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UFGI publication round-up week 5/28

Diabetes. 2018 Apr;67(4):697-703. doi: 10.2337/db17-0937. Epub 2018 Jan 17.

Loss of B-Cell Anergy in Type 1 Diabetes Is Associated With High-Risk HLA and Non-HLA Disease Susceptibility Alleles.

Author information

1
Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO.
2
Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO.
3
Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO.
4
Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL.
5
Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL.
6
Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO john.cambier@ucdenver.edu.

Abstract

Although B cells reactive with islet autoantigens are silenced by tolerance mechanisms in healthy individuals, they can become activated and contribute to the development of type 1 diabetes. We previously demonstrated that high-affinity insulin-binding B cells (IBCs) occur exclusively in the anergic (BND) compartment in peripheral blood of healthy subjects. Consistent with their activation early in disease development, high-affinity IBCs are absent from the BND compartment of some first-degree relatives (FDRs) as well as all patients with autoantibody-positive prediabetes and new-onset type 1 diabetes, a time when they are found in pancreatic islets. Loss of BND IBCs is associated with a loss of the entire BND B-cell compartment consistent with provocation by an environmental trigger or predisposing genetic factors. To investigate potential mechanisms operative in subversion of B-cell tolerance, we explored associations between HLA and non-HLA type 1 diabetes-associated risk allele genotypes and loss of BNDs in FDRs. We found that high-risk HLA alleles and a subset of non-HLA risk alleles (i.e., PTPN2 [rs1893217], INS [rs689], and IKZF3 [rs2872507]), relevant to B- and T-cell development and function are associated with loss of anergy. Hence, the results suggest a role for risk-conferring alleles in perturbation of B-cell anergy during development of type 1 diabetes.
 
 

AMIA Annu Symp Proc. 2018 Apr 16;2017:1848-1857. eCollection 2017.

Identifying High Health Care Utilizers Using Post-Regression Residual Analysis of Health Expenditures from a State Medicaid Program.

Author information

1
Dept. of Computer & Information Science & Engineering University of Florida, Gainesville, FL 32611, USA.
2
Dept. of Health Outcomes & Policy University of Florida, Gainesville, FL 32611, USA.

Abstract

We propose an approach to identify high health care utilizers using residuals from a regression-based health care utilization adjustment model to analyze the variations in health care expenditures. Using a large administrative claims dataset from a state public insurance program, we show that the residuals can identify a group of patients with high residuals whose demographics and categorization of comorbidities are similar to other patients but who have a significant amount of unexplained health care utilization. Additionally, these high utilizers persist from year to year. Correlation analysis with 3M™Potentially Preventable Events (PPE) software shows that a portion of this utilization may be preventable. In addition, these residuals can be useful in predicting future PPEs and hence may be useful in identifying impactable high utilizers.
 
 

PLoS One. 2018 May 24;13(5):e0197776. doi: 10.1371/journal.pone.0197776. eCollection 2018.

Peak oxygen uptake (VO2peak) across childhood, adolescence and young adulthood in Barth syndrome: Data from cross-sectional and longitudinal studies.

Author information

1
Program in Physical Therapy, Washington University School of Medicine, St. Louis, Missouri, United States of America.
2
Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.
3
Department of Electrical and Computer Engineering, Auburn University, Auburn, Alabama, United States of America.
4
Department of Pediatrics, University of Florida, Gainesville, Florida, United States of America.
5
Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, United States of America.

Abstract

Barth syndrome (BTHS) is an ultra-rare, X-linked recessive disorder characterized by cardio-skeletal myopathy, exercise intolerance, and growth delay. Oxygen uptake during peak exercise (VO2peak) has been shown to be severely limited in individuals with BTHS however; the trajectory of VO2peak from childhood to young adulthood is unknown. The objective of this study was to describe VO2peak from childhood through young adulthood in BTHS.

METHODS AND MATERIALS:

VO2peak over time was presented through cross-sectional (n = 33 participants) and a longitudinal analyses (n = 12 participants). Retrospective data were obtained through maximal exercise testing on a cycle ergometer from individuals with BTHS who were or are currently enrolled in a research study during July 2006-September 2017. Participants included in the cross-sectional analysis were divided into 3 groups for analysis: 1) children (n = 13), 2) adolescents (n = 8), and 3) young adults (n = 12). Participants in the longitudinal analysis had at least two exercise tests over a span of 2-9 years.

RESULTS:

VO2peak relative to body weight (ml/kgBW/min), fat-free mass (FFM) and by percent of predicted VO2peak obtained were not significantly different between children, adolescents and young adults. VO2peak did not longitudinally change over a mean time of ~5 years in late adolescent and young adult participants with repeated tests. A model including both cardiac and skeletal muscle variables best predicted VO2peak.

CONCLUSIONS:

In conclusion, VO2peak relative to body weight and fat-free mass demonstrates short- and long-term stability from childhood to young adulthood in BTHS with some variability among individuals.
 
 

Skelet Muscle. 2018 May 31;8(1):17. doi: 10.1186/s13395-018-0163-0.

TRAPPC11 and GOSR2 mutations associate with hypoglycosylation of α-dystroglycan and muscular dystrophy.

Author information

1
Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, Aurora, CO, USA.
2
Department of Biology, Concordia University, Montreal, Canada.
3
Department of Pathology Carver College of Medicine, The University of Iowa, Iowa City, IA, USA.
4
Division of Genetics and Metabolism, University of Florida College of Medicine, Gainesville, FL, USA.
5
Department of Biology, Concordia University, Montreal, Canada. michael.sacher@concordia.ca.
6
Department of Anatomy and Cell Biology, McGill University, Montreal, Canada. michael.sacher@concordia.ca.
7
Department of Pathology Carver College of Medicine, The University of Iowa, Iowa City, IA, USA. steven-moore@uiowa.edu.

Abstract

BACKGROUND:

Transport protein particle (TRAPP) is a supramolecular protein complex that functions in localizing proteins to the Golgi compartment. The TRAPPC11 subunit has been implicated in muscle disease by virtue of homozygous and compound heterozygous deleterious mutations being identified in individuals with limb girdle muscular dystrophy and congenital muscular dystrophy. It remains unclear how this protein leads to muscle disease. Furthermore, a role for this protein, or any other membrane trafficking protein, in the etiology of the dystroglycanopathy group of muscular dystrophies has yet to be found. Here, using a multidisciplinary approach including genetics, immunofluorescence, western blotting, and live cell analysis, we implicate both TRAPPC11 and another membrane trafficking protein, GOSR2, in α-dystroglycan hypoglycosylation.

CASE PRESENTATION:

Subject 1 presented with severe epileptic episodes and subsequent developmental deterioration. Upon clinical evaluation she was found to have brain, eye, and liver abnormalities. Her serum aminotransferases and creatine kinase were abnormally high. Subjects 2 and 3 are siblings from a family unrelated to subject 1. Both siblings displayed hypotonia, muscle weakness, low muscle bulk, and elevated creatine kinase levels. Subject 3 also developed a seizure disorder. Muscle biopsies from subjects 1 and 3 were severely dystrophic with abnormal immunofluorescence and western blotting indicative of α-dystroglycan hypoglycosylation. Compound heterozygous mutations in TRAPPC11 were identified in subject 1: c.851A>C and c.965+5G>T. Cellular biological analyses on fibroblasts confirmed abnormal membrane trafficking. Subject 3 was found to have compound heterozygous mutations in GOSR2: c.430G>T and c.2T>G. Cellular biological analyses on fibroblasts from subject 3 using two different model cargo proteins did not reveal defects in protein transport. No mutations were found in any of the genes currently known to cause dystroglycanopathy in either individual.

CONCLUSION:

Recessive mutations in TRAPPC11 and GOSR2 are associated with congenital muscular dystrophy and hypoglycosylation of α-dystroglycan. This is the first report linking membrane trafficking proteins to dystroglycanopathy and suggests that these genes should be considered in the diagnostic evaluation of patients with congenital muscular dystrophy and dystroglycanopathy.
 
 

Nat Ecol Evol. 2017 Nov;1(11):1737-1746. doi: 10.1038/s41559-017-0331-3. Epub 2017 Oct 9.

Ctenophore relationships and their placement as the sister group to all other animals.

Author information

1
Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA. nathan_whelan@fws.gov.
2
Warm Springs Fish Technology Center, US Fish and Wildlife Service, 5308 Spring St, Warm Springs, GA, 31830, USA. nathan_whelan@fws.gov.
3
Department of Biological Sciences, The University of Alabama, Box 870344, Tuscaloosa, AL, 35487, USA.
4
The Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA.
5
Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
6
The Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA. moroz@whitney.ufl.edu.
7
Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA. moroz@whitney.ufl.edu.
8
Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA. ken@auburn.edu.

Abstract

Ctenophora, comprising approximately 200 described species, is an important lineage for understanding metazoan evolution and is of great ecological and economic importance. Ctenophore diversity includes species with unique colloblasts used for prey capture, smooth and striated muscles, benthic and pelagic lifestyles, and locomotion with ciliated paddles or muscular propulsion. However, the ancestral states of traits are debated and relationships among many lineages are unresolved. Here, using 27 newly sequenced ctenophore transcriptomes, publicly available data and methods to control systematic error, we establish the placement of Ctenophora as the sister group to all other animals and refine the phylogenetic relationships within ctenophores. Molecular clock analyses suggest modern ctenophore diversity originated approximately 350 million years ago ± 88 million years, conflicting with previous hypotheses, which suggest it originated approximately 65 million years ago. We recover Euplokamis dunlapae-a species with striated muscles-as the sister lineage to other sampled ctenophores. Ancestral state reconstruction shows that the most recent common ancestor of extant ctenophores was pelagic, possessed tentacles, was bioluminescent and did not have separate sexes. Our results imply at least two transitions from a pelagic to benthic lifestyle within Ctenophora, suggesting that such transitions were more common in animal diversification than previously thought.
 
 

Sci Rep. 2016 Dec 1;6:38063. doi: 10.1038/srep38063.

The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity.

Author information

1
Department of Chemical Engineering, University of Florida, Bldg. 723, Gainesville, FL 32611, USA.
2
HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
3
Department of Biology, University of Florida, Cancer and Genetics Research Complex, 2033 Mowry Road, Gainesville, FL 32610, USA.
4
Sanford Children’s Health Research Center, Sanford Research, Sioux Falls, SD 57104, USA, Gainesville, FL 32610, USA.
5
Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35186, USA.
6
Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.

Abstract

Mechanical integration of the nucleus with the extracellular matrix (ECM) is established by linkage between the cytoskeleton and the nucleus. This integration is hypothesized to mediate sensing of ECM rigidity, but parsing the function of nucleus-cytoskeleton linkage from other mechanisms has remained a central challenge. Here we took advantage of the fact that the LINC (linker of nucleoskeleton and cytoskeleton) complex is a known molecular linker of the nucleus to the cytoskeleton, and asked how it regulates the sensitivity of genome-wide transcription to substratum rigidity. We show that gene mechanosensitivity is preserved after LINC disruption, but reversed in direction. Combined with myosin inhibition studies, we identify genes that depend on nuclear tension for their regulation. We also show that LINC disruption does not attenuate nuclear shape sensitivity to substrate rigidity. Our results show for the first time that the LINC complex facilitates mechano-regulation of expression across the genome.
 
 

Nucleic Acids Res. 2018 May 29. doi: 10.1093/nar/gky459. [Epub ahead of print]

Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs.

Author information

1
Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA.
2
UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
3
UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.

Abstract

Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi’s Sarcoma-associated herpes virus (KSHV) and Epstein-Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs. In this study, we performed a systematic re-analysis of published datasets from KSHV- and EBV-driven cancers. We used CLIP-seq data from lymphoma cells or EBV-transformed B cells, and a crosslinking, ligation and sequencing of hybrids dataset from KSHV-infected endothelial cells, to identify novel lncRNA targets of viral miRNAs. Here, we catalog the lncRNA targetome of KSHV and EBV miRNAs, and provide a detailed in silico analysis of lncRNA-miRNA binding interactions. Viral miRNAs target several hundred lncRNAs, including a subset previously shown to be aberrantly expressed in human malignancies. In addition, we identified thousands of lncRNAs to be putative targets of human miRNAs, suggesting that miRNA-lncRNA interactions broadly contribute to the regulation of gene expression.
 
 

J Mol Med (Berl). 2018 May 28. doi: 10.1007/s00109-018-1646-5. [Epub ahead of print]

Impact of toll-like receptor 4 stimulation on human neonatal neutrophil spontaneous migration, transcriptomics, and cytokine production.

Author information

1
Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA.
2
Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA.
3
BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Shriners Burns Hospital, Boston, MA, USA.
4
Department of Pediatrics and Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA.
5
Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA. Shawn.Larson@surgery.ufl.edu.

Abstract

Neonates rely on their innate immune system, and neutrophils in particular, to recognize and combat life-threatening bacterial infections. Pretreatment with lipopolysaccharide (LPS), a toll-like receptor (TLR) 4 agonist, improves survival to polymicrobial sepsis in neonatal mice by enhancing neutrophil recruitment. To understand the response of human neonatal neutrophils to TLR4 stimulation, ex vivo spontaneous neutrophil migration, neutrophil transcriptomics, and cytokine production in the presence and absence of LPS were measured directly from whole blood of adults, term neonates, and preterm neonates. Spontaneous neutrophil migration was measured on novel microfluidic devices with time-lapse imaging for 10 h. Genome-wide neutrophil transcriptomics and plasma cytokine concentrations were also determined. Preterm neonates had significantly fewer spontaneously migrating neutrophils at baseline, and both term and preterm neonates had decreased neutrophil velocity, compared to adults. In the presence of LPS stimulation, the number of spontaneously migrating neutrophils was reduced in preterm neonates compared to term neonates and adults. Neutrophil velocity was not significantly different among groups with LPS stimulation. Preterm neonates upregulated expression of genes associated with the recruitment and response of neutrophils following LPS stimulation, but failed to upregulate the expression of genes associated with antimicrobial and antiviral responses. Plasma levels of IL-1β, IL-6, IL-8, MIP-1α, and TNF-α increased in response to LPS stimulation in all groups, but IL-10 was increased only in term and preterm neonates. In conclusion, age-specific changes in spontaneous neutrophil migration counts are not affected by LPS despite changes in gene expression and cytokine production.

KEY MESSAGES:

Preterm neonates have reduced spontaneous neutrophil migration compared to term neonates and adults in the absence and presence of TLR4 stimulation. Preterm and term neonates have reduced neutrophil velocities compared to adults in the absence of TLR4 stimulation but no difference in the presence of TLR4 stimulation. Unique transcriptomic response to TLR4 stimulation is observed in neutrophils from preterm neonates, term neonates, and adults. TLR4 stimulation produces an age-specific cytokine response.

 
 

Chemosphere. 2018 Apr;197:627-633. doi: 10.1016/j.chemosphere.2018.01.062. Epub 2018 Jan 16.

Activated carbon as a means of limiting bioaccumulation of organochlorine pesticides, triclosan, triclocarban, and fipronil from sediments rich in organic matter.

Author information

1
Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA; Department of Veterinary Diagnostic Production and Animal Medicine, Iowa State University, Ames, IA 50010, USA. Electronic address: vdang@iastate.edu.
2
Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA.
3
Biodesign Center for Environmental Health Engineering, The Biodesign Institute and School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA; Indian Health Services, Department of Health and Human Services, Seattle, WA 98121, USA.
4
Biodesign Center for Environmental Health Engineering, The Biodesign Institute and School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA.

Abstract

Addition of activated carbon to contaminated sediment is an established means of remediation but its applicability to sediments high in organic carbon is presently unknown. We evaluated the effects of adding either granular activated carbon (GAC) or pelletized fine-grained activated carbon (PfAC, containing ∼ 50% AC) to contaminated sediments from Lake Apopka featuring a very high total organic carbon content (∼39% w/w dry). Sediments showing background levels of legacy pesticides were spiked with a mixture of 5 chemicals (p,p’-DDE, dieldrin, triclosan, triclocarban, and fipronil) to a nominal concentration of 2 μg/g sediment for each chemical. Following incubation of spiked sediments with the addition of activated carbon for 30 days, we assessed the success on limiting bioaccumulation using Lumbriculus variegatus (blackworm). In contaminant-spiked sediments amended with PfAC, blackworm body burdens of triclosan, triclocarban, and fipronil decreased by >50% and those of p,p’-DDE and dieldrin decreased by <30%. GAC addition to spiked sediments was less impactful, and yielded notable benefits in worm body burden reduction only for fipronil (40%). Fipronil achieved high treatment efficiency within the 30 day amendment with both GAC and PfAC. This is the first study to examine AC treatment in artificially contaminated sediments intrinsically very rich in organic matter content. PfAC exhibited superior performance over GAC for mitigating the uptake of certain organochlorines by aquatic organisms. These results indicate that further studies focusing on additional types of sediments and a broader spectrum of hydrophobic pollutants are warranted.
 
 

J Cell Biochem. 2018 Jan;119(1):599-606. doi: 10.1002/jcb.26219. Epub 2017 Sep 11.

Hydrogen Peroxide Stimulates Exosomal Cathepsin B Regulation of the Receptor for Advanced Glycation End-Products (RAGE).

Author information

1
College of Nursing, Biobehavioral Healthscience Division & College of Medicine, Department of Medicine Division of Translational & Regenerative Medicine, The University of Arizona, Tucson, Arizona.
2
Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida.
3
Department of Physiology and Functional Genomics and Department of Medicine Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida College of Medicine, Gainesville, Florida.

Abstract

Exosomes are nano-sized vesicles that are secreted into the extracellular environment. These vesicles contain various biological effector molecules that can regulate intracellular signaling pathways in recipient cells. The aim of this study was to examine a correlation between exosomal cathepsin B activity and the receptor for advanced glycation end-products (RAGE). Type 1 alveolar epithelial (R3/1) cells were treated with or without hydrogen peroxide and exosomes isolated from the cell conditioned media were characterized by NanoSight analysis. Lipidomic and proteomic analysis showed exosomes released from R3/1 cells exposed to oxidative stress induced by hydrogen peroxide or vehicle differ in their lipid and protein content, respectively. Cathepsin B activity was detected in exosomes isolated from hydrogen peroxide treated cells. The mRNA and protein expression of RAGE increased in cultured R3/1 cells treated with exosomes containing active cathepsin B while depletion of exosomal cathepsin B attenuated RAGE mRNA and protein expression. These results suggest exosomal cathepsin B regulates RAGE in type 1 alveolar cells under conditions of oxidative stress. J. Cell. Biochem. 119: 599-606, 2018.
 
 

Sci Rep. 2016 Aug 11;6:31469. doi: 10.1038/srep31469.

A Comparative Analysis of Sonic Defences in Bombycoidea Caterpillars.

Author information

1
Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada.
2
Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA.

Abstract

Caterpillars have long been used as models for studying animal defence. Their impressive armour, including flamboyant warning colours, poisonous spines, irritating sprays, and mimicry of plant parts, snakes and bird droppings, has been extensively documented. But research has mainly focused on visual and chemical displays. Here we show that some caterpillars also exhibit sonic displays. During simulated attacks, 45% of 38 genera and 33% of 61 species of silk and hawkmoth caterpillars (Bombycoidea) produced sounds. Sonic caterpillars are found in many distantly-related groups of Bombycoidea, and have evolved four distinct sound types- clicks, chirps, whistles and vocalizations. We propose that different sounds convey different messages, with some designed to warn of a chemical defence and others, to startle predators. This research underscores the importance of exploring acoustic communication in juvenile insects, and provides a model system to explore how different signals have evolved to frighten, warn or even trick predators.
 
 

J Am Chem Soc. 2017 Jul 12;139(27):9128-9131. doi: 10.1021/jacs.7b04547. Epub 2017 Jun 29.

Circular Bivalent Aptamers Enable in Vivo Stability and Recognition.

Kuai H1Zhao Z1Mo L1Liu H1Hu X1Fu T1Zhang X1Tan W1,2.

Author information

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

Abstract

Aptamers are powerful candidates for molecular imaging and targeted therapy of cancer based on such appealing features as high binding affinity, high specificity, site-specific modification and rapid tumor penetration. However, aptamers are susceptible to plasma exonucleases in vivo. This seriously affects their in vivo applications. To overcome this key limitation, we herein report the design and development of circular bivalent aptamers. Systematic studies reveal that cyclization of aptamers can improve thermal stability, nuclease resistance and binding affinity. In vivo fluorescence imaging further validates the efficient accumulation and retention of circular bivalent aptamers in tumors compared to “mono-aptamers”. Therefore, this study provides a simple and efficient strategy to boost in vivo aptamer applications in cancer diagnosis and therapy.
 
 

J Am Chem Soc. 2017 Jul 12;139(27):9104-9107. doi: 10.1021/jacs.7b02865. Epub 2017 Jun 29.

Artificial Base zT as Functional “Element” for Constructing Photoresponsive DNA Nanomolecules.

Wang R1,2Jin C1Zhu X1Zhou L1Xuan W1Liu Y1,2Liu Q1Tan W1,2.

Author information

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

Abstract

In contrast to small molecules, DNA and RNA macromolecules can be accurately formulated with base “elements” abbreviated as A, T, U, C, and G. However, the development of functionally artificial bases can result in the generation of new biomaterials with unique properties and applications. Therefore, we herein report the design and synthesis of a photoresponsive base as a new functional or molecular “element” for constructing DNA nanomolecules. The new base is made by fusion of an azobenzene with a natural T base (zT). zT, a new molecular element, is not only the most size-expanded T analogue but also a photoresponsive base capable of specific self-assembly through hydrogen bonding. Our results showed that stable and selective self-assembly of double-stranded DNAs occurred through zT-A base pairing, but it could still be efficiently dissociated by light irradiation. The photoresponsive DNA bases will provide the versatility required for constructing desired DNA nanomolecules and nanodevices.
 
 

Environ Pollut. 2018 May 24;241:136-147. doi: 10.1016/j.envpol.2018.05.033. [Epub ahead of print]

Response of microbial populations regulating nutrient biogeochemical cycles to oiling of coastal saltmarshes from the Deepwater Horizon oil spill.

Author information

1
Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611-0290, USA. Electronic address: hsbae@ufl.edu.
2
Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611-0290, USA.
3
College of the Coast and Environment, Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
4
School of Plant, Environmental, and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.

Abstract

Microbial communities play vital roles in the biogeochemistry of nutrients in coastal saltmarshes, ultimately controlling water quality, nutrient cycling, and detoxification. We determined the structure of microbial populations inhabiting coastal saltmarsh sediments from northern Barataria Bay, Louisiana, USA to gain insight into impacts on the biogeochemical cycles affected by Macondo oil from the 2010 Deepwater Horizon well blowout two years after the accident. Quantitative PCR directed toward specific functional genes revealed that oiled marshes were greatly diminished in the population sizes of diazotrophs, denitrifiers, nitrate-reducers to ammonia, methanogens, sulfate-reducers and anaerobic aromatic degraders, and harbored elevated numbers of alkane-degraders. Illumina 16S rRNA gene sequencing indicated that oiling greatly changed the structure of the microbial communities, including significant decreases in diversity. Oil-driven changes were also demonstrated in the structure of two functional populations, denitrifying and sulfate reducing prokaryotes, using nirS and dsrB as biomarkers, respectively. Collectively, the results from 16S rRNA and functional genes indicated that oiling not only markedly altered the microbial community structures, but also the sizes and structures of populations involved in (or regulating) a number of important nutrient biogeochemical cycles in the saltmarshes. Alterations such as these are associated with potential deterioration of ecological services, and further studies are necessary to assess the trajectory of recovery of microbial-mediated ecosystem functions over time in oiled saltmarsh sediment.
 
 

Appl Microbiol Biotechnol. 2018 May 25. doi: 10.1007/s00253-018-9089-z. [Epub ahead of print]

Microbiota in insect fungal pathology.

Author information

1
Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA.
2
Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
3
Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA. keyhani@ufl.edu.

Abstract

Significant progress has been made in the biochemical and genetic characterization of the host-pathogen interaction mediated by insect pathogenic fungi, with the most widely studied being the Ascomycetes (Hypocrealean) fungi, Metarhizium robertsii and Beauveria bassiana. However, few studies have examined the consequences and effects of host (insect) microbes, whether compatible or antagonistic, on the development and survival of entomopathogenic fungi. Host microbes can act on the insect cuticular surface, within the gut, in specialized insect microbe hosting structures, and within cells, and they include a wide array of facultative and/or obligate exosymbionts and endosymbionts. The insect microbiome differs across developmental stages and in response to nutrition (e.g., different plant hosts for herbivores) and environmental conditions, including exposure to chemical insecticides. Here, we review recent advances indicating that insect-pathogenic fungi have evolved a spectrum of strategies for exploiting or suppressing host microbes, including the production of antimicrobial compounds that are expressed at discrete stages of the infection process. Conversely, there is increasing evidence that some insects have acquired microbes that may be specialized in the production of antifungal compounds to combat infection by (entomopathogenic) fungi. Consideration of the insect microbiome in fungal insect pathology represents a new frontier that can help explain previously obscure ecological and pathological aspects of the biology of entomopathogenic fungi. Such information may lead to novel approaches to improving the efficacy of these organisms in pest control efforts.
 
 

Appl Environ Microbiol. 2018 May 25. pii: AEM.01086-18. doi: 10.1128/AEM.01086-18. [Epub ahead of print]

The Bbgas3 β-glucanosyltransferase contributes to fungal adaptation to extreme alkaline pH.

Luo Z1,2Zhang T3,2Liu P3,2Bai Y3,2Chen Q3,2Zhang Y3,2Keyhani NO4.

Author information

1
Academy of Agricultural Sciences, Southwest University, Chongqing 400716, P. R. China luozb1@163.com.
2
Biotechnology Research Center, Southwest University, Chongqing 400716, P. R. China.
3
Academy of Agricultural Sciences, Southwest University, Chongqing 400716, P. R. China.
4
Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA keyhani@ufl.edu.

Abstract

Fungal β-1,3-glucanosyltransferases are cell wall remodeling enzymes implicated in stress response, cell wall integrity, and virulence, with most fungal genomes containing multiple members. The insect pathogenic fungus Beauveria bassiana displays robust growth over a wide pH range (pH = 4-10). Random insertion mutant library screening for increased sensitivity to alkaline (pH 10) growth conditions resulted in the identification and mapping of a mutant to a β-1,3-glucanosyltransferase gene (Bbgas3). Bbgas3 expression was pH dependent and regulated by the PacC transcription factor, that activates genes in response to neutral/alkaline growth conditions. Targeted gene-knockout of Bbgas3resulted in reduced growth under alkaline conditions, with only minor effects of increased sensitivity to cell wall stress (Congo Red and calcofluor white), and no significant effects on fungal sensitivity to oxidative or osmotic stress. The cell walls of ΔBbgas3 aerial conidia were thinner than wild type and complemented strains in response to alkaline conditions, and β-1,3-glucan antibody and lectin staining revealed alterations in cell surface carbohydrate epitopes. The ΔBbgas3 mutant displayed alterations in cell wall chitin and carbohydrate content in response to alkaline pH. Insect bioassays revealed impaired virulence for the ΔBbgas3 mutant depending upon the pH of the media on which the conidia were grown and harvested. Unexpectedly, a decreased lethal time to kill (LT50, i.e. increased virulence) was seen for the mutant using intra-hemocoel injection assays using conidia grown at acidic pH (5.6). These data show that BbGas3 acts as a pH-responsive cell wall remodeling enzyme involved in resistance to extreme pH (>9).Importance Little is known about adaptations required for growth at high (>9) pH. Here, we show that a specific fungal membrane remodelling β-1,3-glucanosyltransferase (Bbgas3), regulated by the pH-responsive PacC transcription factor forms a critical aspect of the ability of the insect pathogenic fungus, Beauveria bassiana to grow at extreme pH. Loss of Bbgas3 resulted in a unique decreased ability to grow at high pH, with little to no effects seen with respect to other stress conditions, i.e. cell wall integrity, osmotic, and oxidative stress. However, pH-dependent alternations in cell wall properties and virulence were noted for the ΔBbgas3 mutant. These data provide a mechanistic insight into the importance of specific cell wall structure required to stabilize the cell at high pH and link it to the PacC/Pal/Rim pH-sensor and regulatory system.
 
 

Fungal Biol. 2018 Jun;122(6):420-429. doi: 10.1016/j.funbio.2017.07.003. Epub 2017 Jul 19.

Lipid biology in fungal stress and virulence: Entomopathogenic fungi.

Author information

1
Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA. Electronic address: keyhani@ufl.edu.

Abstract

Broad host range insect pathogenic fungi penetrate through the host cuticle, necessitating an ability to confront and overcome surface lipids and other molecules that often include antimicrobial compounds. In this context, induction of lipid assimilatory pathways by exogenous substrates is crucial for successful infection to occur, and lipid growth substrates can have significant effects on the virulence of fungal infectious propagules, e.g. conidia. The production of lipases is a critical part of the cuticle-degrading repertoire and pathways involved in triglyceride metabolism and phospholipid homeostasis have been shown to contribute to host invasion. Mobilization of endogenous lipid stores via the activities of the caleosin and perilipin lipid storage-turnover proteins, have been linked to diverse processes including formation of penetration structures, e.g. germ tubes and appressoria, spore properties and dispersal, and the ability to respond to lipid growth substrates and virulence. Here, we summarize recent advances in our understanding of lipid assimilation and mobilization pathways in the ability of entomogenous fungi to infect and use host substrates. Host surface and internal lipids can alternatively act as antifungal barriers, inducers of pathogenesis-related pathways, and/or as fungal growth substrates. Lipids and lipid assimilation can be considered as forming a co-evolutionary web between the insect host and entomogenous fungi.
 
 

Surgery. 2018 May 25. pii: S0039-6060(18)30160-0. doi: 10.1016/j.surg.2018.04.011. [Epub ahead of print]

Persistent inflammation, immunosuppression, and catabolism and the development of chronic critical illness after surgery.

Author information

1
Department of Surgery, University of Florida College of Medicine, Gainesville. Electronic address: philip.efron@surgery.ufl.edu.
2
Department of Surgery, University of Florida College of Medicine, Gainesville.
3
Department of Medicine, University of Florida College of Medicine, Gainesville.
4
Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville.
5
Institute on Aging and the Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainseville.

Abstract

As early as the 1990s, chronic critical illness, a distinct syndrome of persistent high-acuity illness requiring management in the ICU, was reported under a variety of descriptive terms including the “neuropathy of critical illness,” “myopathy of critical illness,” “ICU-acquired weakness,” and most recently “post-intensive care unit syndrome.” The widespread implementation of targeted shock resuscitation, improved organ support modalities, and evidence-based protocolized ICU care has resulted in significantly decreased in-hospital mortality within surgical ICUs, specifically by reducing early multiple organ failure deaths. However, a new phenotype of multiple organ failure has now emerged with persistent but manageable organ dysfunction, high resource utilization, and discharge to prolonged care facilities. This new multiple organ failure phenotype is now clinically associated with the rapidly increasing incidence of chronic critical illness in critically ill surgery patients. Although the underlying pathophysiology driving chronic critical illness remains incompletely described, the persistent inflammation, immunosuppression, and catabolism syndrome has been proposed as a mechanistic framework in which to explain the increased incidence of chronic critical illness in surgical ICUs. The purpose of this review is to provide a historic perspective of the epidemiologic evolution of multiple organ failure into persistent inflammation, immunosuppression, and catabolism syndrome; describe the mechanism that drives and sustains chronic critical illness, and review the long-term outcomes of surgical patients who develop chronic critical illness.
 
 

Am J Epidemiol. 2018 Jun 1;187(6):1231-1239. doi: 10.1093/aje/kwx368.

Telomere Length and Magnetic Resonance Imaging Findings of Vascular Brain Injury and Central Brain Atrophy: The Strong Heart Study.

Author information

1
Initiative for Research and Education to Advance Community Health, Elson S. Floyd College of Medicine, Washington State University, Seattle, Washington.
2
Department of Radiology, School of Medicine, University of Washington, Seattle, Washington.
3
Texas Biomedical Research Institute, San Antonio, Texas.
4
Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida.
5
Department of Neurology, School of Medicine, University of Washington, Seattle, Washington.
6
Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington.

Abstract

Telomeres are repeating regions of DNA that cap chromosomes. They shorten over the mammalian life span, especially in the presence of oxidative stress and inflammation. Telomeres may play a direct role in cell senescence, serving as markers of premature vascular aging. Leukocyte telomere length (LTL) may be associated with premature vascular brain injury and cerebral atrophy. However, reports have been inconsistent, especially among minority populations with a heavy burden of illness related to vascular aging. We examined associations between LTL and magnetic resonance imaging in 363 American Indians aged 64-93 years from the Strong Heart Study (1989-1991) and its ancillary study, Cerebrovascular Disease and Its Consequences in American Indians (2010-2013). Our results showed significant associations of LTL with ventricular enlargement and the presence of white matter hyperintensities. Secondary models indicated that renal function may mediate these associations, although small case numbers limited inference. Hypertension and diabetes showed little evidence of effect modification. Results were most extreme among participants who evinced the largest decline in LTL. Although this study was limited to cross-sectional comparisons, it represents (to our knowledge) the first consideration of associations between telomere length and brain aging in American Indians. Findings suggest a relationship between vascular aging by cell senescence and severity of brain disease.
 
 

J Anim Sci. 2018 Jun 1. doi: 10.1093/jas/sky224. [Epub ahead of print]

Thermoregulatory Response of Brangus Heifers to Naturally Occurring Heat Exposure on Pasture.

Author information

1
Department of Animal Sciences, University of Florida, Gainesville, FL, USA.

Abstract

Heat stress is a cause of major economic losses to cattle producers, especially in tropical and subtropical environments. The objectives of this study were to assess the phenotypic variability in core body temperature and sweating rate and to evaluate the effect of coat type, temperament, and body weight on core body temperature and sweating rate in Brangus heifers. During August and September of 2016, 725 Brangus heifers on pasture were evaluated in four separate groups (n = 200, 189, 197, and 139). Environmental measurements of dry bulb temperature (Tdb) and relative humidity (RH) were measured every 15 min during the entire time of data collection and the temperature-humidity index (THI) was used to quantify heat stress potential. Coat score, sweating rate, chute score, exit score, and live weight were recorded as the animals passed through the chute. Vaginal temperature was recorded every 5 minutes for 5 consecutive days. There was significant variation in vaginal temperature between heifers in the same environmental conditions (σ2u = 0.049), suggesting opportunities for selective improvements. A repeatability of 0.47 and 0.44 was estimated for sweating rate and vaginal temperature, respectively, suggesting that one measurement would be able to adequately describe the sweating capacity or ability to control the body temperature of an individual.Vaginal temperature increased as THI increased, with approximately one hour lag time in the animal’s response. Vaginal temperature (-0.047°C, P = 0.015) and sweating rate were lower (-5.49 ± 2.12 g/(m 2·h), P < 0.01) for heifers that demonstrated a calmer behavior in the chute. Animals with shorter, smoother hair coats had significantly lower vaginal temperatures when compared to animals with longer hair coats (P < 0.01). Also, heavier heifers in this study maintained lower (P < 0.0001) vaginal temperature than the lighter heifers. Our results showed that hair coat, temperament, and weight influenced vaginal temperature regulation.
 
 

J Dairy Sci. 2017 Jul;100(7):5729-5745. doi: 10.3168/jds.2016-11979. Epub 2017 Apr 27.

Comparison between an exclusive in vitro-produced embryo transfer system and artificial insemination for genetic, technical, and financial herd performance.

Author information

1
Department of Animal Sciences, University of Florida, Gainesville 32611.
2
Department of Animal Sciences, University of Florida, Gainesville 32611. Electronic address: devries@ufl.edu.

Abstract

The objective of this study was to implement an in vitro-produced embryo transfer (IVP-ET) system in an existing stochastic dynamic dairy simulation model with multitrait genetics to evaluate the genetic, technical, and financial performance of a dairy herd implementing an exclusive IVP-ET or artificial insemination (AI) system. In the AI system, sexed semen was used on the genetically best heifers only. In the IVP-ET system, all of the animals in the herd were impregnated with female sexed embryos created through in vitro fertilization of oocytes collected from animals of superior genetics for different traits of interest. Each donor was assumed to yield on average 4.25 transferable embryos per collection. The remaining animals in the herd were used as recipients and received either a fresh embryo or a frozen embryo when fresh embryos were not available. Selection of donors was random or based on the greatest estimated breeding value (EBV) of lifetime net merit (NM$), milk yield, or daughter pregnancy rate. For both the IVP-ET and AI systems, culling of surplus heifer calves not needed to replace culled cows was based on the lowest EBV for the same traits. A herd of 1,000 milking cows was simulated 15 yr over time after the start of the IVP-ET system. The default cost to produce and transfer 1 embryo was set at $165. Prices of fresh embryos at which an exclusive IVP-ET system financially breaks even with the comparable AI system in yr 15 and for an investment period of 15 yr were also estimated. More surplus heifer calves were sold from the IVP-ET systems than from the comparable AI systems. The surplus calves from the IVP-ET systems were also genetically superior to the surplus calves from the comparable AI systems, which might be reflected in their market value as a premium price. The most profitable scenario among the 4 IVP-ET scenarios in yr 15 was the one in which NM$ was maximized in the herd. This scenario had an additional profit of $8/cow compared with a similar AI scenario that maximized NM$, provided that surplus heifer calves could be sold at a premium price based on the superiority of the EBV of NM$. For the IVP-ET system to be at least as profitable as the comparable AI system during a 15-yr investment period, the surplus calves from the IVP-ET system needed to be sold at the premium prices. The break-even price of fresh embryos was estimated to be $84 for the exclusive IVP-ET system. This resulted in the same profit as the AI system, which maximized NM$ for a 15-yr investment period and in which heifer calves were sold at a premium price.
 
 

Mol Biol Evol. 2018 May 31. doi: 10.1093/molbev/msy112. [Epub ahead of print]

Comparative genomics reveals a burst of homoplasy-free numt insertions.

Author information

1
Department of Biology, University of Florida, Gainesville, FL 32611, USA.
2
Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
3
Forestry Research Institute of Hainan Province, Haikou 571100, Hainan, P. R. China.
4
Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093-0359.

Abstract

Mitochondrial DNA sequences are frequently transferred into the nuclear genome, giving rise to numts (nuclear mitochondrial DNA segments). In the absence of whole genomes, avian numts have been suggested to be rare and relatively short. We examined 64 bird genomes to test hypotheses regarding numt frequency, distribution among taxa, and likelihood of homoplasy. We discovered 100-fold variation in numt number across species. Two songbirds, Geospiza fortis (Darwin’s finch) and Zonotrichia albicollis (white-throated sparrow) had the largest number of numts. Ancestral state reconstruction of 957 numt insertions in these two species and their close relatives indicated a remarkable acceleration of numt insertion in the ancestor of Geospiza and Zonotrichia followed by slower, continued accumulation in each lineage. These numts appear to result primarily from de novo insertion with the duplication of existing numts representing a secondary pathway. Insertion events were essentially homoplasy-free and numts appear to represent perfect rare genomic changes.
 
 

PLoS Negl Trop Dis. 2018 May 31;12(5):e0006505. doi: 10.1371/journal.pntd.0006505. [Epub ahead of print]

Detection and phylogenetic characterization of arbovirus dual-infections among persons during a chikungunya fever outbreak, Haiti 2014.

Author information

1
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America.
2
Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America.
3
Department of Pathology, College of Medicine, University of Florida, Gainesville, Florida, United States of America.
4
Department of Health Services Research, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America.
5
Christianville Foundation School Clinic, Gressier, Haiti.
6
Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, United States of America.

Abstract

In the context of recent arbovirus epidemics, questions about the frequency of simultaneous infection of patients with different arbovirus species have been raised. In 2014, a major Chikungunya virus (CHIKV) epidemic impacted the Caribbean and South America. As part of ongoing screening of schoolchildren presenting with acute undifferentiated febrile illness in rural Haiti, we used RT-PCR to identify CHIKV infections in 82 of 100 children with this diagnosis during May-August 2014. Among these, eight were infected with a second arbovirus: six with Zika virus (ZIKV), one with Dengue virus serotype 2, and one with Mayaro virus (MAYV). These dual infections were only detected following culture of the specimen, suggesting low viral loads of the co-infecting species. Phylogenetic analyses indicated that the ZIKV and MAYV strains differ from those detected later in 2014 and 2015, respectively. Moreover, CHIKV and ZIKV strains from co-infected patients clustered monophyletically in their respective phylogeny, and clock calibration traced back the common ancestor of each clade to an overlapping timeframe of introduction of these arboviruses onto the island.
 
 

Nucleic Acids Res. 2018 May 26. doi: 10.1093/nar/gky369. [Epub ahead of print]

Identification of conserved, primary sequence motifs that direct retrovirus RNA fate.

Author information

1
Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA.
2
Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA.

Abstract

Precise stoichiometry of genome-length transcripts and alternatively spliced mRNAs is a hallmark of retroviruses. We discovered short, guanosine and adenosine sequence motifs in the 5’untranslated region of several retroviruses and ascertained the reasons for their conservation using a representative lentivirus and genetically simpler retrovirus. We conducted site-directed mutagenesis of the GA-motifs in HIV molecular clones and observed steep replication delays in T-cells. Quantitative RNA analyses demonstrate the GA-motifs are necessary to retain unspliced viral transcripts from alternative splicing. Mutagenesis of the GA-motifs in a C-type retrovirus validate the similar downregulation of unspliced transcripts and virion structural protein. The evidence from cell-based co-precipitation studies shows the GA-motifs in the 5’untranslated region confer binding by SFPQ/PSF, a protein co-regulated with T-cell activation. Diminished SFPQ/PSF or mutation of either GA-motif attenuates the replication of HIV. The interaction of SFPQ/PSF with both GA-motifs is crucial for maintaining the stoichiometry of the viral transcripts and does not affect packaging of HIV RNA. Our results demonstrate the conserved GA-motifs direct the fate of retrovirus RNA. These findings have exposed an RNA-based molecular target to attenuate retrovirus replication.
 
 

J Dairy Sci. 2017 Jul;100(7):5805-5823. doi: 10.3168/jds.2016-12506. Epub 2017 May 10.

Use of calcitriol to maintain postpartum blood calcium and improve immune function in dairy cows.

Author information

1
Department of Animal Sciences, University of Florida, Gainesville 32611; DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32611.
2
Department of Animal Sciences, University of Florida, Gainesville 32611.
3
DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32611; Department of Large Animal Clinical Sciences, University of Florida, Gainesville 32611.
4
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

Our objectives were to determine the effects of an injectable formulation of calcitriol on mineral metabolism and immune function in postpartum Holstein cows that received an acidogenic diet prepartum to minimize hypocalcemia. In experiment 1, cows within 6 h of calving received calcitriol (0, 200, or 300 μg) to determine the dose needed to increase plasma concentrations of Ca; 300 μg was sufficient to sustain Ca for at least 3 d. In experiment 2, multiparous cows were assigned randomly to receive only vehicle (control, n = 25) or 300 μg of calcitriol (n = 25) subcutaneously within the first 6 h after calving. Blood was sampled before treatment and 12 h later, then daily until 15 d in milk (DIM), and analyzed for concentrations of ionized Ca (iCa), total Ca (tCa), total Mg (tMg), and total P (tP), metabolites, and hormones. Urine was sampled in the first 7 DIM and analyzed for concentrations of tCa, tMg, and creatinine. Neutrophil function was evaluated in the first week postpartum. Dry matter intake and production performance were evaluated for the first 36 DIM. Calcitriol administration increased concentrations of calcitriol in plasma within 12 h of application from 51 to 427 pg/mL, which returned to baseline within 5 d. Concentrations of iCa and tCa increased 24 h after treatment with calcitriol. Concentrations of iCa (control = 1.08 vs. calcitriol = 1.20 mM), tCa (control = 2.23 vs. calcitriol = 2.33 mM), and tP (control = 1.47 vs. calcitriol = 1.81 mM) remained elevated in cows treated with calcitriol until 3, 5, and 7 DIM, respectively, whereas concentration of tMg (control = 0.76 vs. calcitriol = 0.67 mM) was less in calcitriol cows than control cows until 3 DIM. Concentrations of parathyroid hormone decreased in calcitriol cows compared with control cows (control = 441 vs. calcitriol = 336 pg/mL). Calcitriol tended to increase plasma concentrations of β-hydroxybutyrate and serotonin, but concentrations of glucose, nonesterified fatty acids, and C-telopeptide of type I collagen in plasma did not differ between treatments. Cows treated with calcitriol excreted more urinary tCa (control = 0.5 vs. calcitriol = 2.1 g/d) and tMg (control = 4.5 vs. calcitriol = 5.0 g/d) in the first 7 and 2 DIM, respectively, than control cows. Compared with control, calcitriol improved the proportion of neutrophils with oxidative burst (control = 31.9 vs. calcitriol = 40.6%), mean fluorescence intensity for oxidative burst (control = 90,900 vs. calcitriol = 99,746), and mean fluorescence intensity for phagocytosis (control = 23,887 vs. calcitriol = 28,080). Dry matter intake, yields of milk, and milk components did not differ between treatments. Administration of 300 μg of calcitriol at calving was safe and effective in increasing blood concentration of iCa and plasma concentrations of calcitriol, tCa, and tP for the first 6 d after treatment, and improved measures of innate immune function in early-lactation Holstein cows.
 
 

Diabetes. 2018 Apr;67(4):769-781. doi: 10.2337/db17-1034. Epub 2018 Jan 23.

ELOVL4-Mediated Production of Very Long-Chain Ceramides Stabilizes Tight Junctions and Prevents Diabetes-Induced Retinal Vascular Permeability.

Author information

1
Department of Physiology, Michigan State University, East Lansing, MI.
2
Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI.
3
Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI.
4
Ophthalmology and Molecular Genetics and Retina Gene Therapy Group, University of Florida, Gainesville, FL.
5
Department of Physiology, Michigan State University, East Lansing, MI busik@msu.edu.

Abstract

Tight junctions (TJs) involve close apposition of transmembrane proteins between cells. Although TJ proteins have been studied in detail, the role of lipids is largely unknown. We addressed the role of very long-chain (VLC ≥26) ceramides in TJs using diabetes-induced loss of the blood-retinal barrier as a model. VLC fatty acids that incorporate into VLC ceramides are produced by elongase elongation of very long-chain fatty acids protein 4 (ELOVL4). ELOVL4 is significantly reduced in the diabetic retina. Overexpression of ELOVL4 significantly decreased basal permeability, inhibited vascular endothelial growth factor (VEGF)- and interleukin-1β-induced permeability, and prevented VEGF-induced decrease in occludin expression and border staining of TJ proteins ZO-1 and claudin-5. Intravitreal delivery of AAV2-hELOVL4 reduced diabetes-induced increase in vascular permeability. Ultrastructure and lipidomic analysis revealed that ω-linked acyl-VLC ceramides colocalize with TJ complexes. Overall, normalization of retinal ELOVL4 expression could prevent blood-retinal barrier dysregulation in diabetic retinopathy through an increase in VLC ceramides and stabilization of TJs.
 
 

Neurosci Res. 2018 May 29. pii: S0168-0102(18)30084-1. doi: 10.1016/j.neures.2018.05.006. [Epub ahead of print]

In utero electroporation-based translating ribosome affinity purification identifies age-dependent mRNA expression in cortical pyramidal neurons.

Author information

1
Department of Neurosurgery, Xiangya Hospital, Central South University, 85 Xiangya Street, Changsha, 410008, China; Departments of Neurosurgery, and Cellular & Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8082, USA.
2
Departments of Neurosurgery, and Cellular & Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8082, USA.
3
Board of Governors Regenerative Medicine Institute, Center for Neural Science and Medicine, and Department of Biomedical Science Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
4
Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
5
Board of Governors Regenerative Medicine Institute, Center for Neural Science and Medicine, and Department of Biomedical Science Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA; Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
6
Department of Neurosurgery, Xiangya Hospital, Central South University, 85 Xiangya Street, Changsha, 410008, China; Departments of Neurosurgery, and Cellular & Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8082, USA. Electronic address: angelique.bordey@yale.edu.

Abstract

We combined translating ribosome affinity purification (TRAP) with in utero electroporation (IUE), called iTRAP to identify the molecular profile of specific neuronal populations during neonatal development without the need for viral approaches and FACS sorting. We electroporated a plasmid encoding EGFP-tagged ribosomal protein L10a at embryonic day (E) 14-15 to target layer 2-4 cortical neurons of the somatosensory cortex. At three postnatal (P) ages-P0, P7, and P14-when morphogenesis occurs and synapses are forming, TRAP and molecular profiling was performed from electroporated regions. We found that ribosome bound (Ribo)-mRNAs from ∼7,300 genes were significantly altered over time and included classical neuronal genes known to decrease (e.g., Tbr1, Dcx) or increase (e.g., Eno2, Camk2a, Syn1) as neurons mature. This approach led to the identification of specific developmental patterns for Ribo-mRNAs not previously reported to be developmentally regulated in neurons, providing rationale for future examination of their role in selective biological processes. These include upregulation of Lynx1, Nrn1, Cntnap1 over time; downregulation of St8sia2 and Draxin; and bidirectional changes to Fkbp1b. iTRAP is a versatile approach that allows researchers to easily assess the molecular profile of specific neuronal populations in selective brain regions under various conditions, including overexpression and knockdown of target genes, and in disease settings.
 
 

Antimicrob Agents Chemother. 2017 Sep 22;61(10). pii: e01104-17. doi: 10.1128/AAC.01104-17. Print 2017 Oct.

Antibacterial Resistance in Ureaplasma Species and Mycoplasma hominis Isolates from Urine Cultures in College-Aged Females.

Author information

1
Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA.
2
Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA mbbrown@ufl.edu.
3
Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA.

Abstract

Urinary tract infections (UTIs) affect nearly 20% of women age 15 to 29 and account for an estimated $3.5 billion in costs. Antibiotic resistance prolongs UTI treatment, and resistance profiles vary regionally. This regional variation is an important consideration in guiding empirical treatment selection. Regional studies in the United States have identified tetracycline resistance in over one-third of Ureaplasmaspecies isolates, but no studies have evaluated antibiotic resistance levels in college-aged women with a first-time UTI. We tested a panel of antibiotics and determined the MICs of Ureaplasma species (60 U. parvum and 13 U. urealyticum) and 10 Mycoplasma hominis isolates obtained from urine from college-aged women with a first-time UTI. Low antibiotic resistance was found in this population of women with a first-time UTI. All M. hominis and U. urealyticum isolates were sensitive. However, two U. parvum isolates were resistant, with one to levofloxacin (MIC, 4 μg/ml) and one to tetracycline (MIC, 8 μg/ml). For the Ureaplasma spp., the MIC90s were highest against gentamicin (21 μg/ml) and lowest against doxycycline (0.25 μg/ml). In a comparison of MIC levels between Ureaplasma spp., U. urealyticum had significantly higher MICs against each antibiotic except doxycycline. For the resistant isolates, the genetic mechanisms of resistance were determined. PCR amplification identified tetM to be present in the tetracycline-resistant isolate and an S83W mutation within the parC gene of the quinolone-resistant isolate. To our knowledge, this study is the first to provide molecular and phenotypic evidence of the S83W parC mutation conferring levofloxacin resistance in U. parvum isolated from a patient in the United States.
 
 

Bioresour Technol. 2018 May;256:312-320. doi: 10.1016/j.biortech.2018.01.123. Epub 2018 Feb 10.

Largely enhanced bioethanol production through the combined use of lignin-modified sugarcane and xylose fermenting yeast strain.

Author information

1
Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.
2
Center for Natural Products Convergence Research, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea.
3
Agronomy Department, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, IFAS, PO Box 110300, Gainesville, FL 32611, USA.
4
Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea.
5
McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA.
6
Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
7
Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, Daejeon 34113, Republic of Korea. Electronic address: smlee@kist.re.kr.

Abstract

The recalcitrant structure of lignocellulosic biomass is a major barrier in efficient biomass-to-ethanol bioconversion processes. The combination of feedstock engineering via modification in the lignin synthesis pathway of sugarcane and co-fermentation of xylose and glucose with a recombinant xylose utilizing yeast strain produced 148% more ethanol compared to that of the wild type biomass and control strain. The lignin reduced biomass led to a substantially increased release of fermentable sugars (glucose and xylose). The engineered yeast strain efficiently co-utilized glucose and xylose for fermentation, elevating ethanol yields. In this study, it was experimentally demonstrated that the combined efforts of engineering both feedstock and microorganisms largely enhances the bioconversion of lignocellulosic feedstock to bioethanol. This strategy will significantly improve the economic feasibility of lignocellulosic biofuels production.

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