For more info about the Genetics & Genomics Graduate Program, visit the program's homepage
Comments are off

UFGI publications round-up week 01/09/2017

A method for obtaining simian immunodeficiency virus RNA sequences from laser capture microdissected and immune captured CD68+ and CD163+ macrophages from frozen tissue sections of bone marrow and brain.

Author information: Mallard J1, Papazian E1, Soulas C2, Nolan DJ3, Salemi M3, Williams KC4.

1Department of Biology, Boston College, Chestnut Hill, MA, USA.
2Department of Biology, Boston College, Chestnut Hill, MA, USA; Department of Research and Development, Innate Pharma, Marseille, France.
3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Pathology Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA.
4Department of Biology, Boston College, Chestnut Hill, MA, USA. Electronic address:
Journal: Journal of Immunological Methods

Date of e-pub: January 2017

Abstract: Laser capture microdissection (LCM) is used to extract cells or tissue regions for analysis of RNA, DNA or protein. Several methods of LCM are established for different applications, but a protocol for consistently obtaining lentiviral RNA from LCM captured immune cell populations is not described. Obtaining optimal viral RNA for analysis of viral genes from immune-captured cells using immunohistochemistry (IHC) and LCM is challenging. IHC protocols have long antibody incubation times that increase risk of RNA degradation. But, immune capture of specific cell populations like macrophages without staining for virus cannot result in obtaining only a fraction of cells which are productively lentivirally infected. In this study we sought to obtain simian immunodeficiency virus (SIV) RNA from SIV gp120+ and CD68+ monocyte/macrophages in bone marrow (BM) and CD163+ perivascular macrophages in brain of SIV-infected rhesus macaques. Here, we report an IHC protocol with RNase inhibitors that consistently results in optimal quantity and yield of lentiviral RNA from LCM-captured immune cells.



An experimental validation of genomic selection in octoploid strawberry.

Author information: Gezan SA1, Osorio LF2, Verma S2, Whitaker VM2.

1School of Forest Resources and Conservation, University of Florida, 363 Newins-Ziegler Hall, PO Box 110410, Gainesville, FL 32611-0410, USA
2Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA
Journal: Horticulture Research

Date of e-pub: January 2017

Abstract: The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013–2014 and 2014–2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial. High-density genotyping was performed with the Affymetrix Axiom IStraw90 single-nucleotide polymorphism array, and 17 479 polymorphic markers were chosen for analysis. Several methods were compared, including Genomic BLUP, Bayes B, Bayes C, Bayesian LASSO Regression, Bayesian Ridge Regression and Reproducing Kernel Hilbert Spaces. Cross-validation within training populations resulted in higher values than for true validations across trials. For true validations, Bayes B gave the highest predictive abilities on average and also the highest selection efficiencies, particularly for yield traits that were the lowest heritability traits. Selection efficiencies using Bayes B for parent selection ranged from 74% for average fruit weight to 34% for early marketable yield. A breeding strategy is proposed in which advanced selection trials are utilized as training populations and in which genomic selection can reduce the breeding cycle from 3 to 2 years for a subset of untested parents based on their predicted genomic breeding values.



Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data.

Author information: Wang N1, Hosner PA2, Liang B3, Braun EL4, Kimball RT5.

1Department of Biology, University of Florida, Gainesville, FL 32611, USA; Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China. Electronic address:
2Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
3Department of Biology, University of Florida, Gainesville, FL 32611, USA; Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
4Department of Biology, University of Florida, Gainesville, FL 32611, USA.
5Department of Biology, University of Florida, Gainesville, FL 32611, USA. Electronic address:
Journal: Molecular Phylogenetics and Evolution

Date of e-pub: January 2017

Abstract: The phylogeny of the Phasianidae (pheasants, partridges, and allies) has been studied extensively. However, these studies have largely ignored three enigmatic genera because of scarce DNA source material and limited overlapping phylogenetic data: blood pheasants (Ithaginis), snow partridges (Lerwa), and long-billed partridges (Rhizothera). Thus, phylogenetic positions of these three genera remain uncertain in what is otherwise a well-resolved phylogeny. Previous studies using different data types place Lerwa and Ithaginis in similar positions, but the absence of overlapping data means the relationship between them could not be inferred. Rhizothera was originally described in the genus Perdix (true partridges), although a partial cytochrome b (CYB) sequence suggests it is sister to Pucrasia (koklass pheasant). To identify robust relationships among Ithaginis, Lerwa, Rhizothera, and their phasianid relatives, we used 3692 ultra-conserved element (UCE) loci and complete mitogenomes from 19 species including previously hypothesized relatives of the three focal genera and representatives from all major phasianid clades. We used DNA extracted from historical specimen toepads for species that lacked fresh tissue in museum collections. Maximum likelihood and multispecies coalescent UCE analyses strongly supported Lerwa sister to a large clade which included Ithaginis at its base, and also including turkey, grouse, typical pheasants, tragopans, Pucrasia, and Perdix. Rhizothera was also in this clade, sister to a diverse group comprising Perdix, typical pheasants, Pucrasia, turkey and grouse. Mitogenomic genealogies differed from UCEs topologies, supporting a sister relationship between Ithaginis and Lerwa rather than a grade. The position of Rhizothera using mitogenomes depended on analytical choices. Unpartitioned and codon-based analyses placed Rhizothera sister to a tragopan clade, whereas a partitioned DNA model of the mitogenome was congruent with UCE results. In all mitogenome analyses, Pucrasia was sister to a clade including Perdix and the typical pheasants with high support, in contrast to UCEs and published nuclear intron data. Due to the strong support and consistent topology provided by all UCE analyses, we have identified phylogenetic relationships of these three enigmatic, poorly-studied, phasianid taxa.



Retinoic acid receptor regulation of epimorphic and homeostatic regeneration in the axolotl.

Author information: Nguyen M1, Singhal P1, Piet J2, Shefelbine SJ2, Maden M3, Voss SR4,5, Monaghan JR6.

1Department of Biology, Northeastern University, Boston, MA 02115, USA.
2Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA.
3Department of Biology and UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
4Department of Biology, University of Kentucky, Lexington, KY 40506, USA.
5Spinal Cord and Brain Injury Research Center, Lexington, KY 40506, USA.
6Department of Biology, Northeastern University, Boston, MA 02115, USA
Journal: Development (Cambridge, England)

Date of e-pub: January 2017

Abstract: Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we target specific retinoic acid receptors (RARs) to either PD duplicate (RA treatment or RARγ agonist) or truncate (RARβ antagonist) regenerating limbs. RARE-EGFP reporter axolotls showed divergent reporter activity in limbs undergoing PD duplication versus truncation suggesting differences in patterning and skeletal regeneration. Transcriptomics identified expression patterns that explain PD duplication including upregulation of proximal homeobox gene expression and silencing of distal-associated genes whereas limb truncation was associated with disrupted skeletal differentiation. Rarβ antagonism in uninjured limbs induced a loss in skeletal integrity leading to long bone regression and loss of skeletal turnover. Overall, mechanisms were identified that regulate RAR’s multifaceted roles in the salamander limb including regulation of skeletal patterning during epimorphic regeneration, skeletal tissue differentiation during regeneration, and homeostatic regeneration of intact limbs.



The PacC transcription factor regulates secondary metabolite production, stress response, but has only minor effects on virulence in the insect pathogenic fungus Beauveria bassiana.

Author information: Luo Z1,2, Ren H1, Mousa JJ3, Rangel D4, Zhang Y1, Bruner SD3, Keyhani NO5,2.

1Biotechnology Research Center, Southwest University, Chongqing, 400716, P. R. China.
2Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, 32611, USA.
3Deptartment of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
4Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, 746050-50, Brazil.
5Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400045, P.R. China.
Journal: Environmental Microbiology

Date of e-pub: January 2017

Abstract: The PacC transcription factor is an important component of the fungal ambient pH-responsive regulatory system. Loss of pacC in the insect pathogenic fungus Beauveria bassiana resulted in an alkaline pH-dependent decrease in growth and pH-dependent increased susceptibility to osmotic (salt, sorbitol) stress and SDS. Extreme susceptibility to Congo Red was noted irrespective of pH, and ΔBbpacC conidia showed subtle increases in UV susceptibility. The ΔBbPacC mutant showed a reduced ability to acidify media during growth due to failure to produce oxalic acid. The ΔBbPacC mutant failed to produce the insecticidal compound dipicolinic acid, however, production of a yellow-colored compound was noted. The compound, named bassianolone B, was purified and its structure determined. Despite defects in growth, stress resistance, and oxalate/insecticidal compound production, only a small decrease in virulence was seen for the ΔBbpacC strain in topical insect bioassays using larvae from the greater waxmoth, Galleria mellonella or adults of the beetle, Tenebrio molitor. However, slightly more pronounced decreases were seen in virulence via intrahemcoel injection assays (G. mellonella) and in assays using T. molitor larvae. These data suggest important roles for BbpacC in mediating growth at alkaline pH, regulation of secondary metabolite production, and in targeting specific insect stages. This article is protected by copyright. All rights reserved.



Genome Sequence of Porphyromonas gingivalis Strain 381.

Author information: Chastain-Gross RP1,2, Xie G3, Bélanger M4,2, Kumar D5, Whitlock JA4,2, Liu L5, Raines SM4, Farmerie WG5, Daligault HE3, Han CS3, Brettin TS3, Progulske-Fox A1,2.

1Department of Oral Biology, University of Florida, Gainesville, Florida, USA
2Center for Molecular Microbiology, University of Florida, Gainesville, Florida, USA.
3Bioenergy and Biome Sciences (B-11), Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
4Department of Oral Biology, University of Florida, Gainesville, Florida, USA.
5Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA.
Journal: Genome Announcements

Date of e-pub: January 2017

Abstract: Porphyromonas gingivalis is associated with both oral and systemic diseases. Strain-specific P. gingivalis invasion phenotypes do not reliably predict disease presentation during in vivo studies. Here, we present the genome sequence of 381, a common laboratory strain, with a single contig of 2,378,872 bp and a G+C content of 48.36%.



Potentiation of ceftazidime by avibactam against β-lactam-resistant Pseudomonas aeruginosa in an in vitro infection model.

Author information: Sy SK1, Zhuang L1, Beaudoin ME2, Kircher P1, Tabosa MA1, Cavalcanti NC1, Grunwitz C1, Pieper S1, Schuck VJ2, Nichols WW2, Derendorf H3.

1Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, USA.
2AstraZeneca, Waltham, MA, USA.
3Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, USA
Journal: The Journal of Antimicrobial Chemotherapy

Date of e-pub: January 2017

Abstract: This study evaluated the in vitro pharmacodynamics of combinations of ceftazidime and the non-β-lactam β-lactamase inhibitor, avibactam, against ceftazidime-, piperacillin/tazobactam- and meropenem-multiresistant Pseudomonas aeruginosa by a quantitative time-kill method.

MICs of ceftazidime plus 0-16 mg/L avibactam were determined against eight isolates of P. aeruginosa Single-compartment, 24 h time-kill kinetics were investigated for three isolates at 0-16 mg/L avibactam with ceftazidime at 0.25-4-fold the MIC as measured at the respective avibactam concentration. Ceftazidime and avibactam concentrations were measured by LC-MS/MS during the time-kill kinetic studies to evaluate drug degradation.

Avibactam alone displayed no antimicrobial activity. MICs of ceftazidime decreased by 8-16-fold in the presence of avibactam at 4 mg/L. The changes in log10 cfu/mL at both the 10 h and 24 h timepoints (versus 0 h) revealed bacterial killing at ≥1-fold MIC. Significantly higher concentrations of ceftazidime alone, as compared with those of ceftazidime in combination, were required to produce any given kill. Without avibactam, ceftazidime degradation was significant (defined as degradation t1/2 < 24 h), with as little as 19% ± 18% of the original concentration remaining at 8 h for the most resistant strain. In combination with avibactam, ceftazidime degradation at ≥ 1-fold MIC was negligible.

The addition of avibactam protected ceftazidime from degradation in a dose-dependent manner and restored its cidal and static activity at concentrations in combination well below the MIC of ceftazidime alone.



Re-addressing the 2013 consensus guidelines for the diagnosis of insulitis in human type 1 diabetes: is change necessary?

Author information: Campbell-Thompson ML1, Atkinson MA2, Butler AE3, Giepmans BN4, von Herrath MG5, Hyöty H6, Kay TW7, Morgan NG8, Powers AC9, Pugliese A10, Richardson SJ8, In’t Veld PA11.

1Department of Pathology, Immunology, and Laboratory Medicine, 1395 Center Drive, College of Medicine, University of Florida, Gainesville, 32610, FL, USA.
2Department of Pathology, Immunology, and Laboratory Medicine, 1395 Center Drive, College of Medicine, University of Florida, Gainesville, 32610, FL, USA.
3Larry L. Hillblom Islet Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
4Department of Cell Biology, University of Groningen, Groningen, the Netherlands.
5Department of Developmental Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
6Department of Virology, University of Tampere and Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland.
7St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia.
8University of Exeter Medical School, Exeter, UK.
9Vanderbilt University Medical Center, Nashville, TN, USA.
10Miller School of Medicine, University of Miami, Miami, FL, USA.
11Department of Pathology, Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium.
Journal: Diabetologia

Date of e-pub: January 2017

Abstract: N/A



WNT regulation of embryonic development likely involves pathways independent of nuclear CTNNB1.

Author information: Tribulo P1, Moss JI2, Ozawa M3, Jiang Z4, Tian C5, Hansen PJ6.

1P Tribulo, Animal Sciences, University of Florida, Gainesville, United States.
2J Moss, Animal Sciences, University of Florida, Gainesville, United States.
3M Ozawa, Animal Sciences, University of Florida, Gainesville, 32611, United States.
4Z Jiang, Animal Science, University of Connecticut, Storrs, United States.
5C Tian, Animal Science, University of Connecticut, Storrs, 06269-4243, United States.
6P Hansen, Dept. of Animal Sciences, University ofFlorida, Gainesville, 32611-0910, United States
Journal: Reproduction (Cambridge, England)

Date of e-pub: January 2017

Abstract: The bovine was used to examine potential for WNT signaling to affect the preimplantation embryo. Expression of seven key genes involved in canonical WNT signaling declined to a nadir at the morula or blastocyst stage. Expression of 80 genes associated with WNT signaling in the morula and inner cell mass (ICM) and trophectoderm (TE) of the blastocyst was also evaluated. Many genes associated with WNT signaling were characterized by low transcript abundance. Seven genes were different between ICM and TE, and all of them were overexpressed in TE as compared to ICM, including WNT6, FZD1, FZD7, LRP6, PORCN, APC, and SFRP1. Immunoreactive CTNNB1was localized primarily to the plasma membrane at all stages examined from the 2-cell to blastocyst stages of development. Strikingly, neither CTNNB1 nor non-phospho (i.e., active) CTNNB1 was observed in the nucleus of blastomeres at any stage of development even after addition of WNT activators to culture. In contrast, CTNNB1 associated with the plasma membrane was increased by activators of WNT signaling. The planar cell polarity pathway (PCP) could be activated in the embryo as indicated by an experiment demonstrating an increase in phospho-JNK in the nucleus of blastocysts treated with the non-canonical WNT11. Furthermore, WNT11 improved development to the blastocyst stage. In conclusion, canonical WNT signaling is attenuated in the preimplantation bovine embryo but WNT can activate the PCP component JNK. Thus, regulation of embryonic development by WNT is likely to involve activation of pathways independent of nuclear actions of CTNNB1.



FGF19/FGFR4 signaling contributes to the resistance of hepatocellular carcinoma to sorafenib.

Author information: Gao L1, Wang X2,3, Tang Y4, Huang S5, Hu CA6, Teng Y7,8.

1Department of Oral Biology, Dental College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
2Department of Radiology and Imaging Sciences, School of Medicine, University of Utah, Salt Lake City, UT USA
3Experimental Therapeutics Program, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
4Vascular Biology Center, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA USA
5Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL USA
6Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM USA
7Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA USA
Journal: Journal of Experimental & Clinical Cancer Research: CR

Date of e-pub: January 2017

Abstract: Sorafenib, a multi-kinase inhibitor, is used as a standard therapy for advanced hepatocellular carcinoma (HCC). However, complete remission has not been achieved and the molecular basis of HCC resistance to sorafenib remains largely unknown. Previous studies have shown that fibroblast growth factor 19 (FGF19) expression correlates with tumor progression and poor prognosis of HCC. Here, we demonstrate the novel role of FGF19 in HCC resistance to sorafenib therapy.

FGF19 Knockdown cells were achieved by lentiviral-mediated interference, and FGFR4 knockout cells were achieved by CRISPR-Cas9. Protein levels of FGF19, FGFR4 and c-PARP in various HCC cell lines were measured by Western blotting analysis. Cell viability was determined by MTS assay, apoptosis was determined by DAPI nuclear staining and Western blot of c-PRAP, and ROS generation was determined by DCFH-DA staining and electrochemical biosensor.

We showed that FGF19, when overexpressed, inhibited the effect of sorafenib on ROS generation and apoptosis in HCC. In contrast, loss of FGF19 or its receptor FGFR4 led to a remarkable increase in sorafenib-induced ROS generation and apoptosis. In addition, knockdown of FGF19 in sorafenib-resistant HCC cells significantly enhanced the sensitivity to sorafenib. Importantly, targeting FGF19/FGFR4 axis by ponatinib, a third-generation inhibitor of chronic myeloid leukemia, overcomes HCC resistance of sorafenib by enhancing ROS-associated apoptosis in sorafenib-treated HCC.

Our results provide the first evidence that inhibition of FGF19/FGFR4 signaling significantly overcomes sorafenib resistance in HCC. Co-treatment of ponatinib and sorafinib may represent an effective therapeutic approach for eradicating HCC.



A Methodology for Cancer Therapeutics by Systems Pharmacology-Based Analysis: A Case Study on Breast Cancer-Related Traditional Chinese Medicines.

Author information: Li Y1,2, Wang J1,2, Lin F2, Yang Y2, Chen SS1.

1Systems Biology Laboratory, Department of Computer Information Science and Engineering, University of Florida, Gainesville, Florida, United States of America
2Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian, Liaoning, P R China
Southern Illinois University School of Medicine, UNITED STATES
Journal: PLoS One

Date of e-pub: January 2017

Abstract: Breast cancer is the most common carcinoma in women. Comprehensive therapy on breast cancer including surgical operation, chemotherapy, radiotherapy, endocrinotherapy, etc. could help, but still has serious side effect and resistance against anticancer drugs. Complementary and alternative medicine (CAM) may avoid these problems, in which traditional Chinese medicine (TCM) has been highlighted. In this section, to analyze the mechanism through which TCM act on breast cancer, we have built a virtual model consisting of the construction of database, oral bioavailability prediction, drug-likeness evaluation, target prediction, network construction. The 20 commonly employed herbs for the treatment of breast cancer were used as a database to carry out research. As a result, 150 ingredient compounds were screened out as active molecules for the herbs, with 33 target proteins predicted. Our analysis indicates that these herbs 1) takes a ‘Jun-Chen-Zuo-Shi” as rule of prescription, 2) which function mainly through perturbing three pathways involving the epidermal growth factor receptor, estrogen receptor, and inflammatory pathways, to 3) display the breast cancer-related anti-estrogen, anti-inflammatory, regulation of cell metabolism and proliferation activities. To sum it up, by providing a novel in silico strategy for investigation of the botanical drugs, this work may be of some help for understanding the action mechanisms of herbal medicines and for discovery of new drugs from plants.



The primacy of NF1 loss as the driver of tumorigenesis in neurofibromatosis type 1-associated plexiform neurofibromas.

Author information: Pemov A1, Li H2, Patidar R3, Hansen NF4, Sindiri S3, Hartley SW5, Wei JS3, Elkahloun A4, Chandrasekharappa SC4; NISC Comparative Sequencing Program, Boland JF6, Bass S6; NCI DCEG Cancer Genomics Research Laboratory, Mullikin JC4,7, Khan J3, Widemann BC8, Wallace MR2, Stewart DR1.

1Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
2Department of Molecular Genetics and Microbiology, UF Genetics Institute, UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
3Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
4Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Rockville, MD, USA.
5Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
6Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
7NIH Intramural Sequencing Center, National Human Genome Research Institute, Rockville, MD, USA.
8Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
Journal: Oncogene

Date of e-pub: January 2017

Abstract: Neurofibromatosis type 1 (NF1) is a common tumor-predisposition disorder due to germline mutations in the tumor suppressor gene NF1. A virtually pathognomonic finding of NF1 is the plexiform neurofibroma (PN), a benign, likely congenital tumor that arises from bi-allelic inactivation of NF1. PN can undergo transformation to a malignant peripheral nerve sheath tumor, an aggressive soft-tissue sarcoma. To better understand the non-NF1 genetic contributions to PN pathogenesis, we performed whole-exome sequencing, RNASeq profiling and genome-wide copy-number determination for 23 low-passage Schwann cell cultures established from surgical PN material with matching germline DNA. All resected tumors were derived from routine debulking surgeries. None of the tumors were considered at risk for malignant transformation at the time; for example, there was no pain or rapid growth. Deep (~500X) NF1 exon sequencing was also conducted on tumor DNA. Non-NF1 somatic mutation verification was performed using the Ampliseq/IonTorrent platform. We identified 100% of the germline NF1 mutations and found somatic NF1 inactivation in 74% of the PN. One individual with three PNs had different NF1 somatic mutations in each tumor. The median number of somatic mutations per sample, including NF1, was one (range 0-8). NF1 was the only gene that was recurrently somatically inactivated in multiple tumors. Gene Set Enrichment Analysis of transcriptome-wide tumor RNA sequencing identified five significant (FDR<0.01) and seven trending (0.01⩽FDR<0.02) gene sets related to DNA replication, telomere maintenance and elongation, cell cycle progression, signal transduction and cell proliferation. We found no recurrent non-NF1 locus copy-number variation in PN. This is the first multi-sample whole-exome and whole-transcriptome sequencing study of NF1-associated PN. Taken together with concurrent copy-number data, our comprehensive genetic analysis reveals the primacy of NF1 loss as the driver of PN tumorigenesis.Oncogene advance online publication, 9 January 2017; doi:10.1038/onc.2016.464.



Quantification of network structural dissimilarities.

Author information: Schieber TA1, Carpi L2, Díaz-Guilera A3,4, Pardalos PM5, Masoller C2, Ravetti MG1,3.

1Departmento de Engenharia de Produção, Engineering School, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte 31.270-901, Brazil.
2Departament de Física, Universitat Politècnica de Catalunya, 08222 Terrassa, Spain.
3Departament de Física Fonamental, Universitat de Barcelona, 08028 Barcelona, Spain.
4Universitat de Barcelona, Institute of Complex Systems (UBICS), 08028 Barcelona, Spain.
5Industrial and Systems Engineering, University of Florida, Gainesville, Florida 32611-6595, USA.
Journal: Nature Communications

Date of e-pub: January 2017

Abstract: Identifying and quantifying dissimilarities among graphs is a fundamental and challenging problem of practical importance in many fields of science. Current methods of network comparison are limited to extract only partial information or are computationally very demanding. Here we propose an efficient and precise measure for network comparison, which is based on quantifying differences among distance probability distributions extracted from the networks. Extensive experiments on synthetic and real-world networks show that this measure returns non-zero values only when the graphs are non-isomorphic. Most importantly, the measure proposed here can identify and quantify structural topological differences that have a practical impact on the information flow through the network, such as the presence or absence of critical links that connect or disconnect connected components.



Extended time-lapse in vivo imaging of tibia bone marrow to visualize dynamic hematopoietic stem cell engraftment.

Author information: Kim S1,2,3, Lin L1,2, Brown GA1,2, Hosaka K4, Scott EW1,2.

1Program in Stem Cell Biology and Regenerative Medicine, University of Florida College of Medicine, Gainesville, FL, USA.
2Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA.
3Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL, USA.
4Department of Neurosurgery, University of Florida, Gainesville, FL, USA.
Journal: Leukemia

Date of e-pub: January 2017

Abstract: Homing, engraftment and proliferation of hematopoietic stem/progenitor cell (HSC/HPCs) are crucial steps required for success of a bone marrow transplant. Observation of these critical events is limited by the opaque nature of bone. Here we demonstrate how individual HSCs engraft in long bones by thinning one side of the tibia for direct and unbiased observation. Intravital imaging enabled detailed visualization of single Sca-1+, c-Kit+, Lineage- (SKL) cell migration to bone marrow niches and subsequent proliferation to reconstitute hematopoiesis. This longitudinal study allowed direct observation of dynamic HSC/HPC activities during engraftment in full color for up to 6 days in live recipients. Individual SKL cells, but not mature or committed progenitor cells, preferentially homed to a limited number of niches near highly vascularized endosteal regions, and clonally expanded. Engraftment of SKL cells in P-selectin and osteopontin knockout mice showed abnormal homing and expansion of SKL cells. CD150+, CD48- SKL populations initially engrafted in the central marrow region, utilizing only a subset of niches occupied by the parent SKL cells. Our study demonstrates that time-lapse imaging of tibia can be a valuable tool to understand the dynamic characteristics of functional HSC and niche components in various mouse models.Leukemia advance online publication, 13 January 2017; doi:10.1038/leu.2016.354.



Parvovirus Capsid Structures Required for Infection: Mutations Controlling Receptor Recognition and Protease Cleavages.

Author information: Callaway HM1, Feng KH1, Lee DW2, Allison AB1,3, Pinard M4, McKenna R4, Agbandje-McKenna M4, Hafenstein S5, Parrish CR6.

1Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.
2School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.
3Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA.
4Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA.
5Department of Medicine, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.
6Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
Journal: Journal of Virology

Date of e-pub: January 2017

Abstract: Parvovirus capsids are small but complex molecular machines responsible for undertaking many of the steps of cell infection, genome packing, and cell-to-cell as well as host-to-host transfer. The details of parvovirus infection of cells are still not fully understood, but the processes must involve small changes in the capsid structure that allow the endocytosed virus to escape from the endosome, pass through the cell cytoplasm, and deliver the single-stranded DNA (ssDNA) genome to the nucleus, where viral replication occurs. Here, we examine capsid substitutions that eliminate canine parvovirus (CPV) infectivity and identify how those mutations changed the capsid structure or altered interactions with the infectious pathway. Amino acid substitutions on the exterior surface of the capsid (Gly299Lys/Ala300Lys) altered the binding of the capsid to transferrin receptor type 1 (TfR), particularly during virus dissociation from the receptor, but still allowed efficient entry into both feline and canine cells without successful infection. These substitutions likely control specific capsid structural changes resulting from TfR binding required for infection. A second set of changes on the interior surface of the capsid reduced viral infectivity by >100-fold and included two cysteine residues and neighboring residues. One of these substitutions, Cys270Ser, modulates a VP2 cleavage event found in ∼10% of the capsid proteins that also was shown to alter capsid stability. A neighboring substitution, Pro272Lys, significantly reduced capsid assembly, while a Cys273Ser change appeared to alter capsid transport from the nucleus. These mutants reveal additional structural details that explain cell infection processes of parvovirus capsids.

Parvoviruses are commonly found in both vertebrate and invertebrate animals and cause widespread disease. They are also being developed as oncolytic therapeutics and as gene therapy vectors. Most functions involved in infection or transduction are mediated by the viral capsid, but the structure-function correlates of the capsids and their constituent proteins are still incompletely understood, especially in relation to identifying capsid processes responsible for infection and release from the cell. Here, we characterize the functional effects of capsid protein mutations that result in the loss of virus infectivity, giving a better understanding of the portions of the capsid that mediate essential steps in successful infection pathways and how they contribute to viral infectivity.



Isolation of Coronavirus NL63 from Blood from Children in Rural Haiti: Phylogenetic Similarities with Recent Isolates from Malaysia.

Author information: Beau De Rochars VM1,2, Lednicky J1,3, White S1,3, Loeb J1,3, Elbadry MA1,3, Telisma T1,4, Chavannes S1,4, Anilis MG1,4, Cella E1,5,6, Ciccozzi M6, Okech BA1,3, Salemi M1,5, Morris JG Jr7,8.

1Emerging Pathogens Institute, University of Florida, Gainesville, Florida.
2Department of Health Services Research, Management and Policy, College of Public Health and Health Professions, University of Florida, Gainesville, Florida.
3Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida.
4Christianville Foundation, School Clinic, Gressier, Haiti.
5Department of Pathology, Immunology and Laboratory Sciences, College of Medicine, University of Florida, Gainesville, Florida.
6Department of Infectious Parasitic and Immunomediated Diseases, Reference Centre on Phylogeny, Molecular Epidemiology and Microbial Evolution (FEMEM)/Epidemiology Unit, Istituto Superiore di Sanita, Rome, Italy.
7Emerging Pathogens Institute, University of Florida, Gainesville, Florida.
8Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida.
Journal: The American Journal of Tropical Medicine and Hygiene

Date of e-pub: January 2017

Abstract: Human coronavirus (HCoV) NL63 is recognized as a common cause of upper respiratory infections and influenza-like illness. In screening children with acute undifferentiated febrile illness in a school cohort in rural Haiti, we identified HCoV-NL63 in blood samples from four children. Cases clustered over an 11-day period; children did not have respiratory symptoms, but two had gastrointestinal complaints. On phylogenetic analysis, the Haitian HCoV-NL63 strains cluster together in a highly supported monophyletic clade linked most closely with recently reported strains from Malaysia; two respiratory HCoV-NL63 strains identified in north Florida in the same general period form a separate clade, albeit again with close linkages with the Malaysian strains. Our data highlight the variety of presentations that may be seen with HCoV-NL63, and underscore the apparent ease with which CoV strains move among countries, with our data consistent with recurrent introduction of strains into the Caribbean (Haiti and Florida) from Asia.



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

About the Author