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UFGI publication round-up week 6/4

J Am Chem Soc. 2017 Apr 19;139(15):5289-5292. doi: 10.1021/jacs.7b00319. Epub 2017 Apr 7.

Molecular Recognition-Based DNA Nanoassemblies on the Surfaces of Nanosized Exosomes.

Wan S1Zhang L1,2Wang S1Liu Y1,2Wu C1,2Cui C1Sun H1Shi M1,2Jiang Y1,2Li L1Qiu L1,2Tan W1,2.

Author information

1
Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States.
2
Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha 410082, China.

Abstract

Exosomes are membrane-enclosed extracellular vesicles derived from cells, carrying biomolecules that include proteins and nucleic acids for intercellular communication. Owning to their advantages of size, structure, stability, and biocompatibility, exosomes have been used widely as natural nanocarriers for intracellular delivery of theranostic agents. Meanwhile, surface modifications needed to endow exosomes with additional functionalities remain challenging by their small size and the complexity of their membrane surfaces. Current methods have used genetic engineering and chemical conjugation, but these strategies require complex manipulations and have only limited applications. Herein, we present an aptamer-based DNA nanoassemblies on exosome surfaces. This in situ assembly method is based on molecular recognition between DNA aptamers and their exosome surface markers, as well as DNA hybridization chain reaction initiated by an aptamer-chimeric trigger. It further demonstrated selective assembly on target cell-derived exosomes, but not exosomes derived from nontarget cells. The present work shows that DNA nanostructures can successfully be assembled on a nanosized organelle. This approach is useful for exosome modification and functionalization, which is expected to have broad biomedical and bioanalytical applications.
 
 

J Neuroendocrinol. 2017 Oct;29(10). doi: 10.1111/jne.12457.

Hypothalamus Specific Re-Introduction of SNORD116 into Otherwise Snord116 Deficient Mice Increased Energy Expenditure.

Author information

1
Neuroscience Division, Garvan Institute of Medical Research, Sydney, Australia.
2
Diabetes Division, Garvan Institute of Medical Research, Sydney, Australia.
3
Department of Pediatrics, College of Medicine, Center for Smell and Taste, University of Florida, Gainesville, FL, USA.

Abstract

The Snord116 gene cluster has been recognised as a critical contributor to the Prader-Willi syndrome (PWS), with mice lacking Snord116 displaying many classical PWS phenotypes, including low postnatal body weight, reduced bone mass and increased food intake. However, these mice do not develop obesity as a result of increased energy expenditure. To understand the physiological function of SNORD116 better and potentially rescue the altered metabolism of Snord116-/- mice, we used an adeno-associated viral (AAV) approach to reintroduce the product of the Snord116 gene into the hypothalamus in Snord116-/- mice at different ages. The results obtained show that mid-hypothalamic re-introduction of SNORD116 in 6-week-old Snord116-/- mice leads to significantly reduced body weight and weight gain, which is associated with elevated energy expenditure. Importantly, when the intervention targets other areas such as the anterior region of the hypothalamus or the reintroduction occurs in older mice, the positive effects on energy expenditure are diminished. These data indicate that the metabolic symptoms of PWS develop gradually and the Snord116 gene plays a critical role during this process. Furthermore, when we investigated the consequences of SNORD116 re-introduction under conditions of thermoneutrality where the mild cold stress influences are avoided, we also observed a significant increase in energy expenditure. In conclusion, the rescue of mid-hypothalamic Snord116 deficiency in young Snord116 germline deletion mice increases energy expenditure, providing fundamental information contributing to potential virus-mediated genetic therapy in PWS.
 
 

Nat Med. 2018 Jun;24(6):699. doi: 10.1038/s41591-018-0062-2.

Impact of neutralizing antibodies against AAV is a key consideration in gene transfer to nonhuman primates.

Author information

1
Sol Sherry Thrombosis Research Center, Temple University Medical School, Philadelphia, PA, USA. wxiao@temple.edu.
2
Department of Microbiology and Immunology, Temple University Medical School, Philadelphia, PA, USA. wxiao@temple.edu.
3
Cardiovascular Research Center, Temple University Medical School, Philadelphia, PA, USA. wxiao@temple.edu.
4
Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA. guangping.gao@umassmed.edu.
5
Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, FL, USA. lingchen@peds.ufl.edu.
6
Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, FL, USA. rherzog@ufl.edu.
7
Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. xxiao@email.unc.edu.
8
State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. xxiao@email.unc.edu.
9
Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. rjs@med.unc.edu.

 
 

Explore Care Pathways of Colorectal Cancer Patients with Social Network Analysis.

Author information

1
Health Outcomes & Policy, University of Florida, Gainesville, Florida, USA.
2
Hematology/Oncology, University of Florida, Gainesville, Florida, USA.
3
School of Information, Florida State Univeristy, Tallahassee, Florida, USA.
4
Epidemiology, University of Florida, Gainesville, Florida, USA.

Abstract

Patients with colorectal cancer (CRC) often face treatment delays and the exact reasons have not been well studied. This study is to explore clinical workflow patterns for CRC patients using electronic health records (EHR). In particular, we modeled the clinical workflow (provider-provider interactions) of a CRC patient’s workup period as a social network, and identified clusters of workflow patterns based on network characteristics. Understanding of these patterns will help guide healthcare policy-making and practice.
 
 

Neuroscientist. 2018 Jun 1:1073858418780971. doi: 10.1177/1073858418780971. [Epub ahead of print]

Aging in the Brain: New Roles of Epigenetics in Cognitive Decline.

Author information

1
1 Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
2
2 Genetics and Genomics Program, Genetics Institute, University of Florida, Gainesville, FL, USA.

Abstract

Gene expression in the aging brain depends on transcription signals generated by senescent physiology, interacting with genetic and epigenetic programs. In turn, environmental factors influence epigenetic mechanisms, such that an epigenetic-environmental link may contribute to the accumulation of cellular damage, susceptibility or resilience to stressors, and variability in the trajectory of age-related cognitive decline. Epigenetic mechanisms, DNA methylation and histone modifications, alter chromatin structure and the accessibility of DNA. Furthermore, small non-coding RNA, termed microRNA (miRNA) bind to messenger RNA (mRNA) to regulate translation. In this review, we examine key questions concerning epigenetic mechanisms in regulating the expression of genes associated with brain aging and age-related cognitive decline. In addition, we highlight the interaction of epigenetics with senescent physiology and environmental factors in regulating transcription.
 
 

J Virol. 2018 Jun 6. pii: JVI.00812-18. doi: 10.1128/JVI.00812-18. [Epub ahead of print]

In vivo Knock-down of the HSV-1 Latency-Associated Transcript Reduces Reactivation from Latency.

Author information

1
Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA.
2
Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center, New Orleans, LA, USA.
3
Department of Ophthalmology, University of Florida College of Medicine, Gainesville, FL, USA.
4
Department of Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, FL, USA.
5
Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, LA, USA.
6
Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA dbloom@ufl.edu.

Abstract

During Herpes Simplex Virus (HSV) latency, most viral genes are silenced with the exception of one region of the genome encoding the latency-associated transcript (LAT). This long non-coding RNA was originally described as having a role in enhancing HSV-1 reactivation. However, subsequent evidence showing that the LAT blocked apoptosis and promoted efficient establishment of latency suggested that its effects on reactivation were secondary to establishment. Here, we utilize an Adeno-associated Virus (AAV) vector to deliver a LAT-targeting hammerhead ribozyme to HSV-1-infected neurons of rabbits after the establishment of HSV-1 latency. The rabbits were then induced to reactivate latent HSV-1. Using this model, we show that decreasing LAT levels in neurons following the establishment of latency reduced the ability of the virus to reactivate. This demonstrates that the HSV-1 LAT RNA has a role in reactivation that is independent of its function in establishment of latency. In addition these results suggest the potential of AAV vectors expressing LAT-targeting ribozymes as a potential therapy for recurrent HSV disease such as herpes stromal keratitis, a leading cause of infectious blindness.Importance Herpes Simplex Virus (HSV) establishes a life long infection and remains dormant (latent) in our nerve cells. Occasionally HSV reactivates to cause disease, with HSV-1 typically causing cold sores whereas HSV-2 is the most common cause of genital herpes. The details of how HSV reactivates are largely unknown. Most of HSV’s genes are silent during latency with the exception of RNAs made from the latency-associated transcript (LAT) region. While viruses that make less LAT do not reactivate efficiently, these viruses also do not establish latency as efficiently. Here we deliver a ribozyme that can degrade the LAT to the nerve cells of latently infected rabbits using a gene therapy vector. We show that this treatment blocks reactivation in the majority of the rabbits. This work shows that the LAT RNA is important for reactivation and the suggests the potential of this treatment as a therapy for treating HSV infections.
 
 

J Physiol. 2018 Jun 8. doi: 10.1113/JP275661. [Epub ahead of print]

Effects of ketamine on the fetal transcriptomic response to umbilical cord occlusion: comparison to hypoxic hypoxia in the cerebral cortex.

Author information

1
Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, Florida, 32610-0274, USA.

Abstract

Umbilical cord occlusion (UCO) is known to cause neurological disorders in the neonate. Previously, we have reported that hypoxic hypoxia (HH) stimulates the appearance of bacteria in the fetal brain and upregulates the expression of inflammatory markers in fetal cerebral cortex (CTX), and ketamine attenuates these responses. Here, we aimed to test the hypothesis that UCO, like HH, produces an inflammatory response in the fetal CTX, and the treatment with ketamine reduces these effects. In chronically instrumented fetal sheep (∼125d), 30-minute partial UCO decreased fetal Pa O2 levels by approximately 50%. Half of the fetuses received ketamine (3 mg/kg) 10 min prior to UCO (n = 4/group). Fetal brains were collected 1 and 24 hours after the experiment, and mRNA was extracted and hybridized for microarray analyses. Differentially-expressed genes were analyzed for significant association with gene ontologies and pathways. After 1 hour, UCO upregulated nucleic acid processing and chromatin modification, and downregulated metabolic processes compared to control. After 24 hours, UCO upregulated metabolic and protein modification processes. Ketamine produced minimal effects. UCO did not alter the abundance of bacterial DNA in fetal brain, and did not upregulate inflammation pathways when compared to HH. We conclude that UCO produced time dependent responses that did not include bacterial invasion or upregulation of inflammation pathways in fetal CTX. This contrasts with the response to HH, which caused appearance of bacteria in the CTX and upregulated inflammation pathways. These responses in fetal CTX to oxygen deprivation are therefore modified by the maternal or placental response to the stimulus. This article is protected by copyright. All rights reserved.
 
 

Phytopathology. 2018 Apr;108(4):424-435. doi: 10.1094/PHYTO-07-17-0260-RVW. Epub 2018 Jan 24.

Challenges for Managing Candidatus Liberibacter spp. (Huanglongbing Disease Pathogen): Current Control Measures and Future Directions.

Author information

1
First and third authors: Department of Soil and Water Sciences, Genetics Institute, University of Florida, Gainesville; and second author: Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville.

Abstract

Huanglongbing (HLB; “citrus greening” disease) has caused significant damages to the global citrus industry as it has become well established in leading citrus-producing regions and continues to spread worldwide. Insecticidal control has been a critical component of HLB disease management, as there is a direct relationship between vector control and Candidatus Liberibacter spp. (i.e., the HLB pathogen) titer in HLB-infected citrus trees. In recent years, there have been substantial efforts to develop practical strategies for specifically managing Ca. Liberibacter spp.; however, a literature review on the outcomes of such attempts is still lacking. This work summarizes the greenhouse and field studies that have documented the effects and implications of chemical-based treatments (i.e., applications of broad-spectrum antibiotics, small molecule compounds) and nonchemical measures (i.e., applications of plant-beneficial compounds, applications of inorganic fertilizers, biological control, thermotherapy) for phytopathogen control. The ongoing challenges associated with mitigating Ca. Liberibacter spp. populations at the field-scale, such as the seasonality of the phytopathogen and associated HLB disease symptoms, limitations for therapeutics to contact the phytopathogen in planta, adverse impacts of broad-spectrum treatments on plant-beneficial microbiota, and potential implications on public and ecosystem health, are also discussed.
 
 

PLoS One. 2018 Jun 7;13(6):e0198070. doi: 10.1371/journal.pone.0198070. eCollection 2018.

Elimination or more accurate estimation? Investigation of trends in malaria diagnoses in the Ouest Department of Haiti from 2008 to 2017.

Author information

1
Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States of America.
2
Department of Global and Community Health, George Mason University, Fairfax, VA, United States of America.
3
College of Veterinary Medicine, University of Florida, Gainesville, FL, United States of America.
4
African Methodist Episcopal Church Service and Development Agency, Inc., Washington, DC, United States of America.

Abstract

BACKGROUND:

According to the 2016 World Malaria Report, the malaria incidence in Haiti declined by > 40% between 2010 and 2015. Though elimination efforts have likely contributed, this time period also corresponded to a national change in diagnostic methods.

METHODS:

Monthly reports of aggregated patient data were acquired from five clinics in the Ouest Department of Haiti. Generalized linear models were used to compare the number of febrile patients tested, the number of positive tests, and the proportion of tests that were positive (TRP) before and after the national adoption of rapid diagnostic tests (RDTs).

RESULTS:

Prior to the earthquake when microcopy was used for diagnosis, a total of 1,727 patients with 557 (32.3%) positive; post-earthquake testing was reduced and the TPR was variable; during the post recovery period when RDTs were used exclusivly, a total of 5,132 patients were tested using RDTs, only 83 (1.62%) were positive. Compared to the pre-earthquake period, there was a 69% increase in the number of patients tested (IRR: 1.69; 95% CI IRR 1.59, 2.79), and a 97.0% decrease in the proportion of patients with a positive test result (IRR: 0.03; 95% CI IRR 0.02, 0.04) in the post-recovery period.

CONCLUSIONS:

While the decline in malaria indicators between 2010 and 2015 has been cited as evidence of progress towards elimination, these reports derived estimates of the malaria burden in Haiti using two different diagnostic tests. Thus, comparison of these periods in the context of malaria elimination should be made with caution.
 
 

Hum Gene Ther Clin Dev. 2018 Jun 5. doi: 10.1089/humc.2017.142. [Epub ahead of print]

Gene Therapy for Osteoarthritis: Pharmacokinetics of Intra-articular scAAV.IL-1Ra Delivery in an Equine Model.

Author information

1
University of Florida, Orthopaedics and Rehabilitation , PO BOX 100137 , 1600 SW Archer Rd , Gainesville, Florida, United States , 32610 ; watsors@ortho.ufl.edu.
2
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; broomet@ufl.edu.
3
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; andrewsmith@ufl.edu.
4
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; riceb@ufl.edu.
5
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; big.red.gatorfan@gmail.com.
6
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; damyara123@gmail.com.
7
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; hyddmev@ortho.ufl.edu.
8
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; nasrie@ortho.ufl.edu.
9
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; zareza@ortho.ufl.edu.
10
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; plevings@ufl.edu.
11
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; luy@ortho.ufl.edu.
12
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; dacanea@ortho.ufl.edu.
13
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; gfore001@fiu.edu.
14
Mayo Clinic, Rehabilitation Medicine Research Center, Rochester, Minnesota, United States ; Evans.Christopher@mayo.edu.
15
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; mortona@ufl.edu.
16
University of Florida, Small Animal Clinical Sciences, Gainesville, Florida, United States ; mdwinter@ufl.edu.
17
University of Florida, Infectious Diseases and Pathology, Gainesville, Florida, United States ; darkmich@ufl.edu.
18
University of Central Florida, Statistics, Orlando, Florida, United States ; David.Nickerson@ucf.edu.
19
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; colahanp@UFL.EDU.
20
University of Florida, Department of Orthopaedics and Rehabilitation , PO Box 100137, M-210, JHMHC , 1600 SW Archer Rd , Gainesville, Florida, United States , 32610-0137 ; ghivisc@ortho.ufl.edu.

Abstract

142: Toward the treatment of osteoarthritis (OA), we have been investigating self-complementary adeno-associated virus (scAAV) for intra-articular delivery of gene products with therapeutic potential. As OA frequently affects weight-bearing joints, we performed pharmacokinetic studies in the equine forelimb to identify parameters of scAAV gene delivery relevant to clinical translation. Using the coding sequence for interleukin-1 receptor antagonist (IL-1Ra) as a secreted therapeutic reporter we first generated an scAAV vector containing an optimized cDNA for equine IL-1Ra. In dosing studies in vivo we identified a putative ceiling dose of 5 x 1012 viral genomes (vg) which elevated the steady-state eqIL-1Ra in synovial fluids >50-fold for over 6 months. No adverse effects of treatment were seen, and eqIL-1Ra in serum and urine remained at background. Using 5 x 1012 vg and GFP as a cytologic marker, we compared the local and systemic distribution of vector and transduced cells in healthy joints and those with late stage, naturally-occurring OA. Strikingly, a substantial increase in transgenic expression was associated with the articular pathologies characteristic of OA, including synovitis, osteophyte formation and damaged cartilage. Nonetheless, in both the healthy and OA environments the vector and transgene expression were effectively contained within the injected joint. 143: We are investigating self-complementary adeno-associated virus (scAAV) as a vector for intra-articular gene-delivery of IL-1Ra, and its therapeutic capacity in the treatment of osteoarthritis (OA). To model gene-transfer on a scale proportional to the human knee, a frequent site of OA incidence, we focused our studies on the joints of the equine forelimb. Using AAV2.5 capsid and equine IL-1Ra as a homologous transgene, we previously identified a functional ceiling dose of ~5 x 1012 viral genomes, which elevated the steady state levels of eqIL-1Ra in synovial fluids by more than 40-fold over endogenous production for at least 6 months. Here, using an osteochondral fragmentation model of early OA, we examined the functional capacity of scAAV.IL-1Ra gene-delivery in equine joints over a period of 12 weeks. In the disease model, transgenic eqIL-1Ra expression was several-fold higher than seen previously in healthy joints, and correlated directly with the severity of joint pathology at the time of treatment. Despite wide variation in expression, the steady-state eqIL-1Ra in synovial fluids exceeded that of IL-1 by > 400-fold in all animals, and a consistent treatment effect was observed. This included a 30-40% reduction in lameness and ~25% improvement in total joint pathology by both MRI and arthroscopic assessments, which included reduced joint effusion and synovitis, and improved repair of the osteochondral lesion. No vector-related increase in eqIL-1Ra levels in blood or urine was noted. Cumulatively our studies in the equine model indicate scAAV.IL-1Ra administration is reasonably safe and capable of sustained therapeutic IL-1Ra production intra-articularly in joints of human scale. This profile supports consideration for human testing in OA.
 
 

Hum Gene Ther Clin Dev. 2018 Jun 5. doi: 10.1089/humc.2017.143. [Epub ahead of print]

scAAV-Mediated IL-1Ra gene delivery for the Treatment of Osteoarthritis: Test of Efficacy in an Equine Model.

Author information

1
University of Florida, Orthopaedics and Rehabilitation , PO BOX 100137 , 1600 SW Archer Rd , Gainesville, Florida, United States , 32610 ; watsors@ortho.ufl.edu.
2
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; andrewsmith@ufl.edu.
3
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; broomet@ufl.edu.
4
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; riceb@ufl.edu.
5
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; big.red.gatorfan@gmail.com.
6
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; damyara123@gmail.com.
7
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; hyddmark@ortho.ufl.edu.
8
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; elham@ufl.edu.
9
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; zareza@ortho.ufl.edu.
10
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; plevings@ufl.edu.
11
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; luy@ortho.ufl.edu.
12
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; dacanea@ortho.ufl.edu.
13
University of Florida, Orthopaedics and Rehabilitation, Gainesville, Florida, United States ; gfore001@fiu.edu.
14
Mayo Clinic, Rehabilitation Medicine Research Center, Rochester, Minnesota, United States ; Evans.Christopher@mayo.edu.
15
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; mortona@ufl.edu.
16
University of Florida, Small Animal Clinical Sciences, Gainesville, Florida, United States ; mdwinter@ufl.edu.
17
University of Florida, Infectious Diseases and Pathology, Gainesville, Florida, United States ; darkmich@ufl.edu.
18
University of Central Florida, Statistics, Orlando, Florida, United States ; David.Nickerson@ucf.edu.
19
University of Florida, Large Animal Clinical Sciences, Gainesville, Florida, United States ; colahanp@UFL.EDU.
20
University of Florida, Department of Orthopaedics and Rehabilitation , PO Box 100137, M-210, JHMHC , 1600 SW Archer Rd , Gainesville, Florida, United States , 32610-0137 ; ghivisc@ortho.ufl.edu.

Abstract

We are investigating self-complementary adeno-associated virus (scAAV) as a vector for intra-articular gene-delivery of IL-1Ra, and its therapeutic capacity in the treatment of osteoarthritis (OA). To model gene-transfer on a scale proportional to the human knee, a frequent site of OA incidence, we focused our studies on the joints of the equine forelimb. Using AAV2.5 capsid and equine IL-1Ra as a homologous transgene, we previously identified a functional ceiling dose of ~5 x 1012 viral genomes, which elevated the steady state levels of eqIL-1Ra in synovial fluids by more than 40-fold over endogenous production for at least 6 months. Here, using an osteochondral fragmentation model of early OA, we examined the functional capacity of scAAV.IL-1Ra gene-delivery in equine joints over a period of 12 weeks. In the disease model, transgenic eqIL-1Ra expression was several-fold higher than seen previously in healthy joints, and correlated directly with the severity of joint pathology at the time of treatment. Despite wide variation in expression, the steady-state eqIL-1Ra in synovial fluids exceeded that of IL-1 by > 400-fold in all animals, and a consistent treatment effect was observed. This included a 30-40% reduction in lameness and ~25% improvement in total joint pathology by both MRI and arthroscopic assessments, which included reduced joint effusion and synovitis, and improved repair of the osteochondral lesion. No vector-related increase in eqIL-1Ra levels in blood or urine was noted. Cumulatively our studies in the equine model indicate scAAV.IL-1Ra administration is reasonably safe and capable of sustained therapeutic IL-1Ra production intra-articularly in joints of human scale. This profile supports consideration for human testing in OA.
 
 

Front Immunol. 2018 May 9;9:1053. doi: 10.3389/fimmu.2018.01053. eCollection 2018.

Protective Role of Myeloid Cells Expressing a G-CSF Receptor Polymorphism in an Induced Model of Lupus.

Author information

1
Department of Pathology, Immunology, Laboratory Medicine, University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States.

Abstract

The genetic analysis of the lupus-prone NZM2410 mouse has identified a suppressor locus, Sle2c2, which confers resistance to spontaneous lupus in combination with NZM2410 susceptibility loci, or in the chronic graft-versus-host disease (cGVHD) induced model of lupus in the B6.Sle2c2 congenic strain. The candidate gene for Sle2c2, the Csf3r gene encoding the granulocyte colony-stimulating factor receptor (G-CSF-R/CD114), was validated when cGVHD was restored in B6.Sle2c2 mice after treatment with G-CSF. The goal of the project reported herein was to investigate the myeloid cells that confer resistance to cGVHD and to ascertain if the mechanism behind their suppression involves the G-CSF pathway. We showed that despite expressing the highest levels of G-CSF-R, neutrophils play only a modest role in the autoimmune activation induced by cGVHD. We also found reduced expression levels of G-CSF-R on the surface of dendritic cells (DCs) and a differential distribution of DC subsets in response to cGVHD in B6.Sle2c2 versus B6 mice. The CD8α+ DC subset, known for its tolerogenic phenotype, was expanded upon induction of cGVHD in B6.Sle2c2 mice. In addition, the deficiency of CD8α+ DC subset enhanced the severity of cGVHD in B6.Batf3-/- and B6.Sle2c2 mice, confirming their role in suppression of cGVHD. B6.Sle2c2DCs presented lowered activation and antigen presentation abilities and expressed lower levels of genes associated with DC activation and maturation. Exposure to exogenous G-CSF reversed the majority of these phenotypes, suggesting that tolerogenic DCs maintained through a defective G-CSF-R pathway mediated the resistance to cGVHD in B6.Sle2c2 mice.
 
 

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10196-10201. doi: 10.1073/pnas.1711169114. Epub 2017 Sep 5.

Proteoliposome-based full-length ZnT8 self-antigen for type 1 diabetes diagnosis on a plasmonic platform.

Author information

1
Department of Chemistry, Bio-X, and the Biophysics Program, Stanford University, Stanford, CA 94305.
2
Department of Materials Science and Engineering, South University of Science and Technology of China, Shenzhen 518055, China.
3
Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205.
4
Department of Pathology, College of Medicine, University of Florida, Gainesville, FL 32610-0275.
5
Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL 32610-0275.
6
Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205; dfu3@jhmi.edu hdai@stanford.edu.
7
Department of Chemistry, Bio-X, and the Biophysics Program, Stanford University, Stanford, CA 94305; dfu3@jhmi.edu hdai@stanford.edu.

Abstract

Identified as a major biomarker for type 1 diabetes (T1D) diagnosis, zinc transporter 8 autoantibody (ZnT8A) has shown promise for staging disease risk and disease diagnosis. However, existing assays for ZnT8 autoantibody (ZnT8A) are limited to detection by soluble domains of ZnT8, owing to difficulties in maintaining proper folding of a full-length ZnT8 protein outside its native membrane environment. Through a combined bioengineering and nanotechnology approach, we have developed a proteoliposome-based full-length ZnT8 self-antigen (full-length ZnT8 proteoliposomes; PLR-ZnT8) for efficient detection of ZnT8A on a plasmonic gold chip (pGOLD). The protective lipid matrix of proteoliposomes improved the proper folding and structural stability of full-length ZnT8, helping PLR-ZnT8 immobilized on pGOLD (PLR-ZnT8/pGOLD) achieve high-affinity capture of ZnT8A from T1D sera. Our PLR-ZnT8/pGOLD exhibited efficient ZnT8A detection for T1D diagnosis with ∼76% sensitivity and ∼97% specificity (n = 307), superior to assays based on detergent-solubilized full-length ZnT8 and the C-terminal domain of ZnT8. Multiplexed assays using pGOLD were also developed for simultaneous detection of ZnT8A, islet antigen 2 autoantibody, and glutamic acid decarboxylase autoantibody for diagnosing T1D.

 
 

Plant J. 2018 Jun 8. doi: 10.1111/tpj.13986. [Epub ahead of print]

An ecophysiologically-based mapping model identifies a major pleiotropic QTL for leaf growth trajectories of Phaseolus vulgaris.

Author information

1
Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
2
Department of Horticultural Sciences, University of Florida, Gainesville, FL, 32611, USA.
3
Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.

Abstract

Crop modeling, a widely used tool to predict plant growth and development in heterogeneous environments, has been increasingly integrated with genetic information to improve its predictability. This integration can also shed light on the mechanistic path that connects the genotype to a particular phenotype under specific environments. We implemented a bivariate statistical procedure to map and identify quantitative trait loci (QTLs) that can predict the form of plant growth by estimating cultivar-specific growth parameters and incorporating these parameters into a mapping framework. The procedure enables the characterization of how QTLs act differently in response to developmental and environmental cues. We used this procedure to map growth parameters of leaf area and mass in a mapping population of the common bean (Phaseolus vulgaris L.). Different sets of QTLs are responsible for various aspects of growth, including the initiation time of growth, growth rate, inflection point and asymptotic growth. A major QTL of a large effect was identified to pleiotropically affect trait expression in distinct environments and different traits expressed on the same organism. The integration of crop models and QTL mapping through our statistical procedure provides a powerful means of building a more precise predictive model of genotype-phenotype relationships for crops. This article is protected by copyright. All rights reserved.
 
 

PLoS One. 2018 Jun 5;13(6):e0196878. doi: 10.1371/journal.pone.0196878. eCollection 2018.

Bioinformatics core competencies for undergraduate life sciences education.

Author information

1
School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America.
2
Department of Biological Sciences, St. Edward’s University, Austin, Texas, United States of America.
3
Bioinformatics Program, Saint Vincent College, Latrobe, Pennsylvania, United States of America.
4
Department of Biology, Agnes Scott College, Decatur, Georgia, United States of America.
5
Department of Biology, Georgetown University, Washington, D.C., United States of America.
6
Digital World Biology, Seattle, Washington, United States of America.
7
Microbiology and Cell Science Department, University of Florida, Gainesville, Florida, United States of America.
8
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.
9
Department of Biology, San Diego State University, San Diego, California, United States of America.
10
Department of Biology, College of Wooster, Wooster, Ohio, United States of America.
11
College of Natural & Agricultural Sciences, University of California, Riverside, Riverside, California, United States of America.
12
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
13
Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America.
14
Department of Biological Sciences, Hampton University, Hampton, Virginia, United States of America.
15
Department of Agricultural Education and Communication, University of Florida, Gainesville, Florida, United States of America.
16
Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California, United States of America.
17
Department of Teacher Education, University of Nebraska at Omaha, Omaha, Nebraska, United States of America.
18
Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America.
19
Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America.
20
Department of Biology, Lycoming College, Williamsport, Pennsylvania, United States of America.
21
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America.
22
Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America.
23
Department of Natural Sciences, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico, United States of America.
24
Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America.
25
Department of Biology, Susquehanna University, Selinsgrove, Pennsylvania, United States of America.
26
Department of Biology, Chemistry, and Environmental Sciences, Inter American University of Puerto Rico, San Germán Campus, San Germán, Puerto Rico, United States of America.
27
Department of Computer Science, Ohio University, Athens, Ohio, United States of America.
28
Department of Biology Teaching and Learning, University of Minnesota, Saint Paul, Minnesota, United States of America.
29
Center for New Designs in Learning and Scholarship, Georgetown University, Washington, D.C., United States of America.
30
School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, United States of America.

Abstract

Although bioinformatics is becoming increasingly central to research in the life sciences, bioinformatics skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of biology faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondent’s degree of training, time since degree earned, and/or the Carnegie Classification of the respondent’s institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of the syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate biology students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.
 
 

Surg Radiol Anat. 2017 Oct;39(10):1149-1159. doi: 10.1007/s00276-017-1843-x. Epub 2017 Mar 12.

The hippocampus: detailed assessment of normative two-dimensional measurements, signal intensity, and subfield conspicuity on routine 3T T2-weighted sequences.

Author information

1
Department of Radiology, University of Alabama at Birmingham, 619 19th St. S., JT N409, Birmingham, AL, 35249, USA. ehmiddlebrooks@gmail.com.
2
Department of Radiology, University of Florida, Gainesville, FL, USA.
3
Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA.
4
Department of Veterans Affairs Medical Center, Gainesville, FL, USA.
5
Department of Neurology, University of Florida, Gainesville, FL, USA.
6
Department of Neurosurgery, University of Florida, Gainesville, FL, USA.
7
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA.
8
Department of Psychiatry, University of Florida, Gainesville, FL, USA.

Abstract

PURPOSE:

The hippocampus has a critical role in many common disease processes. Currently, routine 3 Tesla structural MRI is a mainstay of clinical diagnosis. The goal of our study is to evaluate the normal variability in size and/or conspicuity of the hippocampal subcomponents in routine clinical 3 Tesla high-resolution T2-weighted images to provide a basis for better defining pathological derangements. Additionally, we utilize diffusion data acquired from a 17.6 Tesla MRI of the hippocampus as a benchmark to better illustrate these subcomponents.

METHODS:

The hippocampus was retrospectively assessed on 104 clinically normal patients undergoing coronal T2-weighted imaging. The conspicuity of the majority of hippocampal subcomponents was assessed in each portion of the hippocampus. Additionally, easily applicable cross-sectional measurements and signal intensities were obtained to evaluate the range of normal, as well as inter- and intra-subject variability.

RESULTS:

The normal range of cross-sectional measurements of the hippocampal subcomponents was calculated. There was minimal side-to-side variability in cross-sectional measurements of hippocampal subcomponents (< 5%) with the exception of the subiculum (R>L by 8.3%) and the CA4/DG (R>L by 5.8%). The internal architecture showed high variability in visibility of subcomponents between different segments of the hippocampus.

CONCLUSIONS:

Confident clinical assessment of the hippocampus requires a thorough knowledge of hippocampal size and signal, but also the internal architecture expected to be seen. The data provided in this study will provide the reader with vital information necessary for distinguishing a normal from abnormal exam.
 
 

Am J Bot. 2017 Oct;104(10):1484-1492. doi: 10.3732/ajb.1700180.

Karyotypic variation and pollen stainability in resynthesized allopolyploids Tragopogon miscellus and T. mirus.

Author information

1
Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA.
2
Department of Biology, University of Florida, Gainesville, Florida 32611, USA.
3
Royal Botanic Gardens, Kew, Natural Capital and Plant Health Department, Richmond, Surrey TW9 3DS, UK.
4
Kangwon National University, Department of Applied Plant Sciences, Chuncheon 24341, Korea.
5
Genetics Institute, University of Florida, Gainesville, Florida 32610, USA.

Abstract

PREMISE OF THE STUDY:

Polyploidy has extensively shaped the evolution of plants, but the early stages of polyploidy are still poorly understood. The neoallopolyploid species Tragopogon mirus and T. miscellus are both characterized by widespread karyotypic variation, including frequent aneuploidy and intergenomic translocations. Our study illuminates the origins and early impacts of this variation by addressing two questions: How quickly does karyotypic variation accumulate in Tragopogon allopolyploids following whole-genome duplication (WGD), and how does the fertility of resynthesized Tragopogon allopolyploids evolve shortly after WGD?

METHODS:

We used genomic in situ hybridization and lactophenol-cotton blue staining to estimate the karyotypic variation and pollen stainability, respectively, of resynthesized T. mirus and T. miscellus during the first five generations after WGD.

KEY RESULTS:

Widespread karyotypic variation developed quickly in synthetics and resembled that of naturally occurring T. mirus and T. miscellus by generation S4 . Pollen stainability in resynthesized allopolyploids was consistently lower than that of natural T. mirus and T. miscellus, as well as their respective diploid progenitor species. Logistic regression showed that mean pollen stainability increased slightly over four generations in resynthesized T. mirus but remained at equivalent levels in T. miscellus.

CONCLUSIONS:

Our results clarify some of the changes that occur in T. mirus and T. miscellus immediately following their origin, most notably the rapid onset of karyotypic variation within these species immediately following WGD.
 
 

Aquat Toxicol. 2018 May 29;201:66-72. doi: 10.1016/j.aquatox.2018.05.024. [Epub ahead of print]

Comparative toxicity of three phenolic compounds on the embryo of fathead minnow, Pimephales promelas.

Author information

1
Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA; College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China.
2
Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA.
3
Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
4
Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA. Electronic address: ndenslow@ufl.edu.

Abstract

Phenols are classified as polar narcotics, which are thought to cause toxicity by non-specific mechanisms, possibly by disrupting membrane structure and function. Here we test three phenolic chemicals, phenol, 2,4-dichlorphenol and pentachlorophenol on embryo development, heartbeat rate and mitochondrial respiration in fathead minnow (Pimephales promelas). While these chemicals have been used on isolated mitochondria, they have not yet been used to verify respiration in intact embryos. Mitochondrial respiration in intact embryos was measured after optimizing the Seahorse XFe24 Extracellular Flux Analyzer. Heartbeat rate and mitochondrial respiration patterns of fathead minnow embryos at different developmental stages were also characterized. Exposures of embryos at developmental stage 20 occurred for 24 h with five concentrations of each phenolic compound ranging from 0.85 to 255 μM for phenol, 0.49 to 147 μM for 2,4-dichlorophenol and 0.3 to 90 μM for pentachlorophenol. Exposure to phenol at the concentrations tested had no effects on development, heartbeat or mitochondrial respiration. However, both 2,4-dichlorophenol and pentachlorophenol showed dose-dependent effects on development, heartbeat rate, and mitochondrial respiration, with the effects occurring at lower concentrations of pentachlorophenol, compared to 2,4-dichlorophenol, highlighting the higher toxicity of the more chlorinated phenols. Both 2,4-dichlorophenol and pentachlorophenol decreased basal mitochondrial respiration of embryos and ATP production. These results indicate that higher chlorinated phenolic chemicals cause developmental toxicity in fathead minnow embryos by decreasing mitochondrial respiration and heartbeat rate.
 
 

Plant Cell Environ. 2017 Nov;40(11):2806-2819. doi: 10.1111/pce.13056. Epub 2017 Oct 12.

Overexpression of DEMETER, a DNA demethylase, promotes early apical bud maturation in poplar.

Author information

1
Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain.
2
School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA.
3
University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
4
Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain.

Abstract

The transition from active growth to dormancy is critical for the survival of perennial plants. We identified a DEMETER-like (CsDML) cDNA from a winter-enriched cDNA subtractive library in chestnut (Castanea sativa Mill.), an economically and ecologically important species. Next, we characterized this DNA demethylase and its putative ortholog in the more experimentally tractable hybrid poplar (Populus tremula × alba), under the signals that trigger bud dormancy in trees. We performed phylogenetic and protein sequence analysis, gene expression profiling, and 5-methyl-cytosine methylation immunodetection studies to evaluate the role of CsDML and its homolog in poplar, PtaDML6. Transgenic hybrid poplars overexpressing CsDML were produced and analysed. Short days and cold temperatures induced CsDML and PtaDML6. Overexpression of CsDML accelerated short-day-induced bud formation, specifically from Stages 1 to 0. Buds acquired a red-brown coloration earlier than wild-type plants, alongside with the up-regulation of flavonoid biosynthesis enzymes and accumulation of flavonoids in the shoot apical meristem and bud scales. Our data show that the CsDML gene induces bud formation needed for the survival of the apical meristem under the harsh conditions of winter.
 
 

Plant Cell Environ. 2017 Oct;40(10):2236-2249. doi: 10.1111/pce.13019. Epub 2017 Aug 30.

Chilling-responsive DEMETER-LIKE DNA demethylase mediates in poplar bud break.

Author information

1
Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain.
2
LBLGC EA1207, USC 1328 INRA, University Orléans, 45067, Orléans, France.
3
School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA.
4
University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
5
Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain.

Abstract

Annual dormancy-growth cycle is a developmental and physiological process essential for the survival of deciduous trees in temperate and boreal forests. Seasonal control of shoot growth in woody perennials requires specific genetic programmes responding to environmental signals. The environmental-controlled mechanisms that regulate the shift between winter dormancy and the growth-promoting genetic programmes are still unknown. Here, we show that dynamics in genomic DNA methylation levels are involved in the regulation of dormancy-growth cycle in poplar. The reactivation of growth in the apical shoot during bud break process in spring is preceded by a progressive reduction of genomic DNA methylation in apex tissue. The induction in apex tissue of a chilling-dependent poplar DEMETER-LIKE 10 (PtaDML10) DNA demethylase precedes shoot growth reactivation. Transgenic poplars showing downregulation of PtaDML8/10 caused delayed bud break. Genome-wide transcriptome and methylome analysis and data mining revealed that the gene targets of DEMETER-LIKE-dependent DNA demethylation are genetically associated with bud break. These data point to a chilling-dependent DEMETER-like DNA demethylase mechanisms being involved in the shift from winter dormancy to a condition that precedes shoot apical vegetative growth in poplar.
 
 

Psychiatry Res. 2018 May 23;267:30-36. doi: 10.1016/j.psychres.2018.05.053. [Epub ahead of print]

Detail-oriented visual processing style: Its role in the relationships between early life adversity and hoarding-related dysfunctions.

Author information

1
Department of Psychiatry, University of California, San Francisco, USA.
2
Department of Psychiatry, University of California, San Francisco, USA; Department of Psychiatry, University of Florida, Gainesville, USA. Electronic address: carolmathews@ufl.edu.

Abstract

Early life adversity, ranging from material deprivation and parental dysfunction to abusive and life-threatening events, has been associated with hoarding symptom severity. Moreover, both victims of early life adversity and individuals with hoarding disorder have been found to have a higher tendency toward detail-oriented visual processing. This study aimed to investigate the role of detail-oriented visual processing in the relationship between early life adversity and hoarding-related dysfunction. Childhood exposure to life adversity, hoarding symptom severity, and emotional attachment to possessions, a hoarding-related dysfunction thought to be most closely related to adversity exposure, were assessed. Detail-oriented visual processing was evaluated using the Central Coherence Index, which was calculated based on the drawing process during the Rey-Osterrieth Complex Figure Test. It was found that detail-oriented visual processing was not significantly associated with hoarding symptom severity, emotional attachment to possessions, or the relationship between early life adversity and hoarding symptom severity. It did, however, act as a significant moderator in the relationship between early life adversity and emotional attachment to possessions. These findings add to the literature by identifying the role of a specific neurocognitive processing style in the mechanism through which early life adversity affects the development of a key hoarding-related dysfunction, elevated emotional attachment to possessions.
 
 

Eur Child Adolesc Psychiatry. 2018 May;27(5):569-579. doi: 10.1007/s00787-017-1074-z. Epub 2017 Nov 2.

Prevalence and predictors of hair pulling disorder and excoriation disorder in Tourette syndrome.

Author information

1
Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
2
Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, CPZN-6254, Boston, MA, 02114, USA.
3
Department of Psychiatry, Youthdale Treatment Centers, University of Toronto and University Health Network, Toronto, ON, Canada.
4
Department of Psychiatry, University of Montreal, Montreal, QC, Canada.
5
Cold Spring Harbor Laboratory, Stanley Institute for Cognitive Genomics, Cold Spring Harbor, NY, USA.
6
Yale Child Study Center, Yale University School of Medicine, New Haven, CT, USA.
7
Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA.
8
Hofstra Northwell School of Medicine, Hempstead, NY, USA.
9
Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
10
Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA.
11
Center for OCD, Anxiety and Related Disorders, University of Florida, Gainesville, FL, USA.
12
Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, CPZN-6254, Boston, MA, 02114, USA. jscharf@partners.org.
13
Department of Neurology, Massachusetts General Hospital, Boston, MA, USA. jscharf@partners.org.
14
Division of Cognitive and Behavioral Neurology, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA. jscharf@partners.org.

Abstract

Trichotillomania/hair pulling disorder (HPD) and excoriation/skin picking disorder (SPD) are childhood-onset, body-focused repetitive behaviors that are thought to share genetic susceptibility and underlying pathophysiology with obsessive-compulsive disorder (OCD) and Tourette syndrome (TS). We sought to determine the prevalence of DSM-5 HPD and SPD in TS patients, and to identify clinical factors most associated with their co-morbidity with TS. Participants included 811 TS patients recruited from TS specialty clinics for a multi-center genetic study. Patients were assessed using standardized, validated semi-structured interviews. HPD and SPD diagnoses were determined using a validated self-report questionnaire. HPD/SPD prevalence rates were calculated, and clinical predictors were evaluated using regression modeling. 3.8 and 13.0% of TS patients met DSM-5 criteria for HPD and SPD, respectively. In univariable analyses, female sex, OCD, and both tic and obsessive-compulsive symptom severity were among those associated with HPD and/or SPD. In multivariable analyses, only lifetime worst-ever motor tic severity remained significantly associated with HPD. Female sex, co-occurring OCD, ADHD, and motor tic severity remained independently associated with SPD. This is the first study to examine HPD and SPD prevalence in a TS sample using semi-structured diagnostic instruments. The prevalence of HPD and SPD in TS patients, and their association with increased tic severity and co-occurring OCD, suggests that clinicians should screen children with TS and related disorders for HPD/SPD, particularly in females and in those with co-occurring OCD. This study also helps set a foundation for subsequent research regarding HPD/SPD risk factors, pathophysiology, and treatment models.
 
 

Am J Bot. 2017 Sep;104(9):1281-1284. doi: 10.3732/ajb.1700281.

Digitization of herbaria enables novel research.

Author information

1
Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA.

 
 

Redox Biol. 2018 Jul;17:432-439. doi: 10.1016/j.redox.2018.05.013. Epub 2018 May 31.

Ceruloplasmin and hephaestin jointly protect the exocrine pancreas against oxidative damage by facilitating iron efflux.

Author information

1
Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, China.
2
Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, FL, USA.
3
QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
4
Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, China. Electronic address: hjchen@nju.edu.cn.

Abstract

Little is known about the iron efflux from the pancreas, but it is likely that multicopper ferroxidases (MCFs) are involved in this process. We thus used hephaestin (Heph) and ceruloplasmin (Cp) single-knockout mice and Heph/Cp double-knockout mice to investigate the roles of MCFs in pancreatic iron homeostasis. We found that both HEPH and CP were expressed in the mouse pancreas, and that ablation of either MCF had limited effect on the pancreatic iron levels. However, ablation of both MCFs together led to extensive pancreatic iron deposition and severe oxidative damage. Perls’ Prussian blue staining revealed that this iron deposition was predominantly in the exocrine pancreas, while the islets were spared. Consistent with these results, plasma lipase and trypsin were elevated in Heph/Cp knockout mice, indicating damage to the exocrine pancreas, while insulin secretion was not affected. These data indicate that HEPH and CP play mutually compensatory roles in facilitating iron efflux from the exocrine pancreas, and show that MCFs are able to protect the pancreas against iron-induced oxidative damage.
 
 

Evol Bioinform Online. 2018 May 8;14:1176934318774546. doi: 10.1177/1176934318774546. eCollection 2018.

aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data.

Author information

1
Florida Museum of Natural History and University of Florida, Gainesville, FL, USA.
2
Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA.

Abstract

Massive strides have been made in technologies for collecting genome-scale data. However, tools for efficiently and flexibly assembling raw outputs into downstream analytical workflows are still nascent. aTRAM 1.0 was designed to assemble any locus from genome sequencing data but was neither optimized for efficiency nor able to serve as a single toolkit for all assembly needs. We have completely re-implemented aTRAM and redesigned its structure for faster read retrieval while adding a number of key features to improve flexibility and functionality. The software can now (1) assemble single- or paired-end data, (2) utilize both read directions in the database, (3) use an additional de novoassembly module, and (4) leverage new built-in pipelines to automate common workflows in phylogenomics. Owing to reimplementation of databasing strategies, we demonstrate that aTRAM 2.0 is much faster across all applications compared to the previous version.
 
 

Mol Microbiol. 2018 Jun 5. doi: 10.1111/mmi.13992. [Epub ahead of print]

Threshold regulation and stochasticity from the MecA/ClpCP proteolytic system in Streptococcus mutans competence.

Author information

1
Department of Physics, University of Florida, Gainesville, FL 32611.
2
Department of Oral Biology, University of Florida, Gainesville, FL 32610.

Abstract

Many bacterial species use the MecA/ClpCP proteolytic system to block entry into genetic competence. In Streptococcus mutans, MecA/ClpCP degrades ComX (also called SigX), an alternative sigma factor for the comY operon and other late competence genes. Although the mechanism of MecA/ClpCP has been studied in multiple Streptococcus species, its role within noisy competence pathways is poorly understood. S. mutans competence can be triggered by two different peptides, CSP and XIP, but it is not known whether MecA/ClpCP acts similarly for both stimuli, how it affects competence heterogeneity, and how its regulation is overcome. We have studied the effect of MecA/ClpCP on the activation of comY in individual S. mutans cells. Our data show that MecA/ClpCP is active under both XIP and CSP stimulation, that it provides threshold control of comY, and that it adds noise in comY expression. Our data agree quantitatively with a model in which MecA/ClpCP prevents adventitious entry into competence by sequestering or intercepting low levels of ComX. Competence is permitted when ComX levels exceed a threshold, but cell-to-cell heterogeneity in MecA levels creates variability in that threshold. Therefore MecA/ClpCP provides a stochastic switch, located downstream of the already noisy comX, that enhances phenotypic diversity. This article is protected by copyright. All rights reserved.
 
 

Phytopathology. 2018 Jun 6. doi: 10.1094/PHYTO-03-18-0088-R. [Epub ahead of print]

Regional spatial-temporal spread of citrus huanglongbing is affected by rain in Florida.

Author information

1
University of Florida, Plant Pathology, Gainesville, Florida, United States ; mpokis@yahoo.com.
2
Gainesville, Florida, United States ; tim.s.schubert@gmail.com.
3
FDACS, Division of Plant Industry, Gainesville, Florida, United States ; matthew.albritton@freshfromflorida.com.
4
Florida Division of Plant Industry, 205102, Gainesville, Florida, United States ; Susan.Halbert@freshfromflorida.com.
5
FDACS, Division of Plant Industry, Gainesville, Florida, United States ; debra.jones@freshfromflorida.com.
6
FDACS, Division of Plant Industry, Gainesville, Florida, United States ; Xiaoan.sun@freshfromflorida.com.
7
University of Florida, Plant Pathology , 2686 SR 29 N , Immokalee, Florida, United States , 34142 ; pdr@ufl.edu.
8
University of Florida, Emerging Pathogens Institute , 2055 Mowry Rd. , Gainesville, Florida, United States , 32610.
9
University of Florida, Emerging Pathogens Institut ; bhsinger@epi.ufl.edu.
10
University of Florida, 3463, Agricultural and Biological engineering, Gainesville, Florida, United States ; wslee@ufl.edu.
11
University of Florida, Plant Patholgoy Dept. , 1453 Fifield Hall , Gainesville, Florida, United States , 32611 ; jbjones@ufl.edu.
12
Tropical Research and Education Center, University of Florida, Plant Pathology , 18905 SW 280th Street , Homestead, Florida, United States , 33031 ; kelly12@ufl.edu.
13
University of Florida, Plant Pathology , 1453 Fifield Hall , Gainesville, Florida, United States , FL 32611 ; ahcvanbruggen@ufl.edu.

Abstract

Citrus huanglongbing (HLB), associated with Candidatus Liberibacter asiaticus (Las), disseminated by Asian Citrus Psyllid (ACP), has devastated citrus in Florida since 2005. Data on HLB occurrence were stored in databases (2005-2012). Cumulative HLB-positive citrus blocks were subjected to kernel density analysis and kriging. Relative disease incidence per county was calculated by dividing HLB numbers by relative tree numbers and maximum incidence. Spatio-temporal HLB distributions were correlated with weather. Relative HLB incidence correlated positively with rainfall. The focus expansion rate was 1626 m month-1, similar to that in Brazil. Relative HLB incidence in counties with primarily large groves increased at a lower rate (0.24 year-1) than in counties with smaller groves in hotspot areas (0.67 year-1), confirming reports that large-scale HLB management may slow epidemic progress.
 
 

Nat Commun. 2018 Jun 6;9(1):2189. doi: 10.1038/s41467-018-04559-0.

Precise temporal regulation of alternative splicing during neural development.

Author information

1
Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA.
2
Department of Automation, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Tsinghua University, Beijing, 100084, China.
3
Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, 10027, USA.
4
Department of Comparative Biology and Safety Sciences, Amgen Inc., Cambridge, MA, 02141, USA.
5
Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, 10032, USA.
6
Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA.
7
Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA. cz2294@columbia.edu.

Abstract

Alternative splicing (AS) is one crucial step of gene expression that must be tightly regulated during neurodevelopment. However, the precise timing of developmental splicing switches and the underlying regulatory mechanisms are poorly understood. Here we systematically analyze the temporal regulation of AS in a large number of transcriptome profiles of developing mouse cortices, in vivo purified neuronal subtypes, and neurons differentiated in vitro. Our analysis reveals early-switch and late-switch exons in genes with distinct functions, and these switches accurately define neuronal maturation stages. Integrative modeling suggests that these switches are under direct and combinatorial regulation by distinct sets of neuronal RNA-binding proteins including Nova, Rbfox, Mbnl, and Ptbp. Surprisingly, various neuronal subtypes in the sensory systems lack Nova and/or Rbfox expression. These neurons retain the “immature” splicing program in early-switch exons, affecting numerous synaptic genes. These results provide new insights into the organization and regulation of the neurodevelopmental transcriptome.
 
 

J Dairy Sci. 2018 Jun 6. pii: S0022-0302(18)30545-9. doi: 10.3168/jds.2018-14580. [Epub ahead of print]

Effects of level of dietary cation-anion difference and duration of prepartum feeding on performance and metabolism of dairy cows.

Author information

1
Department of Animal Sciences, University of Florida, Gainesville 32611.
2
Arm & Hammer Animal Nutrition, Princeton, NJ 08543.
3
Department of Animal Sciences, University of Florida, Gainesville 32611; DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32611. Electronic address: jepsantos@ufl.edu.

Abstract

The objectives were to evaluate the effects of feeding diets with 2 levels of negative dietary cation-anion differences (DCAD) during the last 42 or 21 d of gestation on performance and metabolism in dairy cows. The hypothesis was that extending feeding from 21 to 42 d and reducing the DCAD from -70 to -180 mEq/kg of dry matter (DM) would not be detrimental to performance. Holstein cows at 230 d of gestation were blocked by parity prepartum (48 entering their second lactation and 66 entering their third or greater lactation) and 305-d milk yield, and randomly assigned to 1 of 4 treatments arranged as a 2 × 2 factorial. The 2 levels of DCAD, -70 or -180 mEq/kg of DM, and 2 feeding durations, the last 21 d (short) or the last 42 d (long) prepartum resulted in 4 treatments, short -70 (n = 29), short -180 (n = 29), long -70 (n = 28) and long -180 (n = 28). Cows in the short treatments were fed a diet with DCAD of +110 mEq/kg of DM from -42 to -22 d relative to calving. After calving, cows were fed the same diet and production and disease incidence were evaluated for 42 d in milk, whereas reproduction and survival was evaluated for 305 d in milk. Blood was sampled pre- and postpartum for quantification of metabolites and minerals. Reducing the DCAD linearly decreased prepartum DM intake between -42 and -22 d relative to calving (+110 mEq/kg of DM = 11.5 vs. -70 mEq/kg of DM = 10.7 vs. -180 mEq/kg of DM = 10.2 ± 0.4), and a more acidogenic diet in the last 21 d of the dry period reduced intake by 1.1 kg/d (-70 mEq/kg of DM = 10.8 vs. -180 mEq/kg of DM = 9.7 ± 0.5 kg/d). Cows fed the -180 mEq/kg of DM diet had increased concentrations of ionized Ca in blood on the day of calving (-70 mEq/kg of DM = 1.063 vs. -180 mEq/kg of DM = 1.128 ± 0.020 mM). Extending the duration of feeding the diets with negative DCAD from 21 to 42 d reduced gestation length by 2 d (short = 277.2 vs. long = 275.3 d), milk yield by 2.5 kg/d (short = 40.4 vs. long = 37.9 ± 1.0 kg/d) and tended to increase days open because of reduced pregnancy per artificial insemination (short = 35.0 vs. long = 22.6%). Results suggest that increasing the duration of feeding diets with negative DCAD from 21 to 42 d prepartum might influence milk yield and reproduction of cows in the subsequent lactation, although yields of 3.5% fat- and energy-corrected milk did not differ with treatments. Reducing the DCAD from -70 to -180 mEq/kg of DM induced a more severe metabolic acidosis, increased ionized Ca concentrations prepartum and on the day of calving, and decreased colostrum yield in the first milking, but had no effects on performance in the subsequent lactation. Collectively, these data suggest that extending the feeding of an acidogenic diet beyond 21 d is unnecessary and might be detrimental to dairy cows, and a reduction in the DCAD from -70 to -180 mEq/kg of DM is not needed.

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