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  You have access

  Open access

November, 2015; 4 (11)

RESEARCH ARTICLES

  • Open Access
    Atg9 is required for intraluminal vesicles in amphisomes and autolysosomes
    C. A. Bader, T. Shandala, Y. S. Ng, I. R. D. Johnson, D. A. Brooks
    Biology Open 2015 4: 1345-1355; doi: 10.1242/bio.013979

    Summary: The disappearance of intraluminal vesicles in amphisomes/autolysosomes upon Atg9 depletion suggests that Atg9 has a specific role in intraluminal vesicle formation in autophagic compartments.

  • Open Access
    The zebrafish Kupffer's vesicle as a model system for the molecular mechanisms by which the lack of Polycystin-2 leads to stimulation of CFTR
    Mónica Roxo-Rosa, Raquel Jacinto, Pedro Sampaio, Susana Santos Lopes
    Biology Open 2015 4: 1356-1366; doi: 10.1242/bio.014076

    Summary: Here, we tested the zebrafish Kupffer's vesicle (KV) as a model organ to study, through in vivo imaging of KV volume, the stimulation of cystic fibrosis transmembrane conductance regulator (CFTR) in autosomal dominant polycystic kidney disease ADPKD.

  • Open Access
    Loss of arylformamidase with reduced thymidine kinase expression leads to impaired glucose tolerance
    Alison J. Hugill, Michelle E. Stewart, Marianne A. Yon, Fay Probert, I. Jane Cox, Tertius A. Hough, Cheryl L. Scudamore, Liz Bentley, Gary Wall, Sara E. Wells, Roger D. Cox
    Biology Open 2015 4: 1367-1375; doi: 10.1242/bio.013342

    Summary: Mice homozygous for a tm1b deleted allele have impaired glucose tolerance due to reduced insulin secretion associated with reduced islet mass, but no evidence of renal disease, suggesting a link between abnormal tryptophan metabolism and diabetes.

  • Open Access
    Both ciliary and non-ciliary functions of Foxj1a confer Wnt/β-catenin signaling in zebrafish left-right patterning
    Ping Zhu, Xiaolei Xu, Xueying Lin
    Biology Open 2015 4: 1376-1386; doi: 10.1242/bio.012088

    Summary: Using a targeted overexpression platform, we showed that Wnt activation induces ectopic foxj1a expression and ectopic cilia formation, and revealed two distinct roles of Foxj1a in conferring Wnt-governed left-right patterning.

  • Open Access
    Targeting of ribosomal protein S6 to dendritic spines by in vivo high frequency stimulation to induce long-term potentiation in the dentate gyrus
    Itsuko Nihonmatsu, Noriaki Ohkawa, Yoshito Saitoh, Kaoru Inokuchi
    Biology Open 2015 4: 1387-1394; doi: 10.1242/bio.013243

    Summary: Induction of long-term potentiation, which is a cellular model of learning and memory, mediates the selective targeting of the translational machinery on activated dendritic spines in vivo.

  • Open Access
    Inter- vs intra-individual variation and temporal repeatability of escape responses in the coral reef fish Amblyglyphidodon curacao
    Maïwenn Jornod, Dominique G. Roche
    Biology Open 2015 4: 1395-1399; doi: 10.1242/bio.013508

    Summary: Quantification of the inter- and intra-individual variation in behavioural and kinematic components of escape performance of the tropical damselfish Amblyglyphidodon curacao found no evidence of habituation or fatigue due to repeated stimulations.

  • Open Access
    α1B-Adrenergic receptor signaling controls circadian expression of Tnfrsf11b by regulating clock genes in osteoblasts
    Takao Hirai, Kenjiro Tanaka, Akifumi Togari
    Biology Open 2015 4: 1400-1409; doi: 10.1242/bio.012617

    Summary: This study demonstrates that the circadian regulation of TNFRSF11B is regulated by the clock genes Nr1d1 and Arntl, which are components of the core loop of the circadian clock in osteoblasts, providing a molecular mechanism for the control of bone remodelling by circadian rhythms.

  • Open Access
    Sexual dimorphism in an animal model of Sjögren's syndrome: a potential role for Th17 cells
    Alexandria Voigt, Lida Esfandiary, Cuong Q. Nguyen
    Biology Open 2015 4: 1410-1419; doi: 10.1242/bio.013771

    Summary: Sjogren's syndrome (SjS) is the one of the most common sexual dimorphic autoimmune diseases. This study demonstrates that female C57BL/6.NOD-Aec1Aec2 mice develop earlier onset and more severe symptoms of SjS than male counterparts. Therefore, the C57BL/6.NOD-Aec1Aec2 mouse model could be an appropriate model to study sexual dimorphism in SjS.

  • Open Access
    Cellular population dynamics control the robustness of the stem cell niche
    Adam L. MacLean, Paul D. W. Kirk, Michael P. H. Stumpf
    Biology Open 2015 4: 1420-1426; doi: 10.1242/bio.013714

    Summary: Stem cell niche dynamics are very robust to external and physiological perturbations because proliferation and differentiation are naturally balanced and controlled by the reliance on a shared niche environment.

  • Open Access
    E-cadherin cytoplasmic domain inhibits cell surface localization of endogenous cadherins and fusion of C2C12 myoblasts
    Masayuki Ozawa
    Biology Open 2015 4: 1427-1435; doi: 10.1242/bio.013938

    Summary: This novel approach seeks to overcome the limitations of studying the role of individual cadherins in skeletal muscle fusion in vitro by selecting for myoblasts that express dominant-negative E-cadherin, and provides evidence that cadherins play an essential role in myoblast fusion.

  • Open Access
    Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells
    Catriona M. Manville, Kayleigh Smith, Zbyslaw Sondka, Holly Rance, Simon Cockell, Ian G. Cowell, Ka Cheong Lee, Nicholas J. Morris, Kay Padget, Graham H. Jackson, Caroline A. Austin
    Biology Open 2015 4: 1436-1447; doi: 10.1242/bio.014308

    Summary: Gene ontology enrichment analysis of genes associated with human TOP2B peaks, identified by whole genome ChIP seq used to identify regions of binding, highlighted a number of processes in neuronal development including axonogenesis and axon guidance.

  • Open Access
    Depletion or over-expression of Sh3px1 results in dramatic changes in cell morphology
    Lawrence Hicks, Guojun Liu, Fiona P. Ukken, Sumin Lu, Kathryn E. Bollinger, Kate O'Connor-Giles, Graydon B. Gonsalvez
    Biology Open 2015 4: 1448-1461; doi: 10.1242/bio.013755

    Summary: Proteins containing BAR domains are known to generate membrane curvature. Some BAR domains generate tubules upon over-expression in cells, whereas others generate membrane protrusions. We demonstrate that Sh3px1, the Drosophila ortholog of the Snx9 family, is capable of inducing both tubules and protrusions.

  • Open Access
    Generation of tissue-engineered small intestine using embryonic stem cell-derived human intestinal organoids
    Stacy R. Finkbeiner, Jennifer J. Freeman, Minna M. Wieck, Wael El-Nachef, Christopher H. Altheim, Yu-Hwai Tsai, Sha Huang, Rachel Dyal, Eric S. White, Tracy C. Grikscheit, Daniel H. Teitelbaum, Jason R. Spence
    Biology Open 2015 4: 1462-1472; doi: 10.1242/bio.013235

    Summary: HIO-seeded PGA/PLLA scaffolds thrive in vivo and develop into tissue that looks nearly identical to adult human intestinal tissue. These scaffolds appear to be suitable for further tissue engineering approaches to develop functional intestine.

  • Open Access
    The action of mimetic peptides on connexins protects fibroblasts from the negative effects of ischemia reperfusion
    Beverley J. Glass, Rebecca G. Hu, Anthony R. J. Phillips, David L. Becker
    Biology Open 2015 4: 1473-1480; doi: 10.1242/bio.013573

    Summary: Connexin mimetic peptides can reduce the levels of connexin proteins in cells and can prevent the spread of cell death that occurs following ischemia reperfusion injury, which has therapeutic potential.

  • Open Access
    There are four dynamically and functionally distinct populations of E-cadherin in cell junctions
    Zahra Erami, Paul Timpson, Wu Yao, Ronen Zaidel-Bar, Kurt I. Anderson
    Biology Open 2015 4: 1481-1489; doi: 10.1242/bio.014159

    Summary: Four populations of E-cadherin are identified within cell junctions based on the molecular interactions which determine their size, mobility, and adhesive properties, and support association with the actin cytoskeleton as the first step in adhesion formation.

  • Open Access
    Evolution of enlarged body size of coal tits Parus ater in geographic isolation from two larger competitors, the crested tit Parus cristatus and the willow tit Parus montanus, on six Scandinavian islands
    R. Åke Norberg, Ulla M. Lindhe Norberg
    Biology Open 2015 4: 1490-1508; doi: 10.1242/bio.013839

    Summary: On six widely separated Scandinavian islands, an enlarged food base and intraspecific competition has caused the coal tit Parus ater to evolve morphologically in the direction of two absent competitors.

  • Open Access
    Generation and analysis of knock-in mice carrying pseudohypoaldosteronism type II-causing mutations in the cullin 3 gene
    Yuya Araki, Tatemitsu Rai, Eisei Sohara, Takayasu Mori, Yuichi Inoue, Kiyoshi Isobe, Eriko Kikuchi, Akihito Ohta, Sei Sasaki, Shinichi Uchida
    Biology Open 2015 4: 1509-1517; doi: 10.1242/bio.013276

    Summary: A knock-in mutation in intron 8 of Cul3 in mice led to decreased Cul3 protein expression. Decreased Cul3 protein expression alone did not cause pseudohypoaldosteronism type II (PHAII).

  • Open Access
    Epigenetic regulator Lid maintains germline stem cells through regulating JAK-STAT signaling pathway activity
    Lama Tarayrah, Yuping Li, Qiang Gan, Xin Chen
    Biology Open 2015 4: 1518-1527; doi: 10.1242/bio.013961

    Summary: This study provides new insights into the biological functions of a histone demethylase and sheds light on the interaction between epigenetic mechanisms and signaling pathways in regulating stem cell activities.

  • Open Access
    Do phages impact microbial dynamics, prokaryotic community structure and nutrient dynamics in Lake Bourget?
    Antony Meunier, Stéphan Jacquet
    Biology Open 2015 4: 1528-1537; doi: 10.1242/bio.013003

    Summary: Phages can exert important control on the structure of the bacterial community. By contrast, neither the archaeal community nor the cycling of nutrients seems to be affected by phage abundance.

  • Open Access
    Hox11 genes regulate postnatal longitudinal bone growth and growth plate proliferation
    Kyriel M. Pineault, Ilea T. Swinehart, Kayla N. Garthus, Edward Ho, Qing Yao, Ernestina Schipani, Kenneth M. Kozloff, Deneen M. Wellik
    Biology Open 2015 4: 1538-1548; doi: 10.1242/bio.012500

    Summary: Hox genes are required for postnatal skeletal growth. Hox11 genes function in the zeugopod skeletal elements and regulate longitudinal growth through controlling chondrocyte maturation within the growth plate.

  • Open Access
    Do circadian genes and ambient temperature affect substrate-borne signalling during Drosophila courtship?
    Izarne Medina, José Casal, Caroline C. G. Fabre
    Biology Open 2015 4: 1549-1557; doi: 10.1242/bio.014332

    Summary: We studied the effects of circadian genes and ambient temperature on the substrate-borne signals produced by fruit flies during courtship.

  • Open Access
    Context-specific comparison of sleep acquisition systems in Drosophila
    David S. Garbe, Wesley L. Bollinger, Abigail Vigderman, Pavel Masek, Jill Gertowski, Amita Sehgal, Alex C. Keene
    Biology Open 2015 4: 1558-1568; doi: 10.1242/bio.013011

    Summary: Multiple sleep acquisition systems provide efficient and accurate methods for measuring sleep duration in Drosophila, while video tracking and multibeam analysis allow for increased flexibility of behavioral paradigms and greater resolution of sleep architecture.

  • Open Access
    Novel localization of formin mDia2: importin β-mediated delivery to and retention at the cytoplasmic side of the nuclear envelope
    Xiaowei Shao, Keiko Kawauchi, G. V. Shivashankar, Alexander D. Bershadsky
    Biology Open 2015 4: 1569-1575; doi: 10.1242/bio.013649

    Summary: Formin mDia2 accumulates to the cytoplasmic side of the nuclear envelope and co-localizes with the nuclear pore complexes in an importin β-dependent manner.

  • Open Access
    Mindbomb 2 is dispensable for embryonic development and Notch signalling in zebrafish
    Shohei Mikami, Mizuki Nakaura, Atsuo Kawahara, Takamasa Mizoguchi, Motoyuki Itoh
    Biology Open 2015 4: 1576-1582; doi: 10.1242/bio.014225

    Summary: Mib2 is dispensable for embryonic development and does not have redundant functions with Mib1 in Notch signalling, at least during early development stages in zebrafish.

  • Open Access
    The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals
    Günter Vogt, Cassandra Falckenhayn, Anne Schrimpf, Katharina Schmid, Katharina Hanna, Jörn Panteleit, Mark Helm, Ralf Schulz, Frank Lyko
    Biology Open 2015 4: 1583-1594; doi: 10.1242/bio.014241

    Summary: The triploid marbled crayfish is a rare animal example of speciation by autopolyploidisation and parthenogenesis. It seems to be a particularly suitable model to study how much genetic and epigenetic change is necessary to create a new species.

METHODS & TECHNIQUES

  • Open Access
    Generation of primitive neural stem cells from human fibroblasts using a defined set of factors
    Takumi Miura, Tohru Sugawara, Atsushi Fukuda, Ryo Tamoto, Tomoyuki Kawasaki, Akihiro Umezawa, Hidenori Akutsu
    Biology Open 2015 4: 1595-1607; doi: 10.1242/bio.013151

    Summary: A novel method for the generation of self-renewable, multipotent and neural lineage-restricted LIF-dependent induced primitive neural stem cells (LD-iNSCs) from human fibroblasts with the potential to facilitate human neuronal studies.

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    Integrated Analysis of Cell Shape and Movement in Moving Frame

    Yusri Dwi Heryanto, Chin-Yi Cheng, Yutaka Uchida, Kazushi Mimura, Masaru Ishii, Ryo Yamada
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  • Open Access

    Avoiding being stung or bitten – prey capture behaviors of the ant-eating Texas horned lizard (Phrynosoma cornutum)

    Ismene Fertschai, Wade C. Sherbrooke, Matthias Ott, Boris P. Chagnaud
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  • Open Access

    A Zebrafish Forward Genetic Screen Identifies an Indispensible Threonine Residue in the Kinase Domain of PRKD2

    Panagiota Giardoglou, Despina Bournele, Misun Park, Stavroula Kanoni, George V. Dedoussis, Susan F. Steinberg, Panos Deloukas, Dimitris Beis
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    Interdomain interactions regulate the localization of a lipid transfer protein at ER-PM contact sites

    Bishal Basak, Harini Krishnan, Raghu Padinjat
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    The thermal dependence and molecular basis of physiological color change in Takydromus septentrionalis (Lacertidae)

    Kun Guo, Jun Zhong, Lin Zhu, Fan Xie, Yu Du, Xiang Ji
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