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https://www.readbyqxmd.com/read/28927400/genome-sequencing-of-the-staple-food-crop-white-guinea-yam-enables-the-development-of-a-molecular-marker-for-sex-determination
#1
Muluneh Tamiru, Satoshi Natsume, Hiroki Takagi, Benjamen White, Hiroki Yaegashi, Motoki Shimizu, Kentaro Yoshida, Aiko Uemura, Kaori Oikawa, Akira Abe, Naoya Urasaki, Hideo Matsumura, Pachakkil Babil, Shinsuke Yamanaka, Ryo Matsumoto, Satoru Muranaka, Gezahegn Girma, Antonio Lopez-Montes, Melaku Gedil, Ranjana Bhattacharjee, Michael Abberton, P Lava Kumar, Ismail Rabbi, Mai Tsujimura, Toru Terachi, Wilfried Haerty, Manuel Corpas, Sophien Kamoun, Günter Kahl, Hiroko Takagi, Robert Asiedu, Ryohei Terauchi
BACKGROUND: Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected "orphan" crop that would benefit from crop improvement efforts...
September 19, 2017: BMC Biology
https://www.readbyqxmd.com/read/28915884/q-a-morphological-insights-into-evolution
#2
Neal Anthwal, Abigail S Tucker
In this question and answer article we discuss how evolution shapes morphology (the shape and pattern of our bodies) but also how learning about morphology, and specifically how that morphology arises during development, can shed light on mechanisms that might allow change during evolution. For this we concentrate on recent findings from our lab on how the middle ear has formed in mammals.
September 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28915882/blind-free-living-kiwi-offer-a-unique-window-into-the-ecology-and-evolution-of-vertebrate-vision
#3
Bret A Moore, Joanne R Paul-Murphy, Alan J D Tennyson, Christopher J Murphy
The first report of multiple, blind, wild birds in good health suggests vision is not necessary for the survival of kiwi.
September 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28915805/antibiotic-resistance-it-s-bad-but-why-isn-t-it-worse
#4
REVIEW
Nicholas Waglechner, Gerard D Wright
Antibiotic natural products are ancient and so is resistance. Consequently, environmental bacteria harbor numerous and varied antibiotic resistance elements. Nevertheless, despite long histories of antibiotic production and exposure, environmental bacteria are not resistant to all known antibiotics. This means that there are barriers to the acquisition of a complete resistance armamentarium. The sources, distribution, and movement of resistance mechanisms in different microbes and bacterial populations are mosaic features that act as barriers to slow this movement, thus moderating the emergence of bacterial pan-resistance...
September 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28911321/q-a-the-brain-under-a-mesoscope-the-forest-and-the-trees
#5
Nicholas James Sofroniew
Neurons relevant to a particular behavior are often widely dispersed across the brain. To record activity in groups of individual neurons that might be distributed across large distances, neuroscientists and optical engineers have been developing a new type of microscope called a mesoscope. Mesoscopes have high spatial resolution and a large field of view. This Q&A will discuss this exciting new technology, highlighting a particular instrument, the two-photon random access mesoscope (2pRAM).
September 14, 2017: BMC Biology
https://www.readbyqxmd.com/read/28893259/how-driving-endonuclease-genes-can-be-used-to-combat-pests-and-disease-vectors
#6
REVIEW
H Charles J Godfray, Ace North, Austin Burt
Driving endonuclease genes (DEGs) spread through a population by a non-Mendelian mechanism. In a heterozygote, the protein encoded by a DEG causes a double-strand break in the homologous chromosome opposite to where its gene is inserted and when the break is repaired using the homologue as a template the DEG heterozygote is converted to a homozygote. Some DEGs occur naturally while several classes of endonucleases can be engineered to spread in this way, with CRISPR-Cas9 based systems being particularly flexible...
September 11, 2017: BMC Biology
https://www.readbyqxmd.com/read/28893254/skip-controls-flowering-time-via-the-alternative-splicing-of-sef-pre-mrna-in-arabidopsis
#7
Zhibo Cui, Aizi Tong, Yiqiong Huo, Zhiqiang Yan, Weiqi Yang, Xianli Yang, Xiao-Xue Wang
BACKGROUND: Similar to other eukaryotes, splicing is emerging as an important process affecting development and stress tolerance in plants. Ski-interacting protein (SKIP), a splicing factor, is essential for circadian clock function and abiotic stress tolerance; however, the mechanisms whereby it regulates flowering time are unknown. RESULTS: In this study, we found that SKIP is required for the splicing of serrated leaves and early flowering (SEF) pre-messenger RNA (mRNA), which encodes a component of the ATP-dependent SWR1 chromatin remodeling complex (SWR1-C)...
September 11, 2017: BMC Biology
https://www.readbyqxmd.com/read/28874153/thioester-containing-proteins-regulate-the-toll-pathway-and-play-a-role-in-drosophila-defence-against-microbial-pathogens-and-parasitoid-wasps
#8
Anna Dostálová, Samuel Rommelaere, Mickael Poidevin, Bruno Lemaitre
BACKGROUND: Members of the thioester-containing protein (TEP) family contribute to host defence in both insects and mammals. However, their role in the immune response of Drosophila is elusive. In this study, we address the role of TEPs in Drosophila immunity by generating a mutant fly line, referred to as TEPq (Δ) , lacking the four immune-inducible TEPs, TEP1, 2, 3 and 4. RESULTS: Survival analyses with TEPq (Δ) flies reveal the importance of these proteins in defence against entomopathogenic fungi, Gram-positive bacteria and parasitoid wasps...
September 5, 2017: BMC Biology
https://www.readbyqxmd.com/read/28863777/dosage-sensitive-genes-in-evolution-and-disease
#9
REVIEW
Alan M Rice, Aoife McLysaght
For a subset of genes in our genome a change in gene dosage, by duplication or deletion, causes a phenotypic effect. These dosage-sensitive genes may confer an advantage upon copy number change, but more typically they are associated with disease, including heart disease, cancers and neuropsychiatric disorders. This gene copy number sensitivity creates characteristic evolutionary constraints that can serve as a diagnostic to identify dosage-sensitive genes. Though the link between copy number change and disease is well-established, the mechanism of pathogenicity is usually opaque...
September 1, 2017: BMC Biology
https://www.readbyqxmd.com/read/28859637/q-a-where-did-the-neanderthals-go
#10
Kelley Harris, Rasmus Nielsen
Genomic evidence has demonstrated that humans and Neanderthals interbred. Today, the genomes of most individuals outside Africa contain 2-3% Neanderthal DNA. However, it is still hotly debated why the Neanderthals went extinct and if humans contributed to the Neanderthal extinction. In this Q&A we explore what genomic data might have to say about this issue.
September 1, 2017: BMC Biology
https://www.readbyqxmd.com/read/28859647/blob-ology-and-biology-of-cryo-em-an-interview-with-helen-saibil
#11
Helen R Saibil
Helen Saibil is Bernal Professor of Structural Biology at Birkbeck, University of London. After undergraduate work at McGill University, Canada, Helen moved to London for her PhD at Kings College. After stints at CEA Grenoble and the University of Oxford, she moved to Birkbeck where her lab studies the operation of macromolecular machinery-including molecular chaperones, protein folding/misfolding, and host cell interactions with pathogens. Helen is a Fellow of the Royal Society, Fellow of the Academy of Medical Sciences, and an Honorary Member of both the British Biophysical Society and the Royal Microscopical Society...
August 31, 2017: BMC Biology
https://www.readbyqxmd.com/read/28854926/single-molecule-sequencing-and-hi-c-based-proximity-guided-assembly-of-amaranth-amaranthus-hypochondriacus-chromosomes-provide-insights-into-genome-evolution
#12
D J Lightfoot, D E Jarvis, T Ramaraj, R Lee, E N Jellen, P J Maughan
BACKGROUND: Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of the developing world. Here, we present a reference-quality assembly of the amaranth genome which will assist the agronomic development of the species...
August 31, 2017: BMC Biology
https://www.readbyqxmd.com/read/28854918/ribosome-signatures-aid-bacterial-translation-initiation-site-identification
#13
Adam Giess, Veronique Jonckheere, Elvis Ndah, Katarzyna Chyżyńska, Petra Van Damme, Eivind Valen
BACKGROUND: While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information, developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated...
August 30, 2017: BMC Biology
https://www.readbyqxmd.com/read/28851366/a-widespread-family-of-polymorphic-toxins-encoded-by-temperate-phages
#14
Anne Jamet, Marie Touchon, Bruno Ribeiro-Gonçalves, João André Carriço, Alain Charbit, Xavier Nassif, Mario Ramirez, Eduardo P C Rocha
BACKGROUND: Polymorphic toxins (PTs) are multi-domain bacterial exotoxins belonging to distinct families that share common features in terms of domain organization. PTs are found in all major bacterial clades, including many toxic effectors of type V and type VI secretion systems. PTs modulate the dynamics of microbial communities by killing or inhibiting the growth of bacterial competitors lacking protective immunity proteins. RESULTS: In this work, we identified a novel widespread family of PTs, named MuF toxins, which were exclusively encoded within temperate phages and their prophages...
August 29, 2017: BMC Biology
https://www.readbyqxmd.com/read/28844202/distinct-unfolded-protein-responses-mitigate-or-mediate-effects-of-nonlethal-deprivation-of-c-elegans-sleep-in-different-tissues
#15
Jarred Sanders, Monika Scholz, Ilaria Merutka, David Biron
BACKGROUND: Disrupting sleep during development leads to lasting deficits in chordates and arthropods. To address lasting impacts of sleep deprivation in Caenorhabditis elegans, we established a nonlethal deprivation protocol. RESULTS: Deprivation triggered protective insulin-like signaling and two unfolded protein responses (UPRs): the mitochondrial (UPR(mt)) and the endoplasmic reticulum (UPR(ER)) responses. While the latter is known to be triggered by sleep deprivation in rodent and insect brains, the former was not strongly associated with sleep deprivation previously...
August 28, 2017: BMC Biology
https://www.readbyqxmd.com/read/28821249/erratum-to-charged-residues-next-to-transmembrane-regions-revisited-positive-inside-rule-is-complemented-by-the-negative-inside-depletion-outside-enrichment-rule
#16
James Alexander Baker, Wing-Cheong Wong, Birgit Eisenhaber, Jim Warwicker, Frank Eisenhaber
No abstract text is available yet for this article.
August 18, 2017: BMC Biology
https://www.readbyqxmd.com/read/28814299/biological-function-in-the-twilight-zone-of-sequence-conservation
#17
REVIEW
Chris P Ponting
Strong DNA conservation among divergent species is an indicator of enduring functionality. With weaker sequence conservation we enter a vast 'twilight zone' in which sequence subject to transient or lower constraint cannot be distinguished easily from neutrally evolving, non-functional sequence. Twilight zone functional sequence is illuminated instead by principles of selective constraint and positive selection using genomic data acquired from within a species' population. Application of these principles reveals that despite being biochemically active, most twilight zone sequence is not functional...
August 16, 2017: BMC Biology
https://www.readbyqxmd.com/read/28810920/erratum-to-genomic-innovations-transcriptional-plasticity-and-gene-loss-underlying-the-evolution-and-divergence-of-two-highly-polyphagous-and-invasive-helicoverpa-pest-species
#18
S L Pearce, D F Clarke, P D East, S Elfekih, K H J Gordon, L S Jermiin, A McGaughran, J G Oakeshott, A Papanicolaou, O P Perera, R V Rane, S Richards, W T Tay, T K Walsh, A Anderson, C J Anderson, S Asgari, P G Board, A Bretschneider, P M Campbell, T Chertemps, J T Christeller, C W Coppin, S J Downes, G Duan, C A Farnsworth, R T Good, L B Han, Y C Han, K Hatje, I Horne, Y P Huang, D S T Hughes, E Jacquin-Joly, W James, S Jhangiani, M Kollmar, S S Kuwar, S Li, N-Y Liu, M T Maibeche, J R Miller, N Montagne, T Perry, J Qu, S V Song, G G Sutton, H Vogel, B P Walenz, W Xu, H-J Zhang, Z Zou, P Batterham, O R Edwards, R Feyereisen, R A Gibbs, D G Heckel, A McGrath, C Robin, S E Scherer, K C Worley, Y D Wu
No abstract text is available yet for this article.
August 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28810863/multiple-essential-functions-of-plasmodium-falciparum-actin-1-during-malaria-blood-stage-development
#19
Sujaan Das, Leandro Lemgruber, Chwen L Tay, Jake Baum, Markus Meissner
BACKGROUND: The phylum Apicomplexa includes intracellular parasites causing immense global disease burden, the deadliest of them being the human malaria parasite Plasmodium falciparum, which invades and replicates within erythrocytes. The cytoskeletal protein actin is well conserved within apicomplexans but divergent from mammalian actins, and was primarily reported to function during host cell invasion. However, novel invasion mechanisms have been described for several apicomplexans, and specific functions of the acto-myosin system are being reinvestigated...
August 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28800766/examining-non-ltr-retrotransposons-in-the-context-of-the-evolving-primate-brain
#20
REVIEW
Sara B Linker, Maria C Marchetto, Iñigo Narvaiza, Ahmet M Denli, Fred H Gage
Researchers have long sought to understand the genetic basis of the cognitive differences between primates, with particular focus on the human brain. Although all mutational types have worked in concert with evolutionary forces to generate the current human brain, in this review we will explore the impact of mobile elements, specifically non-LTR retrotransposons. Non-LTR retrotransposons have contributed coding and regulatory sequences to the genome throughout evolution. During primate evolution there have been multiple waves of LINE retrotransposition as well as the birth of new mobile elements such as the SINEs Alu and SVA and we will explore what kinds of impacts these may have had on the evolving human brain...
August 11, 2017: BMC Biology
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