UFGI publication round-up week 03/20/2017
Development of a QTL-environment-based predictive model for node addition rate in common bean.
Author information: Zhang L1, Gezan SA2, Eduardo Vallejos C3, Jones JW1, Boote KJ4, Clavijo-Michelangeli JA4, Bhakta M3, Osorno JM5, Rao I6, Beebe S6, Roman-Paoli E7, Gonzalez A7, Beaver J7, Ricaurte J6, Colbert R5, Correll MJ8.
Date of e-pub: March 2017
Abstract: This work reports the effects of the genetic makeup, the environment and the genotype by environment interactions for node addition rate in an RIL population of common bean. This information was used to build a predictive model for node addition rate. To select a plant genotype that will thrive in targeted environments it is critical to understand the genotype by environment interaction (GEI). In this study, multi-environment QTL analysis was used to characterize node addition rate (NAR, node day- 1) on the main stem of the common bean (Phaseolus vulgaris L). This analysis was carried out with field data of 171 recombinant inbred lines that were grown at five sites (Florida, Puerto Rico, 2 sites in Colombia, and North Dakota). Four QTLs (Nar1, Nar2, Nar3 and Nar4) were identified, one of which had significant QTL by environment interactions (QEI), that is, Nar2 with temperature. Temperature was identified as the main environmental factor affecting NAR while day length and solar radiation played a minor role. Integration of sites as covariates into a QTL mixed site-effect model, and further replacing the site component with explanatory environmental covariates (i.e., temperature, day length and solar radiation) yielded a model that explained 73% of the phenotypic variation for NAR with root mean square error of 16.25% of the mean. The QTL consistency and stability was examined through a tenfold cross validation with different sets of genotypes and these four QTLs were always detected with 50-90% probability. The final model was evaluated using leave-one-site-out method to assess the influence of site on node addition rate. These analyses provided a quantitative measure of the effects on NAR of common beans exerted by the genetic makeup, the environment and their interactions.
Defining the core citrus leaf- and root-associated microbiota: Factors associated with community structure and implications for managing Huanglongbing (Citrus greening) disease.
Author information: Blaustein RAsup>1, Lorca GL2, Meyer JL3, Gonzalez CF2, Teplitski M3.
Date of e-pub: March 2017
Abstract: Stable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that re-structuring of core microbiota may be associated with the progression of Huanlongbing (HLB), the devastating citrus disease caused by Liberibacter asiaticus, L. americanus, and L. africanus The microbial communities of leaves (n=94) and roots (n=79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rDNA. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some over-represented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance of Liberibacter spp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time-series identified a mutually exclusive relationship between Liberibacter spp. and members of Burkholderiaceae, Micromonosporaceae, and Xanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of: (1) plant microbiome selection across multiple variables and (2) changes in (core) community structure that may be a pre-condition to disease establishment and/or be associated with symptom progression.Importance This study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria), but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.
Duvoglustat HCl Increases Systemic and Tissue Exposure of Active Acid α-Glucosidase in Pompe Patients Co-administered with Alglucosidase α.
Author information: Kishnani P1, Tarnopolsky M2, Roberts M3, Sivakumar K4, Dasouki M5, Dimachkie MM5, Finanger E6, Goker-Alpan O7, Guter KA8, Mozaffar T9, Pervaiz MA10, Laforet P11, Levine T12, Adera M13, Lazauskas R14, Sitaraman S14, Khanna R14, Benjamin E14, Feng J14, Flanagan JJ15, Barth J14, Barlow C16, Lockhart DJ17, Valenzano KJ14, Boudes P18, Johnson FK19, Byrne B20.
Date of e-pub: March 2017
Abstract: Duvoglustat HCl (AT2220, 1-deoxynojirimycin) is an investigational pharmacological chaperone for the treatment of acid α-glucosidase (GAA) deficiency, which leads to the lysosomal storage disorder Pompe disease, which is characterized by progressive accumulation of lysosomal glycogen primarily in heart and skeletal muscles. The current standard of care is enzyme replacement therapy with recombinant human GAA (alglucosidase alfa [AA], Genzyme). Based on preclinical data, oral co-administration of duvoglustat HCl with AA increases exposure of active levels in plasma and skeletal muscles, leading to greater substrate reduction in muscle. This phase 2a study consisted of an open-label, fixed-treatment sequence that evaluated the effect of single oral doses of 50 mg, 100 mg, 250 mg, or 600 mg duvoglustat HCl on the pharmacokinetics and tissue levels of intravenously infused AA (20 mg/kg) in Pompe patients. AA alone resulted in increases in total GAA activity and protein in plasma compared to baseline. Following co-administration with duvoglustat HCl, total GAA activity and protein in plasma were further increased 1.2- to 2.8-fold compared to AA alone in all 25 Pompe patients; importantly, muscle GAA activity was increased for all co-administration treatments from day 3 biopsy specimens. No duvoglustat-related adverse events or drug-related tolerability issues were identified.
Selective effects of oral anti-angiogenic tyrosine kinase inhibitors on an animal model of hereditary hemorrhagic telangiectasia.
Author information: Kim YH1, Kim MJ2,3, Choe SW1,4, Sprecher D5, Lee YJ3, Oh SP1,3.
Date of e-pub: March 2017
Abstract: Epistaxis and gastrointestinal (GI) tract hemorrhages are common symptoms of aged hereditary hemorrhagic telangiectasia (HHT) patients that result in anemia. Clinical as well as animal studies have suggested that vascular endothelial growth factor (VEGF) neutralizing antibodies lessen hemorrhage associated with adult onset arteriovenous malformations (AVMs).
The goal of this study is to evaluate potential therapeutic effects of oral delivery of four anti-angiogenic tyrosine-kinase inhibitors (TKIs) in the development of adult onset AVMs in a murine model of HHT.
Adult activin receptor-like kinase 1 (Alk1)-inducible knockout (iKO) model was utilized to evaluate the effect of oral administration of sorafenib, sunitinib, erlotinib, and a pazopanib analog (GW771806), on hemoglobin level, GI hemorrhages, and formation of wound-induced skin AVMs.
Sorafenib and GW771806 significantly improved, yet erlotinib worsened anemia and GI-bleeding in the Alk1-iKO model. However, none of these TKIs appeared to be effective for inhibiting the development of wound-induced skin AVMs. Taken together, these results suggest that oral delivery of anti-angiogenic TKIs are selectively more effective on GI bleeding than mucocutaneous AVMs, and it may provide an experimental basis for selective therapeutic options depending on the symptoms of HHT. This article is protected by copyright. All rights reserved.
Over-expression of the X-linked Inhibitor of Apoptosis Protects Against Retinal Degeneration in a Feline Model of Retinal Detachment.
Author information: Wassmer S1, Leonard B2, Coupland S3, Baker A4, Hamilton J5, Hauswirth WW6, Tsilfidis C7.
Date of e-pub: March 2017
Abstract: Retinal detachment is an acute disorder in humans that is caused by trauma or disease, and it can often lead to permanent visual deficits that result from the death of photoreceptors in the retina. The final pathway for photoreceptor cell death is apoptosis and necroptosis. The X-linked inhibitor of apoptosis (XIAP) has been shown to block both of these cell death pathways. We tested the effects of XIAP on photoreceptor survival in a feline model of retinal detachment. The study was performed in 12 cats, divided into 2 experimental groups. Six animals received a subretinal injection of adeno-associated virus (AAV) carrying the X-linked inhibitor of apoptosis (XIAP) and 6 animals received AAV carrying green fluorescent protein (GFP) as a control. Three weeks after viral delivery, retinas were detached by injecting C3F8 gas into the subretinal space. Optical coherence tomography (OCT) revealed that the retinal detachments resolved within 3-6 weeks as the gas was slowly resorbed. Analysis of histological sections through the plane of the detachment showed significant preservation of the photoreceptor layer in AAV-XIAP-treated animals compared to AAV-GFP-treated animals at 9 weeks after the detachment. XIAP-treated detached retinas were similar to intact controls. These studies support the potential for XIAP therapy in the treatment of human retinal detachment.
AAV: AN OVERVIEW OF UNANSWERED QUESTIONS.
Author information: Berns KI1,2, Muzyczka N3.
Date of e-pub: March 2017
Abstract: Today AAV is one of the most promising and successful gene therapy vectors. AAV vectors have been successful in the treatment of several monogenic diseases in early clinical trials1. Although work in the past has focused primarily on gene replacement, many investigators are now adapting the vector system to new clinical modalities including RNAi and gene modifying strategies such as Crisper/cas91. Moreover, Glybera2 has been licensed for clinical use in the European Union for treatment of a lysosomal storage disease. To reach this level of success has taken more than thirty years from the initial isolation of an infectious AAV clone and the development of AAV vectors for long term expression3-5. This has included the development of so-called scalable production systems that promise to deliver large quantities of vector for both clinical trials and eventually for patient therapies6. We have been studying AAV for 55 years and developing it as a vector for about 35 years. By now we have a fairly good idea of the dimensions of what would be useful to know to optimally employ AAV as a vector, but there are still many unanswered questions within the system. Like all biological systems, each good experiment raises further questions to answer. We will devote this paper to an overview of those areas in which we can identify information we don’t know, and those questions which we haven’t yet recognized. Some of these are touched on in the six review articles in this issue of Human Gene Therapy.
Structural insights into emerging pediatric pathogens human bocaparvoviruses.
Author information: Mietzsch M1, Kailasan S1, Garrison J1, Ilyas M1, Chipman P1, Kantola K2, Janssen ME3, Spear J4, Sousa D4, McKenna R1, Brown K5, Söderlund-Venermo M2, Baker T3, Agbandje-McKenna M6.
Date of e-pub: March 2017
Abstract: Bocaparvoviruses are emerging pathogens of the Parvoviridae family. Human bocaviruses 1 (HBoV1) causes severe respiratory infections and HBoV2-4 gastrointestinal infections in young children. Recent reports of life threatening cases, lack of direct treatment or vaccination, and a limited understanding of their disease mechanisms demand the need to study these pathogens on a molecular and structural level for the development of therapeutics. Towards this end, the capsid structures of HBoV1, HBoV3, and HBoV4 were determined to 2.8 – 3.0 Å resolution using cryo-electron microscopy and 3D image reconstruction. The bocaparvovirus capsids, that display different tissue tropisms, share common features with other parvoviruses, such as depressions at the icosahedral 2-fold and surrounding the 5-fold symmetry axes, protrusions surrounding the 3-fold, and a channel at the 5-fold axis. However, unlike other parvoviruses densities extending the 5-fold channel into the capsid interior are conserved among the bocaparvoviruses and are suggestive of genus specific function. Additionally, their major viral protein 3 contains loops with variable regions at their apexes conferring unique capsid surface topologies relative to other parvoviruses. Structural comparisons at strain (HBoVs) and genus (bovine parvovirus and HBoVs) levels identified differences in surface loops functionally important in host/tissue tropism, pathogenicity, and antigenicity in other parvoviruses, and likely play similar roles for these viruses. This study thus provides a structural framework to characterize determinants of host/tissue tropism, pathogenicity, and antigenicity for the development of anti-viral strategies to control human bocavirus infections.Importance Human bocaviruses are one of only a few members of the Parvoviridae family pathogenic to humans, especially young children and immunocompromised adults. There are currently no treatments or vaccines for these viruses or the related enteric bocaviruses. This study reports the first high-resolution structures of three human bocaparvoviruses determined by cryo-reconstruction. HBoV1 infects the respiratory tract, HBoV3 and HBoV4 the gastrointestinal tract, tissues that are likely targeted by the capsid. Comparison of these viruses provides information on conserved bocaparvovirus-specific features, and variable regions resulting in unique surface topologies that can serve as guides to characterize HBoV determinants of tissue tropism and antigenicity in future experiments. When compared to other existing parvovirus capsid structures this study suggests capsid regions that likely control successful infection, including determinants for receptor attachment, host cell trafficking, and antigenic reactivity. Overall these observations could impact efforts to design anti-viral strategies and vaccines for the HBoVs.
Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris).
Author information: Sessa EB1,2, Juslén A3, Väre H3, Chambers SM4.
Date of e-pub: March 2017
Abstract: Our goal was to infer the phylogenetic relationships and historical biogeography of the genus Dryopteris with a focus on taxa in sub-Saharan Africa and neighboring islands. In general, little is known about the relationships between African fern species and their congeners in other geographic regions, and our aim was to determine whether the sub-Saharan African species of Dryopteris are monophyletic and evolved within Africa or arrived there via repeated dispersals into Africa from other regions.
We obtained sequence data for five chloroplast markers from 214 species of Dryopteris and 18 outgroups. We performed phylogenetic and molecular dating analyses using a Bayesian relaxed clock method in BEAST with fossil and secondary calibration points and estimated ancestral ranges for the genus globally by comparing multiple models in BioGeoBEARS.
We found that 22 of 27 accessions of sub-Saharan African Dryopteris belong to a large clade of 31 accessions that also includes taxa from Indian and Atlantic Ocean islands. Additional accessions of taxa from our regions of interest have Asian, Hawaiian, European, or North American species as their closest relatives.
The majority of sub-Saharan African Dryopteris species are descended from a shared common ancestor that dispersed to Africa from Asia approximately 10 Ma. There have been subsequent dispersal events from the African mainland to islands in the Atlantic and Indian Oceans, including Madagascar. Several additional species are estimated to have descended from ancestors that reached Africa via separate events over the last roughly 20 million years.
DNA probes for monitoring dynamic and transient molecular encounters on live cell membranes.
Author information: You M1,2,3,4, Lyu Y1,2, Han D1,2, Qiu L1,2, Liu Q1, Chen T1,2, Sam Wu C1,2, Peng L2, Zhang L1,2, Bao G5, Tan W1,2.
Date of e-pub: March 2017
Abstract: Cells interact with the extracellular environment through molecules expressed on the membrane. Disruption of these membrane-bound interactions (or encounters) can result in disease progression. Advances in super-resolution microscopy have allowed membrane encounters to be examined, however, these methods cannot image entire membranes and cannot provide information on the dynamic interactions between membrane-bound molecules. Here, we show a novel DNA probe that can transduce transient membrane encounter events into readable cumulative fluorescence signals. The probe, which translocates from one anchor site to another, mimicking motor proteins, is realized through a toehold-mediated DNA strand displacement reaction. Using this probe, we successfully monitored rapid encounter events of membrane lipid domains using flow cytometry and fluorescence microscopy. Our results show a preference for encounters within the same lipid domains.
Aptasensor with Expanded Nucleotide Using DNA Nanotetrahedra for Electrochemical Detection of Cancerous Exosomes.
Author information: Wang S1,2, Zhang L3,2, Wan S2, Cansiz S2, Cui C2, Liu Y3,2, Cai R2, Hong C2, Teng IT2, Shi M3,2, Wu Y3,2, Dong Y1, Tan W3,2.
Date of e-pub: March 2017
Abstract: Exosomes are extracellular vesicles (50-100 nm) circulating in biofluids as intercellular signal transmitters. Although the potential of cancerous exosomes as tumor biomarkers is promising, sensitive and rapid detection of exosomes remains challenging. Herein, we combined the strengths of advanced aptamer technology, DNA-based nanostructure, and portable electrochemical devices to develop a nanotetrahedron (NTH)-assisted aptasensor for direct capture and detection of hepatocellular exosomes. The oriented immobilization of aptamers significantly improved the accessibility of an artificial nucleobase-containing aptamer to suspended exosomes, and the NTH-assisted aptasensor could detect exosomes with 100-fold higher sensitivity when compared to the single-stranded aptamer-functionalized aptasensor. The present study provides a proof-of-concept for sensitive and efficient quantification of tumor-derived exosomes. We thus expect the NTH-assisted electrochemical aptasensor to become a powerful tool for comprehensive exosome studies.
Molecular networks related to the immune system and mitochondria are targets for the pesticide dieldrin in the zebrafish (Danio rerio) central nervous system.
Author information: Cowie AM1, Sarty KI1, Mercer A1, Koh J2, Kidd KA1, Martyniuk CJ3.
Date of e-pub: March 2017
Abstract: The objectives of this study were to determine the behavioral and molecular responses in the adult zebrafish (Danio rerio) central nervous system (CNS) following a dietary exposure to the pesticide dieldrin. Zebrafish were fed pellets spiked with 0.03, 0.15, or 1.8μg/g dieldrin for 21days. Behavioral analysis revealed no difference in exploratory behaviors or those related to anxiety. Transcriptional networks for T-cell aggregation and selection were decreased in expression suggesting an immunosuppressive effect of dieldrin, consistent with other studies investigating organochlorine pesticides. Processes related to oxidative phosphorylation were also differentially affected by dieldrin. Quantitative proteomics (iTRAQ) using a hybrid quadrupole-Orbitrap identified 226 proteins that were different following one or more doses. These proteins included ATP synthase subunits (mitochondrial) and hypoxia up-regulated protein 1 which were decreased and NADH dehydrogenases (mitochondrial) and signal recognition particle 9 which were up-regulated. Thus, proteins affected were functionally associated with the mitochondria and a protein network analysis implicated Parkinson’s disease (PD) and Huntington’s disease as diseases associated with altered proteins. Molecular networks related to mitochondrial dysfunction and T-cell regulation are hypothesized to underlie the association between dieldrin and PD. These data contribute to a comprehensive transcriptomic and proteomic biomarker framework for pesticide exposures and neurodegenerative diseases.
Dieldrin is a persistent organochlorine pesticide that has been associated with human neurodegenerative disease such as Parkinson’s disease. Dieldrin is ranked 18th on the 2015 U.S. Agency for Toxic Substances and Disease Registry and continues to be a pesticide of concern for human health. Transcriptomics and quantitative proteomics (ITRAQ) were employed to characterize the molecular networks in the central nervous system that are altered with dietary exposure to dieldrin. We found that transcriptional and protein networks related to the immune system, mitochondria, and Parkinson’s disease were preferentially affected by dieldrin. The study provides new insight into the mechanisms of dieldrin neurotoxicity that may explain, in part, the association between this pesticide and increased risks to neurodegeneration. These data contribute in a significant way to developing a molecular framework for pesticide induced neurotoxicity.
NOTE: These abstracts were retrieved from the U.S. National Library of Medicine website managed in collaboration with the U.S. National Library of Medicine