ALBERT

Beschreibung: Sources and Transformations of Anthropogenic Nitrogen along an Urban River-Estuarine Continuum Michael J. Pennino, Sujay S. Kaushal, Sudhir Murthy, Joel Blomquist, Jeff Cornwell, and Lora Harris Biogeosciences Discuss., doi:10.5194/bg-2016-264,2016 Manuscript under review for BG (discussion: open, 0 comments) The results of this manuscript report the analysis of the fate and transport of wastewater and anthropogenic nitrogen along the Potomac River Estuary, from Washington D.C. to the Chesapeake Bay. In conjunction with a mass balance approach, nitrate isotopes were used to estimate fluxes and trace the sources and transformations N along the estuary. This study shows that estuaries have a large capacity to transform N inputs, but with large seasonal variability due to hydrological extremes.

Beschreibung: by Eva R. M. Joosten, Shihab A. Shamma, Christian Lorenzi, Peter Neri Sound waveforms convey information largely via amplitude modulations (AM). A large body of experimental evidence has provided support for a modulation (bandpass) filterbank. Details of this model have varied over time partly reflecting different experimental conditions and diverse datasets from distinct task strategies, contributing uncertainty to the bandwidth measurements and leaving important issues unresolved. We adopt here a solely data-driven measurement approach in which we first demonstrate how different models can be subsumed within a common ‘cascade’ framework, and then proceed to characterize the cascade via system identification analysis using a single stimulus/task specification and hence stable task rules largely unconstrained by any model or parameters. Observers were required to detect a brief change in level superimposed onto random level changes that served as AM noise; the relationship between trial-by-trial noisy fluctuations and corresponding human responses enables targeted identification of distinct cascade elements. The resulting measurements exhibit a dynamic complex picture in which human perception of auditory modulations appears adaptive in nature, evolving from an initial lowpass to bandpass modes (with broad tuning, Q∼1) following repeated stimulus exposure.

Beschreibung: by Bihai Shi, Cui Zhang, Caihuan Tian, Jin Wang, Quan Wang, Tengfei Xu, Yan Xu, Carolyn Ohno, Robert Sablowski, Marcus G. Heisler, Klaus Theres, Ying Wang, Yuling Jiao Shoot branching requires the establishment of new meristems harboring stem cells; this phenomenon raises questions about the precise regulation of meristematic fate. In seed plants, these new meristems initiate in leaf axils to enable lateral shoot branching. Using live-cell imaging of leaf axil cells, we show that the initiation of axillary meristems requires a meristematic cell population continuously expressing the meristem marker SHOOT MERISTEMLESS ( STM ). The maintenance of STM expression depends on the leaf axil auxin minimum. Ectopic expression of STM is insufficient to activate axillary buds formation from plants that have lost leaf axil STM expressing cells. This suggests that some cells undergo irreversible commitment to a developmental fate. In more mature leaves, REVOLUTA ( REV ) directly up-regulates STM expression in leaf axil meristematic cells, but not in differentiated cells, to establish axillary meristems. Cell type-specific binding of REV to the STM region correlates with epigenetic modifications. Our data favor a threshold model for axillary meristem initiation, in which low levels of STM maintain meristematic competence and high levels of STM lead to meristem initiation.

Beschreibung: by Lauren A. Richardson Our first ever Open Highlights explores recent Open Access research into the complex relationship between host and pathogen during the course of an infection, and the factors that determine its eventual outcome.

Beschreibung: by Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph Analyses of metagenome data (MG) and metatranscriptome data (MT) are often challenged by a paucity of complete reference genome sequences and the uneven/low sequencing depth of the constituent organisms in the microbial community, which respectively limit the power of reference-based alignment and de novo sequence assembly. These limitations make accurate protein family classification and abundance estimation challenging, which in turn hamper downstream analyses such as abundance profiling of metabolic pathways, identification of differentially encoded/expressed genes, and de novo reconstruction of complete gene and protein sequences from the protein family of interest. The profile hidden Markov model (HMM) framework enables the construction of very useful probabilistic models for protein families that allow for accurate modeling of position specific matches, insertions, and deletions. We present a novel homology detection algorithm that integrates banded Viterbi algorithm for profile HMM parsing with an iterative simultaneous alignment and assembly computational framework. The algorithm searches a given profile HMM of a protein family against a database of fragmentary MG/MT sequencing data and simultaneously assembles complete or near-complete gene and protein sequences of the protein family. The resulting program, HMM-GRASPx, demonstrates superior performance in aligning and assembling homologs when benchmarked on both simulated marine MG and real human saliva MG datasets. On real supragingival plaque and stool MG datasets that were generated from healthy individuals, HMM-GRASPx accurately estimates the abundances of the antimicrobial resistance (AMR) gene families and enables accurate characterization of the resistome profiles of these microbial communities. For real human oral microbiome MT datasets, using the HMM-GRASPx estimated transcript abundances significantly improves detection of differentially expressed (DE) genes. Finally, HMM-GRASPx was used to reconstruct comprehensive sets of complete or near-complete protein and nucleotide sequences for the query protein families. HMM-GRASPx is freely available online from http://sourceforge.net/projects/hmm-graspx.

Beschreibung: by Dazhe Meng, Manu Dubin, Pei Zhang, Edward J. Osborne, Oliver Stegle, Richard M. Clark, Magnus Nordborg The extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis -methylation for hundreds of genes, and many of these associations remained significant after taking SNP effects into account. The pattern of correlations differed markedly between gene body methylation and transposable element methylation. The former was usually positively correlated with expression, and the latter usually negatively correlated, although exceptions were found in both cases. Finally, we developed graphical models of causality that adapt to a sample with heavy population structure, and used them to show that while methylation appears to affect gene expression more often than expression affects methylation, there is also strong support for both being independently controlled. In conclusion, although we find clear evidence for epigenetic regulation, both the number of loci affected and the magnitude of the effects appear to be small compared to the effect of SNPs.

Beschreibung: by Minghua Nie, Emily Arner, John Prudden, Lana Schaffer, Steven Head, Michael N. Boddy Posttranslational modifications (PTMs) provide dynamic regulation of the cellular proteome, which is critical for both normal cell growth and for orchestrating rapid responses to environmental stresses, e.g. genotoxins. Key PTMs include ubiquitin, the Small Ubiquitin-like MOdifier SUMO, and phosphorylation. Recently, SUMO-targeted ubiquitin ligases (STUbLs) were found to integrate signaling through the SUMO and ubiquitin pathways. In general, STUbLs are recruited to target proteins decorated with poly-SUMO chains to ubiquitinate them and drive either their extraction from protein complexes, and/or their degradation at the proteasome. In fission yeast, reducing or preventing the formation of SUMO chains can circumvent the essential and DNA damage response functions of STUbL. This result indicates that whilst some STUbL "targets" have been identified, the crucial function of STUbL is to antagonize SUMO chain formation. Herein, by screening for additional STUbL suppressors, we reveal crosstalk between the serine/threonine phosphatase PP2A-Pab1 B55 and the SUMO pathway. A hypomorphic Pab1 B55 mutant not only suppresses STUbL dysfunction, but also mitigates the phenotypes associated with deletion of the SUMO protease Ulp2, or mutation of the STUbL cofactor Rad60. Together, our results reveal a novel role for PP2A-Pab1 B55 in modulating SUMO pathway output, acting in parallel to known critical regulators of SUMOylation homeostasis. Given the broad evolutionary functional conservation of the PP2A and SUMO pathways, our results could be relevant to the ongoing attempts to therapeutically target these factors.

Beschreibung: by Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction tasks using quantitative microbiome profiles, including species-level relative abundances and presence of strain-specific markers. A comprehensive meta-analysis, with particular emphasis on generalization across cohorts, was performed in a collection of 2424 publicly available metagenomic samples from eight large-scale studies. Cross-validation revealed good disease-prediction capabilities, which were in general improved by feature selection and use of strain-specific markers instead of species-level taxonomic abundance. In cross-study analysis, models transferred between studies were in some cases less accurate than models tested by within-study cross-validation. Interestingly, the addition of healthy (control) samples from other studies to training sets improved disease prediction capabilities. Some microbial species (most notably Streptococcus anginosus ) seem to characterize general dysbiotic states of the microbiome rather than connections with a specific disease. Our results in modelling features of the “healthy” microbiome can be considered a first step toward defining general microbial dysbiosis. The software framework, microbiome profiles, and metadata for thousands of samples are publicly available at http://segatalab.cibio.unitn.it/tools/metaml.

Beschreibung: by Zhenyu Yuan, Heiko Praxenthaler, Nassif Tabaja, Rubben Torella, Anette Preiss, Dieter Maier, Rhett A. Kovall Notch is a conserved signaling pathway that specifies cell fates in metazoans. Receptor-ligand interactions induce changes in gene expression, which is regulated by the transcription factor CBF1/Su(H)/Lag-1 (CSL). CSL interacts with coregulators to repress and activate transcription from Notch target genes. While the molecular details of the activator complex are relatively well understood, the structure-function of CSL-mediated repressor complexes is poorly defined. In Drosophila , the antagonist Hairless directly binds Su(H) (the fly CSL ortholog) to repress transcription from Notch targets. Here, we determine the X-ray structure of the Su(H)-Hairless complex bound to DNA. Hairless binding produces a large conformational change in Su(H) by interacting with residues in the hydrophobic core of Su(H), illustrating the structural plasticity of CSL molecules to interact with different binding partners. Based on the structure, we designed mutants in Hairless and Su(H) that affect binding, but do not affect formation of the activator complex. These mutants were validated in vitro by isothermal titration calorimetry and yeast two- and three-hybrid assays. Moreover, these mutants allowed us to solely characterize the repressor function of Su(H) in vivo.

Beschreibung: by Mario Novkovic, Lucas Onder, Jovana Cupovic, Jun Abe, David Bomze, Viviana Cremasco, Elke Scandella, Jens V. Stein, Gennady Bocharov, Shannon J. Turley, Burkhard Ludewig Fibroblastic reticular cells (FRCs) form the cellular scaffold of lymph nodes (LNs) and establish distinct microenvironmental niches to provide key molecules that drive innate and adaptive immune responses and control immune regulatory processes. Here, we have used a graph theory-based systems biology approach to determine topological properties and robustness of the LN FRC network in mice. We found that the FRC network exhibits an imprinted small-world topology that is fully regenerated within 4 wk after complete FRC ablation. Moreover, in silico perturbation analysis and in vivo validation revealed that LNs can tolerate a loss of approximately 50% of their FRCs without substantial impairment of immune cell recruitment, intranodal T cell migration, and dendritic cell-mediated activation of antiviral CD8 + T cells. Overall, our study reveals the high topological robustness of the FRC network and the critical role of the network integrity for the activation of adaptive immune responses.

Beschreibung: by Jose L. Herrera, Ravi Srinivasan, John S. Brownstein, Alison P. Galvani, Lauren Ancel Meyers As infectious disease surveillance systems expand to include digital, crowd-sourced, and social network data, public health agencies are gaining unprecedented access to high-resolution data and have an opportunity to selectively monitor informative individuals. Contact networks, which are the webs of interaction through which diseases spread, determine whether and when individuals become infected, and thus who might serve as early and accurate surveillance sensors. Here, we evaluate three strategies for selecting sensors—sampling the most connected, random, and friends of random individuals—in three complex social networks—a simple scale-free network, an empirical Venezuelan college student network, and an empirical Montreal wireless hotspot usage network. Across five different surveillance goals—early and accurate detection of epidemic emergence and peak, and general situational awareness—we find that the optimal choice of sensors depends on the public health goal, the underlying network and the reproduction number of the disease ( R 0 ). For diseases with a low R 0 , the most connected individuals provide the earliest and most accurate information about both the onset and peak of an outbreak. However, identifying network hubs is often impractical, and they can be misleading if monitored for general situational awareness, if the underlying network has significant community structure, or if R 0 is high or unknown. Taking a theoretical approach, we also derive the optimal surveillance system for early outbreak detection but find that real-world identification of such sensors would be nearly impossible. By contrast, the friends-of-random strategy offers a more practical and robust alternative. It can be readily implemented without prior knowledge of the network, and by identifying sensors with higher than average, but not the highest, epidemiological risk, it provides reasonably early and accurate information.

Beschreibung: by Liying Guan, Xuehua Ma, Jingyan Zhang, Jia-Jia Liu, Yingchun Wang, Mei Ding Eukaryotic cells extend a variety of surface protrusions to direct cell motility. Formation of protrusions is mediated by coordinated actions between the plasma membrane and the underlying actin cytoskeleton. Here, we found that the single calponin homology (CH) domain-containing protein CHDP-1 induces the formation of cell protrusions in C . elegans . CHDP-1 is anchored to the cortex through its amphipathic helix. CHDP-1 associates through its CH domain with the small GTPase Rac1/CED-10, which is a key regulator of the actin cytoskeleton. CHDP-1 preferentially binds to the GTP-bound active form of the CED-10 protein and preserves the membrane localization of GTP-CED-10. Hence, by coupling membrane expansion to Rac1-mediated actin dynamics, CHDP-1 promotes the formation of cellular protrusions in vivo .

Beschreibung: by Masashi Naito, Masaki Mori, Masayo Inagawa, Kohei Miyata, Naohiro Hashimoto, Sakae Tanaka, Hiroshi Asahara Cell differentiation status is defined by the gene expression profile, which is coordinately controlled by epigenetic mechanisms. Cell type-specific DNA methylation patterns are established by chromatin modifiers including de novo DNA methyltransferases, such as Dnmt3a and Dnmt3b . Since the discovery of the myogenic master gene MyoD , myogenic differentiation has been utilized as a model system to study tissue differentiation. Although knowledge about myogenic gene networks is accumulating, there is only a limited understanding of how DNA methylation controls the myogenic gene program. With an aim to elucidate the role of DNA methylation in muscle development and regeneration, we investigate the consequences of mutating Dnmt3a in muscle precursor cells in mice. Pax3 promoter-driven Dnmt3a -conditional knockout (cKO) mice exhibit decreased organ mass in the skeletal muscles, and attenuated regeneration after cardiotoxin-induced muscle injury. In addition, Dnmt3a -null satellite cells (SCs) exhibit a striking loss of proliferation in culture. Transcriptome analysis reveals dysregulated expression of p57Kip2 , a member of the Cip/Kip family of cyclin-dependent kinase inhibitors (CDKIs), in the Dnmt3a -KO SCs. Moreover, RNAi-mediated depletion of p57Kip2 replenishes the proliferation activity of the SCs, thus establishing a role for the Dnmt3a - p57Kip2 axis in the regulation of SC proliferation. Consistent with these findings, Dnmt3a -cKO muscles exhibit fewer Pax7 + SCs, which show increased expression of p57Kip2 protein. Thus, Dnmt3a is found to maintain muscle homeostasis by epigenetically regulating the proliferation of SCs through p57Kip2 .

Beschreibung: by William Zerges

Beschreibung: Contrasting radiation and soil heat fluxes in Arctic shrub and wet sedge tundra Inge Juszak, Werner Eugster, Monique M. P. D. Heijmans, and Gabriela Schaepman-Strub Biogeosciences, 13, 4049-4064, doi:10.1594/PANGAEA.860561, 2016 Changes in Arctic vegetation composition and structure feed back to climate and permafrost. Using field observations at a Siberian tundra site, we find that dwarf shrubs absorb more solar radiation than wet sedges and thus amplify surface warming, especially during snow melt. On the other hand, permafrost thaw was enhanced below sedges as a consequence of high soil moisture. Standing dead sedge leaves affected the radiation budget strongly and deserve more scientific attention.

Beschreibung: Publication date: 19 July 2016 Source: Cell Reports, Volume 16, Issue 3 Author(s): Sandra Malmgren Hill, Xinxin Hao, Johan Grönvall, Stephanie Spikings-Nordby, Per O. Widlund, Triana Amen, Anna Jörhov, Rebecca Josefson, Daniel Kaganovich, Beidong Liu, Thomas Nyström Age can be reset during mitosis in both yeast and stem cells to generate a young daughter cell from an aged and deteriorated one. This phenomenon requires asymmetry-generating genes (AGGs) that govern the asymmetrical inheritance of aggregated proteins. Using a genome-wide imaging screen to identify AGGs in Saccharomyces cerevisiae , we discovered a previously unknown role for endocytosis, vacuole fusion, and the myosin-dependent adaptor protein Vac17 in asymmetrical inheritance of misfolded proteins. Overproduction of Vac17 increases deposition of aggregates into cytoprotective vacuole-associated sites, counteracts age-related breakdown of endocytosis and vacuole integrity, and extends replicative lifespan. The link between damage asymmetry and vesicle trafficking can be explained by a direct interaction between aggregates and vesicles. We also show that the protein disaggregase Hsp104 interacts physically with endocytic vesicle-associated proteins, such as the dynamin-like protein, Vps1, which was also shown to be required for Vac17-dependent sequestration of protein aggregates. These data demonstrate that two physiognomies of aging—reduced endocytosis and protein aggregation—are interconnected and regulated by Vac17. Graphical abstract Teaser Cellular rejuvenation is enabled by asymmetrical inheritance of damaged proteins. Using a genome-wide imaging screen to identify asymmetry-generating genes, Hill et al. demonstrate a role for vesicle trafficking, membrane fusion, and the myosin-dependent adaptor protein Vac17 in the asymmetric inheritance of misfolded proteins and consequently in the regulation of lifespan.

Beschreibung: by Hunter R. Underhill, Jacob O. Kitzman, Sabine Hellwig, Noah C. Welker, Riza Daza, Daniel N. Baker, Keith M. Gligorich, Robert C. Rostomily, Mary P. Bronner, Jay Shendure Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA) may afford the opportunity to diagnose, monitor recurrence, and evaluate response to therapy solely through a non-invasive blood draw. However, detecting ctDNA against the normally occurring background of cell-free DNA derived from healthy cells has proven challenging, particularly in non-metastatic solid tumors. In this study, distinct differences in fragment length size between ctDNAs and normal cell-free DNA are defined. Human ctDNA in rat plasma derived from human glioblastoma multiforme stem-like cells in the rat brain and human hepatocellular carcinoma in the rat flank were found to have a shorter principal fragment length than the background rat cell-free DNA (134–144 bp vs. 167 bp, respectively). Subsequently, a similar shift in the fragment length of ctDNA in humans with melanoma and lung cancer was identified compared to healthy controls. Comparison of fragment lengths from cell-free DNA between a melanoma patient and healthy controls found that the BRAF V600E mutant allele occurred more commonly at a shorter fragment length than the fragment length of the wild-type allele (132–145 bp vs. 165 bp, respectively). Moreover, size-selecting for shorter cell-free DNA fragment lengths substantially increased the EGFR T790M mutant allele frequency in human lung cancer. These findings provide compelling evidence that experimental or bioinformatic isolation of a specific subset of fragment lengths from cell-free DNA may improve detection of ctDNA.

Beschreibung: Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico) Estelle Couradeau, Daniel Roush, Brandon Scott Guida, and Ferran Garcia-Pichel Biogeosciences Discuss., doi:10.5194/bg-2016-254,2016 Manuscript under review for BG (discussion: open, 0 comments) Endolithic (inside rock) microbial communities are dominated by cyanobacteria, among which the true boring cyanobacteria actively perforate the mineral and play a significant role in the erosion of coastal outcrops that may increase with ocean acidification. We interrogated the microbial communities associated with various intertidal substrates of Mona Island (PR) and brought the first evidence that there exists a mineralogical substrate preference among the pioneers true boring cyanobacteria.

Beschreibung: Publication date: July 2016 Source: Global Ecology and Conservation, Volume 7 Author(s): Lina Mtwana Nordlund How do you, as a university lecturer, change from teacher-centered teaching to a more student-centered, active teaching? This paper aims to inspire you to make a change, big or small, to increase your students’ engagement and learning, by presenting suggestions on what you can do. The ideas and suggestions synthesized here are based on several different teaching philosophies and methods, which are well tested and shown to be effective in the right setting. The selection of suggestions is believed to be specifically suitable for ecology. The paper includes suggestions on how to plan a course or a lecture by setting a good learning environment. Both pre-lecture activities and during lecture activities are included, with a focus on activities to engage students and encourage increased discussion and reflections, as well as what to think about when choosing learning activities and how and why it is important to teach students to think and act like professionals in ecology. While changing teaching methods takes investment of time, time that is limited for many researchers, even small changes in your teaching can make big differences in learning, and the investment will hopefully pay back by making teaching more fun and rewarding. The suggestions presented are understandable without being be conversant in the ‘education literature’, but will provide you with a vocabulary of teaching activities that will be useful if you are inspired to find more information and learn more about teaching.

Beschreibung: by Michal Cagalinec, Mailis Liiv, Zuzana Hodurova, Miriam Ann Hickey, Annika Vaarmann, Merle Mandel, Akbar Zeb, Vinay Choubey, Malle Kuum, Dzhamilja Safiulina, Eero Vasar, Vladimir Veksler, Allen Kaasik Deficiency of the protein Wolfram syndrome 1 (WFS1) is associated with multiple neurological and psychiatric abnormalities similar to those observed in pathologies showing alterations in mitochondrial dynamics. The aim of this study was to examine the hypothesis that WFS1 deficiency affects neuronal function via mitochondrial abnormalities. We show that down-regulation of WFS1 in neurons leads to dramatic changes in mitochondrial dynamics (inhibited mitochondrial fusion, altered mitochondrial trafficking, and augmented mitophagy), delaying neuronal development. WFS1 deficiency induces endoplasmic reticulum (ER) stress, leading to inositol 1,4,5-trisphosphate receptor (IP 3 R) dysfunction and disturbed cytosolic Ca 2+ homeostasis, which, in turn, alters mitochondrial dynamics. Importantly, ER stress, impaired Ca 2+ homeostasis, altered mitochondrial dynamics, and delayed neuronal development are causatively related events because interventions at all these levels improved the downstream processes. Our data shed light on the mechanisms of neuronal abnormalities in Wolfram syndrome and point out potential therapeutic targets. This work may have broader implications for understanding the role of mitochondrial dynamics in neuropsychiatric diseases.

Beschreibung: by Takahiro Ezaki, Yutaka Horita, Masanori Takezawa, Naoki Masuda Direct reciprocity, or repeated interaction, is a main mechanism to sustain cooperation under social dilemmas involving two individuals. For larger groups and networks, which are probably more relevant to understanding and engineering our society, experiments employing repeated multiplayer social dilemma games have suggested that humans often show conditional cooperation behavior and its moody variant. Mechanisms underlying these behaviors largely remain unclear. Here we provide a proximate account for this behavior by showing that individuals adopting a type of reinforcement learning, called aspiration learning, phenomenologically behave as conditional cooperator. By definition, individuals are satisfied if and only if the obtained payoff is larger than a fixed aspiration level. They reinforce actions that have resulted in satisfactory outcomes and anti-reinforce those yielding unsatisfactory outcomes. The results obtained in the present study are general in that they explain extant experimental results obtained for both so-called moody and non-moody conditional cooperation, prisoner’s dilemma and public goods games, and well-mixed groups and networks. Different from the previous theory, individuals are assumed to have no access to information about what other individuals are doing such that they cannot explicitly use conditional cooperation rules. In this sense, myopic aspiration learning in which the unconditional propensity of cooperation is modulated in every discrete time step explains conditional behavior of humans. Aspiration learners showing (moody) conditional cooperation obeyed a noisy GRIM-like strategy. This is different from the Pavlov, a reinforcement learning strategy promoting mutual cooperation in two-player situations.

Beschreibung: by Megan H. Brewer, Rabia Chaudhry, Jessica Qi, Aditi Kidambi, Alexander P. Drew, Manoj P. Menezes, Monique M. Ryan, Michelle A. Farrar, David Mowat, Gopinath M. Subramanian, Helen K. Young, Stephan Zuchner, Stephen W. Reddel, Garth A. Nicholson, Marina L. Kennerson With the advent of whole exome sequencing, cases where no pathogenic coding mutations can be found are increasingly being observed in many diseases. In two large, distantly-related families that mapped to the Charcot-Marie-Tooth neuropathy CMTX3 locus at chromosome Xq26.3-q27.3, all coding mutations were excluded. Using whole genome sequencing we found a large DNA interchromosomal insertion within the CMTX3 locus. The 78 kb insertion originates from chromosome 8q24.3, segregates fully with the disease in the two families, and is absent from the general population as well as 627 neurologically normal chromosomes from in-house controls. Large insertions into chromosome Xq27.1 are known to cause a range of diseases and this is the first neuropathy phenotype caused by an interchromosomal insertion at this locus. The CMTX3 insertion represents an understudied pathogenic structural variation mechanism for inherited peripheral neuropathies. Our finding highlights the importance of considering all structural variation types when studying unsolved inherited peripheral neuropathy cases with no pathogenic coding mutations.

Beschreibung: by Julio C. Morales, Patricia Richard, Praveen L. Patidar, Edward A. Motea, Tuyen T. Dang, James L. Manley, David A. Boothman XRN2 is a 5’-3’ exoribonuclease implicated in transcription termination. Here we demonstrate an unexpected role for XRN2 in the DNA damage response involving resolution of R-loop structures and prevention of DNA double-strand breaks (DSBs). We show that XRN2 undergoes DNA damage-inducible nuclear re-localization, co-localizing with 53BP1 and R loops, in a transcription and R-loop-dependent process. XRN2 loss leads to increased R loops, genomic instability, replication stress, DSBs and hypersensitivity of cells to various DNA damaging agents. We demonstrate that the DSBs that arise with XRN2 loss occur at transcriptional pause sites. XRN2-deficient cells also exhibited an R-loop- and transcription-dependent delay in DSB repair after ionizing radiation, suggesting a novel role for XRN2 in R-loop resolution, suppression of replication stress, and maintenance of genomic stability. Our study highlights the importance of regulating transcription-related activities as a critical component in maintaining genetic stability.

Beschreibung: by Sahar Kassem, Guillaume Gaud, Isabelle Bernard, Mehdi Benamar, Anne S. Dejean, Roland Liblau, Gilbert J. Fournié, Céline Colacios, Bernard Malissen, Abdelhadi Saoudi The guanine nucleotide exchange factor Vav1 is essential for transducing T cell antigen receptor signals and therefore plays an important role in T cell development and activation. Our previous genetic studies identified a locus on rat chromosome 9 that controls the susceptibility to neuroinflammation and contains a non-synonymous polymorphism in the major candidate gene Vav1 . To formally demonstrate the causal implication of this polymorphism, we generated a knock-in mouse bearing this polymorphism (Vav1 R63W ). Using this model, we show that Vav1 R63W mice display reduced susceptibility to experimental autoimmune encephalomyelitis (EAE) induced by MOG 35-55 peptide immunization. This is associated with a lower production of effector cytokines (IFN-γ, IL-17 and GM-CSF) by autoreactive CD4 T cells. Despite increased proportion of Foxp3+ regulatory T cells in Vav1 R63W mice, we show that this lowered cytokine production is intrinsic to effector CD4 T cells and that Treg depletion has no impact on EAE development. Finally, we provide a mechanism for the above phenotype by showing that the Vav1 R63W variant has normal enzymatic activity but reduced adaptor functions. Together, these data highlight the importance of Vav1 adaptor functions in the production of inflammatory cytokines by effector T cells and in the susceptibility to neuroinflammation.

Beschreibung: by Takeshi Matsui, Ian M. Ehrenreich How combinations of gene-environment interactions collectively give rise to genotype-environment interactions is not fully understood. To shed light on this problem, we genetically dissected an environment-specific poor growth phenotype in a cross of two budding yeast strains. This phenotype is detectable when certain segregants are grown on ethanol at 37°C (‘E37’), a condition that differs from the standard culturing environment in both its carbon source (ethanol as opposed to glucose) and temperature (37°C as opposed to 30°C). Using recurrent backcrossing with phenotypic selection, we identified 16 contributing loci. To examine how these loci interact with each other and the environment, we focused on a subset of four loci that together can lead to poor growth in E37. We measured the growth of all 16 haploid combinations of alleles at these loci in all four possible combinations of carbon source (ethanol or glucose) and temperature (30 or 37°C) in a nearly isogenic population. This revealed that the four loci act in an almost entirely additive manner in E37. However, we also found that these loci have weaker effects when only carbon source or temperature is altered, suggesting that their effect magnitudes depend on the severity of environmental perturbation. Consistent with such a possibility, cloning of three causal genes identified factors that have unrelated functions in stress response. Thus, our results indicate that polymorphisms in stress response can show effects that are intensified by environmental stress, thereby resulting in major genotype-environment interactions when multiple of these variants co-occur.

Beschreibung: Anaerobic methane oxidation in an East African great lake (Lake Kivu) Fleur A. E. Roland, François Darchambeau, Cédric Morana, Sean A. Crowe, Bo Thamdrup, and Alberto V. Borges Biogeosciences Discuss., doi:10.5194/bg-2016-300,2016 Manuscript under review for BG (discussion: open, 0 comments) We studied methane consumption in a tropical Great Lake (Lake Kivu, East Africa). Lake Kivu has huge methane concentrations in its deep anoxic waters, but is a very poor emitter of methane to the atmosphere, which suppose a strong methane consumption in the water column. During this study, we put in evidence high aerobic and anaerobic consumption rates, whose relative importance varied with the season (higher aerobic rates in dry season, when the oxic compartment is wider).

Beschreibung: by Samantha B. Shelton, Calder Reinsborough, Blerta Xhemalce RNA levels are widely thought to be predictive of RNA function. However, the existence of more than a hundred chemically distinct modifications of RNA alone is a major indication that these moieties may impart distinct functions to subgroups of RNA molecules that share a primary sequence but display distinct RNA “epigenetic” marks. RNAs can be modified on many sites, including 5′ and 3′ ends, the sugar phosphate backbone, or internal bases, which collectively provide many opportunities for posttranscriptional regulation through a variety of mechanisms. Here, we will focus on how modifications on messenger and microRNAs may affect the process of RNA interference in mammalian cells. We believe that taking RNA modifications into account will not only advance our understanding of this crucial pathway in disease and cancer but will also open the path to exploiting the enzymes that “write” and “erase” them as targets for therapeutic drug development.

Beschreibung: by Armita Nourmohammad, Jakub Otwinowski, Joshua B. Plotkin The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an evolutionary arms race. Here we introduce a mathematical framework to study the coevolutionary dynamics between antibodies and antigens within a host. We focus on changes in the binding interactions between the antibody and antigen populations, which result from the underlying stochastic evolution of genotype frequencies driven by mutation, selection, and drift. We identify the critical viral and immune parameters that determine the distribution of antibody-antigen binding affinities. We also identify definitive signatures of coevolution that measure the reciprocal response between antibodies and viruses, and we introduce experimentally measurable quantities that quantify the extent of adaptation during continual coevolution of the two opposing populations. Using this analytical framework, we infer rates of viral and immune adaptation based on time-shifted neutralization assays in two HIV-infected patients. Finally, we analyze competition between clonal lineages of antibodies and characterize the fate of a given lineage in terms of the state of the antibody and viral populations. In particular, we derive the conditions that favor the emergence of broadly neutralizing antibodies, which may have relevance to vaccine design against HIV.

Beschreibung: by Carole H. Sellem, Jean-Paul di Rago, Jean-Paul Lasserre, Sharon H. Ackerman, Annie Sainsard-Chanet Most of the ATP in living cells is produced by an F-type ATP synthase. This enzyme uses the energy of a transmembrane electrochemical proton gradient to synthesize ATP from ADP and inorganic phosphate. Proton movements across the membrane domain (F O ) of the ATP synthase drive the rotation of a ring of 8–15 c -subunits, which induces conformational changes in the catalytic part (F 1 ) of the enzyme that ultimately promote ATP synthesis. Two paralogous nuclear genes, called Atp9-5 and Atp9-7 , encode structurally different c -subunits in the filamentous fungus Podospora anserina . We have in this study identified differences in the expression pattern for the two genes that correlate with the mitotic activity of cells in vegetative mycelia: Atp9-7 is transcriptionally active in non-proliferating (stationary) cells while Atp9-5 is expressed in the cells at the extremity (apex) of filaments that divide and are responsible for mycelium growth. When active, the Atp9-5 gene sustains a much higher rate of c -subunit synthesis than Atp9-7 . We further show that the ATP9-7 and ATP9-5 proteins have antagonist effects on the longevity of P . anserina . Finally, we provide evidence that the ATP9-5 protein sustains a higher rate of mitochondrial ATP synthesis and yield in ATP molecules per electron transferred to oxygen than the c -subunit encoded by Atp9-7 . These findings reveal that the c -subunit genes play a key role in the modulation of ATP synthase production and activity along the life cycle of P . anserina . Such a degree of sophistication for regulating aerobic energy metabolism has not been described before.

Beschreibung: by Aaron David Goldman, Laura F. Landweber The genome is often described as the information repository of an organism. Whether millions or billions of letters of DNA, its transmission across generations confers the principal medium for inheritance of organismal traits. Several emerging areas of research demonstrate that this definition is an oversimplification. Here, we explore ways in which a deeper understanding of genomic diversity and cell physiology is challenging the concepts of physical permanence attached to the genome as well as its role as the sole information source for an organism.

Beschreibung: Coastal-ocean uptake of anthropogenic carbon Timothée Bourgeois, James C. Orr, Laure Resplandy, Jens Terhaar, Christian Ethé, Marion Gehlen, and Laurent Bopp Biogeosciences, 13, 4167-4185, doi:10.5194/bg-13-4167-2016, 2016 The global coastal ocean took up 0.1 Pg C yr −1 of anthropogenic carbon during 1993–2012 based on new biogeochemical simulations with an eddying 3-D global model. That is about half of the most recent estimate, an extrapolation based on surface areas. It should not be confused with the continental shelf pump, perhaps 10 times larger, which includes natural as well as anthropogenic carbon. Coastal uptake of anthropogenic carbon is limited by its offshore transport.

Beschreibung: Anthropogenically induced environmental changes in the northeastern Adriatic Sea in the last 400 years (Panzano Bay, Gulf of Trieste) Jelena Vidović, Rafał Nawrot, Ivo Gallmetzer, Alexandra Haselmair, Adam Tomašových, Michael Stachowitsch, Vlasta Ćosović, and Martin Zuschin Biogeosciences Discuss., doi:10.5194/bg-2016-273,2016 Manuscript under review for BG (discussion: open, 0 comments) Shallow and sheltered marine embayments in urbanized areas are prone to the accumulation of pollutants, but little is known about the historical baselines of such marine ecosystems. Here we study foraminiferal assemblages, geochemical proxies and sedimentological data from 1.6 m long sediment cores to uncover ~ 400 years of anthropogenic pressure from mining, port and industrial zones in the Gulf of Trieste, Italy. From 1600 to 1900 AD, element concentrations and foraminiferal assemblages point to negligible effects of agricultural activities. The only significant anthropogenic activity during this period is mercury mining in the hinterlands of the gulf, releasing high amounts of mercury into the bay and significantly exceeding today's Italian sediment quality guidelines (SQG) and the standards on the effects of trace elements to benthic organisms (ERL and ERM). Nonetheless, the fluctuations in the concentrations of mercury do not correlate with changes in the composition and diversity of foraminiferal assemblages due to its nonbioavailability. Intensified agricultural and maricultural activities in the first half of the 20th century caused slight nutrient enrichment and a minor increase in foraminiferal diversity. Intensified port and industrial activities in the second half of 20th century increased the normalised trace element concentrations and persistent organic pollutants (PAH, PCB) in the topmost part of the core, with solely Ni exceeding Italian SQG, ERL and ERM. This increase caused only minor changes in the foraminiferal community because foraminifera in Panzano Bay have a long history of adaptation to naturally elevated trace element concentrations. Our study underlines the importance of using an integrated, multidisciplinary approach in reconstructing the history of environmental and anthropogenic changes in marine systems. Given the prolonged human impacts in coastal areas like the Gulf of Trieste, such long term baseline data are crucial for interpreting the present state of marine ecosystems.

Beschreibung: Mechanisms of Trichodesmium demise within the New Caledonian lagoon during the VAHINE mesocosm experiment Dina Spungin, Ulrike Pfreundt, Hugo Berthelot, Sophie Bonnet, Dina AlRoumi, Frank Natale, Wolfgang R. Hess, Kay D. Bidle, and Ilana Berman-Frank Biogeosciences, 13, 4187-4203, doi:10.5194/bg-13-4187-2016, 2016 The marine cyanobacterium Trichodesmium spp. forms massive blooms important to carbon and nitrogen cycling in the oceans that often collapse abruptly. We investigated a Trichodesmium bloom in the lagoon waters of New Caledonia to specifically elucidate the cellular processes mediating the bloom decline. We demonstrate physiological, biochemical, and genetic evidence for nutrient and oxidative stress that induced a genetically controlled programmed cell death (PCD) pathway leading to bloom demise.

Beschreibung: Spring phytoplankton communities of the Labrador Sea (2005–2014): pigment signatures, photophysiology and elemental ratios Glaucia M. Fragoso, Alex J. Poulton, Igor M. Yashayaev, Erica J. H. Head, and Duncan A. Purdie Biogeosciences Discuss., doi:10.5194/bg-2016-295,2016 Manuscript under review for BG (discussion: open, 0 comments) This research describes a detailed analysis of current distributions of spring phytoplankton communities in the Labrador Sea based on ten years of observations. Phytoplankton community composition varied mainly according to the contrasting hydrographical zones of the Labrador Sea. The taxonomic distinctions of these communities influenced the photosynthetic and biochemical signatures of near surface waters, which may have a profound impact on the carbon cycle in high latitude seas.

Beschreibung: by Justin T. Page, Zach S. Liechty, Rich H. Alexander, Kimberly Clemons, Amanda M. Hulse-Kemp, Hamid Ashrafi, Allen Van Deynze, David M. Stelly, Joshua A. Udall

Beschreibung: by Barbara A. Fox, Kiah L. Sanders, Leah M. Rommereim, Rebekah B. Guevara, David J. Bzik Nonreplicating type I uracil auxotrophic mutants of Toxoplasma gondii possess a potent ability to activate therapeutic immunity to established solid tumors by reversing immune suppression in the tumor microenvironment. Here we engineered targeted deletions of parasite secreted effector proteins using a genetically tractable Δ ku80 vaccine strain to show that the secretion of specific rhoptry (ROP) and dense granule (GRA) proteins by uracil auxotrophic mutants of T . gondii in conjunction with host cell invasion activates antitumor immunity through host responses involving CD8α + dendritic cells, the IL-12/interferon-gamma (IFN-γ) T H 1 axis, as well as CD4 + and CD8 + T cells. Deletion of parasitophorous vacuole membrane (PVM) associated proteins ROP5, ROP17, ROP18, ROP35 or ROP38, intravacuolar network associated dense granule proteins GRA2 or GRA12, and GRA24 which traffics past the PVM to the host cell nucleus severely abrogated the antitumor response. In contrast, deletion of other secreted effector molecules such as GRA15, GRA16, or ROP16 that manipulate host cell signaling and transcriptional pathways, or deletion of PVM associated ROP21 or GRA3 molecules did not affect the antitumor activity. Association of ROP18 with the PVM was found to be essential for the development of the antitumor responses. Surprisingly, the ROP18 kinase activity required for resistance to IFN-γ activated host innate immunity related GTPases and virulence was not essential for the antitumor response. These data show that PVM functions of parasite secreted effector molecules, including ROP18, manipulate host cell responses through ROP18 kinase virulence independent mechanisms to activate potent antitumor responses. Our results demonstrate that PVM associated rhoptry effector proteins secreted prior to host cell invasion and dense granule effector proteins localized to the intravacuolar network and host nucleus that are secreted after host cell invasion coordinately control the development of host immune responses that provide effective antitumor immunity against established ovarian cancer.

Beschreibung: by Joshua Mayourian, Ruben M. Savizky, Eric A. Sobie, Kevin D. Costa Human mesenchymal stem cell (hMSC) delivery has demonstrated promise in preclinical and clinical trials for myocardial infarction therapy; however, broad acceptance is hindered by limited understanding of hMSC-human cardiomyocyte (hCM) interactions. To better understand the electrophysiological consequences of direct heterocellular connections between hMSCs and hCMs, three original mathematical models were developed, representing an experimentally verified triad of hMSC families with distinct functional ion channel currents. The arrhythmogenic risk of such direct electrical interactions in the setting of healthy adult myocardium was predicted by coupling and fusing these hMSC models to the published ten Tusscher midcardial hCM model. Substantial variations in action potential waveform—such as decreased action potential duration (APD) and plateau height—were found when hCMs were coupled to the two hMSC models expressing functional delayed rectifier-like human ether à-go-go K + channel 1 (hEAG1); the effects were exacerbated for fused hMSC-hCM hybrid cells. The third family of hMSCs (Type C), absent of hEAG1 activity, led to smaller single-cell action potential alterations during coupling and fusion, translating to longer tissue-level mean action potential wavelength. In a simulated 2-D monolayer of cardiac tissue, re-entry vulnerability with low (5%) hMSC insertion was approximately eight-fold lower with Type C hMSCs compared to hEAG1-functional hMSCs. A 20% decrease in APD dispersion by Type C hMSCs compared to hEAG1-active hMSCs supports the claim of reduced arrhythmogenic potential of this cell type with low hMSC insertion. However, at moderate (15%) and high (25%) hMSC insertion, the vulnerable window increased independent of hMSC type. In summary, this study provides novel electrophysiological models of hMSCs, predicts possible arrhythmogenic effects of hMSCs when directly coupled to healthy hCMs, and proposes that isolating a subset of hMSCs absent of hEAG1 activity may offer increased safety as a cell delivery cardiotherapy at low levels of hMSC-hCM coupling.

Beschreibung: by Angela Lavado-Roldán, Rafael Fernández-Chacón One of the most fascinating properties of the brain is the ability to function smoothly across decades of a lifespan. Neurons are nondividing mature cells specialized in fast electrical and chemical communication at synapses. Often, neurons and synapses operate at high levels of activity through sophisticated arborizations of long axons and dendrites that nevertheless stay healthy throughout years. On the other hand, aging and activity-dependent stress strike onto the protein machineries turning proteins unfolded and prone to form pathological aggregates associated with neurodegeneration. How do neurons protect from those insults and remain healthy for their whole life? Ali and colleagues now present a molecular mechanism by which the enzyme nicotinamide mononucleotide adenylyltransferase 2 (NMNAT2) acts not only as a NAD synthase involved in axonal maintenance but as a molecular chaperone helping neurons to overcome protein unfolding and protein aggregation.

Beschreibung: Sedimentary response to sea ice and atmospheric variability over the instrumental period off Adélie Land, East Antarctica Philippine Campagne, Xavier Crosta, Sabine Schmidt, Marie Noëlle Houssais, Olivier Ther, and Guillaume Massé Biogeosciences, 13, 4205-4218, doi:10.5194/bg-13-4205-2016, 2016 Diatoms and biomarkers have been recently used for palaeoclimate reconstructions in the Southern Ocean. Few sediment-based ecological studies have investigated their relationships with environmental conditions. Here, we compare high-resolution sedimentary records with meteorological data to study relationships between our proxies and recent atmospheric and sea surface changes. Our results indicate that coupled wind pattern and sea surface variability act as the proximal forcing at that scale.

Beschreibung: Observing and modelling phytoplankton community structure in the North Sea: can ERSEM-type models simulate biodiversity? David A. Ford, Johan van der Molen, Kieran Hyder, John Bacon, Rosa Barciela, Veronique Creach, Robert McEwan, Piet Ruardij, and Rodney Forster Biogeosciences Discuss., doi:10.5194/bg-2016-304,2016 Manuscript under review for BG (discussion: open, 0 comments) This study presents a novel set of in situ observations of phytoplankton community structure for the North Sea. These observations were used to validate two physical-biogeochemical ocean model simulations, each of which used different variants of the widely-used European Regional Seas Ecosystem Model (ERSEM). It was found that the ability of the models to reproduce the observed biodiversity was strongly dependent on the details of the biogeochemical model formulations and parameterisations used.

Beschreibung: Evaluation of 4 years of continuous δ 13 C(CO 2 ) data using a moving Keeling plot method Sanam Noreen Vardag, Samuel Hammer, and Ingeborg Levin Biogeosciences, 13, 4237-4251, doi:10.5194/bg-13-4237-2016, 2016 Using a synthetic dataset, we show how to best determine the mean source signature, δ S , at high temporal resolution using continuous CO 2 and δ 13 C(CO 2 ) data. We apply this method to measured data from Heidelberg and find a distinct seasonal cycle of δ S . Disentangling this record into its source components requires the isotopic end members of CO 2 from the biosphere and those from the fuel mix. They can be estimated from the δ S record, but only when their relative share is close to 100 %.

Beschreibung: Long-term drainage reduces CO 2 uptake and increases CO 2 emission on a Siberian floodplain due to shifts in vegetation community and soil thermal characteristics Min Jung Kwon, Martin Heimann, Olaf Kolle, Kristina A. Luus, Edward A. G. Schuur, Nikita Zimov, Sergey A. Zimov, and Mathias Göckede Biogeosciences, 13, 4219-4235, doi:10.5194/bg-13-4219-2016, 2016 A decade-long drainage on an Arctic floodplain has altered dominant plant species and soil temperature regimes. Consequently, CO 2 exchange rates between the atmosphere and the terrestrial ecosystem were modified: CO 2 uptake rates by the terrestrial ecosystem decreased and CO 2 emission rates to the atmosphere increased. Ongoing global warming may thaw ice-rich permafrost and make some regions drier in the Arctic, and this will reduce carbon accumulation in the terrestrial ecosystem.

Beschreibung: Physiological responses of coastal and oceanic diatoms to diurnal fluctuations in seawater carbonate chemistry under two CO 2 concentrations Futian Li, Yaping Wu, David A. Hutchins, Feixue Fu, and Kunshan Gao Biogeosciences Discuss., doi:10.5194/bg-2016-281,2016 Manuscript under review for BG (discussion: open, 0 comments) Ongoing ocean acidification is being superimposed on the natural carbonate buffer system to influence the physiology of phytoplankton. Here, we show that coastal and oceanic diatoms respond differentially to diurnal fluctuating carbonate chemistry in current and ocean acidification scenarios. We propose that the ability to acclimate to dynamic carbonate chemistry may act as one determinant of the spatial distribution of diatom species.

Beschreibung: by Travis J Wiles, Matthew Jemielita, Ryan P Baker, Brandon H Schlomann, Savannah L Logan, Julia Ganz, Ellie Melancon, Judith S Eisen, Karen Guillemin, Raghuveer Parthasarathy The gut microbiota is a complex consortium of microorganisms with the ability to influence important aspects of host health and development. Harnessing this “microbial organ” for biomedical applications requires clarifying the degree to which host and bacterial factors act alone or in combination to govern the stability of specific lineages. To address this issue, we combined bacteriological manipulation and light sheet fluorescence microscopy to monitor the dynamics of a defined two-species microbiota within a vertebrate gut. We observed that the interplay between each population and the gut environment produces distinct spatiotemporal patterns. As a consequence, one species dominates while the other experiences sudden drops in abundance that are well fit by a stochastic mathematical model. Modeling revealed that direct bacterial competition could only partially explain the observed phenomena, suggesting that a host factor is also important in shaping the community. We hypothesized the host determinant to be gut motility, and tested this mechanism by measuring colonization in hosts with enteric nervous system dysfunction due to a mutation in the ret locus, which in humans is associated with the intestinal motility disorder known as Hirschsprung disease. In mutant hosts we found reduced gut motility and, confirming our hypothesis, robust coexistence of both bacterial species. This study provides evidence that host-mediated spatial structuring and stochastic perturbation of communities can drive bacterial population dynamics within the gut, and it reveals a new facet of the intestinal host–microbe interface by demonstrating the capacity of the enteric nervous system to influence the microbiota. Ultimately, these findings suggest that therapeutic strategies targeting the intestinal ecosystem should consider the dynamic physical nature of the gut environment.

Beschreibung: Hydrogen dynamics in soil organic matter as determined by 13 C and 2 H labeling experiments Alexia Paul, Christine Hatté, Lucie Pastor, Yves Thiry, Françoise Siclet, and Jérôme Balesdent Biogeosciences Discuss., doi:10.5194/bg-2016-317,2016 Manuscript under review for BG (discussion: open, 0 comments) The terrestrial environment has been affected by tritium contamination. There is a need to assess the residence time and the dynamics of organic hydrogen in soils organic matter in order to predict the fate of tritium. In the present study we traced carbon and hydrogen from plant derived molecule or from water in different soil types. We showed that water is the main donor of hydrogen in soil and it is dependent on carbon biosynthesis and on soil type.

Beschreibung: Publication date: Available online 28 July 2016 Source: Cell Reports Author(s): Mahesh S. Padanad, Georgia Konstantinidou, Niranjan Venkateswaran, Margherita Melegari, Smita Rindhe, Matthew Mitsche, Chendong Yang, Kimberly Batten, Kenneth E. Huffman, Jingwen Liu, Ximing Tang, Jaime Rodriguez-Canales, Neda Kalhor, Jerry W. Shay, John D. Minna, Jeffrey McDonald, Ignacio I. Wistuba, Ralph J. DeBerardinis, Pier Paolo Scaglioni KRAS is one of the most commonly mutated oncogenes in human cancer. Mutant KRAS aberrantly regulates metabolic networks. However, the contribution of cellular metabolism to mutant KRAS tumorigenesis is not completely understood. We report that mutant KRAS regulates intracellular fatty acid metabolism through Acyl-coenzyme A ( CoA ) synthetase long-chain family member 3 ( ACSL3 ), which converts fatty acids into fatty Acyl-CoA esters, the substrates for lipid synthesis and β - oxidation. ACSL3 suppression is associated with depletion of cellular ATP and causes the death of lung cancer cells. Furthermore, mutant KRAS promotes the cellular uptake, retention, accumulation, and β-oxidation of fatty acids in lung cancer cells in an ACSL3 -dependent manner. Finally, ACSL3 is essential for mutant KRAS lung cancer tumorigenesis in vivo and is highly expressed in human lung cancer. Our data demonstrate that mutant KRAS reprograms lipid homeostasis, establishing a metabolic requirement that could be exploited for therapeutic gain. Graphical abstract Teaser In Brief: Padanad et al. find that ACSL3 is the critical enzyme required for viability of mutant KRAS lung cancer cells in vitro and for lung cancer initiation and progression in vivo. ACSL3 mediates survival and tumorigenesis of mutant KRAS lung cancer cells by promoting uptake, retention, and β-oxidation of fatty acids.

Beschreibung: Publication date: Available online 28 July 2016 Source: Cell Reports Author(s): Junghee Jin, Seung-Nam Kim, Xuqing Liu, Haijun Zhang, Chao Zhang, Ji-Seon Seo, Yong Kim, Tao Sun Emerging evidence has shown that noncoding RNAs, particularly microRNAs (miRNAs), contribute to the pathogenesis of mood and anxiety disorders, although the molecular mechanisms are poorly understood. Here, we show that altered levels of miR-17-92 in adult hippocampal neural progenitors have a significant impact on neurogenesis and anxiety- and depression-related behaviors in mice. miR-17-92 deletion in adult neural progenitors decreases neurogenesis in the dentate gyrus, while its overexpression increases neurogenesis. miR-17-92 affects neurogenesis by regulating genes in the glucocorticoid pathway, especially serum- and glucocorticoid-inducible protein kinase-1 (Sgk1). miR-17-92 knockout mice show anxiety- and depression-like behaviors, whereas miR-17-92 overexpressing mice exhibit anxiolytic and antidepression-like behaviors. Furthermore, we show that miR-17-92 expression in the adult mouse hippocampus responds to chronic stress, and miR-17-92 rescues proliferation defects induced by corticosterone in hippocampal neural progenitors. Our study uncovers a crucial role for miR-17-92 in adult neural progenitors through regulation of neurogenesis and anxiety- and depression-like behaviors. Graphical abstract Teaser The molecular pathogenesis of anxiety and depression disorders is poorly understood. Jin et al. show that microRNA miR-17-92 plays a critical role in regulating adult hippocampal neurogenesis and anxiety- and depression-like behaviors by modifying expression of genes in the glucocorticoid pathway.

Beschreibung: Publication date: Available online 28 July 2016 Source: Cell Reports Author(s): Feng Jiang, Xia Wang, Bei Wang, Lihong Chen, Zhendong Zhao, Nicholas R. Waterfield, Guowei Yang, Qi Jin Pseudomonas aeruginosa is an opportunistic pathogen that regularly causes nosocomial infections in hospitalized patients. The type VI secretion system (T6SS) is responsible for the secretion of numerous virulence effector proteins that can both interfere with competing microbes and manipulate host cells. Here, we report a detailed investigation of a P. aeruginosa H2-T6SS-dependent phospholipase effector, TplE, which acts as a trans-kingdom toxin. Delivery of TplE to the periplasmic space of rival bacteria leads to growth inhibition. Importantly, TplE, also contains a eukaryotic PGAP1-like domain, which targets the host ER apparatus, ultimately leading to disruption of the ER. TplE activity leads to the activation of the unfolded protein response (UPR) through the IRE1α-XBP1 pathway, enhancing autophagic flux. These findings indicate that this T6SS-delivered phospholipase effector is active against both prokaryotic and eukaryotic cellular targets, highlighting the T6SS as a versatile weapon in the Pseudomonas arsenal. Graphical abstract Teaser Jiang et al. report that the P. aeruginosa T6SS PGAP1-like phospholipase effector (TplE) targets the periplasm of competing bacteria to inhibit their growth. TplE can also target and disrupt the ER of eukaryotic cells, leading to ER stress and autophagic flux in the host cells.

Beschreibung: by Tyler W. Doughty, Heather E. Arsenault, Jennifer A. Benanti During mitosis chromosomes are condensed to facilitate their segregation, through a process mediated by the condensin complex. Although several factors that promote maximal condensin activity during mitosis have been identified, the mechanisms that downregulate condensin activity during interphase are largely unknown. Here, we demonstrate that Ycg1, the Cap-G subunit of budding yeast condensin, is cell cycle-regulated with levels peaking in mitosis and decreasing as cells enter G1 phase. This cyclical expression pattern is established by a combination of cell cycle-regulated transcription and constitutive degradation. Interestingly, overexpression of YCG1 and mutations that stabilize Ycg1 each result in delayed cell-cycle entry and an overall proliferation defect. Overexpression of no other condensin subunit impacts the cell cycle, suggesting that Ycg1 is limiting for condensin complex formation. Consistent with this possibility, we find that levels of intact condensin complex are reduced in G1 phase compared to mitosis, and that increased Ycg1 expression leads to increases in both levels of condensin complex and binding to chromatin in G1. Together, these results demonstrate that Ycg1 levels limit condensin function in interphase cells, and suggest that the association of condensin with chromosomes must be reduced following mitosis to enable efficient progression through the cell cycle.

Beschreibung: by Hector M. Vazquez, Christine Vionnet, Carole Roubaty, Shamroop k. Mallela, Roger Schneiter, Andreas Conzelmann While most yeast enzymes for the biosynthesis of glycerophospholipids, sphingolipids and ergosterol are known, genes for several postulated transporters allowing the flopping of biosynthetic intermediates and newly made lipids from the cytosolic to the lumenal side of the membrane are still not identified. An E-MAP measuring the growth of 142'108 double mutants generated by systematically crossing 543 hypomorphic or deletion alleles in genes encoding multispan membrane proteins, both on media with or without an inhibitor of fatty acid synthesis, was generated. Flc proteins, represented by 4 homologous genes encoding presumed FAD or calcium transporters of the ER, have a severe depression of sphingolipid biosynthesis and elevated detergent sensitivity of the ER. FLC1 , FLC2 and FLC3 are redundant in granting a common function, which remains essential even when the severe cell wall defect of flc mutants is compensated by osmotic support. Biochemical characterization of some other genetic interactions shows that Cst26 is the enzyme mainly responsible for the introduction of saturated very long chain fatty acids into phosphatidylinositol and that the GPI lipid remodelase Cwh43, responsible for introducing ceramides into GPI anchors having a C26:0 fatty acid in sn- 2 of the glycerol moiety can also use lyso-GPI protein anchors and various base resistant lipids as substrates. Furthermore, we observe that adjacent deletions in several chromosomal regions show strong negative genetic interactions with a single gene on another chromosome suggesting the presence of undeclared suppressor mutations in certain chromosomal regions that need to be identified in order to yield meaningful E-map data.

Beschreibung: Publication date: Available online 28 July 2016 Source: Cell Reports Author(s): Seung-Hye Lee, Claire E. Le Pichon, Oskar Adolfsson, Valérie Gafner, Maria Pihlgren, Han Lin, Hilda Solanoy, Robert Brendza, Hai Ngu, Oded Foreman, Ruby Chan, James A. Ernst, Danielle DiCara, Isidro Hotzel, Karpagam Srinivasan, David V. Hansen, Jasvinder Atwal, Yanmei Lu, Daniela Bumbaca, Andrea Pfeifer, Ryan J. Watts, Andreas Muhs, Kimberly Scearce-Levie, Gai Ayalon The spread of tau pathology correlates with cognitive decline in Alzheimer’s disease. In vitro, tau antibodies can block cell-to-cell tau spreading. Although mechanisms of anti-tau function in vivo are unknown, effector function might promote microglia-mediated clearance. In this study, we investigated whether antibody effector function is required for targeting tau. We compared efficacy in vivo and in vitro of two versions of the same tau antibody, with and without effector function, measuring tau pathology, neuron health, and microglial function. Both antibodies reduced accumulation of tau pathology in Tau-P301L transgenic mice and protected cultured neurons against extracellular tau-induced toxicity. Only the full-effector antibody enhanced tau uptake in cultured microglia, which promoted release of proinflammatory cytokines. In neuron-microglia co-cultures, only effectorless anti-tau protected neurons, suggesting full-effector tau antibodies can induce indirect toxicity via microglia. We conclude that effector function is not required for efficacy, and effectorless tau antibodies may represent a safer approach to targeting tau. Graphical abstract Teaser Lee et al. report that antibody effector function is not required for targeting tau with antibodies in vivo and in cultured neurons. The authors propose that reducing anti-tau effector function may offer a safer approach for targeting tau by avoiding engagement of microglia that may induce inflammatory responses.

Beschreibung: Publication date: Available online 28 July 2016 Source: Cell Reports Author(s): Rotem Ben-Tov Perry, Ida Rishal, Ella Doron-Mandel, Ashley L. Kalinski, Katalin F. Medzihradszky, Marco Terenzio, Stefanie Alber, Sandip Koley, Albina Lin, Meir Rozenbaum, Dmitry Yudin, Pabitra K. Sahoo, Cynthia Gomes, Vera Shinder, Wasim Geraisy, Eric A. Huebner, Clifford J. Woolf, Avraham Yaron, Alma L. Burlingame, Jeffery L. Twiss, Mike Fainzilber How can cells sense their own size to coordinate biosynthesis and metabolism with their growth needs? We recently proposed a motor-dependent bidirectional transport mechanism for axon length and cell size sensing, but the nature of the motor-transported size signals remained elusive. Here, we show that motor-dependent mRNA localization regulates neuronal growth and cycling cell size. We found that the RNA-binding protein nucleolin is associated with importin β1 mRNA in axons. Perturbation of nucleolin association with kinesins reduces its levels in axons, with a concomitant reduction in axonal importin β1 mRNA and protein levels. Strikingly, subcellular sequestration of nucleolin or importin β1 enhances axonal growth and causes a subcellular shift in protein synthesis. Similar findings were obtained in fibroblasts. Thus, subcellular mRNA localization regulates size and growth in both neurons and cycling cells. Graphical abstract Teaser Perry et al. show that motor-dependent mRNA localization regulates neuronal growth and cycling cell size. They implicate the RNA-binding protein nucleolin in importin β1 mRNA transport to neuronal axons and to the cellular periphery in fibroblasts. Perturbation of this mechanism affects growth and shifts protein synthesis, regulating axon length and cell size.

Beschreibung: Publication date: Available online 28 July 2016 Source: Cell Reports Author(s): Anna Prudova, Vasilena Gocheva, Ulrich auf dem Keller, Ulrich Eckhard, Oakley C. Olson, Leila Akkari, Georgina S. Butler, Nikolaus Fortelny, Philipp F. Lange, Jennifer C. Mark, Johanna A. Joyce, Christopher M. Overall Deregulated cathepsin proteolysis occurs across numerous cancers, but in vivo substrates mediating tumorigenesis remain ill-defined. Applying 8-plex iTRAQ terminal amine isotopic labeling of substrates (TAILS), a systems-level N-terminome degradomics approach, we identified cathepsin B, H, L, S, and Z in vivo substrates and cleavage sites with the use of six different cathepsin knockout genotypes in the Rip1-Tag2 mouse model of pancreatic neuroendocrine tumorigenesis. Among 1,935 proteins and 1,114 N termini identified by TAILS, stable proteolytic products were identified in wild-type tumors compared with one or more different cathepsin knockouts (17%–44% of 139 cleavages). This suggests a lack of compensation at the substrate level by other cathepsins. The majority of neo-N termini (56%–83%) for all cathepsins was consistent with protein degradation. We validated substrates, including the glycolytic enzyme pyruvate kinase M2 associated with the Warburg effect, the ER chaperone GRP78, and the oncoprotein prothymosin-alpha. Thus, the identification of cathepsin substrates in tumorigenesis improves the understanding of cathepsin functions in normal physiology and cancer. Graphical abstract Teaser Cathepsin proteases play a significant role in carcinogenesis, yet their in vivo substrates remain ill-defined. By using systems-level 8-plex TAILS proteomics, Prudova et al. demonstrate that, in the Rip1-Tag2 model of pancreatic cancer, degradation roles for cathepsins predominate, yet many proteins, mostly extracellular ones, are processed to produce stable cleavage products.

Beschreibung: by Nathan Mih, Elizabeth Brunk, Aarash Bordbar, Bernhard O. Palsson Progress in systems medicine brings promise to addressing patient heterogeneity and individualized therapies. Recently, genome-scale models of metabolism have been shown to provide insight into the mechanistic link between drug therapies and systems-level off-target effects while being expanded to explicitly include the three-dimensional structure of proteins. The integration of these molecular-level details, such as the physical, structural, and dynamical properties of proteins, notably expands the computational description of biochemical network-level properties and the possibility of understanding and predicting whole cell phenotypes. In this study, we present a multi-scale modeling framework that describes biological processes which range in scale from atomistic details to an entire metabolic network. Using this approach, we can understand how genetic variation, which impacts the structure and reactivity of a protein, influences both native and drug-induced metabolic states. As a proof-of-concept, we study three enzymes (catechol-O-methyltransferase, glucose-6-phosphate dehydrogenase, and glyceraldehyde-3-phosphate dehydrogenase) and their respective genetic variants which have clinically relevant associations. Using all-atom molecular dynamic simulations enables the sampling of long timescale conformational dynamics of the proteins (and their mutant variants) in complex with their respective native metabolites or drug molecules. We find that changes in a protein’s structure due to a mutation influences protein binding affinity to metabolites and/or drug molecules, and inflicts large-scale changes in metabolism.

Beschreibung: by Linn F. Groeneveld, Sigbjørn Gregusson, Bernt Guldbrandtsen, Sipke J. Hiemstra, Kristian Hveem, Juha Kantanen, Hannes Lohi, Lina Stroemstedt, Peer Berg In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals.

Beschreibung: by Yao Yu, Hongxia Zhou, Yimeng Kong, Bohu Pan, Longxian Chen, Hongbing Wang, Pei Hao, Xuan Li The hydrolytic deamination of adenosine to inosine (A-to-I editing) in precursor mRNA induces variable gene products at the post-transcription level. How and to what extent A-to-I RNA editing diversifies transcriptome is not fully characterized in the evolution, and very little is known about the selective constraints that drive the evolution of RNA editing events. Here we present a study on A-to-I RNA editing, by generating a global profile of A-to-I editing for a phylogeny of seven Drosophila species, a model system spanning an evolutionary timeframe of approximately 45 million years. Of totally 9281 editing events identified, 5150 (55.5%) are located in the coding sequences (CDS) of 2734 genes. Phylogenetic analysis places these genes into 1,526 homologous families, about 5% of total gene families in the fly lineages. Based on conservation of the editing sites, the editing events in CDS are categorized into three distinct types, representing events on singleton genes (type I), and events not conserved (type II) or conserved (type III) within multi-gene families. While both type I and II events are subject to purifying selection, notably type III events are positively selected, and highly enriched in the components and functions of the nervous system. The tissue profiles are documented for three editing types, and their critical roles are further implicated by their shifting patterns during holometabolous development and in post-mating response. In conclusion, three A-to-I RNA editing types are found to have distinct evolutionary dynamics. It appears that nervous system functions are mainly tested to determine if an A-to-I editing is beneficial for an organism. The coding plasticity enabled by A-to-I editing creates a new class of binary variations, which is a superior alternative to maintain heterozygosity of expressed genes in a diploid mating system.

Beschreibung: by John Lalith Charles Richard, Manu Shubhdarshan Shukla, Hervé Menoni, Khalid Ouararhni, Imtiaz Nisar Lone, Yohan Roulland, Christophe Papin, Elsa Ben Simon, Tapas Kundu, Ali Hamiche, Dimitar Angelov, Stefan Dimitrov FACT, in addition to its role in transcription, is likely implicated in both transcription-coupled nucleotide excision repair and DNA double strand break repair. Here, we present evidence that FACT could be directly involved in Base Excision Repair and elucidate the chromatin remodeling mechanisms of FACT during BER. We found that, upon oxidative stress, FACT is released from transcription related protein complexes to get associated with repair proteins and chromatin remodelers from the SWI/SNF family. We also showed the rapid recruitment of FACT to the site of damage, coincident with the glycosylase OGG1, upon the local generation of oxidized DNA. Interestingly, FACT facilitates uracil-DNA glycosylase in the removal of uracil from nucleosomal DNA thanks to an enhancement in the remodeling activity of RSC. This discloses a novel property of FACT wherein it has a co-remodeling activity and strongly enhances the remodeling capacity of the chromatin remodelers. Altogether, our data suggest that FACT may acts in concert with RSC to facilitate excision of DNA lesions during the initial step of BER.

Beschreibung: by Victor Hanson-Smith, Alexander Johnson The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and “resurrect” (that is, synthesize in vivo or in vitro ) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server.

Beschreibung: by Michela Candotti, Modesto Orozco The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed using synthetic agents such as poly(ethylene glycol), whose ability to mimic protein crowders has not been demonstrated. Here we performed a comprehensive atomistic molecular dynamic analysis of the effect of protein crowders on the structure and dynamics of three proteins, namely an intrinsically disordered protein (ACTR), a molten globule conformation (NCBD), and a one-fold structure (IRF-3) protein. We found that crowding does not stabilize the native compact structure, and, in fact, often prevents structural collapse. Poly(ethylene glycol) PEG500 failed to reproduce many aspects of the physiologically-relevant protein crowders, thus indicating its unsuitability to mimic the cell interior. Instead, the impact of protein crowding on the structure and dynamics of a protein depends on its degree of disorder and results from two competing effects: the excluded volume, which favors compact states, and quinary interactions, which favor extended conformers. Such a viscous environment slows down protein flexibility and restricts the conformational landscape, often biasing it towards bioactive conformations but hindering biologically relevant protein-protein contacts. Overall, the protein crowders used here act as unspecific chaperons that modulate the protein conformational space, thus having relevant consequences for disordered proteins.

Beschreibung: by Juliana Bernardes, Gerson Zaverucha, Catherine Vaquero, Alessandra Carbone Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for annotation fail. Here we address the fundamental question of domain identification for highly divergent proteins. By using high performance computing, we demonstrate that the limits of state-of-the-art annotation methods can be bypassed. We design a new strategy based on the observation that many structural and functional protein constraints are not globally conserved through all species but might be locally conserved in separate clades. We propose a novel exploitation of the large amount of data available: 1. for each known protein domain, several probabilistic clade-centered models are constructed from a large and differentiated panel of homologous sequences, 2. a decision-making protocol combines outcomes obtained from multiple models, 3. a multi-criteria optimization algorithm finds the most likely protein architecture. The method is evaluated for domain and architecture prediction over several datasets and statistical testing hypotheses. Its performance is compared against HMMScan and HHblits, two widely used search methods based on sequence-profile and profile-profile comparison. Due to their closeness to actual protein sequences, clade-centered models are shown to be more specific and functionally predictive than the broadly used consensus models. Based on them, we improved annotation of Plasmodium falciparum protein sequences on a scale not previously possible. We successfully predict at least one domain for 72% of P. falciparum proteins against 63% achieved previously, corresponding to 30% of improvement over the total number of Pfam domain predictions on the whole genome. The method is applicable to any genome and opens new avenues to tackle evolutionary questions such as the reconstruction of ancient domain duplications, the reconstruction of the history of protein architectures, and the estimation of protein domain age. Website and software: http://www.lcqb.upmc.fr/CLADE.

Beschreibung: by Anita Sveen, Inger Marie Løes, Sharmini Alagaratnam, Gro Nilsen, Maren Høland, Ole Christian Lingjærde, Halfdan Sorbye, Kaja Christine Graue Berg, Arild Horn, Jon-Helge Angelsen, Stian Knappskog, Per Eystein Lønning, Ragnhild A. Lothe Chromosomal instability is a well-defined hallmark of tumor aggressiveness and metastatic progression in colorectal cancer. The magnitude of genetic heterogeneity among distinct liver metastases from the same patient at the copy number level, as well as its relationship with chemotherapy exposure and patient outcome, remains unknown. We performed high-resolution DNA copy number analyses of 134 liver metastatic deposits from 45 colorectal cancer patients to assess: (i) intra-patient inter-metastatic genetic heterogeneity using a heterogeneity score based on pair-wise genetic distances among tumor deposits; and (ii) genomic complexity, defined as the proportion of the genome harboring aberrant DNA copy numbers. Results were analyzed in relation to the patients’ clinical course; previous chemotherapy exposure and outcome after surgical resection of liver metastases. We observed substantial variation in the level of intra-patient inter-metastatic heterogeneity. Heterogeneity was not associated with the number of metastatic lesions or their genomic complexity. In metachronous disease, heterogeneity was higher in patients previously exposed to chemotherapy. Importantly, intra-patient inter-metastatic heterogeneity was a strong prognostic determinant, stronger than known clinicopathological prognostic parameters. Patients with a low level of heterogeneity (below the median level) had a three-year progression-free and overall survival rate of 23% and 66% respectively, versus 5% and 18% for patients with a high level (hazard ratio0.4, 95% confidence interval 0.2–0.8, P = 0.01; and hazard ratio0.3,95% confidence interval 0.1–0.7, P = 0.007). A low patient-wise level of genomic complexity (below 25%) was also a favorable prognostic factor; however, the prognostic association of intra-patient heterogeneity was independent of genomic complexity in multivariable analyses. In conclusion, intra-patient inter-metastatic genetic heterogeneity is a pronounced feature of metastatic colorectal cancer, and the strong prognostic association reinforces its clinical relevance and places it as a key feature to be explored in future patient cohorts.

Beschreibung: by Yichang Chen, Le Shu, Zhiqun Qiu, Dong Yeon Lee, Sara J. Settle, Shane Que Hee, Donatello Telesca, Xia Yang, Patrick Allard Concerns about the safety of Bisphenol A, a chemical found in plastics, receipts, food packaging and more, have led to its replacement with substitutes now found in a multitude of consumer products. However, several popular BPA-free alternatives, such as Bisphenol S, share a high degree of structural similarity with BPA, suggesting that these substitutes may disrupt similar developmental and reproductive pathways. We compared the effects of BPA and BPS on germline and reproductive functions using the genetic model system Caenorhabditis elegans . We found that, similarly to BPA, BPS caused severe reproductive defects including germline apoptosis and embryonic lethality. However, meiotic recombination, targeted gene expression, whole transcriptome and ontology analyses as well as ToxCast data mining all indicate that these effects are partly achieved via mechanisms distinct from BPAs. These findings therefore raise new concerns about the safety of BPA alternatives and the risk associated with human exposure to mixtures.

Beschreibung: by Xin-Qi Gao, Chang Zhen Liu, Dan Dan Li, Ting Ting Zhao, Fei Li, Xiao Na Jia, Xin-Ying Zhao, Xian Sheng Zhang Pollen–stigma interactions are essential for pollen germination. The highly regulated process of pollen germination includes pollen adhesion, hydration, and germination on the stigma. However, the internal signaling of pollen that regulates pollen–stigma interactions is poorly understood. KINβγ is a plant-specific subunit of the SNF1-related protein kinase 1 complex which plays important roles in the regulation of plant development. Here, we showed that KINβγ was a cytoplasm- and nucleus-localized protein in the vegetative cells of pollen grains in Arabidopsis . The pollen of the Arabidopsis kinβγ mutant could not germinate on stigma, although it germinated normally in vitro . Further analysis revealed the hydration of kinβγ mutant pollen on the stigma was compromised. However, adding water to the stigma promoted the germination of the mutant pollen in vivo , suggesting that the compromised hydration of the mutant pollen led to its defective germination. In kinβγ mutant pollen, the structure of the mitochondria and peroxisomes was destroyed, and their numbers were significantly reduced compared with those in the wild type. Furthermore, we found that the kinβγ mutant exhibited reduced levels of reactive oxygen species (ROS) in pollen. The addition of H 2 O 2 in vitro partially compensated for the reduced water absorption of the mutant pollen, and reducing ROS levels in pollen by overexpressing Arabidopsis CATALASE 3 resulted in compromised hydration of pollen on the stigma. These results indicate that Arabidopsis KINβγ is critical for the regulation of ROS levels by mediating the biogenesis of mitochondria and peroxisomes in pollen, which is required for pollen–stigma interactions during pollination.

Beschreibung: by Wesley R. Lewis, Erik B. Malarkey, Douglas Tritschler, Raqual Bower, Raymond C. Pasek, Jonathan D. Porath, Susan E. Birket, Sophie Saunier, Corinne Antignac, Michael R. Knowles, Margaret W. Leigh, Maimoona A. Zariwala, Anil K. Challa, Robert A. Kesterson, Steven M. Rowe, Iain A. Drummond, John M. Parant, Friedhelm Hildebrandt, Mary E. Porter, Bradley K. Yoder, Nicolas F. Berbari Ciliopathies are genetic disorders arising from dysfunction of microtubule-based cellular appendages called cilia. Different cilia types possess distinct stereotypic microtubule doublet arrangements with non-motile or ‘primary’ cilia having a 9+0 and motile cilia have a 9+2 array of microtubule doublets. Primary cilia are critical sensory and signaling centers needed for normal mammalian development. Defects in their structure/function result in a spectrum of clinical and developmental pathologies including abnormal neural tube and limb patterning. Altered patterning phenotypes in the limb and neural tube are due to perturbations in the hedgehog (Hh) signaling pathway. Motile cilia are important in fluid movement and defects in motility result in chronic respiratory infections, altered left-right asymmetry, and infertility. These features are the hallmarks of Primary Ciliary Dyskinesia (PCD, OMIM 244400). While mutations in several genes are associated with PCD in patients and animal models, the genetic lesion in many cases is unknown. We assessed the in vivo functions of Growth Arrest Specific 8 (GAS8). GAS8 shares strong sequence similarity with the Chlamydomonas Nexin-Dynein Regulatory Complex (NDRC) protein 4 (DRC4) where it is needed for proper flagella motility. In mammalian cells, the GAS8 protein localizes not only to the microtubule axoneme of motile cilia, but also to the base of non-motile cilia. Gas8 was recently implicated in the Hh signaling pathway as a regulator of Smoothened trafficking into the cilium. Here, we generate the first mouse with a Gas8 mutation and show that it causes severe PCD phenotypes; however, there were no overt Hh pathway phenotypes. In addition, we identified two human patients with missense variants in Gas8. Rescue experiments in Chlamydomonas revealed a subtle defect in swim velocity compared to controls. Further experiments using CRISPR/Cas9 homology driven repair (HDR) to generate one of these human missense variants in mice demonstrated that this allele is likely pathogenic.

Beschreibung: Publication date: Available online 29 July 2016 Source: Cell Reports Author(s): Kimberly A. Dowd, Christina R. DeMaso, Rebecca S. Pelc, Scott D. Speer, Alexander R.Y. Smith, Leslie Goo, Derek J. Platt, John R. Mascola, Barney S. Graham, Mark J. Mulligan, Michael S. Diamond, Julie E. Ledgerwood, Theodore C. Pierson Recent epidemics of Zika virus (ZIKV) have been associated with congenital malformation during pregnancy and Guillain-Barré syndrome. There are two ZIKV lineages (African and Asian) that share >95% amino acid identity. Little is known regarding the ability of neutralizing antibodies elicited against one lineage to protect against the other. We investigated the breadth of the neutralizing antibody response following ZIKV infection by measuring the sensitivity of six ZIKV strains to neutralization by ZIKV-confirmed convalescent human serum or plasma samples. Contemporary Asian and early African ZIKV strains were similarly sensitive to neutralization regardless of the cellular source of virus. Furthermore, mouse immune serum generated after infection with African or Asian ZIKV strains was capable of neutralizing homologous and heterologous ZIKV strains equivalently. Because our study only defines a single ZIKV serotype, vaccine candidates eliciting robust neutralizing antibody responses should inhibit infection of both ZIKV lineages, including strains circulating in the Americas. Graphical abstract Teaser Dowd et al. investigate the breadth of the neutralizing antibody response to ZIKV. They demonstrate that contemporary South American, Asian, and early African ZIKV strains are similarly sensitive to neutralization by ZIKV-confirmed convalescent human serum.

Beschreibung: Ocean acidification over the next three centuries using a simple global climate carbon-cycle model: projections and sensitivities Corinne A. Hartin, Benjamin Bond-Lamberty, Pralit Patel, and Anupriya Mundra Biogeosciences, 13, 4329-4342, doi:10.5194/bg-13-4329-2016, 2016 Continued oceanic uptake of anthropogenic CO 2 is projected to significantly alter the chemistry of the upper oceans over the next three centuries, with potentially serious consequences for marine ecosystems. Relatively few models have the capability to make projections of ocean acidification, limiting our ability to assess the impacts and probabilities of ocean changes. In this study we examine the ability of Hector v1.1, a reduced-form global model, to project changes in the upper ocean carbonate system over the next three centuries, and quantify the model's sensitivity to parametric inputs. Hector is run under prescribed emission pathways from the Representative Concentration Pathways (RCPs) and compared to both observations and a suite of Coupled Model Intercomparison (CMIP5) model outputs. Current observations confirm that ocean acidification is already taking place, and CMIP5 models project significant changes occurring to 2300. Hector is consistent with the observational record within both the high- (〉 55°) and low-latitude oceans (〈 55°). The model projects low-latitude surface ocean pH to decrease from preindustrial levels of 8.17 to 7.77 in 2100, and to 7.50 in 2300; aragonite saturation levels (Ω Ar ) decrease from 4.1 units to 2.2 in 2100 and 1.4 in 2300 under RCP 8.5. These magnitudes and trends of ocean acidification within Hector are largely consistent with the CMIP5 model outputs, although we identify some small biases within Hector's carbonate system. Of the parameters tested, changes in [H + ] are most sensitive to parameters that directly affect atmospheric CO 2 concentrations – Q 10 (terrestrial respiration temperature response) as well as changes in ocean circulation, while changes in Ω Ar saturation levels are sensitive to changes in ocean salinity and Q 10 . We conclude that Hector is a robust tool well suited for rapid ocean acidification projections and sensitivity analyses, and it is capable of emulating both current observations and large-scale climate models under multiple emission pathways.

Beschreibung: Decadal and long-term boreal soil carbon and nitrogen sequestration rates across a variety of ecosystems Kristen L. Manies, Jennifer W. Harden, Christopher C. Fuller, and Merritt R. Turetsky Biogeosciences, 13, 4315-4327, doi:10.5194/bg-13-4315-2016, 2016 Boreal soils are important to the global C cycle. We need to understand what controls how C accumulates and is lost from this soil. To help we examined C & N accumulation rates for five boreal ecosystems. Most ecosystems were similar. But the rich fen had higher long-term C & N accumulation rates, likely due to differences in nutrient cycling & because it burns less. Therefore, shifts among ecosystems will not change regional C & N dynamics much, unless there is a shift to or from a rich fen.

Beschreibung: Exploring the distance between nitrogen and phosphorus limitation in mesotrophic surface waters using a sensitive bioassay Enis Hrustic, Risto Lignell, Ulf Riebesell, and Tron Frede Thingstad Biogeosciences Discuss., doi:10.5194/bg-2016-313,2016 Manuscript under review for BG (discussion: open, 0 comments) In the stratified season, phytoplankton in the ocean's top layer are limited by mineral nutrients, normally nitrogen, phosphorous or iron. It is important to know, not only which element is limiting, but also the surplus of the secondary limiting element, referred to as e.g. N* when N is the secondary limiting element. Determination of *N by chemical methods in surface waters is not straight forward. We here show how one instead can "ask the organisms".

Beschreibung: The importance of an estuarine salinity gradient on soil organic carbon stocks of tidal marshes Marijn Van de Broek, Stijn Temmerman, Roel Merckx, and Gerard Govers Biogeosciences Discuss., doi:10.5194/bg-2016-285,2016 Manuscript under review for BG (discussion: open, 0 comments) The results of this study on the OC stocks of tidal marshes show that variations in OC stocks of tidal marshes along estuaries are important and should be taken into account in order to make of accurate estimates of the total amount of OC stored in these ecosystems. Moreover, our results clearly show that most studies underestimate the variation in OC stocks along estuaries due to a shallow sampling depth, neglecting the variation in OC decomposition after burial along estuaries.

Beschreibung: by Fei Liu, Shao-Wu Zhang, Wei-Feng Guo, Ze-Gang Wei, Luonan Chen The inference of gene regulatory networks (GRNs) from expression data can mine the direct regulations among genes and gain deep insights into biological processes at a network level. During past decades, numerous computational approaches have been introduced for inferring the GRNs. However, many of them still suffer from various problems, e.g., Bayesian network (BN) methods cannot handle large-scale networks due to their high computational complexity, while information theory-based methods cannot identify the directions of regulatory interactions and also suffer from false positive/negative problems. To overcome the limitations, in this work we present a novel algorithm, namely local Bayesian network (LBN), to infer GRNs from gene expression data by using the network decomposition strategy and false-positive edge elimination scheme. Specifically, LBN algorithm first uses conditional mutual information (CMI) to construct an initial network or GRN, which is decomposed into a number of local networks or GRNs. Then, BN method is employed to generate a series of local BNs by selecting the k -nearest neighbors of each gene as its candidate regulatory genes, which significantly reduces the exponential search space from all possible GRN structures. Integrating these local BNs forms a tentative network or GRN by performing CMI, which reduces redundant regulations in the GRN and thus alleviates the false positive problem. The final network or GRN can be obtained by iteratively performing CMI and local BN on the tentative network. In the iterative process, the false or redundant regulations are gradually removed. When tested on the benchmark GRN datasets from DREAM challenge as well as the SOS DNA repair network in E . coli , our results suggest that LBN outperforms other state-of-the-art methods (ARACNE, GENIE3 and NARROMI) significantly, with more accurate and robust performance. In particular, the decomposition strategy with local Bayesian networks not only effectively reduce the computational cost of BN due to much smaller sizes of local GRNs, but also identify the directions of the regulations.

Beschreibung: by Hasreet K. Gill, Jennifer D. Cohen, Jesus Ayala-Figueroa, Rachel Forman-Rubinsky, Corey Poggioli, Kevin Bickard, Jean M. Parry, Pu Pu, David H. Hall, Meera V. Sundaram Most epithelial cells secrete a glycoprotein-rich apical extracellular matrix that can have diverse but still poorly understood roles in development and physiology. Zona Pellucida (ZP) domain glycoproteins are common constituents of these matrices, and their loss in humans is associated with a number of diseases. Understanding of the functions, organization and regulation of apical matrices has been hampered by difficulties in imaging them both in vivo and ex vivo . We identified the PAN-Apple, mucin and ZP domain glycoprotein LET-653 as an early and transient apical matrix component that shapes developing epithelia in C . elegans . LET-653 has modest effects on shaping of the vulva and epidermis, but is essential to prevent lumen fragmentation in the very narrow, unicellular excretory duct tube. We were able to image the transient LET-653 matrix by both live confocal imaging and transmission electron microscopy. Structure/function and fluorescence recovery after photobleaching studies revealed that LET-653 exists in two separate luminal matrix pools, a loose fibrillar matrix in the central core of the lumen, to which it binds dynamically via its PAN domains, and an apical-membrane-associated matrix, to which it binds stably via its ZP domain. The PAN domains are both necessary and sufficient to confer a cyclic pattern of duct lumen localization that precedes each molt, while the ZP domain is required for lumen integrity. Ectopic expression of full-length LET-653, but not the PAN domains alone, could expand lumen diameter in the developing gut tube, where LET-653 is not normally expressed. Together, these data support a model in which the PAN domains regulate the ability of the LET-653 ZP domain to interact with other factors at the apical membrane, and this ZP domain interaction promotes expansion and maintenance of lumen diameter. These data identify a transient apical matrix component present prior to cuticle secretion in C . elegans , demonstrate critical roles for this matrix component in supporting lumen integrity within narrow bore tubes such as those found in the mammalian microvasculature, and reveal functional importance of the evolutionarily conserved ZP domain in this tube protecting activity.

Beschreibung: by Tracy L. Callender, Raphaelle Laureau, Lihong Wan, Xiangyu Chen, Rima Sandhu, Saif Laljee, Sai Zhou, Ray T. Suhandynata, Evelyn Prugar, William A. Gaines, YoungHo Kwon, G. Valentin Börner, Alain Nicolas, Aaron M. Neiman, Nancy M. Hollingsworth During meiosis, programmed double strand breaks (DSBs) are repaired preferentially between homologs to generate crossovers that promote proper chromosome segregation at Meiosis I. In many organisms, there are two strand exchange proteins, Rad51 and the meiosis-specific Dmc1, required for interhomolog (IH) bias. This bias requires the presence, but not the strand exchange activity of Rad51, while Dmc1 is responsible for the bulk of meiotic recombination. How these activities are regulated is less well established. In dmc1Δ mutants, Rad51 is actively inhibited, thereby resulting in prophase arrest due to unrepaired DSBs triggering the meiotic recombination checkpoint. This inhibition is dependent upon the meiosis-specific kinase Mek1 and occurs through two different mechanisms that prevent complex formation with the Rad51 accessory factor Rad54: (i) phosphorylation of Rad54 by Mek1 and (ii) binding of Rad51 by the meiosis-specific protein Hed1. An open question has been why inhibition of Mek1 affects Hed1 repression of Rad51. This work shows that Hed1 is a direct substrate of Mek1. Phosphorylation of Hed1 at threonine 40 helps suppress Rad51 activity in dmc1Δ mutants by promoting Hed1 protein stability. Rad51-mediated recombination occurring in the absence of Hed1 phosphorylation results in a significant increase in non-exchange chromosomes despite wild-type levels of crossovers, confirming previous results indicating a defect in crossover assurance. We propose that Rad51 function in meiosis is regulated in part by the coordinated phosphorylation of Rad54 and Hed1 by Mek1.

Beschreibung: Ecological response to collapse of the biological pump following the mass extinction at the Cretaceous-Paleogene boundary Johan Vellekoop, Lineke Woelders, Sanem Açikalin, Jan Smit, Bas van de Schootbrugge, Ismail Ö. Yilmaz, Henk Brinkhuis, and Robert P. Speijer Biogeosciences Discuss., doi:10.5194/bg-2016-275,2016 Manuscript under review for BG (discussion: open, 0 comments) The Cretaceous-Paleogene boundary, ~ 66 Ma, is characterized by a mass-extinction. We studied groups of both surface-dwelling and bottom-dwelling organisms to unravel the oceanographic consequences of these extinctions. Our integrated records indicate that a reduction of the transport of organic matter to the sea floor resulted in enhanced recycling of nutrients in the upper water column and decreased food supply at the sea floor, in the first tens of thousands of years after the extinctions.

Beschreibung: The long-solved problem of the best-fit straight line: Application to isotopic mixing lines Richard Wehr and Scott R . Saleska Biogeosciences Discuss., doi:10.5194/bg-2016-315,2016 Manuscript under review for BG (discussion: open, 0 comments) In 1969, Derek York published a highly general solution to the common problem of how to fit a straight line to points measured with error in both x and y . Unfortunately York’s solution is almost unknown outside the geophysical literature, and new studies wrestle with the problem each year. We introduce York’s solution and demonstrate it using an example from biogeochemistry: the isotopic mixing line. By Monte Carlo simulation, we show that York’s solution is superior to all popular fit methods.

Beschreibung: Publication date: 2 August 2016 Source: Cell Reports, Volume 16, Issue 5 Author(s): Megan Chastain, Qing Zhou, Olga Shiva, Leanne Whitmore, Pingping Jia, Xueyu Dai, Chenhui Huang, Maria Fadri-Moskwik, Ping Ye, Weihang Chai The telomeric CTC1/STN1/TEN1 (CST) complex has been implicated in promoting replication recovery under replication stress at genomic regions, yet its precise role is unclear. Here, we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates the fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association of CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance. Graphical abstract Teaser Chastain et al. find that under replication stress, the telomeric complex CST interacts with RAD51 and is enriched at GC-rich repetitive fragile sites. CST suppression inhibits RAD51 recruitment to fragile sites, resulting in genome instability.

Beschreibung: by Matthew Gruner, Jeremy Grubbs, Aja McDonagh, Dominic Valdes, Ari Winbush, Alexander M. van der Linden Food and feeding-state dependent changes in chemoreceptor gene expression may allow Caenorhabditis elegans to modify their chemosensory behavior, but the mechanisms essential for these expression changes remain poorly characterized. We had previously shown that expression of a feeding state-dependent chemoreceptor gene, srh-234 , in the ADL sensory neuron of C . elegans is regulated via the MEF-2 transcription factor. Here, we show that MEF-2 acts together with basic helix-loop-helix (bHLH) transcription factors to regulate srh-234 expression as a function of feeding state. We identify a cis -regulatory MEF2 binding site that is necessary and sufficient for the starvation-induced down regulation of srh-234 expression, while an E-box site known to bind bHLH factors is required to drive srh-234 expression in ADL. We show that HLH-2 (E/Daughterless), HLH-3 and HLH-4 (Achaete-scute homologs) act in ADL neurons to regulate srh-234 expression. We further demonstrate that the expression levels of srh-234 in ADL neurons are regulated remotely by MXL-3 (Max-like 3 homolog) and HLH-30 (TFEB ortholog) acting in the intestine, which is dependent on insulin signaling functioning specifically in ADL neurons. We also show that this intestine-to-neuron feeding-state regulation of srh-234 involves a subset of insulin-like peptides. These results combined suggest that chemoreceptor gene expression is regulated by both cell-autonomous and non-cell-autonomous transcriptional mechanisms mediated by MEF2 and bHLH factors, which may allow animals to fine-tune their chemosensory responses in response to changes in their feeding state.

Beschreibung: Patterns of carbon processing at the seafloor: the role of faunal and microbial communities in moderating carbon flows Clare Woulds, Steven Bouillon, Gregory L. Cowie, Emily Drake, Jack J. Middelburg, and Ursula Witte Biogeosciences, 13, 4343-4357, doi:10.5194/bg-13-4343-2016, 2016 Estuarine sediments are important locations for carbon cycling and burial. We used tracer experiments to investigate how site conditions affect the way in which seafloor biological communities cycle carbon. We showed that while total respiration rates are primarily determined by temperature, total carbon processing by the biological community is strongly related to its biomass. Further, we saw a distinct pattern of carbon cycling in sandy sediment, in which uptake by bacteria dominates.

Beschreibung: Temporal changes in photoreactivity of dissolved organic carbon and implications for aquatic carbon fluxes from peatlands Amy E. Pickard, Kate V. Heal, Andrew R. McLeod, and Kerry J. Dinsmore Biogeosciences Discuss., doi:10.5194/bg-2016-296,2016 Manuscript under review for BG (discussion: open, 0 comments) Peatland catchments export significant volumes of photoreactive carbon to aquatic systems, particularly headwater streams. Delivery of photoreactive material is subject to seasonal variation, and is also influenced by the timing and magnitude of rainfall events. We suggest that photoprocessing of peatland derived carbon may contribute to carbon dioxide emissions from aquatic systems, although considerable uncertainty remains as to how much material is processed 'in situ' within these systems.

Beschreibung: by Samuel E. Jones, Jessica Tyrrell, Andrew R. Wood, Robin N. Beaumont, Katherine S. Ruth, Marcus A. Tuke, Hanieh Yaghootkar, Youna Hu, Maris Teder-Laving, Caroline Hayward, Till Roenneberg, James F. Wilson, Fabiola Del Greco, Andrew A. Hicks, Chol Shin, Chang-Ho Yun, Seung Ku Lee, Andres Metspalu, Enda M. Byrne, Philip R. Gehrman, Henning Tiemeier, Karla V. Allebrandt, Rachel M. Freathy, Anna Murray, David A. Hinds, Timothy M. Frayling, Michael N. Weedon Disrupted circadian rhythms and reduced sleep duration are associated with several human diseases, particularly obesity and type 2 diabetes, but until recently, little was known about the genetic factors influencing these heritable traits. We performed genome-wide association studies of self-reported chronotype (morning/evening person) and self-reported sleep duration in 128,266 white British individuals from the UK Biobank study. Sixteen variants were associated with chronotype ( P

Beschreibung: by The PLOS Biology Editors PLOS Biology announces a new article type, Open Highlights, which uses a recent research article to nucleate a short synthesis of up to ten related research articles from other PLOS journals and from the wider Open Access corpus.

Beschreibung: by Weitao Chen, Qing Nie, Tau-Mu Yi, Ching-Shan Chou Mating of budding yeast cells is a model system for studying cell-cell interactions. Haploid yeast cells secrete mating pheromones that are sensed by the partner which responds by growing a mating projection toward the source. The two projections meet and fuse to form the diploid. Successful mating relies on precise coordination of dynamic extracellular signals, signaling pathways, and cell shape changes in a noisy background. It remains elusive how cells mate accurately and efficiently in a natural multi-cell environment. Here we present the first stochastic model of multiple mating cells whose morphologies are driven by pheromone gradients and intracellular signals. Our novel computational framework encompassed a moving boundary method for modeling both a-cells and α-cells and their cell shape changes, the extracellular diffusion of mating pheromones dynamically coupled with cell polarization, and both external and internal noise. Quantification of mating efficiency was developed and tested for different model parameters. Computer simulations revealed important robustness strategies for mating in the presence of noise. These strategies included the polarized secretion of pheromone, the presence of the α-factor protease Bar1, and the regulation of sensing sensitivity; all were consistent with data in the literature. In addition, we investigated mating discrimination, the ability of an a-cell to distinguish between α-cells either making or not making α-factor, and mating competition, in which multiple a-cells compete to mate with one α-cell. Our simulations were consistent with previous experimental results. Moreover, we performed a combination of simulations and experiments to estimate the diffusion rate of the pheromone a-factor. In summary, we constructed a framework for simulating yeast mating with multiple cells in a noisy environment, and used this framework to reproduce mating behaviors and to identify strategies for robust cell-cell interactions.

Beschreibung: by Jeffrey B. Joy, Richard H. Liang, Rosemary M. McCloskey, T. Nguyen, Art F. Y. Poon

Beschreibung: by Emily L. Landeen, Christina A. Muirhead, Lori Wright, Colin D. Meiklejohn, Daven C. Presgraves The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation, including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline. In the male germline of Drosophila melanogaster , a novel but poorly understood form of sex chromosome-specific transcriptional regulation occurs that is distinct from canonical sex chromosome dosage compensation or meiotic inactivation. Previous work shows that expression of reporter genes driven by testis-specific promoters is considerably lower—approximately 3-fold or more—for transgenes inserted into X chromosome versus autosome locations. Here we characterize this transcriptional suppression of X-linked genes in the male germline and its evolutionary consequences. Using transgenes and transpositions, we show that most endogenous X-linked genes, not just testis-specific ones, are transcriptionally suppressed several-fold specifically in the Drosophila male germline. In wild-type testes, this sex chromosome-wide transcriptional suppression is generally undetectable, being effectively compensated by the gene-by-gene evolutionary recruitment of strong promoters on the X chromosome. We identify and experimentally validate a promoter element sequence motif that is enriched upstream of the transcription start sites of hundreds of testis-expressed genes; evolutionarily conserved across species; associated with strong gene expression levels in testes; and overrepresented on the X chromosome. These findings show that the expression of X-linked genes in the Drosophila testes reflects a balance between chromosome-wide epigenetic transcriptional suppression and long-term compensatory adaptation by sex-linked genes. Our results have broad implications for the evolution of gene expression in the Drosophila male germline and for genome evolution.

Beschreibung: by Diana P. Bojanova, Seth R. Bordenstein Fecal transplants are increasingly utilized for treatment of recurrent infections (i.e., Clostridium difficile ) in the human gut and as a general research tool for gain-of-function experiments (i.e., gavage of fecal pellets) in animal models. Changes observed in the recipient's biology are routinely attributed to bacterial cells in the donor feces (~10 11 per gram of human wet stool). Here, we examine the literature and summarize findings on the composition of fecal matter in order to raise cautiously the profile of its multipart nature. In addition to viable bacteria, which may make up a small fraction of total fecal matter, other components in unprocessed human feces include colonocytes (~10 7 per gram of wet stool), archaea (~10 8 per gram of wet stool), viruses (~10 8 per gram of wet stool), fungi (~10 6 per gram of wet stool), protists, and metabolites. Thus, while speculative at this point and contingent on the transplant procedure and study system, nonbacterial matter could contribute to changes in the recipient's biology. There is a cautious need for continued reductionism to separate out the effects and interactions of each component.

Beschreibung: Species-specific temporal variation in photosynthesis as a moderator of peatland carbon sequestration Aino Korrensalo, Tomáš Hájek, Pavel Alekseychik, Janne Rinne, Timo Vesala, Lauri Mehtätalo, Ivan Mammarella, and Eeva-Stiina Tuittila Biogeosciences Discuss., doi:10.5194/bg-2016-265,2016 Manuscript under review for BG (discussion: open, 0 comments) Photosynthetic parameters of peatland plant species were measured over one growing season in an ombrotrophic bog. Based on these measurements, ecosystem-level photosynthesis was calculated for the whole growing season and compared with an estimate derived from micrometeorological measurements. These two estimates corresponded well. Species with low areal cover at the site but high photosynthetic efficiency appeared to potentially important for the ecosystem-level carbon balance.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Niloufar Monhasery, Jens Moll, Carly Cuman, Manuel Franke, Larissa Lamertz, Rebecca Nitz, Boris Görg, Dieter Häussinger, Juliane Lokau, Doreen M. Floss, Roland Piekorz, Eva Dimitriadis, Christoph Garbers, Jürgen Scheller Interleukin (IL)-11 signaling is involved in various processes, including epithelial intestinal cell regeneration and embryo implantation. IL-11 signaling is initiated upon binding of IL-11 to IL-11R1 or IL-11R2, two IL-11α-receptor splice variants, and gp130. Here, we show that IL-11 signaling via IL-11R1/2:gp130 complexes occurs on both the apical and basolateral sides of polarized cells, whereas IL-6 signaling via IL-6R:gp130 complexes is restricted to the basolateral side. We show that basolaterally supplied IL-11 is transported and released to the apical extracellular space via transcytosis in an IL-11R1-dependent manner. By contrast, IL-6R and IL-11R2 do not promote transcytosis. In addition, we show that transcytosis of IL-11 is dependent on the intracellular domain of IL-11R1 and that synthetic transfer of the intracellular domain of IL-11R1 to IL-6R promotes transcytosis of IL-6. Our data define IL-11R as a cytokine receptor with transcytotic activity by which IL-11 and IL-6:soluble IL-6R complexes are transported across cellular barriers. Graphical abstract Teaser Monhasery et al. show that interleukin 11 (IL-11) signaling via IL-11 receptor:gp130 complexes occurs on both the apical and basolateral sides of polarized cells. The transcytotic activity of the IL-11 receptor allows IL-11 and interleukin-6:soluble interleukin-6 receptor complexes to be transported across cellular barriers.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Christian Laut Ebbesen, Eric Torsten Reifenstein, Qiusong Tang, Andrea Burgalossi, Saikat Ray, Susanne Schreiber, Richard Kempter, Michael Brecht The medial entorhinal cortex (MEC) and the adjacent parasubiculum are known for their elaborate spatial discharges (grid cells, border cells, etc.) and the precessing of spikes relative to the local field potential. We know little, however, about how spatio-temporal firing patterns map onto cell types. We find that cell type is a major determinant of spatio-temporal discharge properties. Parasubicular neurons and MEC layer 2 (L2) pyramids have shorter spikes, discharge spikes in bursts, and are theta-modulated (rhythmic, locking, skipping), but spikes phase-precess only weakly. MEC L2 stellates and layer 3 (L3) neurons have longer spikes, do not discharge in bursts, and are weakly theta-modulated (non-rhythmic, weakly locking, rarely skipping), but spikes steeply phase-precess. The similarities between MEC L3 neurons and MEC L2 stellates on one hand and parasubicular neurons and MEC L2 pyramids on the other hand suggest two distinct streams of temporal coding in the parahippocampal cortex. Graphical abstract Teaser Neurons in the parahippocampal cortex discharge in elaborate spatiotemporal firing patterns. Ebbesen et al. use juxtacellular recordings to show that the neuronal cell type is a major determinant of temporal discharge patterns such as bursting and phase precession.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Jeannine Gerhardt, Angela D. Bhalla, Jill Sergesketter Butler, James W. Puckett, Peter B. Dervan, Zev Rosenwaks, Marek Napierala Friedreich’s ataxia (FRDA) is caused by the expansion of GAA repeats located in the Frataxin (FXN) gene. The GAA repeats continue to expand in FRDA patients, aggravating symptoms and contributing to disease progression. The mechanism leading to repeat expansion and decreased FXN transcription remains unclear. Using single-molecule analysis of replicated DNA, we detected that expanded GAA repeats present a substantial obstacle for the replication machinery at the FXN locus in FRDA cells. Furthermore, aberrant origin activation and lack of a proper stress response to rescue the stalled forks in FRDA cells cause an increase in 3′-5′ progressing forks, which could enhance repeat expansion and hinder FXN transcription by head-on collision with RNA polymerases. Treatment of FRDA cells with GAA-specific polyamides rescues DNA replication fork stalling and alleviates expansion of the GAA repeats, implicating DNA triplexes as a replication impediment and suggesting that fork stalling might be a therapeutic target for FRDA. Graphical abstract Teaser Gerhardt et al. demonstrate that stable secondary structures, formed at the expanded GAA repeats in Friedreich’s ataxia patient cells, stall DNA replication. In addition, using a single DNA molecule approach to visualize the Frataxin locus, they show that aberrant activation of origins downstream of the GAA repeats alters replication fork direction.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Jacint G. Sanchez, Jessica J. Chiang, Konstantin M.J. Sparrer, Steven L. Alam, Michael Chi, Marcin D. Roganowicz, Banumathi Sankaran, Michaela U. Gack, Owen Pornillos Antiviral response pathways induce interferon by higher-order assembly of signaling complexes called signalosomes. Assembly of the RIG-I signalosome is regulated by K63-linked polyubiquitin chains, which are synthesized by the E3 ubiquitin ligase, TRIM25. We have previously shown that the TRIM25 coiled-coil domain is a stable, antiparallel dimer that positions two catalytic RING domains on opposite ends of an elongated rod. We now show that the RING domain is a separate self-association motif that engages ubiquitin-conjugated E2 enzymes as a dimer. RING dimerization is required for catalysis, TRIM25-mediated RIG-I ubiquitination, interferon induction, and antiviral activity. We also provide evidence that RING dimerization and E3 ligase activity are promoted by binding of the TRIM25 SPRY domain to the RIG-I effector domain. These results indicate that TRIM25 actively participates in higher-order assembly of the RIG-I signalosome and helps to fine-tune the efficiency of the RIG-I-mediated antiviral response. Graphical abstract Teaser Sanchez et al. elucidate the structural requirements for TRIM25 catalytic activation and its effector functions in the antiviral RIG-I pathway. Higher-order oligomerization of TRIM25 is promoted by RIG-I and likely constitutes a regulatory mechanism of cellular antiviral response.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Thomas Liebmann, Nicolas Renier, Karima Bettayeb, Paul Greengard, Marc Tessier-Lavigne, Marc Flajolet Amyloidosis is a major problem in over one hundred diseases, including Alzheimer’s disease (AD). Using the iDISCO visualization method involving targeted molecular labeling, tissue clearing, and light-sheet microscopy, we studied plaque formation in the intact AD mouse brain at up to 27 months of age. We visualized amyloid plaques in 3D together with tau, microglia, and vasculature. Volume imaging coupled to automated detection and mapping enables precise and fast quantification of plaques within the entire intact mouse brain. The present methodology is also applicable to analysis of frozen human brain samples without specialized preservation. Remarkably, amyloid plaques in human brain tissues showed greater 3D complexity and surprisingly large three-dimensional amyloid patterns, or TAPs. The ability to visualize amyloid in 3D, especially in the context of their micro-environment, and the discovery of large TAPs may have important scientific and medical implications. Graphical abstract Teaser Liebmann et al. present 3D renderings of Alzheimer’s disease in an entire mouse brain hemisphere using iDISCO. Volume imaging coupled to automated detection and mapping to the Allen Brain Atlas enables precise and fast quantification of plaques. Plaques in archival human brain samples showed a greater 3D complexity.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Laura Jacox, Justin Chen, Alyssa Rothman, Hillary Lathrop-Marshall, Hazel Sive The mouth arises from the extreme anterior domain (EAD), a region where the ectoderm and endoderm are directly juxtaposed. Here, we identify a “pre-mouth array” in Xenopus that forms soon after the cranial neural crest has migrated to lie on either side of the EAD. Initially, EAD ectoderm comprises a wide and short epithelial mass that becomes narrow and tall with cells and nuclei changing shape, a characteristic of convergent extension. The resulting two rows of cells—the pre-mouth array—later split down the midline to surround the mouth opening. Neural crest is essential for convergent extension and likely signals to the EAD through the Wnt/planar cell polarity (PCP) pathway. Fzl7 receptor is locally required in EAD ectoderm, while Wnt11 ligand is required more globally. Indeed, heterologous cells expressing Wnt11 can elicit EAD convergent extension. The study reveals a precise cellular mechanism that positions and contributes to the future mouth. Graphical abstract Teaser Jacox et al. identify a precise cellular organization of extreme anterior domain (EAD) ectoderm—the “pre-mouth array”—that contributes to the future mouth opening in Xenopus . Their data indicate that the pre-mouth array forms by convergent extension, under control of adjacent neural crest and Wnt/PCP signaling.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Jing-kuan Wei, Wen-chao Wang, Rong-wei Zhai, Yu-hua Zhang, Shang-chuan Yang, Joshua Rizak, Ling Li, Li-qi Xu, Li Liu, Ming-ke Pan, Ying-zhou Hu, Abdelaziz Ghanemi, Jing Wu, Li-chuan Yang, Hao Li, Long-bao Lv, Jia-li Li, Yong-gang Yao, Lin Xu, Xiao-li Feng, Yong Yin, Dong-dong Qin, Xin-tian Hu, Zheng-bo Wang Here, we examine whether neurons differentiated from transplanted stem cells can integrate into the host neural network and function in awake animals, a goal of transplanted stem cell therapy in the brain. We have developed a technique in which a small “hole” is created in the inferior colliculus (IC) of rhesus monkeys, then stem cells are transplanted in situ to allow for investigation of their integration into the auditory neural network. We found that some transplanted cells differentiated into mature neurons and formed synaptic input/output connections with the host neurons. In addition, c-Fos expression increased significantly in the cells after acoustic stimulation, and multichannel recordings indicated IC specific tuning activities in response to auditory stimulation. These results suggest that the transplanted cells have the potential to functionally integrate into the host neural network. Graphical abstract Teaser Integration of differentiated neurons into a functioning neural network is important for the development of stem cell therapies. Wang et al. found that neurons differentiated from transplanted stem cells respond to auditory stimuli in awake monkeys after transplantation.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Nicolas Huguenin-Dezot, Virginia De Cesare, Julien Peltier, Axel Knebel, Yosua Adi Kristaryianto, Daniel T. Rogerson, Yogesh Kulathu, Matthias Trost, Jason W. Chin Ubiquitin is post-translationally modified by phosphorylation at several sites, but the consequences of these modifications are largely unknown. Here, we synthesize multi-milligram quantities of ubiquitin phosphorylated at serine 20, serine 57, and serine 65 via genetic code expansion. We use these phosphoubiquitins for the enzymatic assembly of 20 isomeric phosphoubiquitin dimers, with different sites of isopeptide linkage and/or phosphorylation. We discover that phosphorylation of serine 20 on ubiquitin converts UBE3C from a dual-specificity E3 ligase into a ligase that primarily synthesizes K48 chains. We profile the activity of 31 deubiquitinases on the isomeric phosphoubiquitin dimers in 837 reactions, and we discover that phosphorylation at distinct sites in ubiquitin can activate or repress cleavage of a particular linkage by deubiquitinases and that phosphorylation at a single site in ubiquitin can control the specificity of deubiquitinases for distinct ubiquitin linkages. Graphical abstract Teaser Huguenin-Dezot et al. combine genetic code expansion and enzymatic assembly to synthesize 20 isomeric phosphoubiquitin chains with distinct Ser phosphorylation and/or isopeptide linkage sites. They discover that ubiquitin phosphorylation can control E3 ligase specificity and deubiquitinase specificity.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Minhee Kim, Brian P. O’Rourke, Rajesh Kumar Soni, Prasad V. Jallepalli, Ronald C. Hendrickson, Meng-Fu Bryan Tsou PLK4 is the major kinase driving centriole duplication. Duplication occurs only once per cell cycle, forming one new (or daughter) centriole that is tightly engaged to the preexisting (or mother) centriole. Centriole engagement is known to block the reduplication of mother centrioles, but the molecular identity responsible for the block remains unclear. Here, we show that the centriolar cartwheel, the geometric scaffold for centriole assembly, forms the identity of daughter centrioles essential for the block, ceasing further duplication of the mother centriole to which it is engaged. To ensure a steady block, we found that the cartwheel requires constant maintenance by PLK4 through phosphorylation of the same substrate that drives centriole assembly, revealing a parsimonious control in which “assembly” and “block for new assembly” are linked through the same catalytic reaction to achieve homeostasis. Our results support a recently deduced model that the cartwheel-bound PLK4 directly suppresses centriole reduplication. Graphical abstract Teaser Cellular structures are maintained at constant numbers by balancing the “promotion” and “suppression” of their biogenesis, two processes opposing each other. Through studies on the cell-division organelle, centrioles, Kim et al. found that the two opposing processes are intimately coupled to the same catalytic reaction involving the kinase PLK4, thereby safeguarding centriole homeostasis.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Shengjie Xue, Chang Liu, Xiujie Sun, Weiyun Li, Chi Zhang, Xin Zhou, Yao Lu, Jun Xiao, Chunyang Li, Xiaoyan Xu, Bing Sun, Guoliang Xu, Hongyan Wang Type I interferons (IFNs) play both beneficial and harmful roles in antiviral responses. Precise regulation of host type I IFNs is thus needed to prevent immune dysregulation. Here, we find that the DNA demethylase TET3 is a negative regulator of IFN-β in response to poly(I:C) stimulation or viral infection. Deletion of TET3 enhances antiviral responses, with elevated expression of IFN-β and IFN-stimulated genes. The catalytic domain of TET3 was critical for the suppression of IFN-β production, but TET3 enzymatic activity was dispensable. Instead, the catalytic domain of TET3 interacts with HDAC1 and SIN3A, thus enhancing their binding to the Ifnb1 promoter. Our study demonstrates that TET3 negatively regulates type I IFN production independent of DNA demethylation. This not only sheds light on TET3 as a signaling protein in immune cells for gene regulation but also will help to develop strategies to prevent type I IFN-related disease. Graphical abstract Teaser Xue et al. find that TET3 expression is decreased after viral infection and that TET3 reduction enhances type I IFN production and virus clearance. Mechanistically, TET3 recruits HDAC1 to the Ifnb1 promoter, thus suppressing type I IFN transcription.

Beschreibung: Publication date: Available online 14 July 2016 Source: Cell Reports Author(s): Chieh Hsu, Vincent Jaquet, Mumun Gencoglu, Attila Becskei Bistability plays an important role in cellular memory and cell-fate determination. A positive feedback loop can generate bistability if it contains ultrasensitive molecular reactions. It is often difficult to detect bistability based on such molecular mechanisms due to its intricate interaction with cellular growth. We constructed transcriptional feedback loops in yeast. To eliminate growth alterations, we reduced the protein levels of the transcription factors by tuning the translation rates over two orders of magnitude with designed RNA stem loops. We modulated two ultrasensitive reactions, homodimerization and the cooperative binding of the transcription factor to the promoter. Either of them is sufficient to generate bistability on its own, and when acting together, a particularly robust bistability emerges. This bistability persists even in the presence of a negative feedback loop. Given that protein homodimerization is ubiquitous, it is likely to play a major role in the behavior of regulatory networks. Graphical abstract Teaser Using RNA stem loops to attenuate translation rates, Hsu et al. designed synthetic feedback loops in yeast to study the sources of bistability. They show that cooperative binding of a transcription factor to its promoter or its dimerization generates bistability. Bistability is particularly robust when the dimerizing transcription factor binds to the promoter cooperatively.

Beschreibung: by Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J. Pollard, Alexander Konovalov, Robert M. Flight, Kai Blin, Juan Antonio Vizcaíno

Beschreibung: by Xing Chen, Biao Ren, Ming Chen, Quanxin Wang, Lixin Zhang, Guiying Yan Fungal infection has become one of the leading causes of hospital-acquired infections with high mortality rates. Furthermore, drug resistance is common for fungus-causing diseases. Synergistic drug combinations could provide an effective strategy to overcome drug resistance. Meanwhile, synergistic drug combinations can increase treatment efficacy and decrease drug dosage to avoid toxicity. Therefore, computational prediction of synergistic drug combinations for fungus-causing diseases becomes attractive. In this study, we proposed similar nature of drug combinations: principal drugs which obtain synergistic effect with similar adjuvant drugs are often similar and vice versa. Furthermore, we developed a novel algorithm termed Network-based Laplacian regularized Least Square Synergistic drug combination prediction (NLLSS) to predict potential synergistic drug combinations by integrating different kinds of information such as known synergistic drug combinations, drug-target interactions, and drug chemical structures. We applied NLLSS to predict antifungal synergistic drug combinations and showed that it achieved excellent performance both in terms of cross validation and independent prediction. Finally, we performed biological experiments for fungal pathogen Candida albicans to confirm 7 out of 13 predicted antifungal synergistic drug combinations. NLLSS provides an efficient strategy to identify potential synergistic antifungal combinations.

Beschreibung: by Abbey B. Holt, Dan Wilson, Max Shinn, Jeff Moehlis, Theoden I. Netoff We propose a novel, closed-loop approach to tuning deep brain stimulation (DBS) for Parkinson’s disease (PD). The approach, termed Phasic Burst Stimulation (PhaBS), applies a burst of stimulus pulses over a range of phases predicted to disrupt pathological oscillations seen in PD. Stimulation parameters are optimized based on phase response curves (PRCs), which would be measured from each patient. This approach is tested in a computational model of PD with an emergent population oscillation. We show that the stimulus phase can be optimized using the PRC, and that PhaBS is more effective at suppressing the pathological oscillation than a single phasic stimulus pulse. PhaBS provides a closed-loop approach to DBS that can be optimized for each patient.

Beschreibung: by Kyuha Choi, Carsten Reinhard, Heïdi Serra, Piotr A. Ziolkowski, Charles J. Underwood, Xiaohui Zhao, Thomas J. Hardcastle, Nataliya E. Yelina, Catherine Griffin, Matthew Jackson, Christine Mézard, Gil McVean, Gregory P. Copenhaver, Ian R. Henderson Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance ( R ) genes that encode NBS-LRR domain proteins. Therefore, we sought to test whether NBS-LRR genes would overlap with meiotic crossover hotspots using experimental genetics in Arabidopsis thaliana . NBS-LRR genes tend to physically cluster in plant genomes; for example, in Arabidopsis most are located in large clusters on the south arms of chromosomes 1 and 5. We experimentally mapped 1,439 crossovers within these clusters and observed NBS-LRR gene associated hotspots, which were also detected as historical hotspots via analysis of linkage disequilibrium. However, we also observed NBS-LRR gene coldspots, which in some cases correlate with structural heterozygosity. To study recombination at the fine-scale we used high-throughput sequencing to analyze ~1,000 crossovers within the RESISTANCE TO ALBUGO CANDIDA1 ( RAC1 ) R gene hotspot. This revealed elevated intragenic crossovers, overlapping nucleosome-occupied exons that encode the TIR, NBS and LRR domains. The highest RAC1 recombination frequency was promoter-proximal and overlapped CTT-repeat DNA sequence motifs, which have previously been associated with plant crossover hotspots. Additionally, we show a significant influence of natural genetic variation on NBS-LRR cluster recombination rates, using crosses between Arabidopsis ecotypes. In conclusion, we show that a subset of NBS-LRR genes are strong hotspots, whereas others are coldspots. This reveals a complex recombination landscape in Arabidopsis NBS-LRR genes, which we propose results from varying coevolutionary pressures exerted by host-pathogen relationships, and is influenced by structural heterozygosity.