UFGI publication round-up week 02/06/2017

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics.

Author information: Zhang SD1, Jin JJ1,2, Chen SY1, Chase MW3,4, Soltis DE5,6,7, Li HT1, Yang JB1, Li DZ1, Yi TS1.

1Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
2Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
3Science Directorate, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK.
4School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
5Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA.
6Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
7Genetics Institute, University of Florida, Gainesville, FL, 32608, USA.
Journal: The New Phytologist

Date of e-pub: February 2017

Abstract: Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.



Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade.

Author information: Crowl AA1,2, Myers C2, Cellinese N1.

1Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
2Department of Biology, University of Florida, Gainesville, FL, USA.
Journal: Evolution; International Journal of Organic Evolution

Date of e-pub: February 2017

Abstract: The Mediterranean Basin harbors a remarkable amount of biodiversity, a high proportion of which is endemic to this region. Here we present an in-depth study of an angiosperm species complex, in which cryptic taxonomic diversity has been hypothesized. Specifically, we focus on four currently recognized species in the Roucela complex, a well-supported clade in the Campanulaceae/Campanuloideae: Campanula creutzburgii, C. drabifolia, C. erinus, and C. simulans. This study takes a phylogenomic approach, utilizing near-complete plastomes and 130 nuclear loci, to uncover cryptic diversity and test hypotheses regarding hybridization and polyploidy within this clade. Genome size estimates recovered tetraploid and octoploid lineages within the currently recognized, widespread species C. erinus, showing an east-west geographic pattern. Though genomic data clearly differentiate these two cytotypes, we failed to discern morphological differences. The formation of a cryptic octoploid lineage, distributed across the eastern Mediterranean, is hypothesized to be the result of an allopolyploid event in which one parental morphology is retained. The tetraploid C. erinus and C. creutzburgii (also a tetraploid) are implicated as parental lineages. Our results highlight the utility of target-enrichment approaches for obtaining genomic datasets for thorough assessments of species diversity and the importance of carefully considering gene-tree discordance within such datasets. This article is protected by copyright. All rights reserved.



The development of repetitive motor behaviors in deer mice: Effects of environmental enrichment, repeated testing, and differential mediation by indirect basal ganglia pathway activation.

Author information: Bechard AR1, Bliznyuk N2, Lewis MH1,3.

1Department of Psychology, University of Florida, Gainesville, Florida.
2Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida.
3Department of Psychiatry, University of Florida, Gainesville, Florida.
Journal: Developmental Psychobiology

Date of e-pub: February 2017

Abstract: Little is known about the mechanisms mediating the development of repetitive behaviors in human or animals. Deer mice reared with environmental enrichment (EE) exhibit fewer repetitive behaviors and greater indirect basal ganglia pathway activation as adults than those reared in standard cages. The developmental progression of these behavioral and neural circuitry changes has not been characterized. We assessed the development of repetitive behavior in deer mice using both a longitudinal and cohort design. Repeated testing negated the expected effect of EE, but cohort analyses showed that progression of repetitive behavior was arrested after 1 week of EE and differed significantly from controls after 3 weeks. Moreover, EE reductions in repetitive behavior were associated with increasing activation of indirect pathway nuclei in males across adolescence, but not females. These findings provide the first assessment of developmental trajectories within EE and support indirect pathway mediation of repetitive behavior in male deer mice.



Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin.

Author information: Roesch LF1, Silveira RC2, Corso AL2, Dobbler PT1, Mai V3, Rojas BS2, Laureano ÁM1, Procianoy RS2.

1Centro Interdisciplinar de Pesquisas em Biotecnologia – CIP-Biotec, Campus São Gabriel, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brasil.
2Unidade de Neonatologia do Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil.
3Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America.
Journal: PloS One

Date of e-pub: February 2017

Abstract: Administering intravenous antibiotics during labor to women at risk for transmitting Group B Streptococcus (GBS) can prevent infections in newborns. However, the impact of intrapartum antibiotic prophylaxis on mothers’ microbial community composition is largely unknown. We compared vaginal microbial composition in pregnant women experiencing preterm birth at ≤ 32 weeks gestation that received intrapartum antibiotic prophylaxis with that in controls.

Microbiota in vaginal swabs collected shortly before delivery from GBS positive women that received penicillin intravenously during labor or after premature rupture of membranes was compared to controls. Microbiota was analyzed by 16S rRNA sequencing using the PGM Ion Torrent to determine the effects of penicillin use during hospitalization and GBS status on its composition.

Penicillin administration was associated with an altered vaginal microbial community composition characterized by increased microbial diversity. Lactobacillus sp. contributed only 13.1% of the total community in the women that received penicillin compared to 88.1% in the controls. Streptococcus sp. were present in higher abundance in GBS positive woman compared to controls, with 60% of the total vaginal microbiota in severe cases identified as Streptococcus sp.

Vaginal communities of healthy pregnant women were dominated by Lactobacillus sp. and contained low diversity, while Group B Streptococcus positive women receiving intrapartum antibiotic prophylaxis had a modified vaginal microbiota composition with low abundance of Lactobacillus but higher microbial diversity.



Barcoded nanoparticles for high throughput in vivo discovery of targeted therapeutics.

Author information: Dahlman JE1,2,3,4, Kauffman KJ3,5, Xing Y6,2,3, Shaw TE6,2,3, Mir FF3, Dlott CC3, Langer R6,2,3,5, Anderson DG1,2,3,5, Wang ET7,8.

1Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139; james.dahlman@bme.gatech.edu rlanger@mit.edu dgander@mit.edu eric.t.wang@ufl.edu.
2Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139.
3David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139.
4Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332.
5Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
6Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139.
7David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139; james.dahlman@bme.gatech.edu rlanger@mit.edu dgander@mit.edu eric.t.wang@ufl.edu.
8Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32601.
Journal: Proceedings of the National Academy of Sciences of the United States of America

Date of e-pub: February 2017

Abstract: Nucleic acid therapeutics are limited by inefficient delivery to target tissues and cells and by an incomplete understanding of how nanoparticle structure affects biodistribution to off-target organs. Although thousands of nanoparticle formulations have been designed to deliver nucleic acids, most nanoparticles have been tested in cell culture contexts that do not recapitulate systemic in vivo delivery. To increase the number of nanoparticles that could be tested in vivo, we developed a method to simultaneously measure the biodistribution of many chemically distinct nanoparticles. We formulated nanoparticles to carry specific nucleic acid barcodes, administered the pool of particles, and quantified particle biodistribution by deep sequencing the barcodes. This method distinguished previously characterized lung- and liver- targeting nanoparticles and accurately reported relative quantities of nucleic acid delivered to tissues. Barcode sequences did not affect delivery, and no evidence of particle mixing was observed for tested particles. By measuring the biodistribution of 30 nanoparticles to eight tissues simultaneously, we identified chemical properties promoting delivery to some tissues relative to others. Finally, particles that distributed to the liver also silenced gene expression in hepatocytes when formulated with siRNA. This system can facilitate discovery of nanoparticles targeting specific tissues and cells and accelerate the study of relationships between chemical structure and delivery in vivo.



secHsp70 as a tool to approach amyloid-β42 and other extracellular amyloids.

Author information: de Mena L1, Chhangani D1, Fernandez-Funez P2, Rincon-Limas DE1,3.

1a Department of Neurology , McKnight Brain Institute University of Florida , Gainesville , FL , USA.
2c Department of Biomedical Sciences , University of Minnesota Medical School , Duluth , MN , USA.
3b Department of Neuroscience , Genetics Institute and Center for Translational Research in Neurodegenerative Disease , University of Florida , Gainesville , FL , USA.
Journal: Fly

Date of e-pub: February 2017

Abstract: Self-association of amyloidogenic proteins is the main pathological trigger in a wide variety of neurodegenerative disorders. These aggregates are deposited inside or outside the cell due to hereditary mutations, environmental exposures or even normal aging. Cumulative evidence indicates that the heat shock chaperone Hsp70 possesses robust neuroprotection against various intracellular amyloids in Drosophila and mouse models. However, its protective role against extracellular amyloids was largely unknown as its presence outside the cells is very limited. Our recent manuscript in PNAS revealed that an engineered form of secreted Hsp70 (secHsp70) is highly protective against toxicity induced by extracellular deposition of the amyloid-β42 (Aβ42) peptide. In this Extra View article, we extend our analysis to other members of the heat shock protein family. We created PhiC31-based transgenic lines for human Hsp27, Hsp40, Hsp60 and Hsp70 and compared their activities in parallel against extracellular Aβ42. Strikingly, only secreted Hsp70 exhibits robust protection against Aβ42-triggered toxicity in the extracellular milieu. These observations indicate that the ability of secHsp70 to suppress Aβ42 insults is quite unique and suggest that targeted secretion of Hsp70 may represent a new therapeutic approach against Aβ42 and other extracellular amyloids. The potential applications of this engineered chaperone are discussed.



Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics.

Author information: Zallot R1, Ross R2, Chen WH3, Bruner SD3, Limbach PA2, de Crécy-Lagard V1.

1Department of Microbiology and Cell Science, University of Florida , Gainesville, Florida 32611, United States.
2Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati , Cincinnati, Ohio 45221, United States.
3Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States.
Journal: ACS Chemical Biology

Date of e-pub: February 2017

Abstract: The reduction of epoxyqueuosine (oQ) is the last step in the synthesis of the tRNA modification queuosine (Q). While the epoxyqueuosine reductase (EC enzymatic activity was first described 30 years ago, the encoding gene queG was only identified in Escherichia coli in 2011. Interestingly, queG is absent from a large number of sequenced genomes that harbor Q synthesis or salvage genes, suggesting the existence of an alternative epoxyqueuosine reductase in these organisms. By analyzing phylogenetic distributions, physical gene clustering, and fusions, members of the Domain of Unknown Function 208 (DUF208) family were predicted to encode for an alternative epoxyqueuosine reductase. This prediction was validated with genetic methods. The Q modification is present in Lactobacillus salivarius, an organism missing queG but harboring the duf208 gene. Acinetobacter baylyi ADP1 is one of the few organisms that harbor both QueG and DUF208, and deletion of both corresponding genes was required to observe the absence of Q and the accumulation of oQ in tRNA. Finally, the conversion oQ to Q was restored in an E. coli queG mutant by complementation with plasmids harboring duf208 genes from different bacteria. Members of the DUF208 family are not homologous to QueG enzymes, and thus, duf208 is a non-orthologous replacement of queG. We propose to name DUF208 encoding genes as queH. While QueH contains conserved cysteines that could be involved in the coordination of a Fe/S center in a similar fashion to what has been identified in QueG, no cobalamin was identified associated with recombinant QueH protein.



A Smart, Photocontrollable Drug Release Nanosystem for Multifunctional Synergistic Cancer Therapy.

Author information: Yi Y1, Wang H1, Wang X1, Liu Q1, Ye M1, Tan W1,2.

1Molecular Science and Biomedicine Laboratory, College of Biology, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University , Changsha 410082, China.
2Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Shands Cancer Center, University of Florida Genetics Institute, and McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States.
Journal: ACS Applied Materials & Interfaces

Date of e-pub: February 2017

Abstract: Multifunctional synergistic therapy holds promise in biomedical studies and clinical practice. However, strategies aimed at easily integrating the components of such multimodal therapies are needed. Therefore, we herein report a smart drug release nanosystem able to perform photodynamic therapy, photothermal therapy and chemotherapy in a photocontrollable manner. Doxorubicin (DOX), a chemotherapy drug, and 5, 10, 15, 20-tetrakis (1-methylpyridinium-4-yl) porphyrin (TMPyP4), a photosensitizer, were physically intercalated into a DNA assembly immobilized on gold nanorods. The drugs were efficiently delivered to target cells and released under light irradiation, resulting in a synergism that combined phototherapy and chemotherapy for cancer treatment. This smart, photocontrollable drug release nanosystem promises precisely controlled drug release for multifunctional synergistic cancer therapy.



Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology.

Author information: Zhang L1,2, Wan S2, Jiang Y1,2, Wang Y2, Fu T1, Liu Q1, Cao Z2,3, Qiu L1,2, Tan W1,2.

1Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha 410082, China.
2Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida , Gainesville, Florida 32611, United States.
3School of Pharmacy, Fudan University, Zhangjiang Branch , No. 826 Zhangheng Rd. Pudong New District, Shanghai 201203, China.
Journal: Journal of the American Chemical Society

Date of e-pub: February 2017

Abstract: Disease-related biomarkers are objectively measurable molecular signatures of physiological status that can serve as disease indicators or drug targets in clinical diagnosis and therapy, thus acting as a tool in support of personalized medicine. For example, the prostate-specific antigen (PSA) biomarker is now widely used to screen patients for prostate cancer. However, few such biomarkers are currently available, and the process of biomarker identification and validation is prolonged and complicated by inefficient methods of discovery and few reliable analytical platforms. Therefore, in this Perspective, we look at the advanced chemistry of aptamer molecules and their significant role as molecular probes in biomarker studies. As a special class of functional nucleic acids evolved from an iterative technology termed Systematic Evolution of Ligands by Exponential Enrichment (SELEX), these single-stranded oligonucleotides can recognize their respective targets with selectivity and affinity comparable to those of protein antibodies. Because of their fast turnaround time and exceptional chemical properties, aptamer probes can serve as novel molecular tools for biomarker investigations, particularly in assisting identification of new disease-related biomarkers. More importantly, aptamers are able to recognize biomarkers from complex biological environments such as blood serum and cell surfaces, which can provide direct evidence for further clinical applications. This Perspective highlights several major advancements of aptamer-based biomarker discovery strategies and their potential contribution to the practice of precision medicine.

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