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Identifying the minimum amplicon sequence depth to adequately predict classes in eDNA-based marine biomonitoring using supervised machine learning. Comput Struct Biotechnol J 2021; 19:2256-2268. [PMID: 33995917 PMCID: PMC8093828 DOI: 10.1016/j.csbj.2021.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 01/04/2023] Open
Abstract
Environmental DNA metabarcoding is a powerful approach for use in biomonitoring and impact assessments. Amplicon-based eDNA sequence data are characteristically highly divergent in sequencing depth (total reads per sample) as influenced inter alia by the number of samples simultaneously analyzed per sequencing run. The random forest (RF) machine learning algorithm has been successfully employed to accurately classify unknown samples into monitoring categories. To employ RF to eDNA data, and avoid sequencing-depth artifacts, sequence data across samples are normalized using rarefaction, a process that inherently loses information. The aim of this study was to inform future sampling designs in terms of the relationship between sampling depth and RF accuracy. We analyzed three published and one new bacterial amplicon datasets, using a RF, based initially on the maximal rarefied data available (minimum mean of > 30,000 reads across all datasets) to give our baseline performance. We then evaluated the RF classification success based on increasingly rarefied datasets. We found that extreme to moderate rarefaction (50-5000 sequences per sample) was sufficient to achieve prediction performance commensurate to the full data, depending on the classification task. We did not find that the number of classification classes, data balance across classes, or the total number of sequences or samples, were associated with predictive accuracy. We identified the ability of the training data to adequately characterize the classes being mapped as the most important criterion and discuss how this finding can inform future sampling design for eDNA based biomonitoring to reduce costs and computation time.
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Key Words
- 16S rRNA
- AMBI, AZTI's marine biotic index
- ASV, Amplicon Sequence Variants
- AZE, allowable zone of effect, intermediate impact zone
- BI, biotic index
- BallWa, ballast water dataset
- BasCo, Basque coast dataset
- Biomonitoring
- CE, cage edge
- CV, Coefficient of Variance
- DADA2, Divisive Amplicon Denoising Algorithm
- EQ, environmental quality
- Environmental DNA
- FM, full model
- MDS, multidimensional scaling
- Machine learning
- Marine
- NEB, New England Biolabs
- NW, north west
- NorSa, Norway salmon dataset
- OOB-error, out-of-bag error estimate
- PCR, polymerase chain reaction
- REF, reference site
- RF, random forest algorithm
- SML, supervised machine learning
- ScoSa, Scottish salmon farm dataset
- V3-V4, hypervariable gene regions of the 16s rRNA
- bp, base pairs
- eDNA, environmental deoxyribonucleic acid
- microgAMBI, AZTI's marine biotic index based on microbial genes
- mtry, numbers of variables tried at each split
- n, number
- rRNA, small subunit prokaryotic ribosomal ribonucleic acid
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Gene interactions observed with the HDL-c blood lipid, intakes of protein, sugar and biotin in relation to circulating homocysteine concentrations in a group of black South Africans. Mol Genet Metab Rep 2019; 22:100556. [PMID: 31908954 PMCID: PMC6938949 DOI: 10.1016/j.ymgmr.2019.100556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/05/2019] [Accepted: 12/12/2019] [Indexed: 11/18/2022] Open
Abstract
Background Elevated homocysteine (Hcy) is associated with several pathologies. Gene–diet interactions related to Hcy might be used to customize dietary advice to reduce disease incidence. To explore this possibility, we investigated interactions between anthropometry, biochemical markers and diet and single-nucleotide polymorphisms (SNPs) in relation to Hcy concentrations. Five SNPs of Hcy-metabolizing enzymes were analyzed in 2010 black South Africans. Results Hcy was higher with each additional methylenetetrahydrofolate reductase (MTHFR) C677T minor allele copy, but was lower in methionine synthase (MTR) 2756AA homozygotes than heterozygotes. Individuals harboring cystathionine β synthase (CBS) 833 T/844ins68 had lower Hcy concentrations than others. No interactive effects were observed with any of the anthropometrical markers. MTHFR C677T and CBS T833C/844ins68 homozygote minor allele carriers presented with lower Hcy as high density lipoprotein cholesterol (HDL-c) increased. Hcy concentrations were negatively associated with dietary protein and animal protein intake in the TT and TC genotypes, but positively in the CC genotype of CBS T833C/844ins68. Hcy was markedly higher in TT homozygotes of MTHFR C677T as added sugar intake increased. In CBS T833C/844ins68 major allele carriers, biotin intake was negatively associated with Hcy; but positively in those harboring the homozygous minor allele. Conclusions The Hcy–SNP associations are modulated by diet and open up the possibility of invoking dietary interventions to treat hyperhomocysteinemia. Future intervention trials should further explore the observed gene–diet and gene–blood lipid interactions.
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Key Words
- %TCHO, percentage total carbohydrate intake
- %TE, percentage of total energy
- A, adenine
- Ala, alanine
- Asp, aspartic acid
- Biotin
- Blood lipid–gene interactions
- C, cytosine
- CBS, cystathionine β synthase
- CI, confidence intervals
- CV, coefficient variation
- ES, effect size
- G, guanine
- GGT, gamma glutamyl transferase
- GLM, generalized linear model
- Gene–diet interactions
- Gly, glycine
- HDL-c, high-density lipoprotein cholesterol
- HHcy, hyperhomocysteinemia
- HW, Hardy Weinberg
- HWE, Hardy–Weinberg equilibrium
- HbA1c, glycated hemoglobin
- Hcy, homocysteine
- Hyperhomocysteinemia
- ID, identity
- ISAK, International Society for the Advancement of Kinanthropometry
- Ile, isoleucine
- LD, pairwise linkage-disequilibrium
- LDL-c, low density lipoprotein cholesterol
- MAF, minor allele frequency
- MRC, Medical Research Council
- MT, mutant type
- MTHFR, methylenetetrahydrofolate reductase
- MTR, methionine synthase
- Nutrient–gene interactions
- Nutrigenetics
- PA, physical activity
- PCR, polymerase chain reaction
- PURE, Prospective Urban and Rural Epidemiology
- Precision nutrition
- Protein
- QFFQ, quantitative food frequency questionnaire
- RFLP, restriction fragment length polymorphism
- SD, standard deviations
- SE, standard error
- SFA, saturated fatty acids
- SNP, single-nucleotide polymorphism
- Sugar
- T, thymine
- THUSA, Transition and Health during Urbanization in South Africa
- Thr, threonine
- Total homocysteine
- Val, valine
- WT, wild type.
- bp, base pairs
- d, Cohen's d-value
- ins, insertion
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Identification of novel splice site mutation IVS9 + 1(G > A) and novel complex allele G355R/R359X in Type 1 Gaucher patients heterozygous for mutation N370S. Meta Gene 2016; 9:47-51. [PMID: 27222815 PMCID: PMC4856859 DOI: 10.1016/j.mgene.2016.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/27/2016] [Accepted: 03/17/2016] [Indexed: 11/30/2022] Open
Abstract
Gaucher disease is an autosomal recessive lysosomal storage disorder resulting from deficient glucocerebrosidase activity. More than 350 mutations that cause Gaucher disease have been described to date. Novel mutations can potentially provide insight into the glucocerebrosidase structure–function relationship and biochemical basis of the disease. Here, we report the identification of two novel mutations in two unrelated patients with type I (non-neuronopathic) Gaucher disease: 1) a splice site mutation IVS9 + 1G > A; and (2) a complex allele (cis) G355R/R359X. Both patients have a common N370S mutation in the other allele. The splice site mutation results from an intronic base substitution (G to A, c.1328 + 1, g.5005) at the donor splice site of exon and intron 9. The complex allele results from two point mutations in exon 8 of glucocerebrosidase (G to C at c.1180, g.4396, and T to C at c. 1192, g.4408) substituting glycine by arginine (G355R) and arginine by a premature termination (R359X), respectively. In order to demonstrate that G355R/R359X are in cis arrangement, PCR-amplified glucocerebrosidase exon 8 genomic DNA from the patient was cloned into the vector pJET1.2 in Escherichia coli TOP10® strain. Out of the 15 clones that were sequence analyzed, 10 contained the normal allele sequence and 5 contained the complex allele G355R/R359X sequence showing both mutations in cis arrangement. Restriction fragment length polymorphism analysis using Hph1 restriction endonuclease digest was established for the IVS9 + 1G > A mutation for confirmation and efficient identification of this mutation in future patients. Past literature suggests that mutations affecting splicing patterns of the glucocerebrosidase transcript as well as mutations in Gaucher complex alleles are detrimental to enzyme activity. However, compound heterozygosity with N370S, a mild mutation, will lead to a mild phenotype. The cases reported here support these past findings.
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Key Words
- Complex alleles
- EC, enzyme commission number
- GBA novel mutations
- GBA, glucocerebrosidase enzyme protein
- GBA, glucocerebrosidase gene
- GD, Gaucher disease
- Gaucher disease
- Glucocerebrosidase
- Hb, hemoglobin
- MRI, magnetic resonance imaging
- OMIM, Online Mendelian Inheritance in Man entry number
- PCR, polymerase chain reaction
- RFLP analysis
- RFLP, restriction fragment length polymorphism
- RT-PCR, reverse transcription-PCR
- Sequence analysis
- bp, base pairs
- pJET cloning
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Small Molecule Inhibitors of BAF; A Promising Family of Compounds in HIV-1 Latency Reversal. EBioMedicine 2015; 3:108-121. [PMID: 26870822 PMCID: PMC4739437 DOI: 10.1016/j.ebiom.2015.11.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 11/19/2015] [Accepted: 11/25/2015] [Indexed: 11/23/2022] Open
Abstract
Persistence of latently infected cells in presence of Anti-Retroviral Therapy presents the main obstacle to HIV-1 eradication. Much effort is thus placed on identification of compounds capable of HIV-1 latency reversal in order to render infected cells susceptible to viral cytopathic effects and immune clearance. We identified the BAF chromatin remodeling complex as a key player required for maintenance of HIV-1 latency, highlighting its potential as a molecular target for inhibition in latency reversal. Here, we screened a recently identified panel of small molecule inhibitors of BAF (BAFi's) for potential to activate latent HIV-1. Latency reversal was strongly induced by BAFi's Caffeic Acid Phenethyl Ester and Pyrimethamine, two molecules previously characterized for clinical application. BAFi's reversed HIV-1 latency in cell line based latency models, in two ex vivo infected primary cell models of latency, as well as in HIV-1 infected patient's CD4 + T cells, without inducing T cell proliferation or activation. BAFi-induced HIV-1 latency reversal was synergistically enhanced upon PKC pathway activation and HDAC-inhibition. Therefore BAFi's constitute a promising family of molecules for inclusion in therapeutic combinatorial HIV-1 latency reversal. BAF complex inhibitors (BAFi's) activate latent HIV-1 in cell line models of latency. BAFi's in combination with HDAC inhibitors and PKC activators synergistically activate latent HIV-1. The BAFi's PYR and CAPE reverse HIV-1 latency in primary cell models of latency and in cells obtained from HIV-1 patients.
Access to Combination antiretroviral therapy (cART) has made HIV-1 infection a chronic disease. However, cART is not curative, as a small number of infected cells harboring silent virus with potential to renew the infection persist despite cART. Efforts to cure HIV-1 include activation of these latent cells, making them susceptible to immune clearance. Here we describe the activity of BAF inhibitors in HIV-1 activation in in vitro models of HIV-1 latency as well as in cells obtained from HIV-1 infected patient volunteers. Our data highlight the clinical potential of BAF inhibitors for inclusion in combinatorial therapy to reverse HIV-1 latency.
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Key Words
- BAF complex
- BAF, BRG-Brahma Associated Factors
- BAF250a, BAF Associated Factor 250 a
- BAFi, BAF inhibitor
- BRG-1, Brahma Related Gene 1
- CAPE, caffeic acid phenetyl esther
- ChIP, Chromatin Immunoprecipitation
- Chromatin remodeling
- CycA, Cyclophilin A
- DHS-1, DNase Hypersensitive Site 1
- ES cells, embryonic stem cells
- FAIRE, Formaldehyde Assisted Isolation of Regulatory Elements
- FBS, Fetal Bovine Serum
- GFP, Green Fluorescent Protein
- HDAC, histone deacetylase
- HIV
- HIV-1, human immunodeficiency virus type 1
- IFNß, Interferon beta
- IL10, Interleukin 10
- IL12, Interleukin 12
- IL4, Interleukin 4
- IL6, Interleukin 6
- INI-1, Integrase Interactor 1
- IRES, Internal Ribosome Entry Site
- IκB-α, Inhibitor of NF-κB – alpha
- LRA, latency reversal agent
- LTR, Long Terminal Repeat
- Latency
- MIP26, Major Intrinsic Protein
- MMP9, Matrix Metallopeptidase 9
- NF-κB, Nuclear Factor Kappa-light-chain-enhancer of activated B cells
- PBMC, peripheral blood mononuclear cell
- PBS, Phosphate Buffered Saline
- PKC, Protein Kinase C
- PYR, Pyrimethamine
- RT-qPCR, Reverse Transcriptase, quantitative Polymerase Chain Reaction
- SAHA, Suberoylanilide Hydroxamic Acid
- SD, Standard Deviation
- SOCS3, Suppressor Of Cytokine Signaling 3
- TGF-ß, Transforming Growth Factor beta
- TLR2, Toll-like Receptor 2
- bp, base pairs
- cART, combination Antiretroviral Therapy
- latency reversal agents
- nuc, nucleosome
- siRNA, small interfering RNA
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Soluble form of the ST2 gene product exhibits growth promoting activity in NIH-3T3 cells. Biochem Biophys Rep 2015; 5:8-15. [PMID: 28955802 PMCID: PMC5600422 DOI: 10.1016/j.bbrep.2015.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/10/2015] [Accepted: 11/19/2015] [Indexed: 12/22/2022] Open
Abstract
The ST2 gene is induced in murine fibroblast cells at the start of cell proliferation. Although IL-33 has been identified as a ligand for one of the two major gene products of ST2 – namely, the transmembrane receptor form ST2L – prompting immunological research on inflammation, the roles of the ST2 gene products in cell proliferation remain to be elucidated. Using a cell proliferation assay system with NIH-3T3 cells, a normal murine fibroblast cell line, we found that treatment with recombinant ST2 caused an acceleration of cell proliferation, suggesting that ST2 acts in an autocrine/paracrine fashion. Strikingly, shRNA-induced knockdown of both ST2 gene products, ST2 and ST2L, reduced cell proliferation. This effect was effectively canceled by the expression of shRNA-resistant ST2, but not shRNA-resistant ST2L. The novel enhancement of cell proliferation by ST2 appears to involve positive feedback. Since the ST2 level is increased in various diseases involving inflammation, future investigations into the role of ST2 gene products in relation to various diseases, including malignancies, may be warranted. Soluble ST2 enhanced cell proliferation of NIH-3T3 cells. Reduction of the ST2 gene products highly deteriorated cell growth of NIH-3T3 cells. Cell proliferation was recovered with supplementation of soluble ST2, but not ST2L. Positive feedback system of ST2 on cell proliferation is of great interest.
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Key Words
- Cell proliferation
- DMEM, Dulbecco’s Modified Eagle’s Medium
- EDTA, ethylenediaminetetraacetic acid
- ELISA, enzyme-linked immunosorbent assay
- FBS, fetal bovine serum
- Fibroblast
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- RT-PCR, reverse transcription-polymerase chain reaction
- S.D., standard deviation
- SDS-PAGE, sodium dodecylsulfate-polyacrylamide gel electrophoresis
- ST2 gene
- bp, base pairs
- cDNA, complementary DNA
- shRNA, short hairpin RNA
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Interference of HCV replication by cell penetrable human monoclonal scFv specific to NS5B polymerase. MAbs 2015; 6:1327-39. [PMID: 25517317 DOI: 10.4161/mabs.29978] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A new class of hepatitis C virus (HCV)-targeted therapeutics that is safe, broadly effective and can cope with virus mutations is needed. The HCV's NS5B is highly conserved and different from human protein, and thus it is an attractive target for anti-HCV therapeutics development. In this study, NS5B bound-phage clones selected from a human single chain variable antibody fragment (scFv) phage display library were used to transform appropriate E. coli bacteria. Two scFv inhibiting HCV polymerase activity were selected. The scFvs were linked to a cell penetrating peptide to make cell penetrable scFvs. The transbodies reduced the HCV RNA and infectious virus particles released into the culture medium and inside hepatic cells transfected with a heterologous HCV replicon. They also rescued the innate immune response of the transfected cells. Phage mimotope search and homology modeling/molecular docking revealed the NS5B subdomains and residues bound by the scFvs. The scFv mimotopes matched residues of the NS5B, which are important for nucleolin binding during HCV replication, as well as residues that interconnect the fingers and thumb domains for forming a polymerase active groove. Both scFvs docked on several residues at the thumb armadillo-like fold that could be the polymerase interactive sites of other viral/host proteins for the formation of the replication complex and replication initiation. In conclusion, human transbodies that inhibited HCV RdRp activity and HCV replication and restored the host innate immune response were produced. They are potentially future interferon-free anti-HCV candidates, particularly in combination with other cognates that are specific to NS5B epitopes and other HCV enzymes.
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Key Words
- ABTS, 2, 2′-Azino-di(3-ethylbenzthiazoline-6-sulfonate)
- AE, adverse effects
- BCIP/NBT, 5-bromo-4-chloro-3-indolyl phosphate/nitroblue tetrazolium liquid substrate system
- CDR(s), complementarity determining region(s)
- DMEM, Dulbecco's modified Eagle's medium
- DNA, deoxyribonucleic acid
- DTT, dithiothreitol
- E. coli, Escherichia coli
- ELISA, enzyme-linked immunosorbent assay
- FR(s), immunoglobulin framework region(s)
- Fc, fragment crystallizable of immunoglobulin
- HCV, hepatitis C virus
- HRP, horseradish peroxidase
- Hepatitis C
- IFN-α, interferon-alpha
- IPTG, isopropyl β-D-1-thiogalactopyranoside
- IgG, immunoglobulin G
- LDH, lactic dehydrogenase
- NS, non-structural protein
- NS5B polymerase
- NS5BΔ55, recombinant C-terminally 55 amino acid deleted NS5B
- NTPs, nucleotide triphosphates
- Ni-NTA, nickel-nitrilotriacetic acid
- OD, optical density
- PBS, 0.15 molar phosphate-buffered saline, pH 7.4
- PCR, polymerase chain reaction
- PDB, protein data bank
- PEG, pegylated
- RBV, ribavirin
- RFLP, restriction fragment length polymorphism
- RT-PCR, reverse transcription polymerase chain reaction
- RdRp, RNA-dependent RNA polymerase
- SD, standard deviation
- SDS, sodium dodecyl sulfate
- SOC, standard-of-care
- STAT-C, specifically targeted anti-viral therapy for hepatitis C
- SVR, sustained virologic response
- VH, variable heavy chain domain of conventional four-chain IgG
- VHH, variable heavy chain domain of heavy chain antibody
- VL, variable light chain domain
- bp, base pairs
- cDNA, complementary deoxyribonucleic acid
- hepatitis C virus
- human single-chain variable antibody fragments (human scFv)
- kDa, kilo-Daltons
- mM, millimolars
- nM, nanomolars
- nm, nanometers
- pen/PEN, penetratin gene/protein
- phage display
- qPCR, quantitative real-time reverse transcription polymerase chain reaction
- scFv, single-chain variable antibody fragments
- scfv, gene sequence coding for scFv
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Association of the chicken MHC B haplotypes with resistance to avian coronavirus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:430-437. [PMID: 23178407 PMCID: PMC7103219 DOI: 10.1016/j.dci.2012.10.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/18/2012] [Accepted: 10/19/2012] [Indexed: 06/01/2023]
Abstract
Clinical respiratory illness was compared in five homozygous chicken lines, originating from homozygous B2, B8, B12 and B19, and heterozygous B2/B12 birds after infection with either of two strains of the infectious bronchitis virus (IBV). All chickens used in these studies originated from White Leghorn and Ancona linages. IBV Gray strain infection of MHC homozygous B12 and B19 haplotype chicks resulted in severe respiratory disease compared to chicks with B2/B2 and B5/B5 haplotypes. Demonstrating a dominant B2 phenotype, B2/B12 birds were also more resistant to IBV. Respiratory clinical illness in B8/B8 chicks was severe early after infection, while illness resolved similar to the B5 and B2 homozygous birds. Following M41 strain infection, birds with B2/B2 and B8/B8 haplotypes were again more resistant to clinical illness than B19/B19 birds. Real time RT-PCR indicated that infection was cleared more efficiently in trachea, lungs and kidneys of B2/B2 and B8/B8 birds compared with B19/B19 birds. Furthermore, M41 infected B2/B2 and B8/B8 chicks performed better in terms of body weight gain than B19/B19 chicks. These studies suggest that genetics of B defined haplotypes might be exploited to produce chicks resistant to respiratory pathogens or with more effective immune responses.
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Key Words
- ibv, infectious bronchitis virus
- mhc, major histocompatibility complex
- m41, massachusetts 41
- rt-pcr, reverse transcription polymerase chain reaction
- sars, severe acute respiratory syndrome
- rsv, rous sarcoma virus
- mdv, marek’s disease virus
- spf, specific pathogen free
- pi, post infection
- eid50/ml, embryo infectious dose 50 per ml
- niu, northern illinois university
- pbs, phosphate buffer saline
- rna, ribonucleic acid
- 5′ utr, 5′ untranslated region
- bp, base pairs
- anova, analysis of variance
- ark, arkansas
- ctl, cytotoxic t lymphocyte
- aiv, avian influenza virus
- ifnγ, interferon gamma
- poly i:c, polyinosinic polycytidylic acid
- usda, united states department of agriculture
- nifa, national institute of food and agriculture
- infectious bronchitis virus
- chicken mhc b haplotype
- clinical illness
- infection of trachea
- lungs and kidneys
- resistant
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Age dependent forebrain structural changes in mice deficient in the autism associated gene Met tyrosine kinase. Neuroimage Clin 2012; 1:66-74. [PMID: 24179738 PMCID: PMC3757733 DOI: 10.1016/j.nicl.2012.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 08/13/2012] [Accepted: 09/03/2012] [Indexed: 01/06/2023]
Abstract
The MET tyrosine kinase has been identified as a susceptibility gene in patients with autism spectrum disorders. MET is expressed in the forebrain during prenatal and postnatal development. After birth, MET participates in dendritic outgrowth and circuit formation. Alterations in neuronal development, particularly in the cerebral cortex, may contribute to the pathology of developmental disorders, including autism. Patients with autism can exhibit abnormal cortical volumes and head circumferences. We tested the hypothesis that impaired Met signaling during development alters forebrain structure. We have utilized a conditional mutant mouse line which expresses a kinase-dead Met restricted to the cerebral cortex and hippocampal structures. In these mice, we have used magnetic resonance imaging (MRI) to analyze the structure of the cerebral cortex and related structures across postnatal development. We found that the rostral cortex, caudal hippocampus, dorsal striatum, thalamus, and corpus callosum were all larger in adult, but not juvenile, mutant mice relative to control mice. The specificity of the changes suggests that aberrant expansion of the forebrain is consistent with continued axonal and dendritic growth, potentially leading to improper circuit formation and maintenance.
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Key Words
- ANOVA, analysis of variance
- Autism
- CC, corpus callosum
- Corpus callosum
- Frontal cortex
- H,hipp, hippocampus
- HGF, hepatocyte growth factor
- K–S, Kolmogorov–Smirnov
- MRI
- MRI, magnetic resonance imaging
- Met tyrosine kinase
- Mouse
- P, postnatal day
- PCR, polymerase chain reaction
- RARE, rapid acquisition relaxation enhancement
- SEM, standard error of the mean
- bp, base pairs
- ctx, cerebral cortex
- mm, millimeter
- str, striatum
- th,thal, thalamus
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Restoring virulence to mutants lacking subunits of multiprotein machines: functional complementation of a Brucella virB5 mutant. FEBS Open Bio 2012; 2:71-5. [PMID: 23650582 PMCID: PMC3642115 DOI: 10.1016/j.fob.2012.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 03/29/2012] [Accepted: 03/31/2012] [Indexed: 11/21/2022] Open
Abstract
Complementation for virulence of a non-polar virB5 mutant in Brucella suis 1330 was not possible using a pBBR-based plasmid but was with low copy vector pGL10. Presence of the pBBR-based replicon in wildtype B. suis had a dominant negative effect, leading to complete attenuation in J774 macrophages. This was due to pleiotropic effects on VirB protein expression due to multiple copies of the virB promoter region and over expression of VirB5. Functional complementation of mutants in individual components of multiprotein complexes such as bacterial secretion systems, are often problematic; this study highlights the importance of using a low copy vector.
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Human brain evolution and the "Neuroevolutionary Time-depth Principle:" Implications for the Reclassification of fear-circuitry-related traits in DSM-V and for studying resilience to warzone-related posttraumatic stress disorder. Prog Neuropsychopharmacol Biol Psychiatry 2006; 30:827-53. [PMID: 16563589 PMCID: PMC7130737 DOI: 10.1016/j.pnpbp.2006.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2006] [Indexed: 01/22/2023]
Abstract
The DSM-III, DSM-IV, DSM-IV-TR and ICD-10 have judiciously minimized discussion of etiologies to distance clinical psychiatry from Freudian psychoanalysis. With this goal mostly achieved, discussion of etiological factors should be reintroduced into the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-V). A research agenda for the DSM-V advocated the "development of a pathophysiologically based classification system". The author critically reviews the neuroevolutionary literature on stress-induced and fear circuitry disorders and related amygdala-driven, species-atypical fear behaviors of clinical severity in adult humans. Over 30 empirically testable/falsifiable predictions are presented. It is noted that in DSM-IV-TR and ICD-10, the classification of stress and fear circuitry disorders is neither mode-of-acquisition-based nor brain-evolution-based. For example, snake phobia (innate) and dog phobia (overconsolidational) are clustered together. Similarly, research on blood-injection-injury-type-specific phobia clusters two fears different in their innateness: 1) an arguably ontogenetic memory-trace-overconsolidation-based fear (hospital phobia) and 2) a hardwired (innate) fear of the sight of one's blood or a sharp object penetrating one's skin. Genetic architecture-charting of fear-circuitry-related traits has been challenging. Various, non-phenotype-based architectures can serve as targets for research. In this article, the author will propose one such alternative genetic architecture. This article was inspired by the following: A) Nesse's "Smoke-Detector Principle", B) the increasing suspicion that the "smooth" rather than "lumpy" distribution of complex psychiatric phenotypes (including fear-circuitry disorders) may in some cases be accounted for by oligogenic (and not necessarily polygenic) transmission, and C) insights from the initial sequence of the chimpanzee genome and comparison with the human genome by the Chimpanzee Sequencing and Analysis Consortium published in late 2005. Neuroevolutionary insights relevant to fear circuitry symptoms that primarily emerge overconsolidationally (especially Combat related Posttraumatic Stress Disorder) are presented. Also introduced is a human-evolution-based principle for clustering innate fear traits. The "Neuroevolutionary Time-depth Principle" of innate fears proposed in this article may be useful in the development of a neuroevolution-based taxonomic re-clustering of stress-triggered and fear-circuitry disorders in DSM-V. Four broad clusters of evolved fear circuits are proposed based on their time-depths: 1) Mesozoic (mammalian-wide) circuits hardwired by wild-type alleles driven to fixation by Mesozoic selective sweeps; 2) Cenozoic (simian-wide) circuits relevant to many specific phobias; 3) mid Paleolithic and upper Paleolithic (Homo sapiens-specific) circuits (arguably resulting mostly from mate-choice-driven stabilizing selection); 4) Neolithic circuits (arguably mostly related to stabilizing selection driven by gene-culture co-evolution). More importantly, the author presents evolutionary perspectives on warzone-related PTSD, Combat-Stress Reaction, Combat-related Stress, Operational-Stress, and other deployment-stress-induced symptoms. The Neuroevolutionary Time-depth Principle presented in this article may help explain the dissimilar stress-resilience levels following different types of acute threat to survival of oneself or one's progency (aka DSM-III and DSM-V PTSD Criterion-A events). PTSD rates following exposure to lethal inter-group violence (combat, warzone exposure or intentionally caused disasters such as terrorism) are usually 5-10 times higher than rates following large-scale natural disasters such as forest fires, floods, hurricanes, volcanic eruptions, and earthquakes. The author predicts that both intentionally-caused large-scale bioevent-disasters, as well as natural bioevents such as SARS and avian flu pandemics will be an exception and are likely to be followed by PTSD rates approaching those that follow warzone exposure. During bioevents, Amygdala-driven and locus-coeruleus-driven epidemic pseudosomatic symptoms may be an order of magnitude more common than infection-caused cytokine-driven symptoms. Implications for the red cross and FEMA are discussed. It is also argued that hospital phobia as well as dog phobia, bird phobia and bat phobia require re-taxonomization in DSM-V in a new "overconsolidational disorders" category anchored around PTSD. The overconsolidational spectrum category may be conceptualized as straddling the fear circuitry spectrum disorders and the affective spectrum disorders categories, and may be a category for which Pitman's secondary prevention propranolol regimen may be specifically indicated as a "morning after pill" intervention. Predictions are presented regarding obsessive-compulsive disorder (OCD) (e.g., female-pattern hoarding vs. male-pattern hoarding) and "culture-bound" acute anxiety symptoms (taijin-kyofusho, koro, shuk yang, shook yong, suo yang, rok-joo, jinjinia-bemar, karoshi, gwarosa, Voodoo death). Also discussed are insights relevant to pseudoneurological symptoms and to the forthcoming Dissociative-Conversive disorders category in DSM-V, including what the author terms fright-triggered acute pseudo-localized symptoms (i.e., pseudoparalysis, pseudocerebellar imbalance, psychogenic blindness, pseudoseizures, and epidemic sociogenic illness). Speculations based on studies of the human abnormal-spindle-like, microcephaly-associated (ASPM) gene, the microcephaly primary autosomal recessive (MCPH) gene, and the forkhead box p2 (FOXP2) gene are made and incorporated into what is termed "The pre-FOXP2 Hypothesis of Blood-Injection-Injury Phobia." Finally, the author argues for a non-reductionistic fusion of "distal (evolutionary) neurobiology" with clinical "proximal neurobiology," utilizing neurological heuristics. It is noted that the value of re-clustering fear traits based on behavioral ethology, human-phylogenomics-derived endophenotypes and on ontogenomics (gene-environment interactions) can be confirmed or disconfirmed using epidemiological or twin studies and psychiatric genomics.
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Key Words
- wr-ptsd, warzone-related posttraumatic stress disorder
- foxp2, forkhead box p2
- tcg, transcription controller-gene
- indels, genomic insertion/deletion events
- hpil, hereditary persistence of intestinal lactase
- aspm, abnormal-spindle-like, microcephaly-associated
- mcph, microcephaly primary autosomal recessive
- csac, the chimpanzee sequencing and analysis consortium
- dhea-s, dehydroxyepiandrosterone sulfate
- bp, base pairs
- sines, short interspersed repeats
- snps, single nucleotide polymorphisms
- mrca, most recent common ancestor
- fims, fear-induced malignant syncope
- lc, locus coeruleus
- blna, basolateral-nucleus-of-the-amygdala
- eea, environment of evolutionary adaptedness
- neuroevolutionary-tdp, neuroevolutionary time-depth principle
- eca, epidemiological catchment area
- ncs, national comorbidity survey
- icd, international classification of disease
- ne, norepinephrine
- dsm-iii, dsm-iv, dsm-iv-tr, dsm-v, diagnostic and statistical manual of mental disorders iii, iv, iv-text revision, and v
- ocd, obsessive-compulsive disorder
- ptda, posttraumatic dental-care anxiety
- asd, acute stress disorder
- mya, million years ago
- kya, thousand years ago
- ya, years ago
- wwii, world war two
- va, veterans affairs
- c&p exam, compensation and pension examination
- allele-variant polymorphisms
- anxiety disorders
- combat-related ptsd
- dsm-v
- large-scale disaster
- phobias
- stress and fear circuitry disorders
- war
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Abstract
MB78 is a virulent phage of Salmonella typhimurium that possesses a number of interesting features, making it a suitable organism to study the regulation of gene expression. A detailed physical map of this phage genome has been constructed and is being extensively studied at the molecular level. Here, we demonstrate the expression of two late proteins of bacteriophage MB78 derived from the same gene as a result of possible ribosomal frameshifting. In vitro transcription-translation yields a major protein that migrates as 28kDa, whereas in vivo expression using pET expression vectors yields two equally expressed proteins of molecular sizes 28 and 26kDa. A putative slippery sequence TTTAAAG and a pseudoknot structure, two essential cis elements required for the classical ribosomal frameshifting, are identified in the reading frame. Mutations created at the slippery sequence resulted in a single 28kDa protein and completely abolished the expression of 26kDa protein. Thus, we have produced the first evidence that ribosomal frameshifting occurs in bacteriophage MB78 of Salmonella typhimurium.
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Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B. Gene 1984; 29:87-92. [PMID: 6092234 PMCID: PMC7157916 DOI: 10.1016/0378-1119(84)90169-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/1983] [Revised: 03/01/1984] [Accepted: 03/15/1984] [Indexed: 01/18/2023]
Abstract
DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. 770 bases have been determined which include genomic sequences spanning the 5' termini of the two smallest mRNAs of the 3'-coterminal "nested" set: mRNA A and mRNA B. This region contains the complete coding sequences for mRNA B which are additional to those present in mRNA A. Two open reading frames are present, predicting proteins of Mrs 7500 and 9500.
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