Publications by authors named "Susan J Brown"

85 Publications

Whole-genome classification of rotavirus C and genetic diversity of porcine strains in the USA.

J Gen Virol 2021 May;102(5)

Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA.

Rotavirus C (RVC) is associated with acute diarrhoea in both children and young animals. Because of its frequent occurrence, additional sequences have recently been generated. In this study, we sequenced 21 complete genomes from porcine diarrhoea samples and analysed them together with all available reference sequences collected from the GenBank database [National Center for Biotechnology Information (NCBI)]. Based on phylogenetic analysis and genetic distance calculation, the number of each segment was identified as 31G, 26P, 13I, 5R, 5C, 5M, 12A, 10 N, 9T, 8E and 4 H for genotypes encoding VP7, VP4, VP6, VP1, VP2, VP3 and NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. From the analysis, genotypes G19-G31, P[22]-P[26], R5, A9-A12, N9-N10, T7-T9 and E6-E8 were defined as newly identified genotypes, and genotype C6 was combined with C5, and M6 was combined with M1, due to their closely related nature. Estimated with the identity frequency ratio between the intergenotype and intragenotype, the nucleotide identity cutoff values for different genotypes were determined as 85, 85, 86, 84, 83, 84, 82, 87, 84, 81 and 79 % for VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. Genotyping of the 49 US strains indicated possible segment reassortment in 9 of the 11 segments, with the exceptions being VP1 and NSP5, and the most prevalent genotypes for each segment genes in the USA were G6/G5/G21/G9-P5/P4-I6/I5-R1-C5-M1-A8-N1/N10-T1-E1-H1. Our study updated the genotypes of RVC strains and provided more evidence of RVC strain diversity that may be relevant to better understand genetic diversity, and the distribution and evolution of RVC strains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/jgv.0.001598DOI Listing
May 2021

Undergraduate Virtual Engagement in Community Genome Annotation Provides Flexibility to Overcome Course Disruptions.

J Microbiol Biol Educ 2021 31;22(1). Epub 2021 Mar 31.

Biology Department, Indian River State College, Fort Pierce, FL 34981.

Recently, students and faculty have been forced to deal with unprecedented disruptions to their courses and broader uncertainties that have presented serious challenges to quality instruction. We present a flexible, team-based approach to teaching and learning that can transition seamlessly between face-to-face, hybrid, and fully online instruction when disruptions occur. We have built a community genome annotation program that can be implemented as a module in a biology course, as an entire course, or as directed research projects. This approach maintains an engaging and supportive educational environment and provides students the opportunity to learn and contribute to science with undergraduate research. Students are provided guidance through multiple interactions with faculty and peer mentors to support their progress and encourage learning. Integration of the developed instructional tools with available technology ensures that students can contribute remotely. Through this process, students seamlessly continue their annotation coursework, participate in undergraduate research, and prepare abstracts and posters for virtual conferences. Importantly, this strategy does not impose any additional burden or workload on students, who may already be overwhelmed with the additional work associated with the transition to remote learning. Here, we present tips for implementing this instructional platform, provide an overview of tools that facilitate instruction, and discuss expected educational outcomes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/jmbe.v22i1.2395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8011878PMC
March 2021

Marker location and knee joint constraint affect the reporting of overhead squat kinematics in elite youth football players.

Sports Biomech 2021 Mar 5:1-18. Epub 2021 Mar 5.

School of Applied Sciences Edinburgh, Edinburgh Napier University, Scotland, UK.

Motion capture systems are used in the analysis and interpretation of athlete movement patterns for a variety of reasons, but data integrity remains critical regardless. The extent to which marker location or constraining degrees of freedom (DOF) in the biomechanical model impacts on this integrity lacks consensus. Ten elite academy footballers performed bilateral overhead squats using a marker-based motion capture system. Kinematic data were calculated using four different marker sets with 3DOF and 6DOF configurations for the three joint rotations of the right knee. Root mean squared error differences between marker sets ranged in the sagittal plane between 1.02 and 4.19 degrees to larger values in the frontal (1.30-6.39 degrees) and transverse planes (1.33 and 7.97 degrees). The cross-correlation function of the knee kinematic time series for all eight marker-sets ranged from excellent for sagittal plane motion (>0.99) but reduced for both coronal and transverse planes (<0.9). Two-way ANOVA repeated measures calculated at peak knee flexion revealed significant differences between marker sets for frontal and transverse planes (p < 0.05). Pairwise comparisons showed significant differences between some marker sets. Marker location and constraining DOF while measuring relatively large ranges of motion in this population are important considerations for data integrity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/14763141.2021.1890197DOI Listing
March 2021

Organic contaminants of emerging concern in leachate of historic municipal landfills.

Environ Pollut 2021 May 11;276:116474. Epub 2021 Jan 11.

School of Earth, Environment and Society, McMaster University, Canada; Water Science and Technology Directorate, Environment and Climate Change Canada, Canada. Electronic address:

Many types of contaminants of emerging concern (CECs), including per- and poly-fluoroalkyl substances (PFAS), have been found in leachate of operating municipal landfills. However, there is only limited information on CECs presence in leachate of historic landfills (≥3 decades since closure, often lacking engineered liners or leachate collection systems) at concentrations that may pose a risk to nearby wells and surface water ecosystems. In this study, 48 samples of leachate-impacted groundwater were collected from 20 historic landfills in Ontario, Canada. The CECs measured included artificial sweeteners (ASs), PFAS, organophosphate esters (OPE), pharmaceuticals, bisphenols, sulfamic acid, perchlorate, and substituted phenols. The common presence of the AS saccharin, a known indicator of old landfill leachate, combined with mostly negligible levels of the AS acesulfame, an indicator of modern wastewater, revealed that most samples were strongly influenced by leachate and not cross-contaminated by wastewater (which can contain these same CECs). Several landfills, including ones closed in the 1960s, had total PFAS concentrations similar to those previously measured at modern landfills, with a maximum observed here of 12.7 μg/L. Notably elevated concentrations of several OPE, sulfamic acid, cotinine, and bisphenols A and S were found at many 30-60 year-old landfills. There was little indication of declining concentrations with landfill age, suggesting historic landfills can be long-term sources of CECs to groundwater and that certain CECs may be useful tracers for historic landfill leachate. These findings provide guidance on which CECs may require monitoring at historic landfill sites and wastewater treatment plants receiving their effluent.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.envpol.2021.116474DOI Listing
May 2021

Variable persistence of artificial sweeteners during wastewater treatment: Implications for future use as tracers.

Water Res 2020 Oct 1;184:116124. Epub 2020 Jul 1.

Science and Risk Assessment Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington, Ontario, L7S 1A1, Canada.

For more than a decade the artificial sweeteners acesulfame (ACE) and sucralose (SUC) have been applied as tracers of the input of wastewater to environmental waters. Recently concerns have been raised that degradation of ACE during treatment may hinder or restrict its use as a wastewater tracer. In this study the value of ACE and SUC as tracers was reassessed based on samples of wastewater at 12 municipal wastewater treatment (MWWT) plants and from 7 septic systems and associated septic plumes in groundwater. The results indicated stability of SUC during MWWT at most plants, and variable removal of both sweeteners during some MWWT and in the septic wastewater systems. However, the residual concentrations of ACE and SUC in municipal effluent and in septic plumes indicate that both sweeteners remain valuable wastewater tracers. The mass ratio SUC/ACE was found to be a useful parameter for examining the relative persistence of these sweeteners.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.watres.2020.116124DOI Listing
October 2020

Environmental fluxes of perchlorate in rural catchments, Ontario, Canada.

Sci Total Environ 2020 Jun 20;720:137426. Epub 2020 Feb 20.

Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington, Ontario L7S 1A1, Canada.

Quantitative information about fluxes of perchlorate in the environment is lacking. This study reports analyses of perchlorate in various environmental waters sampled from rural headwater catchments in the Thames River basin in southern Ontario (Canada) that provide evidence about the fluxes and fate of perchlorate in the environment. Concentrations in streams (16 to 1047 ng/L) were used to estimate exports from these rural catchments (228-1843 mg/(ha·year)), atmospheric deposition (1480 ± 230 mg/(ha·year)), as well as variable rates of microbial degradation of perchlorate, which appeared to be enhanced in catchments with higher percentages of wetlands. Groundwater data supported earlier evidence that degradation of perchlorate occurs in the subsurface under oxygen-depleted conditions. The stream data suggest that the rate of degradation varies strongly between catchments and ranges up to >1000 mg/(ha·year).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2020.137426DOI Listing
June 2020

Detections of alkyl-phenoxy-benzenesulfonates in municipal wastewater.

Chemosphere 2020 Jul 29;251:126386. Epub 2020 Feb 29.

Science and Risk Assessment Directorate, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington, Ontario, L7S 1A1, Canada.

This study presents the first reported detections and concentrations of alkyl phenoxy-benzenesulfonate surfactants (APBS) in municipal wastewater. A semi quantitative direct injection LC/MS/MS method was developed. Samples of raw influent and final effluent were obtained from fourteen municipal wastewater treatment plants (WWTPs) at various locations in Canada and were analyzed for APBS, including five homologues of monoalkyldiphenylether disulfonates (MADS) and one monoalkyldiphenylether sulfonate (MAMS) homologue. APBS were detected in all 42 of the wastewater raw influent samples and in 37 of the 42 wastewater final effluent samples; the other 5 final effluent samples had trace levels below the minimum detection limit. In the samples of raw influent from the fourteen municipal treatment plants, the dissolved concentrations of APBS (total) ranged from 0.9 to 13.6 μg/L. In samples of final effluent from the same plants the total APBS ranged from below detection to 4 μg/L. The APBS were more resistant to loss during wastewater treatment compared to previous studies of linear alkylbenzene sulfonates in wastewaters. The most effective wastewater treatments for removal of APBS were those that involved either secondary treatment with aeration or advanced treatment including biological nutrient removal. Available information on ecotoxicity is lacking for evaluating the impacts of APBS surfactants when released to the environment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chemosphere.2020.126386DOI Listing
July 2020

Reinterpretation of 'sperm pump' or 'sperm syringe' function with notes on other male internal reproductive organs in the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae).

Arthropod Struct Dev 2020 Jan 12;54:100915. Epub 2020 Feb 12.

Dept. Biology, Ackert Hall, Kansas State University, Manhattan, KS 66506, USA.

Reproduction is a critical feature in the search for means to manage the Asian citrus psyllid, vector of a devastating bacterial pathogen of citrus. The importance of accuracy in functional, anatomical descriptions and interpretations for use by other disciplines, particularly molecular genetics, cannot be overstressed. The term 'sperm pump' was coined by classical authors on observational appearance of the endoskeleton of the male reproductive apparatus. They described a thimble-shaped cuticle with smooth, cylindrical columns, interpreted as muscles, that ran longitudinally around a central cylinder. They detected transverse lines on the cylinder giving the false impression of a coiled spring. These features fostered the teleological interpretation that the device is a contractile pump. Now obsolete, the term is replaced by 'drum/spout complex'. It is a hypodermis with a sclerotized cuticle that houses the phallus which transports seminal fluid through its lumen to the female for insemination. Between the spout and the external genitalia is a spout extension, conferring flexibility to the apparatus about the abdominal apex. Approximately 21 longitudinal columns extend circumferentially around the cylinder's hemolymph-side, from the thimble's basal plate to its apical plate. These columns are correctly muscle cells, and reinterpreted to exude a lipaceous, lubricating substance for mating.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.asd.2020.100915DOI Listing
January 2020

Research Agenda of the Oncology Nursing Society: 2019-2022.

Oncol Nurs Forum 2019 11;46(6):654-669

Dana-Farber Cancer Institute.

Problem Statement: To define the Oncology Nursing Society Research Agenda for 2019-2022.

Design: Multimethod, consensus-building approach by members of the Research Agenda Project Team.

Data Sources: Expert opinion, literature review, surveys, interviews, focus groups, town hall, and review of research priorities from other cancer care organizations and funding agencies.

Analysis: Content analysis and descriptive statistics were used to synthesize research priority themes that emerged.

Findings: Three priority areas for scientific development were identified.

Implications For Nursing: The Research Agenda can be used to focus oncology nurses' research, scholarship, leadership, and health policy efforts to advance quality cancer care, inform research funding priorities, and align initiatives and resources across the ONS enterprise.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1188/19.ONF.654-669DOI Listing
November 2019

A quick guide for student-driven community genome annotation.

PLoS Comput Biol 2019 04 3;15(4):e1006682. Epub 2019 Apr 3.

Boyce Thompson Institute, Ithaca, New York.

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms and usually have minor or major errors. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447164PMC
April 2019

Expression of teneurin-m/odd Oz during segmentation in the beetle Tribolium castaneum.

Gene Expr Patterns 2019 01 7;31:26-31. Epub 2019 Jan 7.

Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, South Korea; Division of Life Science, Gyeongsang National University, Jinju, 52828, South Korea. Electronic address:

The pair-rule gene teneurin-m/odd Oz (ten-m/odz) is required for the patterning of alternate segment boundaries in the early Drosophila embryo. Mutant phenotypes of ten-m/odz display a typical pair-rule phenotype in which odd-numbered segments are eliminated. Consistent with its pair-rule function, Ten-m/Odz protein is expressed in a seven-stripe pattern before the onset of gastrulation. While expression of ten-m/odz orthologues have been characterized in several vertebrate species, their expression patterns in non-Drosophila arthropods during embryonic segmentation have yet to be reported. Here, we have identified a Tribolium orthologue of ten-m/odz (Tc-ten-m/odz) and analyzed its expression patterns during embryonic segmentation. Tc-ten-m/odz expression was observed in a region of the growth zone, which appeared to be a potential mesodermal region, during germband elongation. Later, segmental expression appeared in the trunk after segments had already formed. In contrast to Drosophila, apparently Tc-ten-m/odz was neither expressed in the ectoderm of the growth zone where segmentation occurs, nor the ectoderm of trunk regions where segmentation is maintained. Our findings suggest that Tc-ten-m/odz may not function as a pair rule gene in Tribolium segmentation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gep.2019.01.002DOI Listing
January 2019

Degenerative Expansion of a Young Supergene.

Mol Biol Evol 2019 03;36(3):553-561

School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.

Long-term suppression of recombination ultimately leads to gene loss, as demonstrated by the depauperate Y and W chromosomes of long-established pairs of XY and ZW chromosomes. The young social supergene of the Solenopsis invicta red fire ant provides a powerful system to examine the effects of suppressed recombination over a shorter timescale. The two variants of this supergene are carried by a pair of heteromorphic chromosomes, referred to as the social B and social b (SB and Sb) chromosomes. The Sb variant of this supergene changes colony social organization and has an inheritance pattern similar to a Y or W chromosome because it is unable to recombine. We used high-resolution optical mapping, k-mer distribution analysis, and quantification of repetitive elements on haploid ants carrying alternate variants of this young supergene region. We find that instead of shrinking, the Sb variant of the supergene has increased in length by more than 30%. Surprisingly, only a portion of this length increase is due to consistent increases in the frequency of particular classes of repetitive elements. Instead, haplotypes of this supergene variant differ dramatically in the amounts of other repetitive elements, indicating that the accumulation of repetitive elements is a heterogeneous and dynamic process. This is the first comprehensive demonstration of degenerative expansion in an animal and shows that it occurs through nonlinear processes during the early evolution of a region of suppressed recombination.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msy236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389315PMC
March 2019

Isolation of High Molecular Weight DNA from Insects.

Methods Mol Biol 2019 ;1858:27-32

Division of Biology, Kansas State University, Manhattan, KS, USA.

Isolation of high molecular weight (HMW) DNA from any organism can be daunting and populations of extremely small insects with hard exoskeletons are no exception. It can be challenging to isolate DNA that is clean enough to enzymatically label, digest or otherwise manipulate without sacrificing length. The method described here was originally developed to isolate HMW DNA for BAC library construction. More recently, it has proven reliable for long range optical mapping as well.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-8775-7_3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8020894PMC
July 2019

Asian citrus psyllid stylet morphology and applicability to the model for inter-instar stylet replacement in the potato psyllid.

Arthropod Struct Dev 2018 Sep 14;47(5):542-551. Epub 2018 Aug 14.

Dept. Biology, Ackert Hall, Kansas State University, Manhattan, KS, 66506, USA.

In Hemiptera, presumptive stylets for each consecutive postembryonic instar are manufactured prior to ecdysis to replace the ecdysial stylets discarded with the exuviae. With the discovery that the bacterium "Candidatus" Liberibacter solanacearum accesses the tissues involved in the stylet replacement process of the potato psyllid, a hypothesis was formed that the bacterium could adhere to the stylets of freshly emerged instars and hence gain access to the host plant when feeding is resumed. Although unproven, it was imperative that a model for stylet replacement be built. Stylet morphology and the stylet replacement process of the Asian citrus psyllid (ACP), vector of "C." L. asiaticus, causal pathogen of citrus greening disease, are comparable to the potato psyllid model system. Morphology consists of a basal terminus with its tab-shaped auricle, a base, shaft, and an apical terminus. Each of the four auricles act as a platform for the replacement apparatus, which is compacted into a tight aggregate of cells, the 'end-cap'. As modeled, on apolysis of larval instar hypodermis, the aggregate 'deconstructs' and expands into a snail shell-shaped tube, the 'atrium', that houses the presumptive stylet as it is synthesized. Completed stylets then despool from the atrium and are fitted into their functional positions as the next instar emerges from its exuviae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.asd.2018.06.007DOI Listing
September 2018

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus).

BMC Biol 2017 Nov 16;15(1):110. Epub 2017 Nov 16.

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.

Background: The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to hybrid de novo genome assembly that incorporates datasets stemming from multiple genomic technologies and methods. We used this approach to improve the gray mouse lemur (Microcebus murinus) genome from early draft status to a near chromosome-scale assembly.

Methods: We used a combination of advanced genomic technologies to iteratively resolve conflicts and super-scaffold the M. murinus genome.

Results: We improved the M. murinus genome assembly to a scaffold N50 of 93.32 Mb. Whole genome alignments between our primary super-scaffolds and 23 human chromosomes revealed patterns that are congruent with historical comparative cytogenetic data, thus demonstrating the accuracy of our de novo scaffolding approach and allowing assignment of scaffolds to M. murinus chromosomes. Moreover, we utilized our independent datasets to discover and characterize sequences associated with centromeres across the mouse lemur genome. Quality assessment of the final assembly found 96% of mouse lemur canonical transcripts nearly complete, comparable to other published high-quality reference genome assemblies.

Conclusions: We describe a new assembly of the gray mouse lemur (Microcebus murinus) genome with chromosome-scale scaffolds produced using a hybrid bioinformatic and sequencing approach. The approach is cost effective and produces superior results based on metrics of contiguity and completeness. Our results show that emerging genomic technologies can be used in combination to characterize centromeres of non-model species and to produce accurate de novo chromosome-scale genome assemblies of complex mammalian genomes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12915-017-0439-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5689209PMC
November 2017

Speed regulation of genetic cascades allows for evolvability in the body plan specification of insects.

Proc Natl Acad Sci U S A 2017 10 25;114(41):E8646-E8655. Epub 2017 Sep 25.

Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91058, Germany;

During the anterior-posterior fate specification of insects, anterior fates arise in a nonelongating tissue (called the "blastoderm"), and posterior fates arise in an elongating tissue (called the "germband"). However, insects differ widely in the extent to which anterior-posterior fates are specified in the blastoderm versus the germband. Here we present a model in which patterning in both the blastoderm and germband of the beetle is based on the same flexible mechanism: a gradient that modulates the speed of a genetic cascade of gap genes, resulting in the induction of sequential kinematic waves of gap gene expression. The mechanism is flexible and capable of patterning both elongating and nonelongating tissues, and hence converting blastodermal to germband fates and vice versa. Using RNAi perturbations, we found that blastodermal fates could be shifted to the germband, and germband fates could be generated in a blastoderm-like morphology. We also suggest a molecular mechanism underlying our model, in which gradient levels regulate the switch between two enhancers: One enhancer is responsible for sequential gene activation, and the other is responsible for freezing temporal rhythms into spatial patterns. This model is consistent with findings in , where gap genes were found to be regulated by two nonredundant "shadow" enhancers.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1702478114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5642680PMC
October 2017

Regulation and function of odd-paired in Tribolium segmentation.

Dev Genes Evol 2017 09 8;227(5):309-317. Epub 2017 Aug 8.

Division of Biology, Kansas State University, Manhattan, KS, USA.

The pair-rule gene odd-paired (opa) is required for the patterning of alternate segment boundaries in the early Drosophila embryo. Mutant phenotypes of opa display a typical pair-rule phenotype in which most of each odd-numbered denticle belt is eliminated. However, among the nine Drosophila pair-rule genes, opa is the only gene that is not expressed in stripes with double segmental periodicity; its transcript and protein are expressed in a broad domain within segmenting embryos. While expression patterns of orthologs of opa have been analyzed in several arthropod species, their regulation and function in segmentation were largely unknown. Here, we analyzed the expression patterns, regulation, and function of the Tribolium ortholog of opa (Tc-opa). Tc-opa is expressed in segmental stripes in the early stages of segmentation and then is expressed in a broad domain at the growth zone of elongating germbands where new segments form. This broad expression of Tc-opa is processed into segmental stripes once the trunk has become segmented. Tc-opa expression is regulated positively and negatively by even-skipped and odd-skipped, respectively. However, knock-down of Tc-opa does not affect embryonic segmentation. Our findings suggest that Tc-opa expression is regulated by the pair-rule gene network even though its requirement for segmentation is uncertain in Tribolium.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00427-017-0590-7DOI Listing
September 2017

Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

Insect Biochem Mol Biol 2016 09 12;76:118-147. Epub 2016 Aug 12.

Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece.

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ibmb.2016.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010457PMC
September 2016

Glyphosate residues in rural groundwater, Nottawasaga River Watershed, Ontario, Canada.

Pest Manag Sci 2016 Oct 8;72(10):1862-72. Epub 2016 Feb 8.

Environment Canada - Water Science and Technology Directorate, Burlington, ON, Canada.

Background: The objective of this study was to investigate the occurrence of glyphosate residues (glyphosate and its metabolite AMPA) in shallow groundwater in a catchment dominated by agriculture, and to examine the potential for this groundwater to store and transmit these compounds to surface waters.

Results: Glyphosate residues were found in some of the groundwater samples collected in riparian (surface seeps), upland (mostly <20 m below ground) and wetland settings (<3 m below ground). Overall, glyphosate and AMPA were detected in 10.5 and 5.0%, respectively, of the groundwater samples analyzed as part of this study. All concentrations of glyphosate were well below Canadian guidelines for drinking water quality and for protection of aquatic life. Seasonal differences in concentrations in riparian seeps were possibly related to cycles of weather, herbicide application and degradation of glyphosate. Highest concentrations were at upland sites (663 ng L(-1) of glyphosate, 698 ng L(-1) of AMPA), apparently related to localized applications. Most glyphosate detections in wetlands were >0.5 km distant from possible areas of application, and, combined with other factors, suggest an atmospheric transport and deposition delivery mechanism. In both upland and wetland settings, highest glyphosate concentrations were sometimes not at the shallowest depths, indicating influence of hydrological factors.

Conclusion: The glyphosate/AMPA detections in riparian seeps demonstrated that these compounds are persistent enough to allow groundwater to store and transmit glyphosate residues to surface waters. Detections in the wetlands support earlier evidence that atmospheric transport and deposition may lead to glyphosate contamination of environments not intended as targets of applications. This interpretation is further supported by detections of both glyphosate and AMPA in precipitation samples collected in the same watershed. © 2016 Her Majesty the Queen in Right of Canada Pest Management Science © 2016 Society of Chemical Industry.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ps.4218DOI Listing
October 2016

The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae).

Genome Biol Evol 2015 Oct 9;7(12):3383-96. Epub 2015 Oct 9.

Department of Genetics, University of Georgia

Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here, we present the assembled and annotated genome of the subsocial beetle Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, do aspects of life history, such as using a carcass to breed, predict overlap in gene models more strongly than phylogeny? We found that the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found strong evidence for an active DNA methylation system. The distribution of methylation was similar to other insects with exons having the most methylated CpGs. Methylation status appears highly conserved; 85% of the methylated genes in N. vespilloides are also methylated in the hymentopteran Nasonia vitripennis. The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality and to address questions about the potential role of methylation in social behavior.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gbe/evv194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700941PMC
October 2015

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool.

BMC Genomics 2015 Sep 29;16:734. Epub 2015 Sep 29.

KSU/K-INBRE Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, USA.

Background: Genome assembly remains an unsolved problem. Assembly projects face a range of hurdles that confound assembly. Thus a variety of tools and approaches are needed to improve draft genomes.

Results: We used a custom assembly workflow to optimize consensus genome map assembly, resulting in an assembly equal to the estimated length of the Tribolium castaneum genome and with an N50 of more than 1 Mb. We used this map for super scaffolding the T. castaneum sequence assembly, more than tripling its N50 with the program Stitch.

Conclusions: In this article we present software that leverages consensus genome maps assembled from extremely long single molecule maps to increase the contiguity of sequence assemblies. We report the results of applying these tools to validate and improve a 7x Sanger draft of the T. castaneum genome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-015-1911-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587741PMC
September 2015

A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor.

Curr Biol 2015 Mar 5;25(5):613-20. Epub 2015 Feb 5.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms that these arthropods use to induce plant galls are poorly understood. We sequenced the genome of the Hessian fly (Mayetiola destructor; Diptera: Cecidomyiidae), a plant parasitic gall midge and a pest of wheat (Triticum spp.), with the aim of identifying genic modifications that contribute to its plant-parasitic lifestyle. Among several adaptive modifications, we discovered an expansive reservoir of potential effector proteins. Nearly 5% of the 20,163 predicted gene models matched putative effector gene transcripts present in the M. destructor larval salivary gland. Another 466 putative effectors were discovered among the genes that have no sequence similarities in other organisms. The largest known arthropod gene family (family SSGP-71) was also discovered within the effector reservoir. SSGP-71 proteins lack sequence homologies to other proteins, but their structures resemble both ubiquitin E3 ligases in plants and E3-ligase-mimicking effectors in plant pathogenic bacteria. SSGP-71 proteins and wheat Skp proteins interact in vivo. Mutations in different SSGP-71 genes avoid the effector-triggered immunity that is directed by the wheat resistance genes H6 and H9. Results point to effectors as the agents responsible for arthropod-induced plant gall formation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cub.2014.12.057DOI Listing
March 2015

Editorial overview: Insect genomics: How to sequence five thousand insect genomes?

Curr Opin Insect Sci 2015 Feb 8;7:iv-v. Epub 2015 Feb 8.

INRA Rennes UMR 1349 IGEPP INRA - Agrocampus Ouest Rennes - Université Rennes 1, BP35327, 35653 Le Rheu cedex, France.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cois.2015.02.006DOI Listing
February 2015

Caudal regulates the spatiotemporal dynamics of pair-rule waves in Tribolium.

PLoS Genet 2014 Oct 16;10(10):e1004677. Epub 2014 Oct 16.

Division of Biology, Kansas State University, Manhattan, Kansas, United States of America.

In the short-germ beetle Tribolium castaneum, waves of pair-rule gene expression propagate from the posterior end of the embryo towards the anterior and eventually freeze into stable stripes, partitioning the anterior-posterior axis into segments. Similar waves in vertebrates are assumed to arise due to the modulation of a molecular clock by a posterior-to-anterior frequency gradient. However, neither a molecular candidate nor a functional role has been identified to date for such a frequency gradient, either in vertebrates or elsewhere. Here we provide evidence that the posterior gradient of Tc-caudal expression regulates the oscillation frequency of pair-rule gene expression in Tribolium. We show this by analyzing the spatiotemporal dynamics of Tc-even-skipped expression in strong and mild knockdown of Tc-caudal, and by correlating the extension, level and slope of the Tc-caudal expression gradient to the spatiotemporal dynamics of Tc-even-skipped expression in wild type as well as in different RNAi knockdowns of Tc-caudal regulators. Further, we show that besides its absolute importance for stripe generation in the static phase of the Tribolium blastoderm, a frequency gradient might serve as a buffer against noise during axis elongation phase in Tribolium as well as vertebrates. Our results highlight the role of frequency gradients in pattern formation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1004677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199486PMC
October 2014

Essential role of eIF5-mimic protein in animal development is linked to control of ATF4 expression.

Nucleic Acids Res 2014 21;42(16):10321-30. Epub 2014 Aug 21.

Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA

Translational control of transcription factor ATF4 through paired upstream ORFs (uORFs) plays an important role in eukaryotic gene regulation. While it is typically induced by phosphorylation of eIF2α, ATF4 translation can be also induced by expression of a translational inhibitor protein, eIF5-mimic protein 1 (5MP1, also known as BZW2) in mammals. Here we show that the 5MP gene is maintained in eukaryotes under strong purifying selection, but is uniquely missing in two major phyla, nematoda and ascomycota. The common function of 5MP from protozoa, plants, fungi and insects is to control translation by inhibiting eIF2. The affinity of human 5MP1 to eIF2β was measured as being equivalent to the published value of human eIF5 to eIF2β, in agreement with effective competition of 5MP with eIF5 for the main substrate, eIF2. In the red flour beetle, Tribolium castaneum, RNA interference studies indicate that 5MP facilitates expression of GADD34, a downstream target of ATF4. Furthermore, both 5MP and ATF4 are essential for larval development. Finally, 5MP and the paired uORFs allowing ATF4 control are conserved in the entire metazoa except nematoda. Based on these findings, we discuss the phylogenetic and functional linkage between ATF4 regulation and 5MP expression in this group of eukaryotes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gku670DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176352PMC
January 2015

Artificial sweeteners in a large Canadian river reflect human consumption in the watershed.

PLoS One 2013 11;8(12):e82706. Epub 2013 Dec 11.

Water Science and Technology Directorate, Environment Canada, Burlington, Ontario, Canada.

Artificial sweeteners have been widely incorporated in human food products for aid in weight loss regimes, dental health protection and dietary control of diabetes. Some of these widely used compounds can pass non-degraded through wastewater treatment systems and are subsequently discharged to groundwater and surface waters. Measurements of artificial sweeteners in rivers used for drinking water production are scarce. In order to determine the riverine concentrations of artificial sweeteners and their usefulness as a tracer of wastewater at the scale of an entire watershed, we analyzed samples from 23 sites along the entire length of the Grand River, a large river in Southern Ontario, Canada, that is impacted by agricultural activities and urban centres. Municipal water from household taps was also sampled from several cities within the Grand River Watershed. Cyclamate, saccharin, sucralose, and acesulfame were found in elevated concentrations despite high rates of biological activity, large daily cycles in dissolved oxygen and shallow river depth. The maximum concentrations that we measured for sucralose (21 µg/L), cyclamate (2.4 µg/L) [corrected], and saccharin (7.2 µg/L) are the highest reported concentrations of these compounds in surface waters to date anywhere in the world. Acesulfame persists at concentrations that are up to several orders of magnitude above the detection limit over a distance of 300 km and it behaves conservatively in the river, recording the wastewater contribution from the cumulative population in the basin. Acesulfame is a reliable wastewater effluent tracer in rivers. Furthermore, it can be used to assess rates of nutrient assimilation, track wastewater plume dilution, separate human and animal waste contributions and determine the relative persistence of emerging contaminants in impacted watersheds where multiple sources confound the usefulness of other tracers. The effects of artificial sweeteners on aquatic biota in rivers and in the downstream Great Lakes are largely unknown.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082706PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3859606PMC
October 2014

Interaction between 25S rRNA A loop and eukaryotic translation initiation factor 5B promotes subunit joining and ensures stringent AUG selection.

Mol Cell Biol 2013 Sep 8;33(18):3540-8. Epub 2013 Jul 8.

Molecular Cellular and Developmental Biology Program, Kansas State University, Manhattan, Kansas, USA.

In yeast, 25S rRNA makes up the major mass and shape of the 60S ribosomal subunit. During the last step of translation initiation, eukaryotic initiation factor 5B (eIF5B) promotes the 60S subunit joining with the 40S initiation complex (IC). Malfunctional 60S subunits produced by misfolding or mutation may disrupt the 40S IC stalling on the start codon, thereby altering the stringency of initiation. Using several point mutations isolated by random mutagenesis, here we studied the role of 25S rRNA in start codon selection. Three mutations changing bases near the ribosome surface had strong effects, allowing the initiating ribosomes to skip both AUG and non-AUG codons: C2879U and U2408C, altering the A loop and P loop, respectively, of the peptidyl transferase center, and G1735A, mapping near a Eukarya-specific bridge to the 40S subunit. Overexpression of eIF5B specifically suppressed the phenotype caused by C2879U, suggesting functional interaction between eIF5B and the A loop. In vitro reconstitution assays showed that C2879U decreased eIF5B-catalyzed 60S subunit joining with a 40S IC. Thus, eIF5B interaction with the peptidyl transferase center A loop increases the accuracy of initiation by stabilizing the overall conformation of the 80S initiation complex. This study provides an insight into the effect of ribosomal mutations on translation profiles in eukaryotes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MCB.00771-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753867PMC
September 2013