bluuebunny/crossref_metadata_2025 huggingface dataset:
Homeodomain interacting protein kinase promotes tumorigenesis and metastatic cell behavior
Authors: Blaquiere Jessica A. , Wong Kenneth Kin Lam , Kinsey Stephen D. , Wu Jin , Verheyen Esther M.
Published: June 2017

Aberrations in signaling pathways that regulate tissue growth often lead to tumorigenesis. Homeodomain interacting protein kinase (Hipk) family members are reported to have distinct and contradictory effects on cell proliferation and tissue growth. From these studies it is clear that much remains to be learned about the roles of Hipk family protein kinases in proliferation and cell behaviour. Previous work has shown that Drosophila Hipk is a potent growth regulator, thus we predicted that it could have a role in tumorigenesis. In our study of Hipk-induced phenotypes, we observed the formation of tumor-like structures in multiple cell types in larvae and adults. Furthermore, elevated Hipk in epithelial cells induces cell spreading, invasion and epithelial-to-mesenchymal transition in the imaginal disc. Further evidence comes from cell culture studies in which we expressed Drosophila Hipk in human breast cancer cells and show that it enhances proliferation and migration. Past studies have shown that Hipk can promote the action of conserved pathways implicated in cancer and EMT, such as Wnt/Wingless, Hippo, Notch and JNK. We show that Hipk-phenotypes are not likely due to activation of a single target, but rather through a cumulative effect on numerous target pathways. Most Drosophila tumor models involve mutations in multiple genes, such as the well-known RasV12model, in which EMT and invasiveness occur after the additional loss of the tumor suppressor genescribble. Our study reveals that elevated levels of Hipk on their own can promote both hyperproliferation and invasive cell behaviour, suggesting that Hipks could be potent oncogenes and drivers of EMT.

Summary statement

The protein kinase Hipk can promote proliferation and invasive behaviors, as well as synergize with known cancer pathways, in a novel Drosophila model for tumorigenesis.
Distribution Shapes Govern the Discovery of Predictive Models for Gene Regulation
Authors: Munsky Brian E. , Li Guoliang , Fox Zachary R. , Shepherd Douglas P. , Neuert Gregor
Published: June 2017

Despite substantial experimental and computational efforts, mechanistic modeling remains more predictive in engineering than in systems biology. The reason for this discrepancy is not fully understood. Although randomness and complexity of biological systems play roles in this concern, we hypothesize that significant and overlooked challenges arise due to specific features of single-molecule events that control crucial biological responses. Here we show that modern statistical tools to disentangle complexity and stochasticity, which assume normally distributed fluctuations or enormous datasets, don't apply to the discrete, positive, and non-symmetric distributions that characterize spatiotemporal mRNA fluctuations in single-cells. We demonstrate an alternate approach that fully captures discrete, non-normal effects within finite datasets. As an example, we integrate single-molecule measurements and these advanced computational analyses to explore Mitogen Activated Protein Kinase induction of multiple stress response genes. We discover and validate quantitatively precise, reproducible, and predictive understanding of diverse transcription regulation mechanisms, including gene activation, polymerase initiation, elongation, mRNA accumulation, spatial transport, and degradation. Our model-data integration approach extends to any discrete dynamic process with rare events and realistically limited data.

Significance Statement

Systems biology seeks to combine experiments with computation to predict complex biological behaviors. However, despite tremendous data and knowledge, most biological models make terrible predictions. By analyzing single-cell-single-molecule measurements of mRNA in yeast during stress response, we explore how prediction accuracy is controlled by experimental distributions shapes. We find that asymmetric data distributions, which arise in measurements of positive quantities, can cause standard modeling approaches to yield excellent fits but make meaningless predictions. We demonstrate advanced computational tools that solve this dilemma and achieve predictive understanding of many spatiotemporal mechanisms of transcription control including RNA polymerase initiation and elongation and mRNA accumulation, transport and decay. Our approach extends to any discrete dynamic process with rare events and realistically limited data.
Histone demethylation and c-MYC activation enhance translational capacity in response to amino acid restriction
Authors: Cheng Chen , Su Trent , Morselli Marco , Kurdistani Siavash K.
Published: June 2017

Nutrient limitation may elicit adaptive epigenetic changes but the nature and mechanisms of the cellular response to specific nutrient deficiencies are incompletely understood. We report that depriving human cells of amino acids (AAs) induces specific loss of H4K20me1 from gene bodies and elevated binding of c-MYC at promoters genome-wide. These effects are most pronounced at ribosomal protein and translation initiation genes, which are upregulated, leading to enhanced protein synthetic capacity. Combination of H4K20 methyltransferase depletion and c-MYC over-expression in rich media is required and sufficient to recapitulate the effects of AA restriction. Our data reveal an unexpected and epigenetically implemented increase in translational capacity when AAs are limiting, likely to safeguard the proteome by making effective use of limited resources.

One Sentence Summary:Combination of H4K20me1 demethylation and c-MYC activation enhance translational capacity in response to amino acid restriction.
winglessis a positive regulator of eyespot color patterns inBicyclus anynanabutterflies
Authors: Özsu Nesibe , Chan Qian Yi , Chen Bin , Gupta Mainak Das , Monteiro Antónia
Published: June 2017

Eyespot patterns of nymphalid butterflies are an example of a novel trait yet, the developmental origin of eyespots is still not well understood. Several genes have been associated with eyespot development but few have been tested for function. One of these genes is the signaling ligand,wingless, which is expressed in the eyespot centers during early pupation and may function in eyespot signaling and color ring differentiation. Here we tested the function ofwinglessin wing and eyespot development by down-regulating it in transgenicBicyclus anynanabutterflies via RNAi driven by an inducible heat-shock promoter. Heat-shocks applied during larval and early pupal development led to significant decreases inwinglessmRNA levels and to decreases in eyespot size and wing size in adult butterflies. We conclude thatwinglessis a positive regulator of eyespot and wing development inB. anynanabutterflies.
Aerobiosis is not associated with GC content and G to T mutations are not the signature of oxidative stress in prokaryotic evolution
Authors: Aslam Sidra , Lan Xin-Ran , Zhang Bo-Wen , Chen Zheng-Lin , Niu Deng-Ke
Published: June 2017

Background:Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines result in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results.

Results:We retrieved 70 aerobe-anaerobe pairs of prokaryotes, and members of each pair were adjacent on the phylogenetic tree. Pairwise comparisons of either whole-genome GC content or the GC content at 4-fold degenerate sites of orthologous genes among these 70 pairs did not show significant differences between aerobes and anaerobes. The signature of guanine oxidation on GC content evolution has not been detected even after extensive controlling of other influencing factors. Furthermore, the anaerobes were not different from the aerobes in the rate of either G to T, C to A, or other directions of substitutions. The presence of the enzymes responsible for guanine oxidation in anaerobic prokaryotes provided additional evidence that guanine oxidation might be prevalent in anaerobic prokaryotes. In either aerobes or anaerobes, the rates of G:C to T:A mutations were not significantly higher than the reverse mutations.

Conclusions:The previous counterintuitive results on the relationship between oxygen requirement and GC content should be attributed to the methodological artefact resulting from phylogenetically non-independence among the analysed samples. Our results showed that aerobiosis does not increase or decrease GC content in evolution. Furthermore, our study challenged the widespread belief that abundant G:C to T:A transversions are the signature of oxidative stress in prokaryotic evolution.
Boosting Felsenstein’s Phylogenetic Bootstrap
Authors: Lemoine F. , Domelevo Entfellner J.-B. , Wilkinson E. , De Oliveira T. , Gascuel O.
Published: June 2017

Felsenstein’s article describing the application of the bootstrap to evolutionary trees, is one of the most cited papers of all time. That statistical method, based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now available for a wide variety of species, and phylogenies with hundreds or thousands of taxa are becoming routine. In that framework, Felsenstein’s bootstrap tends to yield very low supports, especially on deep branches. We propose a revised version, in which the presence of inferred branches in replications is measured using a gradual “transfer” distance, as opposed to the original version using a binary presence/absence index. The resulting supports are higher, while not inducing falsely supported branches. Our method is applied to large simulation, mammal and HIV datasets, for which it reveals the phylogenetic signal, while Felsenstein’s bootstrap fails to do so.
Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer
Authors: Bameta Tripti , Das Dibyendu , Padinhateeri Ranjith
Published: June 2017

Positioning of nucleosomes along the genomic DNA is crucial for many cellular processes that include gene regulation and higher order packaging of chromatin. The question of how nucleosome-positioning information from a parent chromatin gets transferred to the daughter chromatin is highly intriguing. Accounting for experimentally known coupling between replisome movement and nucleosome dynamics, we propose a model that can explain the inheritance of nucleosome positioning. Simulating nucleosome dynamics during replication we argue that short pausing of the replication fork, associated with nucleosome disassembly, can be the event crucial for communicating nucleosome positioning information from parent to daughter. We show that the interplay of timescales between nucleosome disassembly (τp) at the replication fork and nucleosome sliding behind the fork (τs) can give rise to a rich “phase diagram” having different inherited patterns of nucleosome organization. Our model predicts that only whenτp≥τsthe daughter chromatin can inherit the precise nucleosome positioning of the parent.
TRIM9-dependent ubiquitination of DCC constrains kinase signaling, exocytosis, and axon branching
Authors: Plooster Melissa , Menon Shalini , Winkle Cortney C. , Urbina Fabio L. , Monkiewicz Caroline , Phend Kristen D. , Weinberg Richard J. , Gupton Stephanie L.
Published: June 2017

Extracellular netrin-1 and its receptor DCC promote axon branching in developing cortical neurons. Netrin-dependent morphogenesis is preceded by multimerization of DCC, activation of FAK and Src family kinases, and increases in exocytic vesicle fusion, yet how these occurrences are linked is unknown. Here we demonstrate that TRIM9-dependent ubiquitination of DCC blocks the interaction with and phosphorylation of FAK. Upon netrin-1 stimulation TRIM9 promotes DCC multimerization, but TRIM9-dependent ubiquitination of DCC is reduced, which promotes an interaction with FAK and subsequent FAK activation. We found that inhibition of FAK activity blocks elevated frequencies of exocytosisin vitroand elevated axon branchingin vitroandin vivo.Although FAK inhibition decreased SNARE-mediated exocytosis, assembled SNARE complexes and vesicles adjacent to the plasma membrane were increased, suggesting a novel role for FAK in the progression from assembled SNARE complexes to vesicle fusion in developing murine neurons.

Abbreviations used in this paper

DCC

Deleted in Colorectal Cancer

TRIM

Tripartite Motif

SFK

src family kinase

DCCKR

non ubiquitinatable DCC mutant

VAMP

vesicle associated membrane protein

TRIM9ΔRING

TRIM9 lacking the ubiquitin ligase RING domain

TRIM9ΔSPRY

TRIM9 variant lacking the DCC-binding SPRY domain

TIRF

Total Internal Reflection Fluorescence

pY

phosphotyrosine

FAKi

pharmacological FAK inhibitor 14

FRNK

FAK related non-kinase

STX-1A

syntaxin 1A

IP

immunoprecipitate
Computational Investigation of O2Diffusion Through an Intra–molecular Tunnel in AlkB; Influence of Polarization on O2Transport
Authors: Torabifard Hedieh , Cisneros G. Andrés
Published: June 2017

E. ColiAlkB catalyzes the direct dealkylation of various alkylated bases in damaged DNA. The diffusion of molecular Oxygen to the active site in AlkB is an essential step for the oxidative dealkylation activity. Despite detailed studies on the stepwise oxidation mechanism of AlkB, there is no conclusive picture of how O2molecules reach the active site of the protein. Yuet al. (Nature,439, 879) proposed the existence of an intra–molecular tunnel based on their initial crystal structures of AlkB. We have employed computational simulations to investigate possible migration pathways inside AlkB for O2molecules. Extensive molecular dynamics (MD) simulations, including explicit ligand sampling and potential of mean force (PMF) calculations, have been performed to provide a microscopic description of the O2delivery pathway in AlkB. Analysis of intra–molecular tunnels using the CAVER software indicates two possible pathways for O2to diffuse into the AlkB active site. Explicit ligand sampling simulations suggests that only one of these tunnels provides a viable route. The free energy path for an oxygen molecule to travel along each of these tunnels has been determined with AMBER and AMOEBA. Both PMFs indicate passive transport of O2from the surface of the protein. However, the inclusion of explicit polarization shows a very large barrier for diffusion of the co–substrate out of the active site, compared with the non–polarizable potential. In addition, our results suggest that the mutation of a conserved residue along the tunnel, Y178, has dramatic effects on the dynamics of AlkB and on the transport of O2along the tunnel.
Discriminative aversive learning and amygdala responsivity is enhanced in mice with reduced serotonin transporter activity
Authors: Lima João , Sharp Trevor , Taylor Amy M. , Bannerman David M. , McHugh Stephen B.
Published: June 2017

The serotonin (5-HT) transporter (5-HTT) regulates 5-HT availability at the synapse. Low or null 5-HTT expression results in increased 5-HT availability and has been reported to produce anxious and depressive phenotypes, although this remains highly controversial despite two decades of investigation. Paradoxically, SSRIs, which also increase 5-HT availability, reduce the symptoms of anxiety and depression. An emerging ‘network plasticity’ theory of 5-HT function argues that, rather than influencing mood directly, increasing 5-HT availability enhances learning about emotionally-significant events but evidence supporting this theory is inconclusive. Here, we tested one key prediction of this theory: that increased 5-HT availability enhances aversive learning. In experiment 1, we trained 5-HTT knock-out mice (5-HTTKO), which have increased 5-HT availability, and wild-type mice (WT) on an aversive discrimination learning task in which one auditory cue was paired with an aversive outcome whereas a second auditory cue was not. Simultaneously we recorded neuronal and hemodynamic responses from the amygdala, a brain region necessary for aversive learning. 5-HTTKO mice exhibited superior discrimination learning than WTs, and had stronger theta-frequency neuronal oscillations and larger amygdala hemodynamic responses to the aversive cues, which predicted the extent of learning. In experiment 2, we found that acute SSRI treatment (in naïve non-transgenic mice), given specifically before fear learning sessions, enhanced subsequent fear memory recall. Collectively, our data demonstrate that reducing 5-HTT activity (and thereby increasing 5-HT availability) enhances amygdala responsivity to aversive events and facilitates learning for emotionally-relevant cues. Our findings support the network plasticity theory of 5-HT function.
Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters
Authors: Lesaulnier Celine C. , Herbold Craig W. , Pelikan Claus , Berry David , Gérard Cédric , Coz Xavier Le , Gagnot Sophie , Niggemann Jutta , Dittmar Thorsten , Singer Gabriel A. , Loy Alexander
Published: June 2017

Background

Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown.

Results

We performed a multifaceted analysis of microbiota and DOM diversity in twelve natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than ten species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial generaCurvibacter,Aquabacterium, andPolaromonas(Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM.

Conclusions

The bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.
Hippo signaling restricts cells in the second heart field that differentiate into Islet-1-positive atrial cardiomyocytes
Authors: Fukui Hajime , Miyazaki Takahiro , Ishikawa Hiroyuki , Nakajima Hiroyuki , Mochizuki Naoki
Published: June 2017

Abstract

Cardiac precursor cells (CPCs) in the first heart field (FHF) and the second heart field (SHF) present at both arterial and venous poles assemble to form a cardiac tube in zebrafish. Hippo kinase cascade is essential for proper heart formation; however, it remains elusive how Hippo signal contributes to early cardiac fate determination. We here demonstrate that mutants oflarge tumor suppressor kinase 1/2(lats1/2) exhibited an increase in a SHF marker, Islet1 (Isl1)-positive andhand2promoter-activated venous pole atrial cardiomyocytes (CMs) and that those showed expansion of the domain between between the anterior and the posterior lateral plate mesoderm. Consistently, TEAD-8 dependent transcription was activated in caudal region of the left ALPM cells that gave rise to the venous pole atrial CMs. Yap1/Wwtr1-promotedbmp2bexpression was essential for Smad-regulatedhand2expression in the left ALPM, indicating that Hippo signaling restricts the SHF cells originating from the left ALPM that move toward the venous pole.
The Molecular Genetic Basis of Herbivory between Butterflies and their Host-Plants
Authors: Nallu Sumitha , Hill Jason , Don Kristine , Sahagun Carlos , Zhang Wei , Meslin Camille , Snell-Rood Emilie , Clark Nathan L. , Morehouse Nathan I. , Bergelson Joy , Wheat Christopher W. , Kronforst Marcus R.
Published: June 2017

Interactions between herbivorous insects and their host-plants are a central component of terrestrial food webs and a critical topic in agriculture, where a substantial fraction of potential crop yield is lost annually to pests. Important insights into plant-insect interactions have come from research on specific plant defenses and insect detoxification mechanisms. Yet, much remains unknown about the molecular mechanisms that mediate plant-insect interactions. Here we use multiple genome-wide approaches to map the molecular basis of herbivory from both plant and insect perspectives, focusing on butterflies and their larval host-plants. Parallel genome-wide association studies in the Cabbage White butterfly,Pieris rapae, and its host-plant,Arabidopsis thaliana, pinpointed a small number of butterfly and plant genes that influenced herbivory. These genes, along with much of the genome, were regulated in a dynamic way over the time course of the feeding interaction. Comparative analyses, including diverse butterfly/plant systems, showed a variety of genome-wide responses to herbivory, yet a core set of highly conserved genes in butterflies as well as their host-plants. These results greatly expand our understanding of the genomic causes and evolutionary consequences of ecological interactions across two of Nature’s most diverse taxa, butterflies and flowering plants.
Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy
Authors: Wu Yicong , Kumar Abhishek , Smith Corey , Ardiel Evan , Chandris Panagiotis , Christensen Ryan , Rey-Suarez Ivan , Guo Min , Vishwasrao Harshad D. , Chen Jiji , Tang Jianyong , Upadhyaya Arpita , Riviere Patrick J. La , Shroff Hari
Published: June 2017

Light-sheet fluorescence microscopy (LSFM) enables high-speed, high-resolution, gentle imaging of live biological specimens over extended periods. Here we describe a technique that improves the spatiotemporal resolution and collection efficiency of LSFM without modifying the underlying microscope. By imaging samples on reflective coverslips, we enable simultaneous collection of multiple views, obtaining 4 complementary views in 250 ms, half the period it would otherwise take to collect only two views in symmetric dual-view selective plane illumination microscopy (diSPIM). We also report a modified deconvolution algorithm that removes the associated epifluorescence contamination and fuses all views for resolution recovery. Furthermore, we enhance spatial resolution (to < 300 nm in all three dimensions) by applying our method to a new asymmetric diSPIM, permitting simultaneous acquisition of two high-resolution views otherwise difficult to obtain due to steric constraints at high numerical aperture (NA). We demonstrate the broad applicability of our method in a variety of samples of moderate (< 50 μm) thickness, studying mitochondrial, membrane, Golgi, and microtubule dynamics in single cells and calcium activity in nematode embryos.
Analysis of Copy Number Loss of the ErbB4 Receptor Tyrosine Kinase in Glioblastoma
Authors: Jones DeAnalisa C. , Scanteianu Adriana , DiStefano Matthew , Bouhaddou Mehdi , Birtwistle Marc R.
Published: June 2017

Current treatments for glioblastoma multiforme (GBM)—an aggressive form of brain cancer—are minimally effective and yield a median survival of 14.6 months and a two-year survival rate of 30%. Given the severity of GBM and the limitations of its treatment, there is a need for the discovery of novel drug targets for GBM and more personalized treatment approaches based on the characteristics of an individual’s tumor. Most receptor tyrosine kinases—such as EGFR—act as oncogenes, but publicly available data from the Cancer Cell Line Encyclopedia (CCLE) indicates copy number loss in the ERBB4 RTK gene across dozens of GBM cell lines, suggesting a potential tumor suppressor role. This loss is mutually exclusive with loss of its cognate ligand NRG1 in CCLE as well, more strongly suggesting a functional role. The availability of higher resolution copy number data from clinical GBM patients in The Cancer Genome Atlas (TCGA) revealed that a region in Intron 1 of the ERBB4 gene was deleted in 69.1% of tumor samples harboring ERBB4 copy number loss; however, it was also found to be deleted in the matched normal tissue samples from these GBM patients (n = 81). Using the DECIPHER Genome Browser, we also discovered that this mutation occurs at approximately the same frequency in the general population as it does in the disease population. We conclude from these results that this loss in Intron 1 of the ERBB4 gene is neither ade novodriver mutation nor a predisposing factor to GBM, despite the indications from CCLE. A biological role of this significantly occurring genetic alteration is still unknown. While this is a negative result, the broader conclusion is that while copy number data from large cell line-based data repositories may yield compelling hypotheses, careful follow up with higher resolution copy number assays, patient data, and general population analyses are essential to codify initial hypotheses.
Dopamine neuron dependent behaviors mediated by glutamate cotransmission
Authors: Mingote Susana , Chuhma Nao , Kalmbach Abigail , Thomsen Gretchen M. , Wang Yvonne , Mihali Andra , Sferrazza Caroline , Zucker-Scharff Ilana , Siena Anna-Claire , Welch Martha G. , Lizardi-Ortiz José , Sulzer David , Moore Holly , Gaisler-Salomon Inna , Rayport Stephen
Published: June 2017

Dopamine neurons in the ventral tegmental area use glutamate as a cotransmitter. To elucidate the behavioral role of the cotransmission, we targeted the glutamate-recycling enzyme glutaminase (geneGLS1). In mice with a DAT-driven conditional heterozygous (cHET) reduction of GLS1 in their dopamine neurons, dopamine neuron survival and transmission were unaffected, while glutamate cotransmission at phasic firing frequencies was reduced, enabling focusing the cotransmission. DAT GLS1 cHET mice showed normal emotional and motor behaviors, and an unaffected response to acute amphetamine. Strikingly, amphetamine sensitization was reduced and latent inhibition potentiated. These behavioral effects, also seen in global GLS1 HETs with a schizophrenia resilience phenotype, were not seen in mice with an Emx1-driven forebrain reduction affecting most brain glutamatergic neurons. Thus, a reduction in dopamine neuron glutamate cotransmission appears to mediate significant components of the GLS1 HET schizophrenia resilience phenotype, and glutamate cotransmission appears to be important in attribution of motivational salience.
Scaling of optogenetically evoked signaling in a higher-order corticocortical pathway in the anesthetized mouse
Authors: Li Xiaojian , Yamawaki Naoki , Barrett John M. , Körding Konrad P. , Shepherd Gordon M. G.
Published: June 2017

Quantitative analysis of corticocortical signaling is needed to understand and model information processing in cerebral networks. However, higher-order pathways, hodologically remote from sensory input, are not amenable to spatiotemporally precise activation by sensory stimuli. Here, we combined parametric channelrhodopsin-2 (ChR2) photostimulation with multi-unit electrophysiology to study corticocortical driving in a parietofrontal pathway from retrosplenial cortex (RSC) to posterior secondary motor cortex (M2) in micein vivo. Ketamine anesthesia was used both to eliminate complex activity associated with the awake state and to enable stable recordings of responses over a wide range of stimulus parameters. Photostimulation of ChR2-expressing neurons in RSC, the upstream area, produced local activity that decayed quickly. This activity in turn drove downstream activity in M2 that arrived rapidly (5-10 ms latencies), and scaled in amplitude across a wide range of stimulus parameters as an approximately constant fraction (~0.2) of the upstream activity. A model-based analysis could explain the corticocortically driven activity with exponentially decaying kernels (~20 ms time constant) and small delay. Reverse (antidromic) driving was similarly robust. The results show that corticocortical signaling in this pathway drives downstream activity rapidly and scalably, in a mostly linear manner. These properties, identified in anesthetized mice and represented in a simple model, suggest a robust basis for supporting complex non-linear dynamic activity in corticocortical circuits in the awake state.

SIGNIFICANCE STATEMENT

The signaling properties of corticocortical connections are not well understood, particularly for higher-order inter-areal pathways. Here, we developed a paradigm based on parametric optogenetic photostimulation, linear-array electrophysiology, and mathematical modeling to characterize signaling along corticortical connections linking retrosplenial cortex to posterior secondary motor cortex (M2) in anesthetized mice. The results indicate that corticocortically driven activity in the downstream area followed the optogenetically evoked upstream activity in a rapid and scalable manner, and could be described with a simple linear integrator model. These findings suggest that this pathway, when activated selectively in the unconscious state, supports intrinsically linear inter-areal communication.
Neurodegeneration-associated mutant TREM2 proteins abortively cycle between the ER and ER–Golgi intermediate compartment
Authors: Sirkis Daniel W. , Aparicio Renan E. , Schekman Randy
Published: June 2017

Triggering receptor expressed on myeloid cells 2 (TREM2) is a transmembrane protein expressed on microglia within the brain. Several rare mutations inTREM2cause an early-onset form of neurodegeneration when inherited homozygously. Here we investigate how these mutations affect the intracellular transport of TREM2. We find that most pathogenic TREM2 mutant proteins fail to undergo normal maturation in the Golgi complex and show markedly reduced cell surface expression. Prior research has suggested that two such mutants are retained in the endoplasmic reticulum (ER), but we find, using a cell-free COPII vesicle budding reaction, that mutant TREM2 is exported efficiently from the ER. In addition, mutant TREM2 becomes sensitive to cleavage by endoglycosidase D under conditions that inhibit recycling to the ER, indicating that it normally reaches a post-ER compartment. Maturation-defective TREM2 mutants are also efficiently bound by a lectin that recognizesO-glycans added in the ER–Golgi intermediate compartment (ERGIC) andcisGolgi cisterna. Finally, mutant TREM2 accumulates in the ERGIC in cells depleted of COPI. These results indicate that efficient ER export is not sufficient to enable normal cell surface expression of TREM2. Moreover, our findings suggest that the ERGIC may play an underappreciated role as a quality-control center for mutant and/or malformed membrane proteins.
Acquired bilateral telangiectasia macularis eruptiva perstans: A unique clinical feature of photodamaging rather than a subtype of cutaneous mastocytosis
Authors: Moon Hye‐Rim , Kim Young Jae , Jung Joon Min , Won Chong Hyun , Lee Mi Woo , Choi Jee Ho , Chang Sung Eun
Published: June 2017

Telangiectasia macularis eruptiva perstans (TMEP) is a rare subtype of cutaneous mastocytosis, characterized by telangiectatic tan to brown macules on the trunk and extremities. Although TMEP has been descried as an uncommon disease in the literature, we often encounter patients with TMEP lesions in the outpatient clinic. We aimed to assess the clinical and histopathological characteristics of acquired bilateral TMEP, and the pathophysiological mechanism of acquired bilateral TMEP among these patients. We retrospectively reviewed 30 patients (28 men and 2 women) with acquired bilateral TMEP; multiple telangiectatic dark red to brown macules that were symmetrically distributed. The clinical characteristics and general histopathological findings of lesional skin were investigated. The number of mast cells was evaluated using immunohistochemical analysis with an antibody directed against c‐kit (CD117). Acquired bilateral TMEP was predominantly localized on the sun‐exposed area: the upper arm in 30 patients (100%), forearm in 19 patients (63.3%) and anterior chest in 15 patients (50%). A total of 16 patients (53.3%) showed at least one aggravating factor, including UV irradiation, alcohol use and heat exposure. Compared with the mast cell numbers in 19 age‐ and biopsy site‐matched healthy controls (91 ± 29.0/mm2), the number of mast cells in the papillary dermal skin of acquired bilateral TMEP patients was significantly increased (159 ± 37.2/mm2, P < 0.01). In addition, a significant difference in vessel numbers in the papillary dermis was observed between acquired bilateral TMEP patients and healthy controls (10.5 ± 1.9 vs 5.4 ± 1.0/mm2, P < 0.01). Acquired bilateral TMEP is a relatively common disorder in middle‐aged Asian men. An increased number of mast cells and dilated vessels might be a photoaging‐related reactive process of chronic sun‐exposure, which consequently leads to the formation of characteristic telangiectatic hyperpigmentary macules through certain melanogenic mediators.
Field evidence for a rapid adaptive plastic response in morphology and growth of littoral and pelagic brook charr: A reciprocal transplant experiment
Authors: Pépino Marc , Magnan Pierre , Proulx Raphaël
Published: June 2017

Phenotypic plasticity, a process by which individuals modify their morphology, physiology, or behaviour in response to environmental changes, can be seen as the first step in adaptive evolution. Phenotypic plasticity is adaptive if two conditions are met: (1) the phenotype is associated with an environment (plastic response) and (2) the phenotype–environment association increases individual fitness (adaptive response).

Using a reciprocal transplant experiment, we tested the hypothesis that functional morphological responses are correlated with growth at two organizational levels (between and within ecotypes) in brook charr.

Four‐month‐old individuals from four littoral and four pelagic families raised in the laboratory were transferred into eight littoral (3 m × 4 m × 1.5 m depth) and eight pelagic (3 m × 4 m × 6 m depth) lake enclosures for a period of 12 weeks.

Fin length (the main discriminant trait of the littoral and pelagic ecotypes) was less plastic than body shape. Growth was higher in the pelagic than in the littoral habitat, but offspring from littoral and pelagic parental origins did not experience higher growth in their respective habitats (comparison between ecotypes). The body shape of most individuals transplanted to their reciprocal environment shifted toward the form expected in that environment. This plastic response in body shape was functionally correlated with growth within ecotypes, but only in the littoral habitat. Furthermore, the within‐ecotype variance of both morphological traits and growth were higher in the littoral than in the pelagic habitat.

Small phenotypic differences could have direct consequences on fitness in the less favourable habitat, inducing higher inter‐individual variance in growth and stronger phenotype–growth associations. We suggest that phenotypic accommodation and cryptic genetic variation, two mechanisms previously proposed as mechanisms involved in distinct situations, could be simultaneously involved to hasten the process of adaptive evolution in an unfavourable environment.

Aplain language summaryis available for this article.
Detecting elusive aspects of wildlife ecology using drones: New insights on the mating dynamics and operational sex ratios of sea turtles
Authors: Schofield Gail , Katselidis Kostas A. , Lilley Martin K. S. , Reina Richard D. , Hays Graeme C.
Published: June 2017

Offspring and breeding (operational) sex ratios (OSR) are a key component of demographic studies. While offspring sex ratios are often relatively easy to measure, measuring OSRs is often far more problematic. Yet, highly skewed OSRs, and a lack of male–female encounters, may be an important extinction driver.

Using loggerhead sea turtles (Caretta caretta) as a case study, we showed the utility of drones, i.e. unmanned aerial vehicles (UAVs), to distinguish adult males and females in a marine breeding area, using a combination of morphological characteristics (tail length) and behavioural differences (active mating, courting and searching by males versus resting by females). Through repeated surveys, we documented seasonal changes in the OSR.

While the number, and ratio, of males and females on the breeding grounds changed massively, the ratio of receptive females (derived from the rate of influx of new individuals to the area) to breeding males remained close to 1:1 for much of the period before nesting commenced. Hence, we show how large imbalances in the number of adult males and females may translate into relatively balanced OSRs.

Our results suggest that the departure of males from the breeding grounds is linked to a decline in female receptivity, with female sea turtles being known to store sperm to ensure high clutch fertility throughout the nesting season.

In conclusion, while we detected up to three times more females than males at the breeding ground, at present, OSRs appear stable. However, because most males breed annually (vs. biannually by females), there might only be c. 100 males in the adult population (i.e. adult sex ratio of 1:7.5), which might become further skewed under expected climate change scenarios; thus, we need to identify the minimum number of males required to prevent extinction. Finally, we highlight the use of UAVs for assessing the mating dynamics of other marine, terrestrial or avian species, in which adults might exhibit visually detectable differences, such as sexual dimorphism, external body characteristics or grouping tendencies.

A plain language summary is available for this article.
Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models
Authors: Olave Melisa , Avila Luciano J. , Sites Jack W. , Morando Mariana
Published: June 2017

Explanations for gene tree discordance with respect to a species tree are commonly attributed to deep coalescence (also known as incomplete lineage sorting [ILS]), as well as different evolutionary processes such as hybridization, horizontal gene transfer and gene duplication. Among these, deep coalescence is usually quantified as the number of extra linages and has been studied as the principal source of discordance among gene trees, while the other processes that could contribute to gene tree discordance have not been fully explored. This is an important issue for hybridization because interspecific gene flow is well documented and widespread across many plant and animal groups.

Here, we propose a new way to detect gene flow when ILS is present that evaluates the likelihood of different models with various levels of gene flow, by comparing the expected gene tree discordance, using the number of extra lineages. This approach consists of proposing a model, simulating a set of gene trees to infer a distribution of expected extra lineages given the model, and calculating a likelihood function by comparing the fit of the real gene trees to the simulated distribution. To count extra lineages, the gene tree is first reconciled within the species tree, and for a given species tree branch the number of gene lineages minus one is counted. We develop a set of r functions to parallelize software to allow simulations, and to compare hypotheses via a likelihood ratio test to evaluate the presence of gene flow when ILS is present, in a fast and simple way.

Our results show high accuracy under very challenging scenarios of high impact of ILS and low gene flow levels, even using a modest dataset of 5–10 loci and 5–10 individuals per species.

We present a powerful and fast method to detect hybridization in the presence of ILS. We discuss its advantage with large dataset (such as genomic scale), and also identifies possible issues that should be explored with more complex models in future studies.
Structural neuroimaging correlates of alcohol and cannabis use in adolescents and adults
Authors: Thayer Rachel E. , YorkWilliams Sophie , Karoly Hollis C. , Sabbineni Amithrupa , Ewing Sarah Feldstein , Bryan Angela D. , Hutchison Kent E.
Published: June 2017

Background and Aims

Chronic alcohol use is associated with lower gray matter volume, and we reported recently that alcohol use showed negative associations with widespread gray matter (GM) volume even among young adults. The current study aimed to test the strength of association between (1) alcohol use and GM volume; (2) alcohol use and white matter (WM) integrity; (3) cannabis use and GM volume; and (4) cannabis use and WM integrity among adults and adolescents.

Design and Setting

General linear models within large pooled cross‐sectional samples of adolescents and adults who had participated in studies collecting substance use and neuroimaging data in the southwestern United States.

Participants

The current analysis included adults aged 18–55 years (n = 853) and adolescents aged 14–18 years (n = 439) with a range of alcohol and cannabis use.

Measurements

The dependent variable was GM volume or WM integrity, with key predictors of alcohol use [Alcohol Use Disorders Identification Test (AUDIT) score] and cannabis use (past 30‐day use).

Findings

Alcohol use showed large clusters of negative associations (ηp2 = 0.028–0.145, P < 0.001) with GM volume among adults and to a lesser extent (one cluster; ηp2 = 0.070, P < 0.05) among adolescents. Large clusters showed significant associations (ηp2 = 0.050–0.124, P < 0.001) of higher alcohol use with poorer WM integrity, whereas adolescents showed no significant associations between alcohol use and WM. No associations were observed between structural measures and past 30‐day cannabis use in adults or adolescents.

Conclusions

Alcohol use severity is associated with widespread lower gray matter volume and white matter integrity in adults, and with lower gray matter volume in adolescents.
Inhibition of JNK signalling mediates PPARα‐dependent protection against intrahepatic cholestasis by fenofibrate
Authors: Dai Manyun , Yang Julin , Xie Minzhu , Lin Jiao , Luo Min , Hua Huiying , Xu Gangming , Lin Hante , Song Danjun , Cheng Yuqing , Guo Bin , Zhao Jinshun , Gonzalez Frank J , Liu Aiming
Published: June 2017

Background and Purpose

Fenofibrate, a PPARα agonist, is the most widely prescribed drug for treating hyperlipidaemia. Although fibrate drugs are reported to be beneficial for cholestasis, their underlying mechanism has not been determined.

Experimental Approach

Wild‐type mice and Pparα‐null mice were pretreated orally with fenofibrate for 3 days, following which α‐naphthylisothiocyanate (ANIT) was administered to induce cholestasis. The PPARα agonist WY14643 and JNK inhibitor SP600125 were used to determine the role of PPARα and the JNK pathway, respectively, in cholestatic liver injury. The same fenofibrate regimen was applied to investigate its beneficial effects on sclerosing cholangitis in a DDC‐induced cholestatic model.

Key Results

Fenofibrate, 25 mg·kg−1 twice a day, totally attenuated ANIT‐induced cholestasis and liver injury as indicated by biochemical and histological analyses. This protection occurred in wild‐type, but not in Pparα‐null, mice. Alterations in bile acid synthesis and transport were found to be an adaptive response rather than a direct effect of fenofibrate. WY14643 attenuated ANIT‐induced cholestasis and liver injury coincident with inhibition of JNK signalling. Although SP600125 did not affect cholestasis, it inhibited liver injury in the ANIT model when the dose of fenofibrate used was ineffective. Fenofibrate was also revealed to have a beneficial effect in the sclerosing cholangitis model.

Conclusions and Implications

These data suggest that the protective effects of fenofibrate against cholestasis‐induced hepatic injury are dependent on PPARα and fenofibrate dose, and are mediated through inhibition of JNK signalling. This mechanism of fenofibrate protection against intrahepatic cholestasis may offer additional therapeutic opportunities for cholestatic liver diseases.
WMJ‐8‐B, a novel hydroxamate derivative, induces MDA‐MB‐231 breast cancer cell death via the SHP‐1‐STAT3‐survivin cascade
Authors: Chuang Yu‐Fan , Huang Shiu‐Wen , Hsu Ya‐Fen , Yu Meng‐Chieh , Ou George , Huang Wei‐Jan , Hsu Ming‐Jen
Published: June 2017

Background and Purpose

Histone deacetylase (HDAC) inhibitors have been demonstrate to have broad‐spectrum anti‐tumour properties and have attracted lots of attention in the field of drug discovery. However, the underlying anti‐tumour mechanisms of HDAC inhibitors remain incompletely understood. In this study, we aimed to characterize the underlying mechanisms through which the novel hydroxamate‐based HDAC inhibitor, WMJ‐8‐B, induces the death of MDA‐MB‐231 breast cancer cells.

Experimental Approach

Effects of WMJ‐8‐B on cell viability, cell cycle distribution, apoptosis and signalling molecules were analysed by the MTT assay, flowcytometric analysis, immunoblotting, reporter assay, chromatin immunoprecipitation analysis and use of siRNAs. A xenograft model was used to determine anti‐tumour effects of WMJ‐8‐B in vivo.

Key Results

WMJ‐8‐B induced survivin reduction, G2/M cell cycle arrest and apoptosis in MDA‐MB‐231 cells. STAT3 phosphorylation, transactivity and its binding to the survivin promoter region were reduced in WMJ‐8‐B‐treated cells. WMJ‐8‐B activated the protein phosphatase SHP‐1 and when SHP‐1 signalling was blocked, the effects of WMJ‐8‐B on STAT3 phosphorylation and survivin levels were abolished. However, WMJ‐8‐B increased the transcription factor Sp1 binding to the p21 promoter region and enhanced p21 levels. Moreover, WMJ‐8‐B induced α‐tubulin acetylation and disrupted microtubule assembly. Inhibition of HDACs was shown to contribute to WMJ‐8‐B′s actions. Furthermore, WMJ‐8‐B suppressed the growth of MDA‐MB‐231 xenografts in mammary fat pads in vivo.

Conclusions and Implications

The SHP‐1‐STAT3‐survivin and Sp1‐p21 cascades are involved in WMJ‐8‐B‐induced MDA‐MB‐231 breast cancer cell death. These results also indicate the potential of WMJ‐8‐B as a lead compound for treatment of breast cancer and warrant its clinical development.