bluuebunny/crossref_metadata_2025 huggingface dataset:
Experience-dependent mushroom body plasticity in butterflies: consequences of search complexity and host range
Authors: van Dijk Laura J. A. , Janz Niklas , Schäpers Alexander , Gamberale-Stille Gabriella , Carlsson Mikael A.
Published: November 2017

An ovipositing insect experiences many sensory challenges during her search for a suitable host plant. These sensory challenges become exceedingly pronounced when host range increases, as larger varieties of sensory inputs have to be perceived and processed in the brain. Neural capacities can be exceeded upon information overload, inflicting costs on oviposition accuracy. One presumed generalist strategy to diminish information overload is the acquisition of a focused search during its lifetime based on experiences within the current environment, a strategy opposed to a more genetically determined focus expected to be seen in relative specialists. We hypothesized that a broader host range is positively correlated with mushroom body (MB) plasticity, a brain structure related to learning and memory. To test this hypothesis, butterflies with diverging host ranges (
Polygonia c-album
,
Aglais io
and
Aglais urticae
) were subjected to differential environmental complexities for oviposition, after which ontogenetic MB calyx volume differences were compared among species. We found that the relative generalist species exhibited remarkable plasticity in ontogenetic MB volumes; MB growth was differentially stimulated based on the complexity of the experienced environment. For relative specialists, MB volume was more canalized. All in all, this study strongly suggests an impact of host range on brain plasticity in Nymphalid butterflies.
Identification of a molecular pH sensor in coral
Authors: Barott Katie L. , Barron Megan E. , Tresguerres Martin
Published: November 2017

Maintaining stable intracellular pH (pHi) is essential for homeostasis, and requires the ability to both sense pH changes that may result from internal and external sources, and to regulate downstream compensatory pH pathways. Here we identified the cAMP-producing enzyme soluble adenylyl cyclase (sAC) as the first molecular pH sensor in corals. sAC protein was detected throughout coral tissues, including those involved in symbiosis and calcification. Application of a sAC-specific inhibitor caused significant and reversible pHi acidosis in isolated coral cells under both dark and light conditions, indicating sAC is essential for sensing and regulating pHi perturbations caused by respiration and photosynthesis. Furthermore, pHi regulation during external acidification was also dependent on sAC activity. Thus, sAC is a sensor and regulator of pH disturbances from both metabolic and external origin in corals. Since sAC is present in all coral cell types, and the cAMP pathway can regulate virtually every aspect of cell physiology through post-translational modifications of proteins, sAC is likely to trigger multiple homeostatic mechanisms in response to pH disturbances. This is also the first evidence that sAC modulates pHi in any non-mammalian animal. Since corals are basal metazoans, our results indicate this function is evolutionarily conserved across animals.
Culture of an aphid heritable symbiont demonstrates its direct role in defence against parasitoids
Authors: Brandt Jayce W. , Chevignon Germain , Oliver Kerry M. , Strand Michael R.
Published: November 2017

Heritable symbionts are common in insects with many contributing to host defence.
Hamiltonella defensa
is a facultative, bacterial symbiont of the pea aphid,
Acyrthosiphon pisum
that provides protection against the endoparasitoid wasp
Aphidius ervi
. Protection levels vary among strains of
H. defensa
that are differentially infected by bacteriophages named APSEs. By contrast, little is known about mechanism(s) of resistance owing to the intractability of host-restricted microbes for functional study. Here, we developed methods for culturing strains of
H. defensa
that varied in the presence and type of APSE. Most
H. defensa
strains proliferated at 27°C in co-cultures with the TN5 cell line or as pure cultures with no insect cells. The strain infected by APSE3, which provides high levels of protection
in vivo
, produced a soluble factor(s) that disabled development of
A. ervi
embryos independent of any aphid factors. Experimental transfer of APSE3 also conferred the ability to disable
A. ervi
development to a phage-free strain of
H. defensa
. Altogether, these results provide a critical foundation for characterizing symbiont-derived factor(s) involved in host protection and other functions. Our results also demonstrate that phage-mediated transfer of traits provides a mechanism for innovation in host restricted symbionts.
GeTFEP: A general transfer free energy profile of transmembrane proteins
Authors: Tian Wei , Naveed Hammad , Lin Meishan , Liang Jie
Published: November 2017

Free energy of transferring amino acid side–chains from aqueous environment into lipid bilayers, known as transfer free energy (TFE), provides important information on the thermodynamic stability of membrane proteins. In this study, we derived a TFE profile named General Transfer Free Energy Profile (GeTFEP) based on computation of the TFEs of 58β–barrel membrane proteins (βMPs). The GeTFEP agrees well with experimentally measured and computationally derived TFEs. Analysis based on the GeTFEP shows that residues in different regions of the TM segments ofβMPs have different roles during the membrane insertion process. Results further reveal the importance of the sequence pattern of transmembrane strands in stabilizingβMPs in the membrane environment. In addition, we show that GeTFEP can be used to predict the positioning and the orientation ofβMPs in the membrane. We also show that GeTFEP can be used to identify structurally or functionally important amino acid residue sites ofβMPs. Furthermore, the TM segments ofα–helical membrane proteins can be accurately predicted with GeTFEP, suggesting that the GeTFEP captures fundamental thermodynamic properties of amino acid residues inside membrane, and is of general applicability in studying membrane protein.
Genomic Locus Modulating IOP in the BXD RI Mouse Strains
Authors: King Rebecca , Li Ying , Wang Jiaxing , Struebing Felix L. , Geisert Eldon E.
Published: November 2017

Purpose

Intraocular pressure (IOP) is the primary risk factor for developing glaucoma. The present study examines genomic contribution to the normal regulation of IOP in the mouse.

Methods

The BXD recombinant inbred (RI) strain set was used to identify genomic loci modulating IOP. We measured the IOP from 532 eyes from 34 different strains. The IOP data will be subjected to conventional quantitative trait analysis using simple and composite interval mapping along with epistatic interactions to define genomic loci modulating normal IOP.

Results

The analysis defined one significant quantitative trait locus (QTL) on Chr.8 (100 to 106 Mb). The significant locus was further examined to define candidate genes that modulate normal IOP. There are only two good candidate genes within the 6 Mb over the peak, Cdh8 (Cadherin 8) and Cdh11 (Cadherin 11). Expression analysis on gene expression and immunohistochemistry indicate that Cdh11 is the best candidate for modulating the normal levels of IOP.

Conclusions

We have examined the genomic regulation of IOP in the BXD RI strain set and found one significant QTL on Chr. 8. Within this QTL that are two potential candidates for modulating IOP with the most likely gene being Cdh11.
The trauma severity model: An ensemble machine learning approach to risk prediction
Authors: Gorczyca Michael T. , Toscano Nicole C. , Cheng Julius D.
Published: November 2017

Statistical theory indicates that a flexible model can attain a lower generalization error than an inflexible model, provided that the setting is appropriate. This is highly relevant in the context of mortality risk prediction for trauma patients, as researchers have focused exclusively on the use of generalized linear models for risk prediction, and generalized linear models may be too inflexible to capture the potentially complex relationships in trauma data. Due to this, we propose a machine learning model, the Trauma Severity Model (TSM), for risk prediction. In order to validate TSM’s performance, this study compares TSM to three established risk prediction models: the Bayesian Logistic Injury Severity Score, the Harborview Assessment for Risk of Mortality, and the Trauma Mortality Prediction Model. Our results indicate that TSM has superior performance, and thereby provides improved risk prediction.

Highlights:

We propose an ensemble machine learning model for trauma risk prediction.

A hyper-parameter search scheme is proposed for model development.

We compare our model to established models for trauma risk prediction.

Our model improves over established models for each performance metric considered.
Carry-over effects of larval microclimate on the transmission potential of a mosquito-borne pathogen
Authors: Evans Michelle V. , Shiau Justine C. , Solano Nicole , Brindley Melinda A. , Drake John M. , Murdock Courtney C.
Published: November 2017

Climate shapes the transmission of mosquito-borne pathogens through impacts on both the vector and the pathogen. In addition to direct effects of the environment, carry-over effects from previous life history stages can influence mosquito traits relevant to disease transmission. While this has been explored in a laboratory setting, the net effect of temperature-mediated carry-over effects due to relevant environmental variation in the larval stage is ambiguous. Here, we use data collected from a semi-field experiment investigating dengue dynamics inAedes albopictusacross a natural environmental gradient to parameterize a dengue transmission model. We rearedAe. albopictusacross three different land classes characterized by their proportion of impervious surface. Emerged females were offered a dengue infectious bloodmeal, kept at a constant 27 °C, and assayed for infection, dissemination, and infectiousness 21 days post infection. Incorporating carry-over effects of larval environment on measures of vector competence resulted in lower predicted dengue transmission potential across land class and season, however a strong positive relationship with larval environmental temperature remained. Given the significant impact of carry-over effects, future mechanistic models of disease transmission should include both direct and carry-over effects of environmental temperature.
Phosphorylation of the synaptonemal complex protein SYP-1 promotes meiotic chromosome segregation
Authors: Sato-Carlton Aya , Nakamura-Tabuchi Chihiro , Chartrand Stephane Kazuki , Uchino Tomoki , Carlton Peter Mark
Published: November 2017

Chromosomes that have undergone crossing-over in meiotic prophase must maintain sister chromatid cohesion somewhere along their length between the first and second meiotic divisions. While many eukaryotes use the centromere as a site to maintain cohesion, the holocentric organismC. elegansinstead creates two chromosome domains of unequal length termed the short arm and long arm, which become the first and second site of cohesion loss at meiosis I and II. The mechanisms that confer distinct functions to the short and long arm domains remain poorly understood. Here, we show that phosphorylation of the synaptonemal complex protein SYP-1 is required to create these domains. Once crossovers are made, phosphorylated SYP-1 and PLK-2 become cooperatively confined to short arms and guide phosphorylated histone H3 and the chromosomal passenger complex to the site of meiosis I cohesion loss. Our results show that PLK-2 and phosphorylated SYP-1 ensure creation of the short arm subdomain, promoting disjunction of chromosomes in meiosis I.
A size-invariant bud-duration timer enables robustness in yeast cell size control
Authors: Allard Corey A.H. , Decker Franziska , Weiner Orion D. , Toettcher Jared E. , Graziano Brian R.
Published: November 2017

Cell size drives key aspects of cell physiology, including organelle abundance [1, 2] and DNA ploidy [3]. While cells employ diverse strategies to regulate size [4–11], it is unclear how they are integrated to provide robust, systems-level control. In budding yeast, a molecular size sensor restricts passage of small cells through G1, enabling them to gain proportionally more volume than larger cells before progressing to Start [7, 12, 13]. Size control post-Start is less clear. S/G2/M duration in wildtype cells shows only a weak dependence on cell size; and since yeast exhibit exponential growth, larger cells would be expected to add more volume than smaller ones [7, 14–17]. However, even large mother cells produce smaller daughters, suggesting that additional regulation may occur during S/G2/M [7]. To gain further insight into post-Start size control, we prepared ‘giant’ yeast (>10-fold larger than typical volume) using two approaches to reversibly block cell cycle progression but not growth: optogenetic disruption of the cell polarity factor Bem1 [18, 19] and a temperature-sensitivecdk1allele [20]. We reasoned that giant yeast would satisfy pre-Start size control while enabling us to uncover post-Start size-limiting mechanisms though the identification of invariant growth parameters. Upon release from their block, giant mothers reenter the cell cycle and their progeny rapidly return to the original unperturbed size. This behavior is consistent with a size-invariant ‘timer’ specifying the duration of S/G2/M and indicates that yeast use at least two distinct mechanisms at different cell cycle phases to ensure size homeostasis.
Lessons from simple marine models on the bacterial regulation of eukaryotic development
Authors: Woznica Arielle , King Nicole
Published: November 2017

Molecular cues from environmental bacteria influence important developmental decisions in diverse marine eukaryotes. Yet, relatively little is understood about the mechanisms underlying these interactions, in part because marine ecosystems are dynamic and complex. With the help of simple model systems, including the choanoflagellate Salpingoeca rosetta, we have begun to uncover the bacterial cues that shape eukaryotic development in the ocean. Here, we review how diverse bacterial cues – from lipids to macromolecules – regulate development in marine eukaryotes. It is becoming clear that there are networks of chemical information circulating in the ocean, with both eukaryotes and bacteria acting as nodes; one eukaryote can precisely respond to cues from several diverse environmental bacteria, and a single environmental bacterium can regulate the development of different eukaryotes.

Highlights

Cues from environmental bacteria influence the development of many marine eukaryotes

The molecular cues produced by environmental bacteria are structurally diverse

Eukaryotes can respond to many different environmental bacteria

Some environmental bacteria act as “information hubs” for diverse eukaryotes

Experimentally tractable systems, like the choanoflagellate S. rosetta, promise to reveal molecular mechanisms underlying these interactions
High-resolution modeling of thermal thresholds and multiple environmental influences on coral bleaching for regional and local reef managements
Authors: Kumagai Naoki H. , Yamano Hiroya ,   Committee Sango-Map-Project
Published: November 2017

Corals are one of the communities most threatened by global and local stressors. Excessive summer sea temperatures can cause coral bleaching, resulting in decreases in living coral coverage. Coral bleaching may begin with rising sea temperatures, although the widely used threshold of 1 °C over the local climatological maximum sea temperature has been reconsidered. In this study, we refine thermal indices predicting coral bleaching at high resolution (1 km) by statistically optimizing the thermal threshold and multiple environmental influences on bleaching, such as ultraviolet (UV) radiation, water turbidity, and cooling effects on corals. We use a dataset of coral bleaching events observed during 2004–2016 in Japan derived from the Web-based monitoring system, the Sango (Coral) Map Project, aiming at regional to local conservation of Japanese corals. We show how the ability to predict coral bleaching is improved by the choice of thermal index, statistical optimization of thermal thresholds, usage of multiple environmental influences, and modeling methods (generalized linear model and random forest). After optimization, the differences among the thermal indices in the ability to predict coral bleaching were slight. Among environmental influences, cooling effects, UV radiation, and water turbidity, in addition to a thermal index, well explain the occurrence of coral bleaching. Prediction based on the best explanatory model reveals that recent Japanese coral reefs are experiencing bleaching in many areas, although we show a practical way to reduce bleaching frequency significantly by screening UV radiation. Thus, our high-resolution models may provide a quantitative basis for the management of local reefs under current global and local stressors. The results of this study may be useful to other researchers for selecting a predictive method according to their needs or skills.
Probabilistic Count Matrix Factorization for Single Cell Expression Data Analysis
Authors: Durif G. , Modolo L. , Mold J. E. , Lambert-Lacroix S. , Picard F.
Published: November 2017

Motivation

The development of high throughput single-cell sequencing technologies now allows the investigation of the population diversity of cellular transcriptomes. The expression dynamics (gene-to-gene variability) can be quantified more accurately, thanks to the measurement of lowly-expressed genes. In addition, the cell-to-cell variability is high, with a low proportion of cells expressing the same genes at the same time/level. Those emerging patterns appear to be very challenging from the statistical point of view, especially to represent a summarized view of single-cell expression data. PCA is a most powerful tool for high dimensional data representation, by searching for latent directions catching the most variability in the data. Unfortunately, classical PCA is based on Euclidean distance and projections that poorly work in presence of over-dispersed count data with dropout events like single-cell expression data.

Results

We propose a probabilistic Count Matrix Factorization (pCMF) approach for single-cell expression data analysis, that relies on a sparse Gamma-Poisson factor model. This hierarchical model is inferred using a variational EM algorithm. It is able to jointly build a low dimensional representation of cells and genes. We show how this probabilistic framework induces a geometry that is suitable for single-cell data visualization, and produces a compression of the data that is very powerful for clustering purposes. Our method is competed against other standard representation methods like t-SNE, and we illustrate its performance for the representation of single-cell expression (scRNA-seq) data.

Availability

Our work is implemented in the pCMF R-package1.
HDAC11 is a fatty-acid deacylase
Authors: Kutil Zsofia , Novakova Zora , Meleshin Marat , Mikesova Jana , Schutkowski Mike , Barinka Cyril
Published: November 2017

Histone deacetylase 11 (HDAC11) is a sole member of the class IV HDAC subfamily with negligible intrinsic deacetylation activity. Here we reportin vitroprofiling of HDAC11 deacylase activities, and our data unequivocally show that the enzyme efficiently removes acyl moieties spanning 8–18 carbons from the side chain nitrogen of the lysine residue of a peptidic substrate. Additionally, N-linked lipoic acid and biotin are removed by the enzyme, although with lower efficacy. Catalytic efficiencies toward dodecanoylated and myristoylated peptides exceed 70,000 M−1s−1making HDAC11 the most proficient fatty acid deacylase of the HDAC family. Interestingly, HDAC11 is strongly inhibited by free myristic, palmitic and stearic acids with inhibition constants of 6.5 µM, 0.9 µM, and 1.6 µM, respectively. At the same time, its deacylase activity is stimulated more than 2.5-fold by both palmitoyl-coenzyme A and myristoyl-coenzyme A, pointing toward metabolic control of the enzymatic activity by fatty acid metabolites. Our data reveal novel enzymatic activity of HDAC11 that can, in turn, facilitate the uncovering of additional biological functions of the enzyme as well as the design of isoform-specific HDAC inhibitors.
Flow-mediated self-organization of ventilation in honeybee nests
Authors: Peters Jacob M. , Peleg Orit , Mahadevan L.
Published: November 2017

European honey bees (Apis mellifera) live in large congested nest cavities with a single opening that limits passive ventilation. These nests are actively ventilated by individual bees which fan their wings at the nest entrance when the local air temperature exceeds a threshold. Here we show that colonies with relatively large nest entrances use an emergent ventilation strategy where fanning bees self-organize to form fanning groups, separating regions of continuous inflow and outflow. The observed spatio-temporal patterns correlate the air velocity and air temperature along the entrances to the distribution of fanning bees. A mathematical model that couples these variables to known fanning behavior of individuals recapitulates their collective dynamics. Additionally, the model makes predictions about the temporal stability of the fanning group as a function of the temperature difference between the environment and the nest. Consistent with these predictions, we observe that the fanning groups drift, cling to the entrance boundaries, break-up and reform as the ambient temperature varies over a period of days. Overall, our study shows how honeybees use flow-mediated communication to self-organize into a steady-state in fluctuating environments.
Universal scaling across biochemical networks on Earth
Authors: Kim Hyunju , Smith Harrison B. , Mathis Cole , Raymond Jason , Walker Sara I.
Published: November 2017

The application of network science to biology has advanced our understanding of the metabolism of individual organisms and the organization of ecosystems but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, we constructed biochemical networks using a global database of 28,146 annotated genomes and metagenomes, and 8,658 cataloged biochemical reactions. We uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical networks to random chemical networks reveals the observed biological scaling is not solely a product of the biochemistry shared across life on Earth. Instead, it emerges due to how the global inventory of biochemical reactions is partitioned into individuals. We show the three domains of life are topologically distinguishable, with > 80% accuracy in predicting evolutionary domain based on biochemical network size and average topology. Taken together our results point to a deeper level of organization in biochemical networks than what has been understood so far.
Planar cell polarity: thepricklegene acts independently on both the Ds/Ft and the Stan Systems
Authors: Casal José , Ibáñez-Jiménez Beatriz , Lawrence Peter A.
Published: November 2017

Epithelial cells are polarised within the plane of the epithelium, forming oriented structures whose coordinated and consistent polarity (planar cell polarity, PCP) relates to the principal axes of the body or organ. InDrosophilaat least two separate molecular systems generate and interpret intercellular polarity signals: Dachsous/Fat, and the “core” or Stan system. Here we study thepricklegene and its protein products Prickle and Spiny leg. Much research on PCP has focused on the asymmetric localisation of core proteins in the cell and as a resultpricklewas placed in the heart of the Stan system. Here we ask if this view is correct and how thepricklegene relates to the two systems. We find thatpricklecan affect, separately, both systems — however, neither Pk nor Sple are essential components of the Ds/Ft or the Stan system, nor do they act as a functional link between the two systems.
Ligand-Mediated Biofilm Formation via Enhanced Physical Interaction Between a Diguanylate Cyclase and Its Receptor
Authors: Giacalone David , Jarrod Smith T. , Collins Alan J. , Sondermann Holger , Koziol Lori J. , O’Toole George A.
Published: November 2017

The second messenger, cyclic dimeric GMP (c-di-GMP) regulates biofilm formation for many bacteria. The binding of c-d¡-GMP by the inner-membrane protein LapD controls biofilm formation, and the LapD receptor is central to a complex network of c-di-GMP-mediated biofilm formation. In this study, we examine how c-di-GMP signaling specificity by a diguanylate cyclase (DGC), GcbC, is achieved via interactions with the LapD receptor and by small ligand sensing via GcbC’s calcium channel chemotaxis (CACHE) domain. We provide evidence that biofilm formation is stimulated by the environmentally relevant organic acid citrate (and a related compound, isocitrate) in a GcbC-dependent manner through enhanced GcbC-LapD interaction, which results in increased LapA localization to the cell surface. Furthermore, GcbC shows little ability to synthesize c-di-GMP in isolation. However, when LapD is present GcbC activity is significantly enhanced ~8-fold, indicating that engaging the LapD receptor stimulates the activity of this DGC; citrate-enhanced GcbC-LapD interaction further stimulates c-di-GMP synthesis. We propose that the l-site of GcbC serves two roles beyond allosteric control of this enzyme: promoting GcbC-LapD interaction and stabilizing the active conformation of GcbC in the GcbC-LapD complex. Finally, given that LapD can interact with a dozen different DGCs of P. fluorescens, many of which have ligand-binding domains, the ligand-mediated enhanced signaling via LapD-GcbC interaction described here is likely a conserved mechanism of signaling in this network. Consistent with this idea, we identify a second example of ligand-mediated enhancement of DGC-LapD interaction that promotes biofilm formation.

Importance

In many bacteria, dozens of enzymes produce the dinucleotide signal c-di-GMP, however it is unclear how undesired crosstalk is mitigated in the context of this soluble signal, and how c-di-GMP signaling is regulated by environmental inputs. We demonstrate that GcbC, a DGC, shows little ability to synthesize c-d¡-GMP in the absence of its cognate receptor LapD; GcbC-LapD interaction enhances c-di-GMP synthesis by GcbC, likely mediated by the l-site of GcbC. We further show evidence for a ligand-mediated mechanism of signaling specificity via increased physical interaction of a DGC with its cognate receptor. We envision a scenario wherein a “cloud” of weakly active DGCs can increase their activity by specific interaction with their receptor in response to appropriate environmental signals, concomitantly boosting c-di-GMP production, ligand-specific signaling and biofilm formation.
Growing Bacteriophage M13 in Liquid Culture
Authors: Green Michael R. , Sambrook Joseph
Published: November 2017

Stocks of bacteriophage M13 are usually grown in liquid culture. The infected bacteria do not lyse but, instead, grow at a slower than normal rate to form a dilute suspension. The inoculum of bacteriophage is almost always a freshly picked plaque or a suspension of bacteriophage particles obtained from a single plaque, as described here. Infected cells contain up to 200 copies of double-stranded, replicative-form DNA and extrude several hundred bacteriophage particles per generation. Thus, a 1-mL culture of infected cells can produce enough double-stranded viral DNA (1–2 mg) for restriction mapping and recovery of cloned DNA inserts and sufficient single-stranded DNA (∼5–10 mg) for site-directed mutagenesis, DNA sequencing, or synthesis of radiolabeled probes. The titer of bacteriophages in the supernatant from infected cells is so high (∼1012 pfu/mL) that a small aliquot serves as a permanent stock of the starting plaque.
In Vitro Fertilization in Mice
Authors: Taft Robert
Published: November 2017

In vitro fertilization (IVF) involves fertilization of mature oocytes with capacitated sperm in a tissue culture dish. This technique can generate large numbers of cleavage-stage embryos without using a significant number of single-caged stud males for mating. In addition, sperm penetration is synchronous during incubation with mature oocytes, leading to synchronous development, unlike fertilization in vivo, when natural ovulation is usually spread over time. These embryos can be used for a variety of applications including rapid strain expansion and generation of age-matched experimental cohorts as well as cryopreservation at the two-cell stage (speed cryo). Another use of IVF is to generate offspring from cryopreserved sperm and from mice that, for one reason or another, will not mate or carry litters to term, that is, strain rescue. The method described here was refined at The Jackson Laboratory and has been in use for several years. There are many published alternative approaches and/or modifications, but this method, which can be used for both fresh and cryorecovered sperm, is relatively simple and effective for a wide variety of strains, although embryo yield varies considerably among strains as a function of response to superovulation and fertilization rate. Optimal results are dependent on practice and attention to detail.
DNA Bisulfite Sequencing for Single-Nucleotide-Resolution DNA Methylation Detection
Authors: Lizardi Paul M. , Yan Qin , Wajapeyee Narendra
Published: November 2017

DNA methylation plays an important role in multiple biological processes. Therefore, methodologies that can detect changes in DNA methylation are of general importance. A popular and reliable method for measuring DNA methylation status is DNA bisulfite sequencing. This protocol details the steps required for bisulfite conversion and analysis of either genes or a specific genomic region. Denatured DNA (i.e., single-stranded DNA) is treated with sodium bisulfite under conditions that preferentially convert unmethylated cytosine (C) residues to uracil (U) residues while methylated cytosines remain unmodified. The converted DNA can then be amplified using a gene-specific primer. U is amplified as thymidine (T) in polymerase chain reaction (PCR) and detected as T during DNA sequencing.
Illumina Sequencing of Bisulfite-Converted DNA Libraries
Authors: Lizardi Paul M. , Yan Qin , Wajapeyee Narendra
Published: November 2017

Here we describe a standard MethylC-seq protocol using single-read sequencing on an Illumina Genome Analyzer II platform. The protocol involves ligation of methylated sequencing adaptors to sonicated genomic DNA, gel purification, sodium bisulfite conversion, polymerase chain reaction (PCR) amplification, and sequencing.
Harvesting Tissue from Immunized Mice, Rats, and Hamsters
Authors: Greenfield Edward A.
Published: November 2017

Immunologically active organs such as the spleen and lymph nodes are rich sources of antibodies; they are also major sites in the body where antibody-producing B cells accumulate. The lymph nodes, in particular, can be targeted when deciding where to inject an animal with antigen. Once an immunized animal has developed a sufficient serum antibody titer, these organs can be harvested for hybridoma fusion and monoclonal antibody production.
CRIME, FEAR, AND MENTAL HEALTH IN MEXICO
Authors: VILLARREAL ANDRÉS , YU WEI‐HSIN
Published: November 2017

This article examines the effect of exposure to criminal violence on fear of crime and mental health in Mexico, a country that has experienced a dramatic rise in violent events resulting from the operation of drug trafficking organizations (DTOs). Data are drawn from more than 30,000 respondents to a national longitudinal survey of Mexican households. We use fixed‐effects models which allow us to control for time‐invariant individual and municipal characteristics affecting both exposure to violence and mental health. The results indicate a substantial increase in fear and psychological distress for individuals living in communities that suffered a rise in the local homicide rate even when exposure to other forms of victimization and more personal experiences with crime are taken into account. Because DTO killings occur in response to factors external to a specific neighborhood, they generate fear and psychological distress at a larger geographical scale. They also seem to create a generalized sense of insecurity, leading to increased fear of other types of crimes. We examine the effect of large surges in homicide and the presence of military and paramilitary groups combatting DTOs as these conditions may approximate those in conflict zones elsewhere in the world. We also explore differences in the relative sensitivity to homicide rates between sociodemographic groups.
Managing Uncertainty in Runoff Estimation with the U.S. Environmental Protection Agency National Stormwater Calculator
Authors: Schifman L.A. , Tryby M.E. , Berner J. , Shuster W.D.
Published: November 2017

The U.S. Environmental Protection Agency National Stormwater Calculator (NSWC) simplifies the task of estimating runoff through a straightforward simulation process based on the EPA Stormwater Management Model. The NSWC accesses localized climate and soil hydrology data, and options to experiment with low‐impact development (LID) features for parcels up to 5 ha in size. We discuss how the NSWC treats the urban hydrologic cycle and focus on the estimation uncertainty in soil hydrology and its impact on runoff simulation by comparing field‐measured soil hydrologic data from 12 cities to corresponding NSWC estimates in three case studies. The default NSWC hydraulic conductivity is 10.1 mm/h, which underestimates conductivity measurements for New Orleans, Louisiana (95 ± 27 mm/h) and overestimates that for Omaha, Nebraska (3.0 ± 1.0 mm/h). Across all cities, the NSWC prediction, on average, underestimated hydraulic conductivity by 10.5 mm/h compared to corresponding measured values. In evaluating how LID interact with soil hydrology and runoff response, we found direct hydrologic interaction with pre‐existing soil shows high sensitivity in runoff prediction, whereas LID isolated from soils show less impact. Simulations with LID on higher permeability soils indicate that nearly all of pre‐LID runoff is treated; while features interacting with less‐permeable soils treat only 50%. We highlight the NSWC as a screening‐level tool for site runoff dynamics and its suitability in stormwater management.
Different EGFR gene mutations in two patients with synchronous multiple lung cancers: A case report
Authors: Sakai Hiroki , Saji Hisashi , Kimura Hiroyuki , Tsuda Masataka , Wakiyama Yoichi , Miyazawa Tomoyuki , Marushima Hideki , Kojima Koji , Hoshikawa Masahiro , Takagi Masayuki , Nakamura Haruhiko
Published: November 2017

Routine clinical and pathological evaluations to determine the relationship between different lesions are often not completely conclusive. Interestingly, detailed genetic analysis of tumor samples may provide important additional information and identify second primary lung cancers. In the present study, we report cases of two synchronous lung adenocarcinomas composed of two distinct pathological subtypes with different EGFR gene mutations: a homozygous deletion in exon 19 of the papillary adenocarcinoma subtype and a point mutation of L858R in exon 21 of the tubular adenocarcinoma. The present report highlights the clinical importance of molecular cancer biomarkers to guide management decisions in cases involving multiple lung tumors.
Macular thinning in prediabetes or type 2 diabetes without diabetic retinopathy: the Maastricht Study
Authors: De Clerck Eline E.B. , Schouten Jan S.A.G. , Berendschot Tos T.J.M. , Goezinne Fleur , Dagnelie Pieter C. , Schaper Nicolaas C. , Schram Miranda T. , Stehouwer Coen D.A. , Webers Carroll A.B.
Published: November 2017

Purpose

To assess macular thinning in individuals with prediabetes or type 2 diabetes without diabetic retinopathy (DM2 w/o DR) compared with individuals with normal glucose metabolism (NGM).

Methods

Using spectral domain optical coherence tomography (SD‐OCT), we measured macular thickness in six subfields as defined by the Early Treatment Diabetic Retinopathy Study (ETDRS) in 1838 participants from The Maastricht Study, a population‐based cohort study (mean age 59 ± 8 years, 49% men, 1087 NGM, 279 prediabetes, 472 DM2 w/o DR). Multivariable linear regression was used to assess the association between macular thickness and glucose metabolism status.

Results

After adjustment for age, sex and spherical equivalent, individuals with prediabetes showed a significant decrease in pericentral superior macular thickness [β = −2.14 μm (95% confidence interval (CI): −4.24 to −0.03), p < 0.05] compared with individuals with NGM. In individuals with DM2 w/o DR, the fovea [β = −4.05 μm (95% CI: −6.30 to −1.79), p < 0.001] and the four pericentral quadrants (range: β = −4.64 to −5.29 μm, p < 0.001) were significantly thinner compared with individuals with NGM. There was a significant linear trend of macular thinning with severity of glucose metabolism status in five subfields (p < 0.001).

Conclusion

Macular thickness is reduced in prediabetes and a greater reduction occurs in DM2, even before DR is clinically present. About half of the thinning observed in DM2 w/o DR was already found in prediabetes. Generalized thinning of the macula could be related to thinning of the temporal side of the optic nerve head through the connecting papillo‐macular bundle.
Computer‐aided diagnosis based on enhancement of degraded fundus photographs
Authors: Jin Kai , Zhou Mei , Wang Shaoze , Lou Lixia , Xu Yufeng , Ye Juan , Qian Dahong
Published: November 2017

Purpose

Retinal imaging is an important and effective tool for detecting retinal diseases. However, degraded images caused by the aberrations of the eye can disguise lesions, so that a diseased eye can be mistakenly diagnosed as normal. In this work, we propose a new image enhancement method to improve the quality of degraded images.

Methods

A new method is used to enhance degraded‐quality fundus images. In this method, the image is converted from the input RGB colour space to LAB colour space and then each normalized component is enhanced using contrast‐limited adaptive histogram equalization. Human visual system (HVS)‐based fundus image quality assessment, combined with diagnosis by experts, is used to evaluate the enhancement.

Results

The study included 191 degraded‐quality fundus photographs of 143 subjects with optic media opacity. Objective quality assessment of image enhancement (range: 0–1) indicated that our method improved colour retinal image quality from an average of 0.0773 (variance 0.0801) to an average of 0.3973 (variance 0.0756). Following enhancement, area under curves (AUC) were 0.996 for the glaucoma classifier, 0.989 for the diabetic retinopathy (DR) classifier, 0.975 for the age‐related macular degeneration (AMD) classifier and 0.979 for the other retinal diseases classifier.

Conclusion

The relatively simple method for enhancing degraded‐quality fundus images achieves superior image enhancement, as demonstrated in a qualitative HVS‐based image quality assessment. This retinal image enhancement may, therefore, be employed to assist ophthalmologists in more efficient screening of retinal diseases and the development of computer‐aided diagnosis.
Immune‐suppressive effects of interleukin‐6 on T‐cell‐mediated anti‐tumor immunity
Authors: Tsukamoto Hirotake , Fujieda Koji , Senju Satoru , Ikeda Tokunori , Oshiumi Hiroyuki , Nishimura Yasuharu
Published: November 2017

Accompanied by the growing clinical applications of immunotherapy in the treatment of cancer patients, development of novel therapeutic approaches to reverse the immune‐suppressive environment in cancer patients is eagerly anticipated, because the success of cancer immunotherapy is currently limited by immune‐suppressive effects in tumor‐bearing hosts. Interleukin (IL)‐6, a pleotropic proinflammatory cytokine, participates in tumor cell‐autonomous processes that are required for their survival and growth, and is therefore known as a poor prognostic factor in cancer patients. In addition, an emerging role of IL‐6 in modulating multiple functions of immune cells including T cells, dendritic cells, and macrophages is responsible for the dysfunction of innate and adaptive immunity against tumors. Therefore, the IL‐6‐targeting approach is of value as a promising strategy for desensitization and prevention of immune‐suppressive effects, and should be an effective treatment when combined with current immunotherapies. The aim of the present review is to discuss the immune‐suppressive aspects of IL‐6, notably with modification of T‐cell functions in cancer patients, and their relationship to anti‐tumor immune responses and cancer immunotherapy.
Haunted Infrastructure: Religious Ruins and Urban Obstruction in Vietnam
Authors: Schwenkel Christina
Published: November 2017

This essay examines encounters between urban infrastructure and the spirit world, or what I am calling “haunted infrastructure.” It does so through the case study of an historic pagoda in Vinh City, Vietnam, that was destroyed by US aerial bombing in 1968, leaving only the charred front gate standing. As one of the last visible ruins of war that mark a history of imperial violence to the landscape, the pagoda's remains have been designated a site worthy of remembrance and preservation as architectural heritage. For urban residents, this symbolic space of urban destruction—and subsequent myth‐making—has remained one of the most affect‐laden places in the city and the center of renewed religious practices through the spontaneous reconstruction of the pagoda and its altars. In the essay, I trace the dynamic social life of Diệc Pagoda—co‐constituted by spirits, legends, and practitioners—as it abetted and disrupted colonial, socialist, and market‐oriented urban development. Drawing on Edensor's () notion of the productive capacity of the ruin to contest state power, I argue that religious ruins, as animated materiality that channel collective energies, have emerged as powerful sites to protest the encroachment of socialist development in and through the ghosts that inhabit them. While contemporary practices at Diệc Pagoda speak to religious diversification across urban Vietnam, they do so through obstructing, rather than enabling state projects of modernization. Haunted infrastructures and their attenuating myths thus reveal deep‐seated ambivalences about the postcolonial state and the specter of foreignness in the city. [Ruins; Urbanization; Infrastructure; Socialism; Urban Heritage; Religiosity; Ghosts]
Aβ exacerbates α‐synuclein‐induced neurotoxicity through impaired insulin signaling in α‐synuclein‐overexpressed human SK‐N‐MC neuronal cells
Authors: Chang Ching‐Chi , Li Hsin‐Hua , Chang Yen‐Ting , Ho Ying‐Jui , Hsieh Ling‐Jia , Chiu Pai‐Yi , Cheng Yu‐Shih , Lin Chih‐Li , Lai Te‐Jen
Published: November 2017

Aim

α‐Synuclein (αSyn) is known as a small soluble protein abundantly expressed in neuronal cells. Although its physiological role is still unclear, the aggregation of αSyn has been recognized as responsible for some neurodegenerative disorders such as dementia with Lewy bodies (DLB). In most cases, intracellular abnormal aggregates are caused by protein‐coding mutations that alter primary structure and therefore increase propensity toward aggregation. However, no pathogenic alterations or polymorphisms in αSyn are found in DLB patients so far, suggesting genetic mutations may not play a major role in DLB pathogenesis. In contrast, emerging evidence reveals that amyloid β (Aβ) may contribute to aggregate formation and exacerbate neurotoxicity of αSyn. However, the underlying mechanism of action has remained unclear.

Methods

To investigate molecular pathways involved in Aβ‐mediated αSyn pathology, we established an in vitro model for inducible αSyn overexpression in SK‐N‐MC human neuronal cells.

Results

Our results demonstrated that Aβ treatment in αSyn‐overexpressed neuronal cells significantly increases αSyn intracellular aggregation and cytotoxicity. Moreover, Aβ also caused AMP‐activated protein kinase (AMPK) inhibition and impaired insulin sensitivity, which leads to significant downregulation of nuclear factor erythroid 2‐related factor 2 (NRF2)/heme oxygenase 1 (HO‐1) antioxidant signaling to elicit αSyn aggregation.

Conclusions

This raised the possibility that insulin resistance could be one of the causative factors of αSyn toxicity, and the strategies for insulin sensitization may have therapeutic potential for synucleinopathies including DLB.
Outcome of restorative proctocolectomy with an ileo‐anal pouch for ulcerative colitis: effect of changes in clinical practice
Authors: Germain A. , de Buck van Overstraeten A. , Wolthuis A. , Ferrante M. , Vermeire S. , Van Assche G. , D'Hoore A.
Published: November 2017

Aim

Surgery for ileal pouch–anal anastomosis (IPAA) has evolved over time, especially since the introduction of laparoscopy. The aim of this retrospective study was to report the impact of surgical evolution on outcome over a period of 25 years.

Method

All patients who had IPAA surgery for ulcerative colitis from 1990 to 2015 at the University Hospitals of Leuven were included. Patients were divided into three period arms (period A 1990–1999; period B 2000–2009; period C 2010–2015). The main outcome measure was anastomotic leakage.

Results

A total of 335 patients (58.8% male) with a median age of 39 years (interquartile range 32–49 years) at surgery were included. Median follow‐up was 5 years (interquartile range 2–10 years). Overall anastomotic leakage (grades A–C) was 14.9%. A significant decrease in leakage rate was observed over time (from 21.4% in period A to 12.1% in period B to 10.0% in period C; P = 0.04). The defunctioning ileostomy rate at the time of pouch construction decreased from 91.7% (period A) to 40.3% (period B) to 11.1% (period C) (P < 0.001). We observed an increase in the use of laparoscopy (23.9% in period A vs 72.6% in period B, vs 84.4% in period C; P = 0.001) and a shift to a modified two‐stage procedure (4.1% in period A, vs 66.7% in period C; P < 0.0001). In a monocentric study with some of the data retrieved retrospectively it was not possible to account for the impact of preoperative nutritional status (weight loss, serum albumin level) or disease burden. Other outcome factors were not measured, for example sexual function and fecundity.

Conclusion

A higher rate of laparoscopic IPAA surgery, together with a shift towards modified two‐stage procedures, was associated with a lower leakage rate despite a reduction in the use of defunctioning ileostomy.
House Prices, Wealth Effects and Labour Supply
Authors: Disney Richard , Gathergood John
Published: November 2017

We examine the impact of house prices on labour supply decisions using UK microdata. We combine household survey data with local‐level house price measures and controls for local labour demand. Our microdata also allow us to control for individual level income expectations. We find significant house price effects on labour supply, consistent with leisure being a normal good. Labour supply responses to house prices are concentrated among young married female owners and older owners. This finding suggests that house prices affect the decisions of marginal workers in the economy. Our estimates imply that house prices are economically important in the participation decisions for these workers.