Biology Open

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List of Papers (Total 596)

Simultaneous expression of ClopHensor and SLC26A3 reveals the nature of endogenous oxalate transport in CHO cells

ClopHensor, a fluorescent fusion protein, is a dual function biosensor that has been utilized as a tool for the simultaneous measurement of intracellular chloride and pH in cells. ClopHensor has traditionally been used in conjunction with fluorescence microscopy for single cell measurements. Here, we present a promising multi-well format advancement for the use of ClopHensor as a...

Microenvironmental stimuli induce different macrophage polarizations in experimental models of emphysema

Macrophages play a pivotal role in the development of emphysema and depending on the microenvironment stimuli can be polarized into M1- or M2-like macrophage phenotypes. We compared macrophage polarizations in cigarette smoke (CS)- and porcine pancreatic elastase (PPE)-induced emphysema models. C57BL/6 mice were subdivided into four experimental groups. In the PPE group, animals...

Automated morphometry toolbox for analysis of microscopic model organisms using simple bright-field imaging

Model organisms with compact genomes, such as yeast and C aenorhabditis elegans , are particularly useful for understanding organism growth and life/cell cycle. Organism morphology is a critical parameter to measure in monitoring growth and stage in the life cycle. However, manual measurements are both time consuming and potentially inaccurate, due to variations among users and...

Alteration of 28S rRNA 2′-O-methylation by etoposide correlates with decreased SMN phosphorylation and reduced Drosha levels

The most common types of modification in human rRNA are pseudouridylation and 2′- O ribose methylation. These modifications are performed by small nucleolar ribonucleoproteins (snoRNPs) which contain a guide RNA (snoRNA) that base pairs at specific sites within the rRNA to direct the modification. rRNA modifications can vary, generating ribosome heterogeneity. One possible method...

Tracking diphyodont development in miniature pigs in vitro and in vivo

Abnormalities of tooth number in humans, such as agenesis and supernumerary tooth formation, are closely related to diphyodont development. There is an increasing demand to understand the molecular and cellular mechanisms behind diphyodont development through the use of large animal models, since they are the most similar to the mechanism of human tooth development. However...

Antimicrobial potential of actinomycetes isolated from the unexplored hot Merzouga desert and their taxonomic diversity

The absence of new antibiotics is guiding more and more researchers to specific ecosystems. One hundred and 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...

From polar bears to cell polarity and everything in between: 2018 in review

It was all change in the BiO Editor team in 2018, with Steven Kelly replacing departing founding Editor-in-Chief Jordan Raff ([Kelly, 2018][1]; [Raff, 2018][2]). We were delighted to announce the appointment of Tristan Rodríguez (Imperial College London, UK) and Yong Peng (Sichuan University, China

GFP-Forked, a genetic reporter for studying Drosophila oocyte polarity

The polarized organization of the Drosophila oocyte can be visualized by examining the asymmetric localization of mRNAs, which is supported by networks of polarized microtubules (MTs). In this study, we used the gene forked , the putative Drosophila homologue of espin , to develop a unique genetic reporter for asymmetric oocyte organization. We generated a null allele of the...

A neurodevelopmental TUBB2B β-tubulin mutation impairs Bim1 (yeast EB1)-dependent spindle positioning

Malformations of the human cerebral cortex can be caused by mutations in tubulins that associate to compose microtubules. Cerebral cortical folding relies on neuronal migration and on progenitor proliferation partly dictated by microtubule-dependent mitotic spindle positioning. A single amino acid change, F265L, in the conserved TUBB2B β-tubulin gene has been identified in...

Correction: DARPins recognizing mTFP1 as novel reagents for in vitro and in vivo protein manipulations (doi:10.1242/bio.036749)

There were errors published in [Biology Open (2018) 11, bio036749][1] ([doi:10.1242/bio.036749)][2]. The article title originally used the word ‘recognize’, where the word used should have been ‘recognizing’. The correct title appears above and both the online full-text and PDF versions

An in vivo translation-reporter system for the study of protein synthesis in zebrafish embryos

Control of gene expression at the translation level is increasingly regarded as a key feature in many biological processes. Simple, inexpensive and reliable procedures to visualize sites of protein production are required to allow observation of the spatiotemporal patterns of mRNA translation at subcellular resolution. We present a method, named SPoT (for Subcellular Patterns of...

Endodermal pouch-expressed dmrt2b is important for pharyngeal cartilage formation

Pharyngeal pouches, a series of outpocketings derived from the foregut endoderm, are essential for craniofacial skeleton formation. However, the molecular mechanisms underlying endodermal pouch-regulated head cartilage development are not fully understood. In this study, we find that zebrafish dmrt2b , a gene encoding Doublesex- and Mab-3-related transcription factor, is...

A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics

Animals with large adipose stores, such as marine mammals, may provide insights into the evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can be rapidly obtained by proteomics and transcriptomics, but their application to adipose tissue is hindered by low nucleic acid and protein yields. We...

Neuronal cell culture from transgenic zebrafish models of neurodegenerative disease

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 of human fused in sarcoma (FUS) and ataxin-3...

A model of mucopolysaccharidosis type IIIB in pigs

Mucopolysaccharidosis type IIIB (MPS IIIB) is a rare genetic disorder caused by loss-of-function mutations in the NAGLU gene. Pigs are an ideal large animal model for human diseases; however, a porcine model of MPS IIIB has not been reported. We have previously generated a heterozygous NAGLU -deficient ( NAGLU +/-) Large White boar via a transgenic approach. Here we characterized...

Correction: Do wild-caught urban house sparrows show desensitized stress responses to a novel stressor? (doi:10.1242/bio.031849)

[There were errors published in Biology Open (2018) 7, [bio031849][2] ([doi:10.1242/bio.031849)][3]][3] D. Strubbe's second affiliation and funders were omitted from the original manuscript. This has now been amended in the online version. The author apologises for any inconvenience. []: /lookup

Viability of dietary substitution of live microalgae with dry Ulva rigida in broodstock conditioning of the Pacific oyster (Crassostrea gigas)

The current study evaluated the microalgae replacement by dry macroalgae ( Ulva rigida ) in the reproductive success and biochemical composition of the 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) and 100...

Correction: Characterization of a cdc14 null allele in Drosophila melanogaster (doi:10.1242/bio.035394)

[There were errors published in Biology Open 2018 7: bio035394 [doi:10.1242/bio.035394][2]][2] Incorrect versions of [Figure 2][2]B and [Figure S5B][3] were used for the published version of this article. The corrected figures are shown below. ![Fig. 2.][4] Fig. 2. cdc14 null males

Efficient genome editing using CRISPR/Cas9 ribonucleoprotein approach in cultured Medaka fish cells

Gene editing with CRISPR/Cas9 is a powerful tool to study the function of target genes. Although this technology has demonstrated wide efficiency in many species, including fertilized zebrafish and medaka fish embryos when microinjected, its application to achieve efficient gene editing in cultured fish cells have met some difficulty. Here, we report an efficient and reliable...