TY - JOUR TI - Agricultural production: assessment of the potential use of Cas9-mediated gene drive systems for agricultural pest control AU - Scott, Maxwell J. AU - Gould, Fred AU - Lorenzen, Marcé AU - Grubbs, Nathaniel AU - Edwards, Owain AU - O’Brochta, David T2 - Journal of Responsible Innovation AB - To highlight how gene drives could be useful for control of agricultural insect pests, we selected species that are pests of animals (New World screwworm), plants (spotted wing Drosophila, diamondback moth, Bemisia tabaci whitefly), or stored grains (red flour beetle). With the exception of whitefly, routine methods for delivering DNA to the germline and selecting for genetically modified insects have been developed. The traditional approach in agriculture has been to suppress insect pest populations using insecticides and other farming practices. Similarly, we suggest the main use of gene drives in agriculture will be for population suppression through targeting essential genes. We provide examples of gene drives that target specific genes including female-essential genes. Further, we discuss issues related to containment in the laboratory and eventual field testing of strains harboring a Cas9-mediated gene drive system. DA - 2017/12/11/ PY - 2017/12/11/ DO - 10.1080/23299460.2017.1410343 VL - 5 IS - sup1 SP - S98-S120 J2 - Journal of Responsible Innovation LA - en OP - SN - 2329-9460 2329-9037 UR - http://dx.doi.org/10.1080/23299460.2017.1410343 DB - Crossref ER - TY - RPRT TI - Translation regulation of uORFs-containing genes in Arabidopsis AU - Merchante, C. AU - Yun, J. AU - Valpuesta-Fernandez, V. AU - Stepanova, A. AU - Alonso, J. DA - 2017/// PY - 2017/// ER - TY - JOUR TI - The potential for the use of gene drives for pest control in New Zealand: a perspective AU - Dearden, Peter K. AU - Gemmell, Neil J. AU - Mercier, Ocean R. AU - Lester, Philip J. AU - Scott, Maxwell J. AU - Newcomb, Richard D. AU - Buckley, Thomas R. AU - Jacobs, Jeanne M. E. AU - Goldson, Stephen G. AU - Penman, David R. T2 - Journal of the Royal Society of New Zealand AB - Genetic technologies such as gene editing and gene drive systems have recently emerged as potential tools for pest control. Gene drives, in particular, have been described as potential solutions to the pest problems that beset New Zealand. Here we describe the current state of gene drive technologies and present a series of examples to examine the potential benefits and problems arising from gene drive approaches for pest control in New Zealand. We consider the risks and barriers, both biological and social, that would need to be addressed to deploy such systems against our key pests with particular reference to the unique characteristics of New Zealand’s biota, environment and peoples. Gene drives are a potentially useful technology for the eradication of pests in New Zealand but a great deal of research and understanding, as well as public acceptance, is required before they can be implemented. DA - 2017/10/25/ PY - 2017/10/25/ DO - 10.1080/03036758.2017.1385030 VL - 48 IS - 4 SP - 225-244 J2 - Journal of the Royal Society of New Zealand LA - en OP - SN - 0303-6758 1175-8899 UR - http://dx.doi.org/10.1080/03036758.2017.1385030 DB - Crossref KW - Bioheritage KW - bioprotection KW - CRISPR KW - gene drives KW - pest control KW - social licence ER - TY - JOUR TI - Regulation of Drosophila Lifespan by bellwether Promoter Alleles AU - Garcia, Júlia Frankenberg AU - Carbone, Mary Anna AU - Mackay, Trudy F. C. AU - Anholt, Robert R. H. T2 - Scientific Reports AB - Longevity varies among individuals, but how natural genetic variation contributes to variation in lifespan is poorly understood. Drosophila melanogaster presents an advantageous model system to explore the genetic underpinnings of longevity, since its generation time is brief and both the genetic background and rearing environment can be precisely controlled. The bellwether (blw) gene encodes the α subunit of mitochondrial ATP synthase. Since metabolic rate may influence lifespan, we investigated whether alternative haplotypes in the blw promoter affect lifespan when expressed in a co-isogenic background. We amplified 521 bp upstream promoter sequences containing alternative haplotypes and assessed promoter activity both in vitro and in vivo using a luciferase reporter system. The AG haplotype showed significantly greater expression of luciferase than the GT haplotype. We then overexpressed a blw cDNA construct driven by either the AG or GT haplotype promoter in transgenic flies and showed that the AG haplotype also results in greater blw cDNA expression and a significant decrease in lifespan relative to the GT promoter haplotype, in male flies only. Thus, our results show that naturally occurring regulatory variants of blw affect lifespan in a sex-specific manner. DA - 2017/6/23/ PY - 2017/6/23/ DO - 10.1038/S41598-017-04530-X VL - 7 IS - 1 J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/S41598-017-04530-X DB - Crossref ER - TY - JOUR TI - Foundational and Translational Research Opportunities to Improve Plant Health AU - Michelmore, Richard AU - Coaker, Gitta AU - Bart, Rebecca AU - Beattie, Gwyn AU - Bent, Andrew AU - Bruce, Toby AU - Cameron, Duncan AU - Dangl, Jeffery AU - Dinesh-Kumar, Savithramma AU - Edwards, Rob AU - Eves-van den Akker, Sebastian AU - Gassmann, Walter AU - Greenberg, Jean T. AU - Hanley-Bowdoin, Linda AU - Harrison, Richard J. AU - Harvey, Jagger AU - He, Ping AU - Huffaker, Alisa AU - Hulbert, Scot AU - Innes, Roger AU - Jones, Jonathan D. G. AU - Kaloshian, Isgouhi AU - Kamoun, Sophien AU - Katagiri, Fumiaki AU - Leach, Jan AU - Ma, Wenbo AU - McDowell, John AU - Medford, June AU - Meyers, Blake AU - Nelson, Rebecca AU - Oliver, Richard AU - Qi, Yiping AU - Saunders, Diane AU - Shaw, Michael AU - Smart, Christine AU - Subudhi, Prasanta AU - Torrance, Lesley AU - Tyler, Bret AU - Valent, Barbara AU - Walsh, John T2 - Molecular Plant-Microbe Interactions AB - The white paper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on nonsustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture. DA - 2017/7// PY - 2017/7// DO - 10.1094/mpmi-01-17-0010-cr VL - 30 IS - 7 SP - 515-516 J2 - MPMI LA - en OP - SN - 0894-0282 UR - http://dx.doi.org/10.1094/mpmi-01-17-0010-cr DB - Crossref ER - TY - JOUR TI - Genetics of Hereditary Ataxia in Scottish Terriers AU - Urkasemsin, G. AU - Nielsen, D.M. AU - Singleton, A. AU - Arepalli, S. AU - Hernandez, D. AU - Agler, C. AU - Olby, N.J. T2 - Journal of Veterinary Internal Medicine AB - Background Scottish Terriers have a high incidence of juvenile onset hereditary ataxia primarily affecting the Purkinje neuron of the cerebellar cortex and causing slowly progressive cerebellar dysfunction. Objective To identify chromosomal regions associated with hereditary ataxia in Scottish Terriers. Animals One hundred and fifty‐three Scottish Terriers were recruited through the Scottish Terrier Club of America. Materials and Methods Prospective study. Dogs were classified as affected if they had slowly progressive cerebellar signs. When possible, magnetic resonance imaging and histopathological evaluation of the brain were completed as diagnostic aids. To identify genomic regions connected with the disease, genome‐wide mapping was performed using both linkage‐ and association‐based approaches. Pedigree evaluation and homozygosity mapping were also performed to examine mode of inheritance and to investigate the region of interest, respectively. Results Linkage and genome‐wide association studies in a cohort of Scottish Terriers both identified a region on CFA X strongly associated with the disease trait. Homozygosity mapping revealed a 4 Mb region of interest. Pedigree evaluation failed to identify the possible mode of inheritance due to the lack of complete litter information. Conclusion and Clinical Importance This finding suggests that further genetic investigation of the potential region of interest on CFA X should be considered in order to identify the causal mutation as well as develop a genetic test to eliminate the disease from this breed. DA - 2017/5/29/ PY - 2017/5/29/ DO - 10.1111/jvim.14738 VL - 31 IS - 4 SP - 1132-1139 J2 - J Vet Intern Med LA - en OP - SN - 0891-6640 UR - http://dx.doi.org/10.1111/jvim.14738 DB - Crossref KW - Canine KW - Cerebellar abiotrophy KW - Cerebellar ataxia KW - Neurodegeneration ER - TY - CHAP TI - The triple response assay and its use to characterize ethylene mutants in arabidopsis AU - Merchante, C. AU - Stepanova, A.N. T2 - Methods in Molecular Biology AB - Exposure of plants to ethylene results in drastic morphological changes. Seedlings germinated in the dark in the presence of saturating concentrations of ethylene display a characteristic phenotype known as the triple response. This phenotype is robust and easy to score. In Arabidopsis the triple response is usually evaluated at 3 days post germination in seedlings grown in the dark in rich media supplemented with 10 μM of the ethylene precursor ACC in air or in unsupplemented media in the presence of 10 ppm ethylene. The triple response in Arabidopsis consists of shortening and thickening of hypocotyls and roots and exaggeration of the curvature of apical hooks. The search for Arabidopsis mutants that fail to show this phenotype in ethylene or, vice versa, display the triple response in the absence of exogenously supplied hormone has allowed the identification of the key components of the ethylene biosynthesis and signaling pathways. Herein, we describe a simple protocol for assaying the triple response in Arabidopsis. The method can also be employed in many other dicot species, with minor modifications to account for species-specific differences in germination. We also compiled a comprehensive table of ethylene-related mutants of Arabidopsis, including many lines with auxin-related defects, as wild-type levels of auxin biosynthesis, transport, signaling, and response are necessary for the normal response of plants to ethylene. PY - 2017/// DO - 10.1007/978-1-4939-6854-1_13 VL - 1573 SP - 163-209 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85015705453&partnerID=MN8TOARS KW - Phytohormone KW - Ethylene KW - ACC KW - Triple response KW - Arabidopsis KW - Seedlings KW - Germination KW - Hypocotyl KW - Root KW - Apical hook KW - Mutants ER - TY - JOUR TI - Editorial: Relevance of translational regulation on plant growth and environmental responses AU - Ferrando, A. AU - Castellano, M.M. AU - Lisón, P. AU - Leister, D. AU - Stepanova, A.N. AU - Hanson, J. T2 - Frontiers in Plant Science AB - EDITORIAL article Front. Plant Sci., 19 December 2017Sec. Plant Physiology Volume 8 - 2017 | https://doi.org/10.3389/fpls.2017.02170 DA - 2017/// PY - 2017/// DO - 10.3389/fpls.2017.02170 VL - 8 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85040509996&partnerID=MN8TOARS KW - mRNA translation KW - translation factors KW - post-transcriptional regulation KW - translatome KW - organellar gene expression ER - TY - JOUR TI - The triple response assay and its use to characterize ethylene mutants in Arabidopsis AU - Merchante, C. AU - Stepanova, A. N. T2 - Ethylene signaling: methods and protocols DA - 2017/// PY - 2017/// VL - 1573 SP - 163-209 ER - TY - JOUR TI - Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development AU - Sehra, Bhupinder AU - Franks, Robert G. T2 - FRONTIERS IN PLANT SCIENCE AB - In the Arabidopsis thaliana seed pod, pod shatter and seed dispersal properties are in part determined by the development of a longitudinally-orientated dehiscence zone that derives from cells of the gynoecial valve margin. Transcriptional regulation of the MADS protein encoding transcription factors genes SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2) are critical for proper valve margin (VM) identity specification and later on for dehiscence zone (DZ) development. Current models of SHP1 and SHP2 regulation indicate that the transcription factors FRUITFULL (FUL) and REPLUMLESS (RPL) repress these SHP genes in the developing valve and replum domains, respectively. Thus the expression of the SHP genes is restricted to the VM. FUL encodes a MADS-box containing transcription factor that is predicted to act through CArG-box containing cis-regulatory motifs. Here we delimit functional modules within the SHP2 cis-regulatory region and examine the functional importance of CArG box motifs within these regulatory regions. We have characterized a 2.2kb region upstream of the SHP2 translation start site that drives early and late medial domain expression in the gynoecium, as well as expression within the VM and DZ. We identified two separable, independent cis-regulatory modules, a 1kb promoter region and a 700bp enhancer region, that are capable of giving valve margin and dehiscence zone expression. Our results argue for multiple independent cis-regulatory modules that support SHP2 expression during VM development and may contribute to the robustness of SHP2 expression in this tissue. Additionally, three closely positioned CArG box motifs located in the SHP2 upstream regulatory region were mutated in the context of the 2.2kb reporter construct. Mutating simultaneously all three CArG boxes caused a moderate de-repression of the SHP2 reporter that was detected within the valve domain, suggesting that these CArG boxes are involved in SHP2 repression in the valve. DA - 2017/10/16/ PY - 2017/10/16/ DO - 10.3389/fpls.2017.01712 VL - 8 SP - SN - 1664-462X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85034058138&partnerID=MN8TOARS KW - SHATTERPROOF genes KW - FRUITFULL KW - seedpod dehiscence KW - valve margin KW - fruit patterning KW - transcriptional regulation ER - TY - JOUR TI - Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals AU - Theilmann, Mia C. AU - Goh, Yong Jun AU - Nielsen, Kristian Fog AU - Klaenhammer, Todd R. AU - Barrangou, Rodolphe AU - Abou Hachem, Maher T2 - MBIO AB - ABSTRACT Therapeutically active glycosylated phytochemicals are ubiquitous in the human diet. The human gut microbiota (HGM) modulates the bioactivities of these compounds, which consequently affect host physiology and microbiota composition. Despite a significant impact on human health, the key players and the underpinning mechanisms of this interplay remain uncharacterized. Here, we demonstrate the growth of Lactobacillus acidophilus on mono- and diglucosyl dietary plant glycosides (PGs) possessing small aromatic aglycones. Transcriptional analysis revealed the upregulation of host interaction genes and identified two loci that encode phosphotransferase system (PTS) transporters and phospho-β-glucosidases, which mediate the uptake and deglucosylation of these compounds, respectively. Inactivating these transport and hydrolysis genes abolished or severely reduced growth on PG, establishing the specificity of the loci to distinct groups of PGs. Following intracellular deglucosylation, the aglycones of PGs are externalized, rendering them available for absorption by the host or for further modification by other microbiota taxa. The PG utilization loci are conserved in L. acidophilus and closely related lactobacilli, in correlation with versatile growth on these compounds. Growth on the tested PG appeared more common among human gut lactobacilli than among counterparts from other ecologic niches. The PGs that supported the growth of L. acidophilus were utilized poorly or not at all by other common HGM strains, underscoring the metabolic specialization of L. acidophilus . These findings highlight the role of human gut L. acidophilus and select lactobacilli in the bioconversion of glycoconjugated phytochemicals, which is likely to have an important impact on the HGM and human host. IMPORTANCE Thousands of therapeutically active plant-derived compounds are widely present in berries, fruits, nuts, and beverages like tea and wine. The bioactivity and bioavailability of these compounds, which are typically glycosylated, are altered by microbial bioconversions in the human gut. Remarkably, little is known about the bioconversion of PGs by the gut microbial community, despite the significance of this metabolic facet to human health. Our work provides the first molecular insights into the metabolic routes of diet relevant and therapeutically active PGs by Lactobacillus acidophilus and related human gut lactobacilli. This taxonomic group is adept at metabolizing the glucoside moieties of select PG and externalizes their aglycones. The study highlights an important role of lactobacilli in the bioconversion of dietary PG and presents a framework from which to derive molecular insights into their metabolism by members of the human gut microbiota. DA - 2017/// PY - 2017/// DO - 10.1128/mbio.01421-17 VL - 8 IS - 6 SP - SN - 2150-7511 KW - Lactobacillus KW - beta-glucoside KW - bioavailability KW - gut microbiota KW - phytochemical KW - polydatin KW - polyphenols KW - resveratrol KW - xenobiotic metabolism ER - TY - JOUR TI - Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips AU - Wear, Emily E. AU - Song, Jawon AU - Zynda, Gregory J. AU - LeBlanc, Chantal AU - Lee, Tae-Jin AU - Mickelson-Young, Leigh AU - Concia, Lorenzo AU - Mulvaney, Patrick AU - Szymanski, Eric S. AU - Allen, George C. AU - Martienssen, Robert A. AU - Vaughn, Matthew W. AU - Hanley-Bowdoin, Linda AU - Thompson, William F. T2 - PLANT CELL AB - All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the “Repli-seq” assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ∼32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase. DA - 2017/9// PY - 2017/9// DO - 10.1105/tpc.17.00037 VL - 29 IS - 9 SP - 2126-2149 SN - 1532-298X UR - http://europepmc.org/abstract/med/28842533 ER - TY - JOUR TI - Review of research advances in the screwworm eradication program over the past 25 years AU - Scott, Maxwell J. AU - Concha, Carolina AU - Welch, John B. AU - Phillips, Pamela L. AU - Skoda, Steven R. T2 - Entomologia Experimentalis et Applicata AB - Abstract New World screwworms, C ochliomyia hominivorax ( C oquerel) ( D iptera: C alliphoridae: C hrysomyinae), are devastating pests of warm‐blooded animals that cause significant economic damage to livestock. The successful campaign to eradicate screwworms from continental N orth A merica, led by the US Department of Agriculture and using the sterile insect technique, continues to receive research support that has resulted in improved technologies for all aspects of the program. The process and ingredients for mass‐rearing screwworms is more efficient and sustainable, and there is now a standardized protocol for developing new strains used in mass rearing. Cryopreservation of screwworm embryos allows strains to be preserved and recovered if necessary and also reduces rearing requirements for backup and research strains. Sterile fly release procedures and equipment have been updated leading to optimized sterile fly release rates. Surveillance for screwworm infestations and outbreaks have incorporated new trap designs, habitat analysis, and molecular genetic techniques that enhance monitoring the progress of the program as well as early detection and response to outbreaks. Genetic analyses of screwworm populations across their current range have increased the understanding of genetic differentiation, which may aide in developing new strains and determining the geographic origin of screwworms causing outbreaks when they occur. The ability to release only sterile males, which has been a goal of the program for over 60 years, has recently been accomplished through the development of transgenic sexing strains. The strains carry a conditional female lethal gene and are comparable to the wild‐type strain for several biological parameters that are important for mass production and performance in the field. The strains should improve efficiency of population suppression of the current and future eradication and prevention programs against screwworms. These research advances as well as future considerations are presented. DA - 2017/8/30/ PY - 2017/8/30/ DO - 10.1111/eea.12607 VL - 164 IS - 3 SP - 226-236 J2 - Entomologia Exp Applicata LA - en OP - SN - 0013-8703 1570-7458 UR - http://dx.doi.org/10.1111/eea.12607 DB - Crossref KW - New World screwworm KW - Cochliomyia hominivorax KW - Diptera KW - Calliphoridae KW - Chrysomyinae KW - sterile insect technique KW - SIT KW - insect mass rearing KW - obligate myiasis KW - insect genetics KW - male-only strains KW - insect surveillance ER - TY - JOUR TI - Linkage map construction and QTL analysis for internal heat necrosis in autotetraploid potato AU - Schumann, Mitchell J. AU - Zeng, Zhao-Bang AU - Clough, Mark E. AU - Yencho, G. Craig T2 - THEORETICAL AND APPLIED GENETICS DA - 2017/10// PY - 2017/10// DO - 10.1007/s00122-017-2941-1 VL - 130 IS - 10 SP - 2045-2056 SN - 1432-2242 ER - TY - JOUR TI - Disparate gain and loss of parasitic abilities among nematode lineages AU - Holterman, Martijn AU - Karegar, Akbar AU - Mooijman, Paul AU - Megen, Hanny AU - Elsen, Sven AU - Vervoort, Mariette T. W. AU - Quist, Casper W. AU - Karssen, Gerrit AU - Decraemer, Wilfrida AU - Opperman, Charles H. AU - Bird, David M. AU - Kammenga, Jan AU - Goverse, Aska AU - Smant, Geert AU - Helder, Johannes T2 - PLOS ONE AB - Plant parasitism has arisen time and again in multiple phyla, including bacteria, fungi, insects and nematodes. In most of these organismal groups, the overwhelming diversity hampers a robust reconstruction of the origins and diversification patterns of this trophic lifestyle. Being a moderately diversified phylum with ≈ 4,100 plant parasites (15% of total biodiversity) subdivided over four independent lineages, nematodes constitute a major organismal group for which the genesis of plant parasitism could be mapped. Since substantial crop losses worldwide have been attributed to less than 1% of these plant parasites, research efforts are severely biased towards this minority. With the first molecular characterisation of numerous basal and supposedly harmless plant parasites as well as their non-parasitic relatives, we were able to generate a comprehensive molecular framework that allows for the reconstruction of trophic diversification for a complete phylum. In each lineage plant parasites reside in a single taxonomic grouping (family or order), and by taking the coverage of the next lower taxonomic level as a measure for representation, 50, 67, 100 and 85% of the known diversity was included. We revealed distinct gain and loss patterns with regard to plant parasitism per se as well as host exploitation strategies between these lineages. Our map of parasitic nematode biodiversity also revealed an unanticipated time reversal in which the two most ancient lineages showed the lowest level of ecological diversification and vice versa. DA - 2017/9/21/ PY - 2017/9/21/ DO - 10.1371/journal.pone.0185445 VL - 12 IS - 9 SP - SN - 1932-6203 ER - TY - JOUR TI - A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency AU - Edwards, K. D. AU - Fernandez-Pozo, N. AU - Drake-Stowe, K. AU - Humphry, M. AU - Evans, A. D. AU - Bombarely, A. AU - Allen, F. AU - Hurst, R. AU - White, B. AU - Kernodle, S. P. AU - Bromley, J. R. AU - Sanchez-Tamburrino, J. P. AU - Lewis, R. S. AU - Mueller, L. A. T2 - BMC GENOMICS AB - Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation.Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production.Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species. DA - 2017/6/19/ PY - 2017/6/19/ DO - 10.1186/s12864-017-3791-6 VL - 18 SP - SN - 1471-2164 KW - Sequencing KW - Nicotiana KW - Nicotiana tabacum KW - tobacco KW - Solanaceae KW - Nitrogen use efficiency KW - Nitrogen utilization efficiency KW - EGY1 KW - Map-based cloning KW - Polyploidy ER - TY - JOUR TI - Alterations of CorTFL1 and CorAP1 expression correlate with major evolutionary shifts of inflorescence architecture in Cornus (Cornaceae) - a proposed model for variation of closed inflorescence forms AU - Ma, Qing AU - Liu, Xiang AU - Franks, Robert G. AU - Xiang, Qiu-Yun T2 - NEW PHYTOLOGIST AB - TFL1-, AP1- and LFY-like genes are known to be key regulators of inflorescence development. However, it remains to be tested whether the evolutionary modifications of inflorescence morphology result from shifts in their expression patterns. We compared the spatiotemporal expression patterns of CorTFL1, CorAP1 and CorLFY in six closely related Cornus species that display four types of closed inflorescence morphology using quantitative real-time polymerase chain reaction (qRT-PCR) and RNA in situ hybridization. Character mapping on the phylogeny was conducted to identify evolutionary changes and to assess the correlation between changes in gene expression and inflorescence morphology. Results demonstrated variation of gene expression patterns among species and a strong correlation between CorTFL1 expression and the branch index of the inflorescence type. Evolutionary changes in CorTFL1 and CorAP1 expression co-occurred on the phylogeny with the morphological changes underpinning inflorescence divergence. The study found a clear correlation between the expression patterns of CorTFL1 and CorAP1 and the inflorescence architecture in a natural system displaying closed inflorescences. The results suggest a role for the alteration in CorTFL1 and CorAP1 expression during the evolutionary modification of inflorescences in Cornus. We propose that a TFL1-like and AP1-like gene-based model may explain variation of closed inflorescences in Cornus and other lineages. DA - 2017/10// PY - 2017/10// DO - 10.1111/nph.14197 VL - 216 IS - 2 SP - 519-535 SN - 1469-8137 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84988892931&partnerID=MN8TOARS KW - CorAP1 KW - Cornus KW - CorTFL1 KW - evolutionary development KW - gene expression KW - inflorescence KW - in situ hybridization KW - quantitative real-time polymerase chain reaction (qRT-PCR) ER - TY - JOUR TI - A VIGS screen identifies immunity in the Arabidopsis Pla-1 accession to viruses in two different genera of the Geminiviridae AU - Reyes, Maria Ines AU - Flores-Vergara, Miguel A. AU - Guerra-Peraza, Orlene AU - Rajabu, Cyprian AU - Desai, Jigar AU - Hiromoto-Ruiz, Yokiko H. AU - Ndunguru, Joseph AU - Hanley-Bowdoin, Linda AU - Kjemtrup, Susanne AU - Ascencio-Ibanez, Jose T. AU - Robertson, Dominique T2 - PLANT JOURNAL AB - Summary Geminiviruses are DNA viruses that cause severe crop losses in different parts of the world, and there is a need for genetic sources of resistance to help combat them. Arabidopsis has been used as a source for virus‐resistant genes that derive from alterations in essential host factors. We used a virus‐induced gene silencing ( VIGS ) vector derived from the geminivirus Cabbage leaf curl virus (Ca LC uV) to assess natural variation in virus–host interactions in 190 Arabidopsis accessions. Silencing of CH ‐42 , encoding a protein needed to make chlorophyll, was used as a visible marker to discriminate asymptomatic accessions from those showing resistance. There was a wide range in symptom severity and extent of silencing in different accessions, but two correlations could be made. Lines with severe symptoms uniformly lacked extensive VIGS , and lines that showed attenuated symptoms over time (recovery) showed a concomitant increase in the extent of VIGS . One accession, Pla‐1, lacked both symptoms and silencing, and was immune to wild‐type infectious clones corresponding to Ca LC uV or Beet curly top virus ( BCTV ), which are classified in different genera in the Geminiviridae. It also showed resistance to the agronomically important Tomato yellow leaf curl virus ( TYLCV ). Quantitative trait locus mapping of a Pla‐1 X Col‐0 F 2 population was used to detect a major peak on chromosome 1, which is designated gip‐1 ( geminivirus immunity Pla‐1‐1 ). The recessive nature of resistance to Ca LC uV and the lack of obvious candidate genes near the gip‐1 locus suggest that a novel resistance gene(s) confers immunity. DA - 2017/12// PY - 2017/12// DO - 10.1111/tpj.13716 VL - 92 IS - 5 SP - 796-807 SN - 1365-313X KW - Arabidopsis KW - BCTV KW - CaLCuV KW - geminivirus KW - gip-1 KW - immunity KW - Pla-1 KW - VIGS ER - TY - JOUR TI - Repliscan: a tool for classifying replication timing regions AU - Zynda, Gregory J. AU - Song, Jawon AU - Concia, Lorenzo AU - Wear, Emily E. AU - Hanley-Bowdoin, Linda AU - Thompson, William F. AU - Vaughn, Matthew W. T2 - BMC BIOINFORMATICS AB - Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing.To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds.Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage. DA - 2017/8/7/ PY - 2017/8/7/ DO - 10.1186/s12859-017-1774-x VL - 18 SP - 1-14 SN - 1471-2105 UR - http://europepmc.org/abstract/med/28784090 KW - DNA replication KW - Repli-seq KW - Classification ER - TY - JOUR TI - Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster AU - Lee, Yuh Chwen G. AU - Yang, Qian AU - Chi, Wanhao AU - Turkson, Susie A. AU - Du, Wei A. AU - Kemkemer, Claus AU - Zeng, Zhao-Bang AU - Long, Manyuan AU - Zhuang, Xiaoxi T2 - GENOME BIOLOGY AND EVOLUTION AB - Foraging behavior is critical for the fitness of individuals. However, the genetic basis of variation in foraging behavior and the evolutionary forces underlying such natural variation have rarely been investigated. We developed a systematic approach to assay the variation in survival rate in a foraging environment for adult flies derived from a wild Drosophila melanogaster population. Despite being such an essential trait, there is substantial variation of foraging behavior among D. melanogaster strains. Importantly, we provided the first evaluation of the potential caveats of using inbred Drosophila strains to perform genome-wide association studies on life-history traits, and concluded that inbreeding depression is unlikely a major contributor for the observed large variation in adult foraging behavior. We found that adult foraging behavior has a strong genetic component and, unlike larval foraging behavior, depends on multiple loci. Identified candidate genes are enriched in those with high expression in adult heads and, demonstrated by expression knock down assay, are involved in maintaining normal functions of the nervous system. Our study not only identified candidate genes for foraging behavior that is relevant to individual fitness, but also shed light on the initial stage underlying the evolution of the behavior. DA - 2017/5// PY - 2017/5// DO - 10.1093/gbe/evx089 VL - 9 IS - 5 SP - 1357-1369 SN - 1759-6653 KW - genome-wide association study KW - foraging behavior KW - Drosophila melanogaster KW - inbreeding depression ER - TY - JOUR TI - Transcriptomic Analysis in Strawberry Fruits Reveals Active Auxin Biosynthesis and Signaling in the Ripe Receptacle (vol 8, pg 889, 2017) AU - Estrada-Johnson, Elizabeth AU - Csukasi, Fabiana AU - Pizarro, Carmen M. AU - Vallarino, Jose G. AU - Kiryakova, Yulia AU - Vioque, Amalia AU - Merchante, Catharina AU - Brumos, Javier AU - Medina-Escobar, Nieves AU - Botella, Miguel A. AU - Alonso, Jose M. AU - Fernie, Alisdair R. AU - Sanchez-Sevilla, Jose F. AU - Osorio, Sonia AU - Valpuesta, Victoriano T2 - FRONTIERS IN PLANT SCIENCE AB - [This corrects the article on p. 889 in vol. 8, PMID: 28611805.]. DA - 2017/7/24/ PY - 2017/7/24/ DO - 10.3389/fpls.2017.01305 VL - 8 SP - SN - 1664-462X KW - auxin KW - fruit KW - strawberry KW - transcriptome regulation KW - ripening ER - TY - JOUR TI - The S-layer Associated Serine Protease Homolog PrtX Impacts Cell Surface-Mediated Microbe-Host Interactions of Lactobacillus acidophilus NCFM AU - Johnson, Brant R. AU - O'Flaherty, Sarah AU - Goh, Yong Jun AU - Carroll, Ian AU - Barrangou, Rodolphe AU - Klaenhammer, Todd R. T2 - FRONTIERS IN MICROBIOLOGY AB - Health-promoting aspects attributed to probiotic microorganisms, including adhesion to intestinal epithelia and modulation of the host mucosal immune system, are mediated by proteins found on the bacterial cell surface. Notably, certain probiotic and commensal bacteria contain a surface (S-) layer as the outermost stratum of the cell wall. S-layers are non-covalently bound semi-porous, crystalline arrays of self-assembling, proteinaceous subunits called S-layer proteins (SLPs). Recent evidence has shown that multiple proteins are non-covalently co-localized within the S-layer, designated S-layer associated proteins (SLAPs). In Lactobacillus acidophilus NCFM, SLP and SLAPs have been implicated in both mucosal immunomodulation and adhesion to the host intestinal epithelium. In this study, a S-layer associated serine protease, PrtX (prtX, lba1578), was deleted from the chromosome of L. acidophilus NCFM. Compared to the parent strain, the PrtX-deficient strain (∆prtX) demonstrated increased autoaggregation, an altered cellular morphology, and pleiotropic increases in adhesion to mucin and fibronectin, in vitro. Furthermore, ∆prtX demonstrated increased in vitro immune stimulation of IL-6, IL-12, and IL-10 compared to wild-type, when exposed to mouse dendritic cells. Finally, in vivo colonization of germ-free mice with ∆prtX led to an increase in epithelial barrier integrity. The absence of PrtX within the exoproteome of a ∆prtX strain caused morphological changes, resulting in a pleiotropic increase of the organisms' immunomodulatory properties and interactions with some intestinal epithelial cell components. DA - 2017/6/30/ PY - 2017/6/30/ DO - 10.3389/fmicb.2017.01185 VL - 8 SP - SN - 1664-302X KW - serine protease KW - S-layer KW - S-layer associated proteins KW - Lactobacillus KW - probiotic KW - intestinal barrier integrity KW - mucin KW - fibronectin ER - TY - JOUR TI - Germline transformation of the western corn rootworm, Diabrotica virgifera virgifera AU - Chu, F. AU - Klobasa, W. AU - Wu, P. AU - Pinzi, S. AU - Grubbs, N. AU - Gorski, S. AU - Cardoza, Y. AU - Lorenzen, M. D. T2 - INSECT MOLECULAR BIOLOGY AB - Abstract The western corn rootworm (WCR), a major pest of maize, is notorious for rapidly adapting biochemically, behaviourally and developmentally to a variety of control methods. Despite much effort, the genetic basis of WCR adaptation remains a mystery. Since transformation‐based applications such as transposon tagging and enhancer trapping have facilitated genetic dissection of model species such as Drosophila melanogaster , we developed a germline‐transformation system for WCR in an effort to gain a greater understanding of the basic biology of this economically important insect. Here we report the use of a fluorescent‐marked Minos element to create transgenic WCR. We demonstrate that the transgenic strains express both an eye‐specific fluorescent marker and piggyBac transposase . We identified insertion‐site junction sequences via inverse PCR and assessed insertion copy number using digital droplet PCR (ddPCR). Interestingly, most WCR identified as transgenic via visual screening for DsRed fluorescence proved to carry multiple Minos insertions when tested via ddPCR. A total of eight unique insertion strains were created by outcrossing the initial transgenic strains to nontransgenic WCR mates. Establishing transgenic technologies for this beetle is the first step towards bringing a wide range of transformation‐based tools to bear on understanding WCR biology. DA - 2017/8// PY - 2017/8// DO - 10.1111/imb.12305 VL - 26 IS - 4 SP - 440-452 SN - 1365-2583 KW - Minos KW - piggyBac KW - small-scale rearing KW - embryonic microinjection ER - TY - JOUR TI - The Tobacco Trichome Exudate Z-abienol and Its Relationship With Plant Resistance to Phytophthora nicotianae AU - Steede, William T. AU - Ma, Justin M. AU - Eickholt, David P. AU - Drake-Stowe, Katherine E. AU - Kernodle, Sheri P. AU - Shew, H. David AU - Danehower, David A. AU - Lewis, Ramsey S. T2 - PLANT DISEASE AB - In previous research, we discovered a favorable quantitative trait locus (QTL) in cigar tobacco cultivar 'Beinhart 1000' designated as Phn15.1, which provides a high level of partial resistance to the black shank disease caused by Phytophthora nicotianae. A very close genetic association was also found between Phn15.1 and the ability to biosynthesize Z-abienol, a labdanoid diterpene exuded by the trichomes onto above-ground plant parts, and that imparts flavor and aroma characteristics to Oriental and some cigar tobacco types. Because accumulation of Z-abienol is considered to be undesirable for cultivars of other tobacco types, we herein describe a series of experiments to gain insight on whether this close association is due to genetic linkage or pleiotropy. First, in an in vitro bioassay, we observed Z-abienol and related diterpenes to inhibit hyphal growth of P. nicotianae at concentrations between 0.01 and 100 ppm. Secondly, we field-tested transgenic versions of Beinhart 1000 carrying RNAi constructs for downregulating NtCPS2 or NtABS, two genes involved in the biosynthesis of Z-abienol. Thirdly, we also field tested a recombinant inbred line population segregating for a truncation mutation in NtCPS2 leading to an interrupted Z-abienol pathway. We observed no correlation between field resistance to P. nicotianae and the ability to accumulate Z-abienol in either the transgenic materials or the mapping population. Results suggest that, although Z-abienol may affect P. nicotianae when applied at high concentrations in in vitro assays, the compound has little effect on black shank disease development under natural field conditions. Thus, it should be possible to disassociate Phn15.1-mediated black shank resistance identified in cigar tobacco cultivar Beinhart 1000 from the ability to accumulate Z-abienol, an undesirable secondary metabolite for burley and flue-cured tobacco cultivars. DA - 2017/7// PY - 2017/7// DO - 10.1094/pdis-10-16-1512-re VL - 101 IS - 7 SP - 1214-1221 SN - 1943-7692 ER - TY - JOUR TI - Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping AU - Guo, Y. AU - Fudali, S. AU - Gimeno, J. AU - DiGennaro, P. AU - Chang, S. AU - Williamson, V.M. AU - Bird, D.M. AU - Nielsen, D.M. T2 - Genetics AB - Abstract Interactions between species are pervasive among plants, animals, and microbes, and identifying the molecular signals involved is an active area of research.. Organisms engage in extensive cross-species molecular dialog, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of 98 isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla. With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites. The effects of parasite genotypes on plant gene expression were often substantial, with up to 90-fold (P = 3.2 × 10−52) changes in expression levels caused by individual parasite loci. Mapped loci included a number of pleiotropic sites, including one 87-kb parasite locus that modulated expression of >60 host genes. The 213 host genes identified were substantially enriched for transcription factors. We distilled higher-order connections between polymorphisms and genes from both species via network inference. To replicate our results and test whether effects were conserved across a broader host range, we performed a confirmatory experiment using M. hapla-infected tomato. This revealed that homologous genes were similarly affected. Finally, to validate the broader utility of cross-species eQTL mapping, we applied the strategy to data from a Salmonella infection study, successfully identifying polymorphisms in the human genome affecting bacterial expression. DA - 2017/// PY - 2017/// DO - 10.1534/genetics.117.202531 VL - 206 IS - 4 SP - 2175-2184 SN - 1943-2631 KW - transspecies KW - trans-eQTL KW - host-pathogen interaction KW - symbiosis KW - RNA-Seq ER - TY - JOUR TI - Genital morphology and allometry differ by species and sex in Malawi cichlid fishes AU - Moore, Emily C. AU - Roberts, Reade B. T2 - HYDROBIOLOGIA AB - The African cichlid fishes show great diversity in mating displays and reproductive strategies, yet species differences in genital morphology have been little studied. Observational notes have described broad sex differences in external genital shape between males and females, but these differences have not been quantified. We examined three aspects of genital morphology (relative anogenital distance, relative vent length, and relative external genital area) in two riverine and eleven Lake Malawi African cichlid species from eight genera. We find the most sexually distinct morphology in the Lake Malawi rock cichlids and the least sexual dimorphism in the riverine outgroup; additionally, diversity in metrics within genus indicates that these traits are recently evolving. Sexual dimorphism in morphology is present in most species, and, in the Lake Malawi species, multivariate discriminant analysis allows for accurate assignment of gonadal sex based on genital morphology and body size. This will serve as a useful method for sexing fish in a nonlethal fashion and provides a starting point for further examination of the evolution of genital morphology in this diverse group of fishes. DA - 2017/5// PY - 2017/5// DO - 10.1007/s10750-016-2912-6 VL - 791 IS - 1 SP - 127-143 SN - 1573-5117 KW - Genital morphology KW - Cichlid fishes KW - Sexual dimorphism KW - Anogenital distance KW - Genital papilla ER - TY - JOUR TI - Genetic sex determination in Astatotilapia calliptera, a prototype species for the Lake Malawi cichlid radiation AU - Peterson, Erin N. AU - Cline, Maggie E. AU - Moore, Emily C. AU - Roberts, Natalie B. AU - Roberts, Reade B. T2 - SCIENCE OF NATURE DA - 2017/6// PY - 2017/6// DO - 10.1007/s00114-017-1462-8 VL - 104 IS - 5-6 SP - SN - 1432-1904 KW - Sex chromosome KW - Genetic sex determination KW - Cichlid KW - Fish KW - Astatotilapia calliptera ER - TY - JOUR TI - Deletion of lipoteichoic acid synthase impacts expression of genes encoding cell surface proteins in lactobacillus acidophilus AU - Selle, K. AU - Goh, Y. J. AU - Johnson, B. R. AU - O'Flaherty, S. AU - Andersen, J. M. AU - Barrangou, R. AU - Klaenhammer, T. R. T2 - Frontiers in Microbiology AB - Lactobacillus acidophilus NCFM is a well-characterized probiotic microorganism, supported by a decade of genomic and functional phenotypic investigations. L. acidophilus deficient in lipoteichoic acid (LTA), a major immunostimulant in Gram-positive bacteria, has been shown to shift immune system responses in animal disease models. However, the pleiotropic effects of removing LTA from the cell surface in lactobacilli are unknown. In this study, we surveyed the global transcriptional and extracellular protein profiles of two strains of L. acidophilus deficient in LTA. Twenty-four differentially expressed genes specific to the LTA-deficient strains were identified, including a predicted heavy metal resistance operon and several putative peptidoglycan hydrolases. Cell morphology and manganese sensitivity phenotypes were assessed in relation to the putative functions of differentially expressed genes. LTA-deficient L. acidophilus exhibited elongated cellular morphology and their growth was severely inhibited by elevated manganese concentrations. Exoproteomic surveys revealed distinct changes in the composition and relative abundances of several extracellular proteins and showed a bias of intracellular proteins in LTA-deficient strains of L. acidophilus. Taken together, these results elucidate the impact of ltaS deletion on the transcriptome and extracellular proteins of L. acidophilus, suggesting roles of LTA in cell morphology and ion homeostasis as a structural component of the Gram positive cell wall. DA - 2017/// PY - 2017/// DO - 10.3389/fmicb.2017.00553 VL - 8 ER - TY - JOUR TI - An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid fish AU - Roberts, Reade B. AU - Moore, Emily C. AU - Kocher, Thomas D. T2 - MOLECULAR ECOLOGY AB - Despite long-standing interest in the evolution and maintenance of discrete phenotypic polymorphisms, the molecular genetic basis of such polymorphism in the wild is largely unknown. Female sex-associated blotched colour polymorphisms found in cichlids of Lake Malawi, East Africa, represent a highly successful polymorphic phenotype, found and maintained in four genera across the geographic expanse of the lake. Previously, we identified an association with an allelic variant of the paired-box transcription factor gene pax7a and blotched colour morphs in Lake Malawi cichlid fishes. Although a diverse range of blotched phenotypes are present in Lake Malawi cichlid species, they all appeared to result from an allele of pax7a that produces increased levels of transcript. Here, we examine the developmental and genetic basis of variation among blotched morphs. First, we confirm that pax7a-associated blotch morphs result primarily from modulation of melanophore development and survival. From laboratory crosses and natural population studies, we identify at least three alleles of pax7a associated with discrete subtypes of blotched morphs, in addition to the ancestral pax7a allele. Genotypes at pax7a support initial evolution of a novel pax7a allele to produce the blotched class of morphs, followed by subsequent evolution of that pax7a blotched allele to produce additional alleles associated with discrete colour morphs. Variant alleles of pax7a produce different levels of pax7a transcript, correlating with pigmentation phenotype at the cellular level. This naturally selected allelic series should serve as a case study for understanding the molecular genetic control of pax7a expression and the evolution of sex-associated alleles. DA - 2017/5// PY - 2017/5// DO - 10.1111/mec.13975 VL - 26 IS - 10 SP - 2625-2639 SN - 1365-294X KW - allelic series KW - cichlid fish KW - colour morphs KW - pax7 KW - pigmentation ER - TY - JOUR TI - Variation in Recombination Rate: Adaptive or Not? AU - Ritz, Kathryn R. AU - Noor, Mohamed A. F. AU - Singh, Nadia D. T2 - TRENDS IN GENETICS AB - Rates of meiotic recombination are widely variable both within and among species. However, the functional significance of this variation remains largely unknown. Is the observed within-species variation in recombination rate adaptive? Recent work has revealed new insight into the scale and scope of population-level variation in recombination rate. These data indicate that the magnitude of within-population variation in recombination is similar among taxa. The apparent similarity of the variance in recombination rate among individuals between distantly related species suggests that the relative costs and benefits of recombination that establish the upper and lower bounds may be similar across species. Here we review the current data on intraspecific variation in recombination rate and discuss the molecular and evolutionary costs and benefits of recombination frequency. We place this variation in the context of adaptation and highlight the need for more empirical studies focused on the adaptive value of variation in recombination rate. DA - 2017/5// PY - 2017/5// DO - 10.1016/j.tig.2017.03.003 VL - 33 IS - 5 SP - 364-374 SN - 1362-4555 ER - TY - JOUR TI - Building early-larval sexing systems for genetic control of the Australian sheep blow fly Lucilia cuprina using two constitutive promoters AU - Yan, Ying AU - Linger, Rebecca J. AU - Scott, Maxwell J. T2 - Scientific Reports AB - Transgenic sexing strains (TSS) that carry conditional female lethal genes are advantageous for genetic control programs based on the sterile insect technique (SIT). It is desirable if females die early in development as larval diet is a major cost for mass production facilities. This can be achieved by using a gene promoter that is only active in embryos to drive expression of the tetracycline transactivator (tTA), the transcription factor commonly used in two-component TSS. While an embryo-specific promoter is ideal it may not be essential for assembling an effective TSS as tTA can be repressed by addition of tetracycline to the diet at larval and/or adult stages. Here we have investigated this idea by isolating and employing the promoters from the Lucilia spitting image and actin 5C genes to drive tTA expression in embryos and later stages. L. cuprina TSS with the tTA drivers and tTA-regulated tetO-Lshid effectors produced only females when raised on a limited tetracycline diet. The Lshid transgene contains a sex-specific intron and as a consequence only females produce LsHID protein. TSS females died at early larval stages, which makes the lines advantageous for an SIT program. DA - 2017/5/31/ PY - 2017/5/31/ DO - 10.1038/s41598-017-02763-4 VL - 7 IS - 1 SP - J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-017-02763-4 DB - Crossref ER - TY - JOUR TI - Translation regulation in plants: an interesting past, an exciting present and a promising future AU - Merchante, Catharina AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - PLANT JOURNAL AB - Summary Changes in gene expression are at the core of most biological processes, from cell differentiation to organ development, including the adaptation of the whole organism to the ever‐changing environment. Although the central role of transcriptional regulation is solidly established and the general mechanisms involved in this type of regulation are relatively well understood, it is clear that regulation at a translational level also plays an essential role in modulating gene expression. Despite the large number of examples illustrating the critical role played by translational regulation in determining the expression levels of a gene, our understanding of the molecular mechanisms behind such types of regulation has been slow to emerge. With the recent development of high‐throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein–RNA interactions and ribosome occupancy at the genome level, a renewed enthusiasm toward studying translation regulation is warranted. The use of these new powerful technologies in well‐established and uncharacterized translation‐dependent processes holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation. DA - 2017/5// PY - 2017/5// DO - 10.1111/tpj.13520 VL - 90 IS - 4 SP - 628-653 SN - 1365-313X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85017002891&partnerID=MN8TOARS KW - translation KW - upstream open reading frames KW - internal ribosomal entry sites KW - gene-specific translation KW - global regulation of translation KW - RNA-binding protein ER - TY - JOUR TI - Transcriptomic analysis in strawberry fruits reveals active auxin biosynthesis and signaling in the ripe receptacle AU - Estrada-Johnson, E. AU - Csukasi, F. AU - Pizarro, C. M. AU - Vallarino, J. G. AU - Kiryakova, Y. AU - Vioque, A. AU - Brumos, J. AU - Medina-Escobar, N. AU - Botella, M. A. AU - Alonso, J. M. AU - Fernie, A. R. AU - Sanchez-Sevilla, J. F. AU - Osorio, S. AU - Valpuesta, V. T2 - Frontiers in Plant Science DA - 2017/// PY - 2017/// VL - 8 ER - TY - JOUR TI - Deciphering the routes of invasion of Drosophila suzukii by means of ABC random forest AU - Fraimout, A. AU - Debat, V. AU - Fellous, S. AU - Hufbauer, R. A. AU - Foucaud, J. AU - Pudlo, P. AU - Marin, J. M. AU - Price, D. K. AU - Cattel, J. AU - Chen, X. AU - Depra, M. AU - Duyck, P. F. AU - Guedot, C. AU - Kenis, M. AU - Kimura, M. T. AU - Loeb, G. AU - Loiseau, A. AU - Martinez-Sanudo, I. AU - Pascual, M. AU - al., T2 - Molecular Biology and Evolution DA - 2017/// PY - 2017/// VL - 34 IS - 4 SP - 980-996 ER - TY - JOUR TI - CRISPR-Cas Technologies and Applications in Food Bacteria AU - Stout, Emily AU - Klaenhammer, Todd AU - Barrangou, Rodolphe T2 - ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 8 AB - Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity. DA - 2017/// PY - 2017/// DO - 10.1146/annurev-food-072816-024723 VL - 8 SP - 413-437 SN - 1941-1421 KW - probiotics KW - cultures KW - strain-typing KW - phage resistance KW - plasmid vaccination KW - antimicrobial KW - genome editing ER - TY - JOUR TI - An Extracellular Cell-Attached Pullulanase Confers Branched alpha-Glucan Utilization in Human Gut Lactobacillus acidophilus AU - Moller, Marie S. AU - Goh, Yong Jun AU - Rasmussen, Kasper Bowig AU - Cypryk, Wojciech AU - Celebioglu, Hasan Ufuk AU - Klaenhammer, Todd R. AU - Svensson, Birte AU - Abou Hachem, Maher T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT Of the few predicted extracellular glycan-active enzymes, glycoside hydrolase family 13 subfamily 14 (GH13_14) pullulanases are the most common in human gut lactobacilli. These enzymes share a unique modular organization, not observed in other bacteria, featuring a catalytic module, two starch binding modules, a domain of unknown function, and a C-terminal surface layer association protein (SLAP) domain. Here, we explore the specificity of a representative of this group of pullulanases, Lactobacillus acidophilus Pul13_14 ( La Pul13_14), and its role in branched α-glucan metabolism in the well-characterized Lactobacillus acidophilus NCFM, which is widely used as a probiotic. Growth experiments with L. acidophilus NCFM on starch-derived branched substrates revealed a preference for α-glucans with short branches of about two to three glucosyl moieties over amylopectin with longer branches. Cell-attached debranching activity was measurable in the presence of α-glucans but was repressed by glucose. The debranching activity is conferred exclusively by La Pul13_14 and is abolished in a mutant strain lacking a functional La Pul13_14 gene. Hydrolysis kinetics of recombinant La Pul13_14 confirmed the preference for short-branched α-glucan oligomers consistent with the growth data. Curiously, this enzyme displayed the highest catalytic efficiency and the lowest K m reported for a pullulanase. Inhibition kinetics revealed mixed inhibition by β-cyclodextrin, suggesting the presence of additional glucan binding sites besides the active site of the enzyme, which may contribute to the unprecedented substrate affinity. The enzyme also displays high thermostability and higher activity in the acidic pH range, reflecting adaptation to the physiologically challenging conditions in the human gut. IMPORTANCE Starch is one of the most abundant glycans in the human diet. Branched α-1,6-glucans in dietary starch and glycogen are nondegradable by human enzymes and constitute a metabolic resource for the gut microbiota. The role of health-beneficial lactobacilli prevalent in the human small intestine in starch metabolism remains unexplored in contrast to colonic bacterial residents. This study highlights the pivotal role of debranching enzymes in the breakdown of starchy branched α-glucan oligomers (α-limit dextrins) by human gut lactobacilli exemplified by Lactobacillus acidophilus NCFM, which is one of the best-characterized strains used as probiotics. Our data bring novel insight into the metabolic preference of L. acidophilus for α-glucans with short α-1,6-branches. The unprecedented affinity of the debranching enzyme that confers growth on these substrates reflects its adaptation to the nutrient-competitive gut ecological niche and constitutes a potential advantage in cross-feeding from human and bacterial dietary starch metabolism. DA - 2017/6// PY - 2017/6// DO - 10.1128/aem.00402-17 VL - 83 IS - 12 SP - SN - 1098-5336 KW - glycoside hydrolase family 13 KW - human gut microbiota KW - starch KW - starch binding modules ER - TY - JOUR TI - A Nonparametric survival function estimator via censored kernel quantile regressions AU - Shin, S. J. AU - Zhang, H. H. AU - Wu, Y. C. T2 - Statistica Sinica DA - 2017/// PY - 2017/// VL - 27 IS - 1 SP - 457-478 ER - TY - JOUR TI - Soybean cyst nematode culture collections and field populations from North Carolina and Missouri reveal high incidences of infection by viruses AU - Ruark, Casey L. AU - Koenning, Stephen R. AU - Davis, Eric L. AU - Opperman, Charles H. AU - Lommel, Steven A. AU - Mitchum, Melissa G. AU - Sit, Tim L. T2 - PLOS ONE AB - Five viruses were previously discovered infecting soybean cyst nematodes (SCN; Heterodera glycines) from greenhouse cultures maintained in Illinois. In this study, the five viruses [ScNV, ScPV, ScRV, ScTV, and SbCNV-5] were detected within SCN greenhouse and field populations from North Carolina (NC) and Missouri (MO). The prevalence and titers of viruses in SCN from 43 greenhouse cultures and 25 field populations were analyzed using qRT-PCR. Viral titers within SCN greenhouse cultures were similar throughout juvenile development, and the presence of viral anti-genomic RNAs within egg, second-stage juvenile (J2), and pooled J3 and J4 stages suggests active viral replication within the nematode. Viruses were found at similar or lower levels within field populations of SCN compared with greenhouse cultures of North Carolina populations. Five greenhouse cultures harbored all five known viruses whereas in most populations a mixture of fewer viruses was detected. In contrast, three greenhouse cultures of similar descent to one another did not possess any detectable viruses and primarily differed in location of the cultures (NC versus MO). Several of these SCN viruses were also detected in Heterodera trifolii (clover cyst) and Heterodera schachtii (beet cyst), but not the other cyst, root-knot, or reniform nematode species tested. Viruses were not detected within soybean host plant tissue. If nematode infection with viruses is truly more common than first considered, the potential influence on nematode biology, pathogenicity, ecology, and control warrants continued investigation. DA - 2017/1/31/ PY - 2017/1/31/ DO - 10.1371/journal.pone.0171514 VL - 12 IS - 1 SP - SN - 1932-6203 ER -