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BMC Biology

Ginger L Hunter, Li He, Norbert Perrimon, Guillaume Charras, Edward Giniger, Buzz Baum
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...
February 11, 2019: BMC Biology
ThankGod E Ebenezer, Martin Zoltner, Alana Burrell, Anna Nenarokova, Anna M G Novák Vanclová, Binod Prasad, Petr Soukal, Carlos Santana-Molina, Ellis O'Neill, Nerissa N Nankissoor, Nithya Vadakedath, Viktor Daiker, Samson Obado, Sara Silva-Pereira, Andrew P Jackson, Damien P Devos, Julius Lukeš, Michael Lebert, Sue Vaughan, Vladimίr Hampl, Mark Carrington, Michael L Ginger, Joel B Dacks, Steven Kelly, Mark C Field
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. gracilis has been a popular model organism and of considerable biotechnological interest, but the absence of a gene catalogue has hampered both basic research and translational efforts. RESULTS: We report a detailed transcriptome and partial genome for E...
February 7, 2019: BMC Biology
Aimee A Malzahn, Xu Tang, Keunsub Lee, Qiurong Ren, Simon Sretenovic, Yingxiao Zhang, Hongqiao Chen, Minjeong Kang, Yu Bao, Xuelian Zheng, Kejun Deng, Tao Zhang, Valeria Salcedo, Kan Wang, Yong Zhang, Yiping Qi
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...
January 31, 2019: BMC Biology
Aneesh P H Bose, Jonathan M Henshaw, Holger Zimmermann, Karoline Fritzsche, Kristina M Sefc
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. We combine theoretical modeling with a detailed genetic study on a socially monogamous wild fish, Variabilichromis moorii, which displays biparental care despite exceptionally high rates of extra-pair paternity...
January 31, 2019: BMC Biology
Dario Leister
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...
January 30, 2019: BMC Biology
Lianhua Qin, Jie Wang, Junmei Lu, Hua Yang, Ruijuan Zheng, Zhonghua Liu, Xiaochen Huang, Yonghong Feng, Zhongyi Hu, Baoxue Ge
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. One marker found in all Beijing/W Mtb strains is a deletion of RD105 region that results in a gene fusion, Rv0071/74, with a variable number (3-9 m) of VDP (V: Val, D: Asp; P: Pro) repeats (coded by gtggacccg repeat sequences) at the N-terminal...
January 25, 2019: BMC Biology
Lisui Bao, Changxu Tian, Shikai Liu, Yu Zhang, Ahmed Elaswad, Zihao Yuan, Karim Khalil, Fanyue Sun, Yujia Yang, Tao Zhou, Ning Li, Suxu Tan, Qifan Zeng, Yang Liu, Yueru Li, Yun Li, Dongya Gao, Rex Dunham, Kenneth Davis, Geoffrey Waldbieser, Zhanjiang Liu
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...
January 25, 2019: BMC Biology
Sarah A Middleton, James Eberwine, Junhyong Kim
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., in neuronal dendrites, localization is a critical step for long-lasting synaptic potentiation. However, there is little consensus regarding which RNAs are localized and the role of alternative isoforms in localization. A comprehensive catalog of localized RNA can help dissect RBP/RNA interactions and localization motifs...
January 24, 2019: BMC Biology
Viola Grugni, Alessandro Raveane, Linda Ongaro, Vincenza Battaglia, Beniamino Trombetta, Giulia Colombo, Marco Rosario Capodiferro, Anna Olivieri, Alessandro Achilli, Ugo A Perego, Jorge Motta, Maribel Tribaldos, Scott R Woodward, Luca Ferretti, Fulvio Cruciani, Antonio Torroni, Ornella Semino
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...
January 24, 2019: BMC Biology
Alba Carreras, Luna Simona Pane, Roberto Nitsch, Katja Madeyski-Bengtson, Michelle Porritt, Pinar Akcakaya, Amir Taheri-Ghahfarokhi, Elke Ericson, Mikael Bjursell, Marta Perez-Alcazar, Frank Seeliger, Magnus Althage, Ralph Knöll, Ryan Hicks, Lorenz M Mayr, Rosie Perkins, Daniel Lindén, Jan Borén, Mohammad Bohlooly-Y, Marcello Maresca
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...
January 15, 2019: BMC Biology
Axelle Kerstens, Nikky Corthout, Benjamin Pavie, Zengjin Huang, Frank Vernaillen, Greetje Vande Velde, Sebastian Munck
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...
January 7, 2019: BMC Biology
Matthew A Coelho, Songyuan Li, Luna Simona Pane, Mike Firth, Giovanni Ciotta, Jonathan D Wrigley, Maria Emanuela Cuomo, Marcello Maresca, Benjamin J M Taylor
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...
December 28, 2018: BMC Biology
Chenzi Zhang, Xiangjun He, Yvonne K Kwok, Feng Wang, Junyi Xue, Hui Zhao, Kin Wah Suen, Chi Chiu Wang, Jianwei Ren, George G Chen, Paul B S Lai, Jiangchao Li, Yin Xia, Andrew M Chan, Wai-Yee Chan, Bo Feng
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...
December 28, 2018: BMC Biology
Ailís O'Carroll, Brieuc Chauvin, James W P Brown, Ava Meagher, Joanne Coyle, Jurgen Schill, Akshay Bhumkhar, Dominic J B Hunter, Thomas Ve, Bostjan Kobe, Emma Sierecki, Yann Gambin
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...
December 24, 2018: BMC Biology
Christian Tudorache, Hans Slabbekoorn, Yuri Robbers, Eline Hin, Johanna H Meijer, Herman P Spaink, Marcel J M Schaaf
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...
December 21, 2018: BMC Biology
Ziyun Wu, Megan M Senchuk, Dylan J Dues, Benjamin K Johnson, Jason F Cooper, Leira Lew, Emily Machiela, Claire E Schaar, Heather DeJonge, T Keith Blackwell, Jeremy M Van Raamsdonk
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...
December 18, 2018: BMC Biology
Graham P Bell, Mirna Kvajo
No abstract text is available yet for this article.
December 17, 2018: BMC Biology
Matthew D Herron, Seyed A Zamani-Dahaj, William C Ratcliff
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. Since collective-level trait values are functions of lower-level trait values, collective-level heritability is related to particle-level heritability...
December 13, 2018: BMC Biology
Yuehui Tian, Shiqiang Gao, Eva Laura von der Heyde, Armin Hallmann, Georg Nagel
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. Characterization of new opsins would help to understand the green algae photobiology and to develop new tools for optogenetics. RESULTS: Here we report the characterization of a novel opsin family from these green algae: light-inhibited guanylyl cyclases regulated through a two-component-like phosphoryl transfer, called "two-component cyclase opsins" (2c-Cyclops)...
December 6, 2018: BMC Biology
Jan Mölter, Lilach Avitan, Geoffrey J Goodhill
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...
November 28, 2018: BMC Biology
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