ethics and know your customer principle to be implemented.

Practical implications

This paper can serve as a resource that explores the functions of lawyers and other professional advisers as reporting parties whose aim is to prevent financial and economic crime in Indonesia.

Originality/value

This paper encourages lawyers, other professional advisers, and public and private institutions to implement a code of ethics, and also integrity and professionalism, with a view to preventing economic and financial crimes. According to the code, the functions and obligations of lawyers and other professional advisers include discouraging such offenses. The code becomes effective when legal professionals adhere to legal ethics and integrity.
Faith and Failure on the Australian Goldfields: Gendered Interpretations of Piety and the “Good Death”
Authors: Jones Jennifer
Published: November 2019

Gold‐seeking in the 1850s Australian gold rush provided opportunity for James and Maggie Hoey, a young Scottish couple, to pursue wealth, experience adventure, and escape some of the strictures of their United Presbyterian religious culture. They hoped that Providence would guide their paths to independence, prosperity, and eventual return to Scotland. Instead, they experienced repeated failure and suffering, becoming keenly aware of the absence of familiar avenues of support and solace. This article examines the gendered strategies family members developed to maintain or reclaim piety under unfavourable conditions on the goldfields. The disparity between their expectations and outcomes draws attention to the ways in which religious beliefs shaped individual response to suffering. The dogged, but ultimately futile, quest for gold undermined the capacity of James Hoey to fulfil his gendered roles, impacting upon his hope in, and assurance of, election to eternal life.
Eliding the Esoteric: R. J. Campbell and Early Twentieth Century Protestant Discourse in Britain
Authors: McNamara Brendan
Published: November 2019

R. J. Campbell was arguably the most renowned British religious figure of his generation, a prominent promoter of reform as a leader of non‐conforming Protestantism in Britain at the turn of the twentieth century. He is generally regarded as a promulgator of pre‐war optimism, a universalist who courted personal fame and who sparked an intra‐Protestant sectarian crisis when he initiated a new reformist movement, the “New Theology.” Most of the analysis, including Campbell's suspect retrospective memoir, treat this religious ferment as rooted in Protestant/Christian perturbation. This perspective does not allow for a wider consideration of the vibrant religious milieu of enquiry then in vogue which brought Campbell into contact with a variety of esoteric ideas and philosophies and their interlocutors. Absent this focus, important figures participating in that religious colloquy are marginalised. My article seeks to fill out the commonly accepted version of events. Material not previously examined is interrogated towards illuminating Campbell's wider interests. It postulates that Campbell was one of a number of contributors to a broad discussion on religious ideas and their relationship to Christianity, one of a number of figures shaped by, as much as shaping, the contemporary discursive environment.
Chalcolithic settlement of Bahra 1 and its possible functions
Authors: Bieliński Piotr
Published: November 2019

Excavations of the Kuwaiti–Polish Archaeological Mission at the site of Bahra 1 in Kuwait uncovered the remains of a large settlement from the sixth millennium BC, associated with the Mesopotamian Ubaid culture. This connection is made clear by the presence of Ubaid Ware from the Ubaid 2/3 phase that appears alongside Red Coarse Ware typical for the Arabian Neolithic. Architecture of the settlement resembled the Ubaid one with orthogonal, multi‐chambered houses. In one part of the site they form a dense block with traits that indicate some degree of spatial planning. This type of spatial arrangement is absent in Arabian Neolithic settlements and is also unknown from Ubaid settlements in Mesopotamia. One of the buildings discovered at Bahra 1 has a ground plan reminiscent of a sanctuary from Eridu XVI and was probably associated with cultic activities, as was a circular stone enclosure (Unit 6), representing local building traditions. The character of Bahra 1 architecture and the presence of cultic buildings at the site suggest that the settlements served as a local ceremonial and/or cultic centre.
Patient preference and operating time for digital versus conventional impressions: a network meta‐analysis
Authors: Sivaramakrishnan G , Alsobaiei M , Sridharan K
Published: November 2019

Background

Digital impression techniques have seen many advancements, with new hardware and software being developed each year. The technical advantages of these systems are real‐time visualization, evaluation and archive, segmental capture, ease of recapture if necessary, economical in terms of no use of impression material or trays or disinfection, easy file transfer and communication with the laboratory. However patient satisfaction is one major factor that might influence the choice of impression technique. The aim of this network meta‐analysis was to identify statistically the evidence on overall patient preferences relative to digital versus conventional impression techniques, in addition to the time taken in making these impressions.

Methodology

Randomized or prospective clinical studies were identified based on the inclusion criteria in PUBMED, DARE and COCHRANE databases; subsequently pertinent data were extracted. Risk of bias of the included studies was assessed using the Cochrane risk of bias tool and Newcastle‐Ottawa scale. Heterogeneity amongst the studies in direct comparison was assessed by Chi‐square and I2 tests using the Inverse variance heterogeneity model. Direct comparison estimates were derived by pooling the data from studies that compared the same intervention. Indirect comparison pooled estimates were derived by using the data amongst the studies, through a common comparator, using MetaXL software. Mean differences and Odds ratio at 95% confidence interval were used as the effect estimates, while inconsistencies were evaluated by H‐statistics. GRADE working group approach was used to assess the quality of available evidence.

Results

Fourteen studies were included. Results from 11 studies  on 471 patients (236‐Digital; 235‐conventional) were pooled for patient preference with 95% confidence interval. The Forest plot showed a pooled estimate of 31.23 [5.95, 163.87], showing a statistically significant number of patients favouring digital impressions. Results from 11 studies reported the time taken in 589 patients (278‐digital; 311 conventional). The pooled estimate (2.72 [0.08, 5.32]) (95% confidence interval) showed a statistically significant increase in the time required to make digital impressions. The overall time taken in minutes for the interventions in the digital group in decreasing order were: LAVA Cos (8.14[3.64,12,26] (statistically significant); I tero (4.11[‐1.02,9.24]; CEREC (0.34[‐4.14,4.82]).

Conclusion

There was an overall preference for digital impressions, although the time required is longer. The factors related to the digital system, the operator and the patient were studied, with recommendations forming a basis for possible hardware and software upgrades of the digital systems that can produce significant improvement in the acceptance rate for both the patient and the clinician.
Berberine protects against diabetic kidney disease via promoting PGC‐1α‐regulated mitochondrial energy homeostasis
Authors: Qin Xin , Jiang Ming , Zhao Yan , Gong Jing , Su Hao , Yuan Fen , Fang Ke , Yuan Xiaoyi , Yu Xiao , Dong Hui , Lu Fuer
Published: November 2019

Background and Purpose

Disordered lipid metabolism and disturbed mitochondrial bioenergetics play pivotal roles in the initiation and development of diabetic kidney disease (DKD). Berberine is a plant alkaloid, used in Chinese herbal medicine. It has multiple therapeutic actions on diabetes mellitus and its complications, including regulation of glucose and lipid metabolism, improvement of insulin sensitivity, and alleviation of oxidative damage. Here, we investigated the reno‐protective effects of berberine.

Experimental Approach

We used samples from DKD patients and experiments with models of DKD (db/db mice) and cultured podocytes, to characterize energy metabolism profiles using metabolomics. Molecular targets and mechanisms involved in the regulation of mitochondrial function and bioenergetics by berberine were investigated, along with its effects on metabolic alterations in DKD mice.

Key Results

Metabolomic analysis suggested altered mitochondrial fuel usage and generalized mitochondrial dysfunction in patients with DKD. In db/db mice, berberine treatment reversed the disordered metabolism, podocyte damage and glomerulosclerosis. Lipid accumulation, excessive generation of mitochondrial ROS, mitochondrial dysfunction, and deficient fatty acid oxidation in DKD mouse models and in cultured podocytes were suppressed by berberine. These protective effects of berberine were accompanied by activation of the peroxisome proliferator‐activated receptor γ coactivator‐1α (PGC‐1α) signalling pathway, which promoted mitochondrial energy homeostasis and fatty acid oxidation in podocytes.

Conclusion and Implications

PGC‐1α‐mediated mitochondrial bioenergetics could play a key role in lipid disorder‐induced podocyte damage and development of DKD in mice. Restoration of PGC‐1α activity and the energy homeostasis by berberine might be a potential therapeutic strategy against DKD.