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Biology Open

M Alessandra Vigano, Dimitri Bieli, Jonas V Schaefer, Roman Peter Jakob, Shinya Matsuda, Timm Maier, Andreas Plückthun, Markus Affolter
Over the last few years, protein-based affinity reagents have proven very helpful in cell and developmental biology. While many of these versatile small proteins can be expressed both in the intracellular and extracellular milieu in cultured cells and in living organisms, they can also be functionalized by fusing them to different protein domains in order to regulate or modulate their target proteins in diverse manners. For example, protein binders have been employed to degrade, trap, localize or enzymatically modify specific target proteins...
September 20, 2018: Biology Open
Elise Hennebert, Edwicka Gregorowicz, Patrick Flammang
Many marine invertebrates use adhesive secretions to attach to underwater surfaces and functional groups borne by their adhesive proteins and carbohydrates, such as catechols and phosphates, play a key role in adhesion. The occurrence of sulfates as recurrent moieties in marine bioadhesives suggests that they could also be involved. However, in most cases, their presence in the adhesive material remains speculative. We investigated the presence of sulfated biopolymers in five marine invertebrates representative of the four types of adhesion encountered in the sea: mussels and tubeworms for permanent adhesion, limpets for transitory adhesion, sea stars for temporary adhesion, and sea cucumbers for instantaneous adhesion...
September 20, 2018: Biology Open
Cátia Crespo, Elisabeth Knust
Photoreceptor cells (PRCs) mature from simple epithelial cells, a process characterised by growth and compartmentalisation of the apical membrane into an inner and an outer segment. So far, a PRC subtype-specific description of morphological and cellular changes in the developing zebrafish retina is missing. Here, we performed an in-depth characterisation of four of the five PRC subtypes of the zebrafish retina between 51 and 120 hours post fertilisation, including quantification of the size of different compartments, localisation of polarity proteins and positioning of organelles...
September 20, 2018: Biology Open
Lauren E Nadler, Shaun S Killen, Paolo Domenici, Mark I McCormick
Animals are exposed to variable and rapidly changing environmental flow conditions, such as wind in terrestrial habitats and currents in aquatic systems. For fishes, previous work suggests that individuals exhibit flow-induced changes in aerobic swimming performance. Yet, no one has examined whether similar plasticity is found in fast-start escape responses, which are modulated by anaerobic swimming performance, sensory stimuli and neural control. In this study, we used fish from wild schools of the tropical damselfish Chromis viridis from shallow reefs surrounding Lizard Island in the Great Barrier Reef, Australia...
September 20, 2018: Biology Open
Jamie Rae Acosta, Maxinne Watchon, Kristy C Yuan, Jennifer Fifita, Adam J Svahn, Emily K Don, Ian P Blair, Garth A Nicholson, Nicholas J Cole, Claire Goldsbury, Angela S Laird
We describe a protocol for culturing neurons from transgenic zebrafish embryos to investigate the subcellular distribution and protein aggregation status of neurodegenerative disease-causing proteins. The utility of the protocol was demonstrated on cell cultures from zebrafish that transgenically express disease-causing variants, human FUS and ataxin-3 proteins, in order to study amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia type-3 (SCA3), respectively. A mixture of neuronal subtypes, including motor neurons, exhibited differentiation and neurite outgrowth in the cultures...
September 6, 2018: Biology Open
Vedad Delic, Kenyaria Noble, Sandra Zivkovic, Tam-Anh Phan, Christian Reynes, Yumeng Zhang, Oluwakemi Phillips, Charles Claybaker, Yen Ta, Vinh B Dinh, Josean Cruz, Tomas A Prolla, Patrick C Bradshaw
Mitochondrial DNA mutations accumulate with age and may play a role in stem cell aging as suggested by the premature aging phenotype of mitochondrial DNA polymerase gamma (POLG) exonuclease-deficient mice. Therefore, E1A immortalized murine embryonic fibroblasts (MEFs) from POLG exonuclease-deficient and WT mice were constructed. Surprisingly, when some E1A immortalized MEF lines were cultured in pyruvate containing media they slowly became addicted to the pyruvate. The POLG exonuclease-deficient MEFs were more sensitive to several mitochondrial inhibitors and showed increased reactive oxygen species production under standard conditions...
September 3, 2018: Biology Open
Madelyn K Logan, Marilyn F Burke, Michael D Hebert
Small Cajal body-specific RNAs (scaRNAs) are part of small Cajal body-specific ribonucleoproteins (scaRNPs) that modify small nuclear RNA (snRNA) in Cajal Bodies (CBs). Several scaRNAs (scaRNA 2, 9 and 17) have been found to generate smaller, nucleolus-enriched fragments. We hypothesize that the fragments derived from scaRNA 2, 9 and 17 form regulatory RNPs that influence the level of modifications within rRNA by altering small nucleolar RNP (snoRNP) activity. Here we show that external factors such as DNA damaging agents can alter the scaRNA9 full-length to processed fragment ratio...
September 3, 2018: Biology Open
Jiude Mao, Chad O'Gorman, Miriam Sutovsky, Michal Zigo, Kevin D Wells, Peter Sutovsky
Ubiquitin A-52 residue ribosomal protein fusion product 1 ( Uba52 ), a ubiquitin-ribosomal fusion gene is a major source of ubiquitin protein for covalent modification of proteinaceous substrates recycled by ubiquitin-proteasome system (UPS). Its role in early embryo development has not been studied. Using CRISPR/cas9 gene editing tool, the objective of this study was to determine if UBA52 protein is required for mammalian embryogenesis. Matured metaphase II porcine oocytes were injected with CRISPR Cas9+guide RNAs (Uba52 gRNA) or cas9 without gRNAs as control, followed by in vitro fertilization (IVF) and embryo culture to day 7...
August 22, 2018: Biology Open
Michael Brand, Matthias Sommer, Frank Jermusek, William E Fahl, Michael Uder
The aim of our study was to determine the protective efficacy of the PrC-210 aminothiol radioprotector against X-ray-induced DNA damage in normal human cells and to establish dose- and time-effect models for future PrC-210 use in humans. The PrC-210 structure has a branched structure which enables scavenging of reactive oxygen species (ROS) away from DNA. Normal human blood lymphocytes, fibroblasts, and naked genomic DNA were exposed to PrC-210 from seconds to hours prior to irradiation. Biological (γ-H2AX foci), chemical (8-oxo-deoxyguanosine), and physical (genomic DNA electrophoretic migration) DNA damage endpoints were scored to determine the ability of PrC-210 to suppress radiation-induced DNA damage...
August 22, 2018: Biology Open
Daniel Terheyden-Keighley, Xiaoqing Zhang, Beate Brand-Saberi, Carsten Theiss
During the development of the peripheral nervous system, a subgroup of neural crest cells migrate away from the neural tube and coalesce into clusters of sensory neurons (ganglia). Mechanisms involved in the formation of the dorsal root ganglia (DRG) from neural crest cells are currently unclear. Mice carrying mutations in Cxcr4 , which is known to control neural crest migration, exhibit malformed DRG. In order to investigate this phenomenon, we modelled sensory neuron differentiation in vitro by directing the differentiation of human induced pluripotent stem cells into sensory neurons under SDF1 (agonist), AMD3100 (antagonist) or control conditions...
August 22, 2018: Biology Open
Timothy Jakobi, Dmitry Kolomenskiy, Teruaki Ikeda, Simon Watkins, Alex Fisher, Hao Liu, Sridhar Ravi
Flight is a complicated task at small scales in part due to the ubiquitous unsteady air which contains it. Flying organisms deal with these difficulties using active and passive control mechanisms to steer their body motion. Body attitudes of flapping organisms are linked with their resultant flight trajectories and performance, yet little is understood about how discrete unsteady aerodynamic phenomena affect the interlaced dynamics of such systems. In this study, we examined freely flying bumblebees subject to a single discrete gust to emulate aerodynamic disturbances encountered in nature...
August 22, 2018: Biology Open
Ana Rato, Sandra Joaquim, Tânia G Tavares, Zita E Martins, A Catarina Guedes, Luís F Pereira, Jorge Machado, A Margarete Matias, José F M Gonçalves, Paulo Vaz-Pires, Leonardo J Magnoni, Rodrigo O A Ozório, Domitília Matias
The current study evaluated the microalgae replacement by dry macroalgae ( Ulva rigida ) in the reproductive success and biochemical composition of pacific oyster ( Crassostrea gigas ) during broodstock conditioning. Five nutritional regimes were tested: 100% macroalgae (Diet 1); 50% macroalgae+50% microalgae (Diet 2); 25% macroalgae+75% microalgae (Diet 3); 100% microalgae (Diet 4). An Unfed group was used as a negative control. The microalgae blend was composed by 33% Isochrysis galbana and 67% diatoms (75% Skeletonema costatum +25% Chaetoceros calcitrans )...
August 20, 2018: Biology Open
Koichi Fujisawa, Taro Takami, Yumi Fukui, Takahiro Nagatomo, Issei Saeki, Toshihiko Matsumoto, Isao Hidaka, Naoki Yamamoto, Takeshi Okamoto, Makoto Furutani-Seiki, Isao Sakaida
Fatty liver, which has been continuously growing in the number of patients, is the most common liver disease. For detailed analysis, a useful model of fatty liver is desired and fish is considered as a candidate of the models. We assessed direct observation of the liver, which is the most conventional method for the non-invasive analysis of the progression in fatty liver. By using transparent medaka, changes in fat deposition in the liver were able to be observed. An analysis of the assessment of the progression in fatty liver using Ultrasound showed a significant increase in echo intensity, which indicates that this is a useful examination method...
August 20, 2018: Biology Open
Alexander G Knorr, Céline M Gravot, Clayton Gordy, Stefan Glasauer, Hans Straka
Passive and interactive virtual reality (VR) environments are becoming increasingly popular in the field of behavioral neuroscience. While the technique was originally developed for human observers, corresponding applications have been adopted for the research of visual-driven behavior and neural circuits in animals. RGB color reproduction using red, green and blue primary color pixels is generally calibrated for humans, questioning if the distinct parameters are also readily transferable to other species. In particular, a visual image in the RGB color space has a clearly defined contrast pattern for humans, but this may not necessarily be the case for other mammals or even non-mammalian species, thereby impairing any interpretation of color-related behavioral or neuronal results...
August 20, 2018: Biology Open
Zhibo Wang, Guofang Li, Hanqing Sun, Li Ma, Yanping Guo, Zhengyang Zhao, Hua Gao, Lixin Mei
In our study, the effects of water stress on photosynthesis and photosynthetic electron transport chain (PETC) were studied through several ways including monitoring the change of gas exchange parameters, modulated chlorophyll fluorescence, rapid fluorescence induction kinetics, reactive oxygen species, antioxidant enzymes activities and D1 protein in apple leaves. Our results showed when the leaf water potential ( ψ w ) was above -1.5MPa, the stomatal limitation should be the main reason for the drop of photosynthesis...
August 20, 2018: Biology Open
Piotr Duchnowski, Tomasz Hryniewiecki, Mariusz Kuśmierczyk, Piotr Szymanski
PURPOSE The aim of the study was to evaluate the prognostic value of RDW for multiple organ dysfunction syndrome (MODS) in the early postoperative period in patients undergoing valve replacement or repair surgery. METHODS A prospective study was conducted on a group of 713 consecutive patients with haemodynamically significant valvular heart disease who underwent elective valvular surgery. The primary end-point at the 30-day follow-up was postoperative MODS. The secondary end-point was death from all causes in patients with MODS...
August 20, 2018: Biology Open
Lahcen Ouchari, Amal Boukeskasse, Brahim Bouizgarne, Yedir Ouhdouch
The absence of new antibiotics is guiding more and more researchers to specific ecosystems. One hundred sixty-three Actinobacteria isolates were isolated from Merzouga sand and screened for their antibacterial and antifungal activities. To test the antimicrobial effect of isolates, four microorganisms known as human potential pathogens were used. The electrophoretic profiles of isolates obtained by repetitive element PCR fingerprinting (rep-PCR) were compared by clustering. Results showed that among the tested isolates, 59% were active against one or more of testing Gram positive, Gram negative and the yeast Candida albicans The importance of culture media for the activity expression was revealed...
August 20, 2018: Biology Open
David Holowka, Kankanit Thanapuasuwan, Barbara Baird
Lipid phase heterogeneity in plasma membranes is thought to play a key role in targeting cellular signaling, but efforts to test lipid raft and related hypotheses are limited by the spatially dynamic nature of these phase-based structures in cells and by experimental characterization tools. We suggest that perturbation of plasma membrane structure by lipid derivatives offers a general method for assessing functional roles for ordered lipid regions in membrane and cell biology. We previously reported that short chain ceramides with either C2 or C6 acyl chains inhibit antigen-stimulated Ca2+ mobilization (Gidwani et al...
August 10, 2018: Biology Open
Tal Frolinger, Francis Herman, Ali Sharma, Steven Sims, Jun Wang, Giulio Maria Pasinetti
In this study, we developed an experimental protocol leveraging enhanced reduced representation bisulphite sequencing to investigate methylation and gene expression patterns in the hippocampus in response to polyphenolic compounds. We report that the administration of a standardized bioavailable polyphenolic preparation (BDPP) differentially influences methylated cytosine patterns in introns, UTR and exons in hippocampal genes. We subsequently established that dietary BDPP-mediated changes in methylation influenced the transcriptional pattern of select genes that are involved in synaptic plasticity...
July 3, 2018: Biology Open
Yordano E Jimenez, Ariel L Camp, Jonathan D Grindall, Elizabeth L Brainerd
Many suction-feeding fish use neurocranial elevation to expand the buccal cavity for suction feeding, a motion necessarily accompanied by the dorsal flexion of joints in the axial skeleton. How much dorsal flexion the axial skeleton accommodates and where that dorsal flexion occurs may vary with axial skeletal morphology, body shape and the kinematics of neurocranial elevation. We measured three-dimensional neurocranial kinematics in three species with distinct body forms: laterally compressed Embiotoca lateralis , fusiform Micropterus salmoides , and dorsoventrally compressed Leptocottus armatus The area just caudal to the neurocranium occupied by bone was 42±1...
September 20, 2018: Biology Open
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