1,412 results match your criteria Bmc Biology[Journal]


Derivation of adult canine intestinal organoids for translational research in gastroenterology.

BMC Biol 2019 Apr 11;17(1):33. Epub 2019 Apr 11.

Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA.

Background: Large animal models, such as the dog, are increasingly being used for studying diseases including gastrointestinal (GI) disorders. Dogs share similar environmental, genomic, anatomical, and intestinal physiologic features with humans. To bridge the gap between commonly used animal models, such as rodents, and humans, and expand the translational potential of the dog model, we developed a three-dimensional (3D) canine GI organoid (enteroid and colonoid) system. Read More

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http://dx.doi.org/10.1186/s12915-019-0652-6DOI Listing
April 2019
4 Reads

Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons.

BMC Biol 2019 Apr 10;17(1):30. Epub 2019 Apr 10.

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.

Background: Epigenetic mechanisms play fundamental roles in brain function and behavior and stressors such as social isolation can alter animal behavior via epigenetic mechanisms. However, due to cellular heterogeneity, identifying cell-type-specific epigenetic changes in the brain is challenging. Here, we report the first use of a modified isolation of nuclei tagged in specific cell type (INTACT) method in behavioral epigenetics of Drosophila melanogaster, a method we call mini-INTACT. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-019-0646-4DOI Listing
April 2019
1 Read

Correction to: Q&A: insulin secretion and type 2 diabetes: why do β-cells fail?

BMC Biol 2019 Apr 9;17(1):32. Epub 2019 Apr 9.

Department of Physiology, Anatomy & Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.

Upon publication of the original article [1], the authors noticed that they had accidently omitted to acknowledge funding from the European Research Council. Read More

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http://dx.doi.org/10.1186/s12915-019-0650-8DOI Listing

Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes.

BMC Biol 2019 Apr 8;17(1):31. Epub 2019 Apr 8.

Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.

Background: Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. Anthropogenic activity may contribute to the spread of bacterial resistance cycling through natural environments, including through the release of human waste, as sewage treatment only partially removes antibiotic-resistant bacteria. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-019-0649-1DOI Listing
April 2019
2 Reads

Selective processing of all rotational and translational optic flow directions in the zebrafish pretectum and tectum.

BMC Biol 2019 Mar 29;17(1):29. Epub 2019 Mar 29.

Werner Reichardt Centre for Integrative Neuroscience, Institute of Neurobiology, University of Tübingen, 72076, Tübingen, Germany.

Background: The processing of optic flow in the pretectum/accessory optic system allows animals to stabilize retinal images by executing compensatory optokinetic and optomotor behavior. The success of this behavior depends on the integration of information from both eyes to unequivocally identify all possible translational or rotational directions of motion. However, it is still unknown whether the precise direction of ego-motion is already identified in the zebrafish pretectum or later in downstream premotor areas. Read More

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http://dx.doi.org/10.1186/s12915-019-0648-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441171PMC

The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation.

BMC Biol 2019 Mar 29;17(1):28. Epub 2019 Mar 29.

Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, Republic of Korea.

Background: Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura's jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations. Read More

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http://dx.doi.org/10.1186/s12915-019-0643-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441219PMC

Modelling the potential of genetic control of malaria mosquitoes at national scale.

BMC Biol 2019 Mar 29;17(1):26. Epub 2019 Mar 29.

Oxford Martin School, University of Oxford, Oxford, UK.

Background: The persistence of malaria in large parts of sub-Saharan Africa has motivated the development of novel tools to complement existing control programmes, including gene-drive technologies to modify mosquito vector populations. Here, we use a stochastic simulation model to explore the potential of using a driving-Y chromosome to suppress vector populations in a 10 km area of West Africa including all of Burkina Faso.

Results: The consequence of driving-Y introductions is predicted to vary across the landscape, causing elimination of the target species in some regions and suppression in others. Read More

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http://dx.doi.org/10.1186/s12915-019-0645-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440076PMC
March 2019
1 Read

Be the change you seek in science.

BMC Biol 2019 Mar 27;17(1):27. Epub 2019 Mar 27.

MATTER Lab, Child Mind Institute, New York, NY, USA.

Few would argue that science is better done in silos, with no transparency or sharing of methods and resources. Yet scientists and scientific stakeholders (e.g. Read More

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http://dx.doi.org/10.1186/s12915-019-0647-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436210PMC

Correction to: SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis.

BMC Biol 2019 Mar 20;17(1):25. Epub 2019 Mar 20.

Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China.

Upon publication of the original article [1], the authors noticed that they omitted Additional file 16: Table S10 from the Additional file list. Additional file 16: Table S10 can be found attached to this Correction and the caption of this Additional file can be found below. Read More

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http://dx.doi.org/10.1186/s12915-019-0640-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425691PMC

GSK-3β protects fetal oocytes from premature death via modulating TAp63 expression in mice.

BMC Biol 2019 03 12;17(1):23. Epub 2019 Mar 12.

State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.

Background: Female mammals have a limited reproductive lifespan determined by the size of the primordial follicle pool established perinatally. Over two thirds of fetal oocytes are abolished via programmed cell death during early folliculogenesis. However, the underlying mechanisms governing fetal oocyte attrition remain largely elusive. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-019-0641-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417224PMC
March 2019
6 Reads

A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits.

BMC Biol 2019 03 12;17(1):24. Epub 2019 Mar 12.

Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.

Background: The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. Read More

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http://dx.doi.org/10.1186/s12915-019-0642-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417139PMC
March 2019
2 Reads

Mesencephalic origin of the inferior lobe in zebrafish.

BMC Biol 2019 03 8;17(1):22. Epub 2019 Mar 8.

Paris-Saclay Institute of Neuroscience (Neuro-PSI), CNRS UMR9197, Univ Paris Sud, Université Paris-Saclay, CNRS Bâtiment 5, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France.

Background: Although the overall brain organization is shared in vertebrates, there are significant differences within subregions among different groups, notably between Sarcopterygii (lobe-finned fish) and Actinopterygii (ray-finned fish). Recent comparative studies focusing on the ventricular morphology have revealed a large diversity of the hypothalamus. Here, we study the development of the inferior lobe (IL), a prominent structure forming a bump on the ventral surface of the teleost brain. Read More

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http://dx.doi.org/10.1186/s12915-019-0631-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407210PMC

Correction to: Detecting neural assemblies in calcium imaging data.

BMC Biol 2019 03 6;17(1):21. Epub 2019 Mar 6.

Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.

Upon publication of the original article, [1], the authors noticed that the first authors' affiliation contained an error. Read More

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http://dx.doi.org/10.1186/s12915-019-0644-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404314PMC

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations.

BMC Biol 2019 03 6;17(1):20. Epub 2019 Mar 6.

Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, No. 168, Huaguan Road, Chengdu, 610052, Sichuan, China.

Background: Microbial communities are susceptible to the public goods dilemma, whereby individuals can gain an advantage within a group by utilizing, but not sharing the cost of producing, public goods. In bacteria, the development of quorum sensing (QS) can establish a cooperation system in a population by coordinating the production of costly and sharable extracellular products (public goods). Cooperators with intact QS system and robust ability in producing public goods are vulnerable to being undermined by QS-deficient defectors that escape from QS but benefit from the cooperation of others. Read More

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http://dx.doi.org/10.1186/s12915-019-0639-3DOI Listing
March 2019
5 Reads

Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida.

BMC Biol 2019 03 1;17(1):19. Epub 2019 Mar 1.

Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.

Background: Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species can infiltrate the blood stream of their hosts eventually colonizing organs, skin and gills. How this presumed anaerobe can persist and invade oxygenated tissues, despite having a strictly anaerobic metabolism, remains elusive. Read More

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http://dx.doi.org/10.1186/s12915-019-0634-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397501PMC

The golden death bacillus Chryseobacterium nematophagum is a novel matrix digesting pathogen of nematodes.

BMC Biol 2019 02 28;17(1):10. Epub 2019 Feb 28.

School of Veterinary Medicine, University of Glasgow, Scotland, UK.

Background: Nematodes represent important pathogens of humans and farmed animals and cause significant health and economic impacts. The control of nematodes is primarily carried out by applying a limited number of anthelmintic compounds, for which there is now widespread resistance being reported. There is a current unmet need to develop novel control measures including the identification and characterisation of natural pathogens of nematodes. Read More

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http://dx.doi.org/10.1186/s12915-019-0632-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394051PMC
February 2019
2 Reads

Q&A: modern crop breeding for future food security.

BMC Biol 2019 02 25;17(1):18. Epub 2019 Feb 25.

Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.

Farmers around the world have recently experienced significant crop losses due to severe heat and drought. Such extreme weather events and the need to feed a rapidly growing population have raised concerns for global food security. While plant breeding has been very successful and has delivered today's highly productive crop varieties, the rate of genetic improvement must double to meet the projected future demands. Read More

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http://dx.doi.org/10.1186/s12915-019-0638-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390336PMC
February 2019
1 Read

Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa.

BMC Biol 2019 02 22;17(1):16. Epub 2019 Feb 22.

Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA.

Background: Metazoan lineages exhibit a wide range of regenerative capabilities that vary among developmental stage and tissue type. The most robust regenerative abilities are apparent in the phyla Cnidaria, Platyhelminthes, and Echinodermata, whose members are capable of whole-body regeneration (WBR). This phenomenon has been well characterized in planarian and hydra models, but the molecular mechanisms of WBR are less established within echinoderms, or any other deuterostome system. Read More

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http://dx.doi.org/10.1186/s12915-019-0633-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385403PMC
February 2019
7.984 Impact Factor

Open questions: how to get developmental biology into shape?

BMC Biol 2019 02 22;17(1):17. Epub 2019 Feb 22.

Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.

Recent technical advances have provided unprecedented insights into the selective deployment of the genome in developing organisms, but how such differential gene expression is used to sculpt the complex shapes and sizes of organs remains unclear. Here, we outline major open questions in organogenesis and suggest how a synthesis between developmental biology and physics can help to address them. Read More

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http://dx.doi.org/10.1186/s12915-019-0636-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6387480PMC
February 2019

Role of self-organising myddosome oligomers in inflammatory signalling by Toll-like receptors.

Authors:
Nicholas J Gay

BMC Biol 2019 02 20;17(1):15. Epub 2019 Feb 20.

Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.

A paper published in BMC Biology characterises biophysically oligomeric and filamentous structures formed spontaneously by the Toll-like receptor signalling adaptor MyD88. Naturally occurring mutants of MyD88 that cause immunodeficiency are unable to form these structures. By contrast a somatic mutant that promotes the survival of tumour cells forms oligomers much more readily than the wild-type protein. Read More

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http://dx.doi.org/10.1186/s12915-019-0637-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383289PMC
February 2019

Circadian oscillator proteins across the kingdoms of life: structural aspects.

BMC Biol 2019 02 18;17(1):13. Epub 2019 Feb 18.

Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany.

Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms in organisms from bacteria to animals. These periodic rhythms result from a complex interplay among clock components that are specific to the organism, but share molecular mechanisms across kingdoms. A full understanding of these processes requires detailed knowledge, not only of the biochemical properties of clock proteins and their interactions, but also of the three-dimensional structure of clockwork components. Read More

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http://dx.doi.org/10.1186/s12915-018-0623-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378743PMC
February 2019

Identification of functional long non-coding RNAs in C. elegans.

BMC Biol 2019 02 18;17(1):14. Epub 2019 Feb 18.

Earlham Institute, Norwich Research Park, Norwich, UK.

Background: Functional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing 20 years ago. The last decade of research has seen a tremendous increase in the number of non-coding RNAs identified in various organisms. While we have mechanistic understandings of small non-coding RNA pathways, long non-coding RNAs represent a diverse class of active transcripts whose function remains less well characterised. Read More

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http://dx.doi.org/10.1186/s12915-019-0635-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378714PMC
February 2019

A role for actomyosin contractility in Notch signaling.

BMC Biol 2019 02 11;17(1):12. Epub 2019 Feb 11.

MRC-LMCB, University College London, London, WC1E6BT, UK.

Background: Notch-Delta signaling functions across a wide array of animal systems to break symmetry in a sheet of undifferentiated cells and generate cells with different fates, a process known as lateral inhibition. Unlike many other signaling systems, however, since both the ligand and receptor are transmembrane proteins, the activation of Notch by Delta depends strictly on cell-cell contact. Furthermore, the binding of the ligand to the receptor may not be sufficient to induce signaling, since recent work in cell culture suggests that ligand-induced Notch signaling also requires a mechanical pulling force. Read More

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http://dx.doi.org/10.1186/s12915-019-0625-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369551PMC
February 2019

Transcriptome, proteome and draft genome of Euglena gracilis.

BMC Biol 2019 02 7;17(1):11. Epub 2019 Feb 7.

School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.

Background: Photosynthetic euglenids are major contributors to fresh water ecosystems. Euglena gracilis in particular has noted metabolic flexibility, reflected by an ability to thrive in a range of harsh environments. E. Read More

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http://dx.doi.org/10.1186/s12915-019-0626-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366073PMC
February 2019
2 Reads

Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis.

BMC Biol 2019 01 31;17(1). Epub 2019 Jan 31.

Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.

Background: CRISPR-Cas12a (formerly Cpf1) is an RNA-guided endonuclease with distinct features that have expanded genome editing capabilities. Cas12a-mediated genome editing is temperature sensitive in plants, but a lack of a comprehensive understanding on Cas12a temperature sensitivity in plant cells has hampered effective application of Cas12a nucleases in plant genome editing.

Results: We compared AsCas12a, FnCas12a, and LbCas12a for their editing efficiencies and non-homologous end joining (NHEJ) repair profiles at four different temperatures in rice. Read More

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http://dx.doi.org/10.1186/s12915-019-0629-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357469PMC
January 2019
4 Reads

Thawing out frozen metabolic accidents.

Authors:
Dario Leister

BMC Biol 2019 01 30;17(1). Epub 2019 Jan 30.

Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany.

Photosynthesis and nitrogen fixation became evolutionarily immutable as "frozen metabolic accidents" because multiple interactions between the proteins and protein complexes involved led to their co-evolution in modules. This has impeded their adaptation to an oxidizing atmosphere, and reconfiguration now requires modification or replacement of whole modules, using either natural modules from exotic species or non-natural proteins with similar interaction potential. Ultimately, the relevant complexes might be reconstructed (almost) from scratch, starting either from appropriate precursor processes or by designing alternative pathways. Read More

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http://dx.doi.org/10.1186/s12915-018-0621-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354398PMC
January 2019
1 Read

Inclusive fitness benefits mitigate costs of cuckoldry to socially paired males.

BMC Biol 2019 01 31;17(1). Epub 2019 Jan 31.

Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.

Background: In socially monogamous species, reproduction is not always confined to paired males and females. Extra-pair males commonly also reproduce with paired females, which is traditionally thought to be costly to the females' social partners. However, we suggest that when the relatedness between reproducing individuals is considered, cuckolded males can suffer lower fitness losses than otherwise expected, especially when the rate of cuckoldry is high. Read More

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http://dx.doi.org/10.1186/s12915-018-0620-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354359PMC
January 2019
1 Read

A deletion in the RD105 region confers resistance to multiple drugs in Mycobacterium tuberculosis.

BMC Biol 2019 01 25;17(1). Epub 2019 Jan 25.

Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.

Background: The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), especially those that are multidrug resistant poses a serious threat to global tuberculosis control. However, the mechanism underlying the occurrence of drug resistance against more than one drug is poorly understood. Given that the Beijing/W strains are associated with outbreaks and multidrug resistance, they may harbor a genetic advantage and provide useful insight into the disease. Read More

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http://dx.doi.org/10.1186/s12915-019-0628-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347829PMC
January 2019
6 Reads

The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish.

BMC Biol 2019 01 25;17(1). Epub 2019 Jan 25.

Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY, 13244, USA.

Background: Sex determination mechanisms in teleost fish broadly differ from mammals and birds, with sex chromosomes that are far less differentiated and recombination often occurring along the length of the X and Y chromosomes, posing major challenges for the identification of specific sex determination genes. Here, we take an innovative approach of comparative genome analysis of the genomic sequences of the X chromosome and newly sequenced Y chromosome in the channel catfish.

Results: Using a YY channel catfish as the sequencing template, we generated, assembled, and annotated the Y genome sequence of channel catfish. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-019-0627-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346536PMC
January 2019
27 Reads

Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons.

BMC Biol 2019 01 24;17(1). Epub 2019 Jan 24.

Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, 160 BRB II/III - 421 Curie Blvd, Philadelphia, PA, 19104-6064, USA.

Background: RNA localization involves cis-motifs that are recognized by RNA-binding proteins (RBP), which then mediate localization to specific sub-cellular compartments. RNA localization is critical for many different cell functions, e.g. Read More

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http://dx.doi.org/10.1186/s12915-019-0630-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344992PMC
January 2019
2 Reads

Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas.

BMC Biol 2019 01 24;17(1). Epub 2019 Jan 24.

Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.

Background: Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America by an ancestral Beringian population, from which two well-differentiated components originated and subsequently mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analysis of the Y-chromosome haplogroup Q, which is the only Pan-American haplogroup and accounts for virtually all Native American Y chromosomes in Mesoamerica and South America.

Results: Our analyses of 1. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-018-0622-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345020PMC
January 2019
7.984 Impact Factor

In vivo genome and base editing of a human PCSK9 knock-in hypercholesterolemic mouse model.

BMC Biol 2019 01 15;17(1). Epub 2019 Jan 15.

Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 43 183, Gothenburg, Sweden.

Background: Plasma concentration of low-density lipoprotein (LDL) cholesterol is a well-established risk factor for cardiovascular disease. Inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9), which regulates cholesterol homeostasis, has recently emerged as an approach to reduce cholesterol levels. The development of humanized animal models is an important step to validate and study human drug targets, and use of genome and base editing has been proposed as a mean to target disease alleles. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-018-0624-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334452PMC
January 2019
9 Reads

A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples.

BMC Biol 2019 01 7;17(1). Epub 2019 Jan 7.

VIB Bio Imaging Core, Herestraat 49, Box 602, 3000, Leuven, Belgium.

Background: Current mesoscale 3D imaging techniques are limited to transparent or cleared samples or require the use of X-rays. This is a severe limitation for many research areas, as the 3D color surface morphology of opaque samples-for example, intact adult Drosophila, Xenopus embryos, and other non-transparent samples-cannot be assessed. We have developed "ALMOST," a novel optical method for 3D surface imaging of reflective opaque objects utilizing an optical projection tomography device in combination with oblique illumination and optical filters. Read More

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http://dx.doi.org/10.1186/s12915-018-0614-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323867PMC
January 2019
5 Reads

BE-FLARE: a fluorescent reporter of base editing activity reveals editing characteristics of APOBEC3A and APOBEC3B.

BMC Biol 2018 12 28;16(1):150. Epub 2018 Dec 28.

Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK.

Background: Base Editing is a precise genome editing method that uses a deaminase-Cas9 fusion protein to mutate cytidine to thymidine in target DNA in situ without the generation of a double-strand break. However, the efficient enrichment of genetically modified cells using this technique is limited by the ability to detect such events.

Results: We have developed a Base Editing FLuorescent Activity REporter (BE-FLARE), which allows for the enrichment of cells that have undergone editing of target loci based on a fluorescence shift from BFP to GFP. Read More

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http://dx.doi.org/10.1186/s12915-018-0617-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309101PMC
December 2018
2 Reads

Homology-independent multiallelic disruption via CRISPR/Cas9-based knock-in yields distinct functional outcomes in human cells.

BMC Biol 2018 12 28;16(1):151. Epub 2018 Dec 28.

School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.

Background: Cultured human cells are pivotal models to study human gene functions, but introducing complete loss of function in diploid or aneuploid cells has been a challenge. The recently developed CRISPR/Cas9-mediated homology-independent knock-in approach permits targeted insertion of large DNA at high efficiency, providing a tool for insertional disruption of a selected gene. Pioneer studies have showed promising results, but the current methodology is still suboptimal and functional outcomes have not been well examined. Read More

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http://dx.doi.org/10.1186/s12915-018-0616-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310992PMC
December 2018
2 Reads

Pathological mutations differentially affect the self-assembly and polymerisation of the innate immune system signalling adaptor molecule MyD88.

BMC Biol 2018 12 24;16(1):149. Epub 2018 Dec 24.

EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW, 2052, Australia.

Background: Higher-order self-assembly of proteins, or "prion-like" polymerisation, is now emerging as a simple and robust mechanism for signal amplification, in particular within the innate immune system, where the recognition of pathogens or danger-associated molecular patterns needs to trigger a strong, binary response within cells. MyD88, an important adaptor protein downstream of TLRs, is one of the most recent candidates for involvement in signalling by higher order self-assembly. In this new light, we set out to re-interpret the role of polymerisation in MyD88-related diseases and study the impact of disease-associated point mutations L93P, R196C, and L252P/L265P at the molecular level. Read More

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http://dx.doi.org/10.1186/s12915-018-0611-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304784PMC
December 2018
3 Reads

Biological clock function is linked to proactive and reactive personality types.

BMC Biol 2018 12 21;16(1):148. Epub 2018 Dec 21.

Institute of Biology, Leiden University, Leiden, The Netherlands.

Background: Many physiological processes in our body are controlled by the biological clock and show circadian rhythmicity. It is generally accepted that a robust rhythm is a prerequisite for optimal functioning and that a lack of rhythmicity can contribute to the pathogenesis of various diseases. Here, we tested in a heterogeneous laboratory zebrafish population whether and how variation in the rhythmicity of the biological clock is associated with the coping styles of individual animals, as assessed in a behavioural assay to reliably measure this along a continuum between proactive and reactive extremes. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-018-0618-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303931PMC
December 2018
29 Reads

Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathways.

BMC Biol 2018 12 18;16(1):147. Epub 2018 Dec 18.

Department of Genetics, Harvard Medical School, Boston, MA, USA.

Background: The mitochondrial unfolded protein response (mitoUPR) is a stress response pathway activated by disruption of proteostasis in the mitochondria. This pathway has been proposed to influence lifespan, with studies suggesting that mitoUPR activation has complex effects on longevity.

Results: Here, we examined the contribution of the mitoUPR to the survival and lifespan of three long-lived mitochondrial mutants in Caenorhabditis elegans by modulating the levels of ATFS-1, the central transcription factor that mediates the mitoUPR. Read More

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http://dx.doi.org/10.1186/s12915-018-0615-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298126PMC
December 2018
1 Read

Tackling waste in publishing through portable peer review.

BMC Biol 2018 12 17;16(1):146. Epub 2018 Dec 17.

Springer Nature, New York, USA.

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http://dx.doi.org/10.1186/s12915-018-0619-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297941PMC
December 2018
1 Read

Trait heritability in major transitions.

BMC Biol 2018 12 13;16(1):145. Epub 2018 Dec 13.

School of Biological Sciences, Georgia Institute of Technology, North Avenue, Atlanta, GA, 30332, USA.

Background: Increases in biological complexity and the origins of life's hierarchical organization are described by the "major transitions" framework. A crucial component of this paradigm is that after the transition in complexity or organization, adaptation occurs primarily at the level of the new, higher-level unit. For collective-level adaptations to occur, though, collective-level traits-properties of the group, such as collective size-must be heritable. Read More

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http://dx.doi.org/10.1186/s12915-018-0612-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6293664PMC
December 2018
2 Reads

Two-component cyclase opsins of green algae are ATP-dependent and light-inhibited guanylyl cyclases.

BMC Biol 2018 12 6;16(1):144. Epub 2018 Dec 6.

Botanik I, Julius-Maximilians-Universität Würzburg, Biozentrum, Julius-von-Sachs-Platz 2, 97082, Würzburg, Germany.

Background: The green algae Chlamydomonas reinhardtii and Volvox carteri are important models for studying light perception and response, expressing many different photoreceptors. More than 10 opsins were reported in C. reinhardtii, yet only two-the channelrhodopsins-were functionally characterized. Read More

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http://dx.doi.org/10.1186/s12915-018-0613-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284317PMC
December 2018
1 Read

Detecting neural assemblies in calcium imaging data.

BMC Biol 2018 11 28;16(1):143. Epub 2018 Nov 28.

Queensland Brian Institute, The University of Queensland, Brisbane, 4072, Australia.

Background: Activity in populations of neurons often takes the form of assemblies, where specific groups of neurons tend to activate at the same time. However, in calcium imaging data, reliably identifying these assemblies is a challenging problem, and the relative performance of different assembly-detection algorithms is unknown.

Results: To test the performance of several recently proposed assembly-detection algorithms, we first generated large surrogate datasets of calcium imaging data with predefined assembly structures and characterised the ability of the algorithms to recover known assemblies. Read More

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http://dx.doi.org/10.1186/s12915-018-0606-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6262979PMC
November 2018
1 Read

Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids.

BMC Biol 2018 11 28;16(1):137. Epub 2018 Nov 28.

Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.

Background: The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis). The timing and frequency of secondary endosymbiosis during eukaryotic evolution is currently unclear but may be resolved in part by studying cryptomonads, a group of single-celled eukaryotes comprised of both photosynthetic and non-photosynthetic species. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-018-0593-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260743PMC
November 2018
14 Reads

Genome of tiny predator with big appetite.

BMC Biol 2018 11 28;16(1):140. Epub 2018 Nov 28.

School of BioSciences, University of Melbourne, VIC, 3010, Australia.

The capture and enslavement of eukaryotic algae by unicellular predators to acquire photosynthesis was a major driving force in early eukaryotic diversification. A genome presented in BMC Biology provides a glimpse of how such a tiny predator might have preyed on red algae and detained them to create new lineages of photosynthetic organisms. Read More

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http://dx.doi.org/10.1186/s12915-018-0610-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260725PMC
November 2018
1 Read

Migration through a small pore disrupts inactive chromatin organization in neutrophil-like cells.

BMC Biol 2018 11 26;16(1):142. Epub 2018 Nov 26.

Liggins Institute, University of Auckland, Auckland, New Zealand.

Background: Mammalian cells are flexible and can rapidly change shape when they contract, adhere, or migrate. The nucleus must be stiff enough to withstand cytoskeletal forces, but flexible enough to remodel as the cell changes shape. This is particularly important for cells migrating through confined spaces, where the nuclear shape must change in order to fit through a constriction. Read More

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http://dx.doi.org/10.1186/s12915-018-0608-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6257957PMC
November 2018
1 Read

Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria.

BMC Biol 2018 11 22;16(1):141. Epub 2018 Nov 22.

Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Průmyslová 595, 252 50, Vestec, Czech Republic.

Background: Bacteria and mitochondria contain translocases that function to transport proteins across or insert proteins into their inner and outer membranes. Extant mitochondria retain some bacterial-derived translocases but have lost others. While BamA and YidC were integrated into general mitochondrial protein transport pathways (as Sam50 and Oxa1), the inner membrane TAT translocase, which uniquely transports folded proteins across the membrane, was retained sporadically across the eukaryote tree. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-018-0607-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251230PMC
November 2018
17 Reads

Precise A•T to G•C base editing in the zebrafish genome.

BMC Biol 2018 11 20;16(1):139. Epub 2018 Nov 20.

Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.

Background: Base editors are a class of genome editing tools with the ability to efficiently induce point mutations in genomic DNA, without inducing double-strand breaks or relying on homology-direct repair as in other such technologies. Recently, adenine base editors (ABEs) have been developed to mediate the conversion of A•T to G•C in genomic DNA of human cells, mice, and plants. Here, we investigated the activity and efficiency of several adenine base editors in zebrafish and showed that base editing can be used to create new models of pathogenic diseases caused by point mutations. Read More

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http://dx.doi.org/10.1186/s12915-018-0609-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247682PMC
November 2018
18 Reads

Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions.

BMC Biol 2018 11 15;16(1):138. Epub 2018 Nov 15.

Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Ihnestraße 63-73, Berlin, 14195, Germany.

Background: Characterizing recurring sequence patterns in human promoters has been a challenging undertaking even nowadays where a near-complete overview of promoters exists. However, with the more recent availability of genomic location (ChIP-seq) data, one can approach that question through the identification of characteristic patterns of transcription factor occupancy and histone modifications.

Results: Based on the ENCODE annotation and integration of sequence motifs as well as three-dimensional chromatin data, we have undertaken a re-analysis of occupancy and sequence patterns in human promoters. Read More

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http://dx.doi.org/10.1186/s12915-018-0585-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6238301PMC
November 2018
1 Read

15 years of BMC Biology.

BMC Biol 2018 11 1;16(1):135. Epub 2018 Nov 1.

Springer Nature, New York, USA.

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http://dx.doi.org/10.1186/s12915-018-0602-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219252PMC
November 2018
1 Read

Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida.

BMC Biol 2018 11 5;16(1):136. Epub 2018 Nov 5.

Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.

Background: Complex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Homeobox TFs in the TALE superclass are deeply embedded in the gene regulatory networks that orchestrate embryogenesis. Knotted-like homeobox (KNOX) TFs, homologous to animal MEIS, have been found to drive the haploid-to-diploid transition in both unicellular green algae and land plants via heterodimerization with other TALE superclass TFs, demonstrating remarkable functional conservation of a developmental TF across lineages that diverged one billion years ago. Read More

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https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-01
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http://dx.doi.org/10.1186/s12915-018-0605-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219170PMC
November 2018
18 Reads