1,392 results match your criteria BMC Biology [Journal]


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

BMC Biol 2019 Feb 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
February 2019

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

BMC Biol 2019 Feb 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
February 2019

A role for actomyosin contractility in Notch signaling.

BMC Biol 2019 Feb 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 Feb 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

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

BMC Biol 2019 Jan 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
1 Read

Thawing out frozen metabolic accidents.

Authors:
Dario Leister

BMC Biol 2019 Jan 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

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

BMC Biol 2019 Jan 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 Jan 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
3 Reads

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

BMC Biol 2019 Jan 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
10 Reads

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

BMC Biol 2019 Jan 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
1 Read

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

BMC Biol 2019 Jan 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 Jan 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 Jan 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
1 Read

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
1 Read

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
2 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
17 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
11 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
13 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
14 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
16 Reads

On microbes, aging and the worm: an interview with David Weinkove.

Authors:
David Weinkove

BMC Biol 2018 11 1;16(1):125. Epub 2018 Nov 1.

Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK.

David Weinkove is an associate professor at Durham University, UK, studying host-microbe interactions in the model organism Caenorhabditis elegans. David has been focusing on the way microbes affect the physiology of their hosts, including the process of aging. In this interview, he discusses the questions shaping his research, how they evolved over the years, and his guiding principles for leading a lab. Read More

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http://dx.doi.org/10.1186/s12915-018-0600-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211589PMC
November 2018
1 Read

Open questions: why are babies rarely born with cancer?

Authors:
Michelle Monje

BMC Biol 2018 11 1;16(1):129. Epub 2018 Nov 1.

Departments of Neurology and Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA, USA.

Childhood cancer is fundamentally a disease of dysregulated development. Why does it rarely occur during the fetal period, a time of enormous growth and development? Read More

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http://dx.doi.org/10.1186/s12915-018-0601-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211449PMC
November 2018
1 Read

Communicating through scents: an interview with Jane Hurst.

Authors:
Jane Hurst

BMC Biol 2018 11 1;16(1):126. Epub 2018 Nov 1.

Mammalian Behaviour & Evolution Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

Jane Hurst is a William Prescott Professor of Animal Science at the University of Liverpool, UK, studying scent communication in mammals and its role in behaviours. In this interview, Jane discusses how scents encode complex information in rodents, driving behaviours such as kinship interactions and choosing a mate, how understanding natural behaviours of animals can inform experimental designs, and what is the connection between Jane Austin and pheromones. Read More

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http://dx.doi.org/10.1186/s12915-018-0596-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211507PMC
November 2018
1 Read

Open questions: why should we care about ER-phagy and ER remodelling?

Authors:
Ivan Dikic

BMC Biol 2018 11 1;16(1):131. Epub 2018 Nov 1.

Institute for Biochemistry II and Frankfurt Cancer Institute, Goethe University, Theodor Stern Kai 7, 60590, Frankfurt, Germany.

The endoplasmic reticulum (ER) is one of the most complex organelles in the eukaryotic cell. Recent findings suggest that a process called ER-phagy plays a major role in maintaining the ER's shape and function. Read More

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November 2018
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Systems biology of meristems: an interview with Teva Vernoux.

Authors:
Teva Vernoux

BMC Biol 2018 11 1;16(1):120. Epub 2018 Nov 1.

Laboratoire Reproduction et Développement des Plantes, Université de Lyon, CNRS, INRA, ENS de Lyon, UCB Lyon 1, F-69342, Lyon, France.

Teva Vernoux is a plant developmental biologist and holds positions as the Director of the Institute for Reproduction and Development of Plants at ENS de Lyon, and as a Research Director at Centre National de la Recherche Scientifique. Teva spoke to us about the need for multidisciplinary approaches to tackle multi-scale problems, how to go beyond a list of genes, and the importance of constructive reviews. Read More

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http://dx.doi.org/10.1186/s12915-018-0591-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211413PMC
November 2018
2 Reads

From plant immunity to food security: an interview with Ksenia Krasileva.

Authors:
Ksenia Krasileva

BMC Biol 2018 11 1;16(1):123. Epub 2018 Nov 1.

Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.

Ksenia Krasileva is an Assistant Professor at UC Berkley, studying innate immunity in plants. Ksenia's work combines plant genomics and plant-microbe interactions with new technologies, spanning basic studies and translational research in agriculture. In this interview Ksenia shares her experience with research and leading a lab, as well as thoughts on innovations in publishing. Read More

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http://dx.doi.org/10.1186/s12915-018-0597-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211597PMC
November 2018
7 Reads

Studying the microbiome and its complexities: an interview with Alan Walker.

Authors:
Alan W Walker

BMC Biol 2018 11 1;16(1):134. Epub 2018 Nov 1.

The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.

Alan Walker is a Senior Lecturer at the University of Aberdeen, UK, studying the intestinal microbiota and its interactions with the host's diet. In this interview, Alan discusses his research interests, earlier studies of the ways contaminants can affect microbiome analyses, the excitement of experiments going well, and why science doesn't need to be combative. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211542PMC
November 2018
11 Reads

Evolving eukaryotes: an interview with Joel Dacks.

Authors:
Joel B Dacks

BMC Biol 2018 11 1;16(1):119. Epub 2018 Nov 1.

Faculty of Medicine and Dentistry, University of Alberta, 5-31 Medical Science Building, Edmonton, Alberta, Canada.

Joel Dacks is an Associate Professor and Canada Research Chair in Evolutionary Cell Biology at the University of Alberta, a Scientific Associate at the Natural History Museum (London), and the current President of the International Society for Evolutionary Protistology. His research group studies the evolution and diversity of the eukaryotic membrane-trafficking system, from origins to potential disease therapeutics. In this interview, Joel shares some perspectives on gaining a balanced view of comparative cell biology and the importance of a constructive peer review process. Read More

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http://dx.doi.org/10.1186/s12915-018-0586-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211498PMC
November 2018
1 Read

Evolutionary development and morphological modifications of the brain: an interview with Angelika Stollewerk.

BMC Biol 2018 11 1;16(1):117. Epub 2018 Nov 1.

School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.

Angelika Stollewerk is a Reader at Queen Mary University of London, where her lab uses a diverse range of species to study the evolution of the arthropod nervous system. Angelika spoke to us about social spiders, the future of evo-devo, and open peer review. Read More

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http://dx.doi.org/10.1186/s12915-018-0590-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211559PMC
November 2018
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Unraveling rain forest biodiversity: an interview with Thomas Couvreur.

BMC Biol 2018 11 1;16(1):127. Epub 2018 Nov 1.

IRD, UMR DIADE, Univ. Montpellier, Montpellier, France.

Thomas Couvreur is a researcher and botanist at the Institut de Recherche pour le Développement (IRD), based in Montpellier, France, studying tropical biosystems. He is using diverse approaches-from taxonomy, molecular phylogenetics, phylogeography, to modeling species distribution-to understand the evolution and resilience of biodiversity in rain forests. In this interview, Thomas describes the ongoing research in his lab, the most urgent challenges and opportunities in biodiversity research, and the importance of knowing how to code. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211545PMC
November 2018
1 Read

Open questions: what are the genes underlying antagonistic coevolution?

Authors:
Dieter Ebert

BMC Biol 2018 11 1;16(1):114. Epub 2018 Nov 1.

Department of Environmental Sciences, University of Basel, Zoology, Vesalgasse 1, 4051, Basel, Switzerland.

Although the idea of coevolution was first presented 150 years ago, we still only vaguely understand the genetic basis of its workings. Identifying the genes responsible for coevolutionary interactions would enable us to distinguish between fundamentally different models of coevolution and would represent a milestone in population genetics and genomics. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211428PMC
November 2018
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When a physicist wanders into biology…: an interview with KC Huang.

BMC Biol 2018 11 1;16(1):130. Epub 2018 Nov 1.

Bioengineering Department, Stanford University, Stanford, CA, USA.

Kerwyn Casey ("KC") Huang is an Associate Professor at Stanford University, studying the physical nature of biological systems and the underpinnings of fundamental processes such as cell shape determination, cell division, and intracellular and microbial community organization. In this interview, KC discusses how the ability to pursue insights at scales from molecules to cellular communities can shed new light on longstanding questions, the necessity for new tools in exploring the microbiome, how to create an empowering lab environment, and why integrating chemistry with physics and biology can bring us closer to asking the right questions. Read More

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http://dx.doi.org/10.1186/s12915-018-0595-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211556PMC
November 2018
2 Reads

Host-parasite interactions: an interview with Emily Troemel.

Authors:
Emily Troemel

BMC Biol 2018 11 1;16(1):133. Epub 2018 Nov 1.

Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.

Emily Troemel is a Professor at the University of California San Diego, where her lab uses Caenorhabditis elegans to study host-pathogen interactions and the shaping of the immune response. In this interview, Emily shared her thoughts on peer review and its role in training future scientists, and the possibility of a new form of immunity in epithelia. Read More

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http://dx.doi.org/10.1186/s12915-018-0592-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211567PMC
November 2018
1 Read

Dissecting the forces that shape crops: an interview with Ryohei Terauchi.

Authors:
Ryohei Terauchi

BMC Biol 2018 11 1;16(1):132. Epub 2018 Nov 1.

Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.

Ryohei Terauchi is a Professor at Kyoto University and a Group Leader at the Iwate Biotechnology Research Center, Japan, studying the evolution of crops and their pathogens. In this interview, Ryohei describes his research interests, how the revolution in sequencing technology helped improve our understanding of orphan crops, and who are the scientists that inspire him. Read More

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http://dx.doi.org/10.1186/s12915-018-0598-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211442PMC
November 2018
1 Read
7.984 Impact Factor

Horizons in evolutionary genomics: an interview with David Ferrier.

BMC Biol 2018 11 1;16(1):124. Epub 2018 Nov 1.

The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK.

David Ferrier is a Reader at the University of St Andrews and Deputy Director of the Scottish Oceans Institute, where his lab studies how the diversity of form in the animal kingdom evolved, with an emphasis on using comparative genomics. In this interview, David shares his thoughts on how to escape the 'straitjacket' of traditional model systems, transparency in peer review, and the past and future of genome sequencing. Read More

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http://dx.doi.org/10.1186/s12915-018-0587-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211512PMC
November 2018
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Open questions: respiratory chain supercomplexes-why are they there and what do they do?

Authors:
Judy Hirst

BMC Biol 2018 11 1;16(1):111. Epub 2018 Nov 1.

The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.

In the mitochondrial inner membrane the respiratory enzymes associate to form supramolecular assemblies known as supercomplexes. The existence of supercomplexes is now widely accepted-but what functional or structural advantages, if any, do they confer? Read More

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http://dx.doi.org/10.1186/s12915-018-0577-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211484PMC
November 2018
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From bacterial genomics to clinical epidemiology: an interview with Bill Hanage.

Authors:
William P Hanage

BMC Biol 2018 11 1;16(1):122. Epub 2018 Nov 1.

Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, USA.

Bill Hanage is an Associate Professor of Epidemiology at Harvard School of Public Health, where he studies fundamental and applied epidemiology using genomic and evolutionary methods. Bill spoke to us about the different types of selection that determine pathogen populations, asking reviewers to highlight positives of papers, and whether we're closer to a causal framework for studying the microbiome. Read More

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http://dx.doi.org/10.1186/s12915-018-0588-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211398PMC
November 2018
2 Reads

Startling responses of zebrafish: an interview with Harold Burgess.

Authors:
Harold A Burgess

BMC Biol 2018 11 1;16(1):118. Epub 2018 Nov 1.

Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA.

Harold Burgess is a Senior Investigator at the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), part of the National Institutes of Health. Work in his lab combines genetic and imaging techniques to study neural circuits required for sensory guided behavior in zebrafish. In this interview Harold shares his thoughts on the changing field of neural development, pre-publication review, and 'Darwinian experiments' of peer review. Read More

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http://dx.doi.org/10.1186/s12915-018-0589-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211441PMC
November 2018
2 Reads

Correction to: The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches.

BMC Biol 2018 10 30;16(1):128. Epub 2018 Oct 30.

Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.

Reinvestigation of the raw data revealed an unfortunate error in Ugelvig et al. 2008 [1]. Read More

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http://dx.doi.org/10.1186/s12915-018-0604-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208041PMC
October 2018
4 Reads

Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences.

BMC Biol 2018 10 25;16(1):121. Epub 2018 Oct 25.

Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.

Background: The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. Read More

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http://dx.doi.org/10.1186/s12915-018-0581-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6202837PMC
October 2018
1 Read