Cilia, essential motile and sensory organelles, have several compartments: the basal body, transition zone, and the middle and distal axoneme segments. The distal segment accommodates key functions, ...including cilium assembly and sensory activities. While the middle segment contains doublet microtubules (incomplete B-tubules fused to complete A-tubules), the distal segment contains only A-tubule extensions, and its existence requires coordination of microtubule length at the nanometer scale. We show that three conserved proteins, two of which are mutated in the ciliopathy Joubert syndrome, determine the geometry of the distal segment, by controlling the positions of specific microtubule ends. FAP256/CEP104 promotes A-tubule elongation. CHE-12/Crescerin and ARMC9 act as positive and negative regulators of B-tubule length, respectively. We show that defects in the distal segment dimensions are associated with motile and sensory deficiencies of cilia. Our observations suggest that abnormalities in distal segment organization cause a subset of Joubert syndrome cases.
Computational inference of mutation effects is necessary for genetic studies in which many mutations must be considered as etiologic candidates. Programs such as PolyPhen-2 predict the relative ...severity of damage caused by missense mutations, but not the actual probability that a mutation will reduce/eliminate protein function. Based on genotype and phenotype data for 116,330 ENU-induced mutations in the Mutagenetix database, we calculate that putative null mutations, and PolyPhen-2-classified "probably damaging", "possibly damaging", or "probably benign" mutations have, respectively, 61%, 17%, 9.8%, and 4.5% probabilities of causing phenotypically detectable damage in the homozygous state. We use these probabilities in the estimation of genome saturation and the probability that individual proteins have been adequately tested for function in specific genetic screens. We estimate the proportion of essential autosomal genes in Mus musculus (C57BL/6J) and show that viable mutations in essential genes are more likely to induce phenotype than mutations in non-essential genes.
PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for the analysis of shotgun proteomic data. The contained modules allow for ...formatting of sequence databases, peptide spectrum matching, statistical filtering and data organization, extracting quantitative information from label-free and chemically labeled data, and analyzing statistics for differential proteomics. PatternLab also has modules to perform similarity-driven studies with de novo sequencing data, to evaluate time-course experiments and to highlight the biological significance of data with regard to the Gene Ontology database. The PatternLab for proteomics 4.0 package brings together all of these modules in a self-contained software environment, which allows for complete proteomic data analysis and the display of results in a variety of graphical formats. All updates to PatternLab, including new features, have been previously tested on millions of mass spectra. PatternLab is easy to install, and it is freely available from http://patternlabforproteomics.org.
Diabetic nephropathy (DN) is one of the major microvascular complications of diabetes and it is defined as a rise in the urinary albumin excretion (UAE) rate and abnormal renal function. Currently, ...changes in albuminuria are considered a hallmark of onset or progression of DN. However, some patients with diabetes have advanced renal pathological changes and progressive kidney function decline even if urinary albumin levels are in the normal range, indicating that albuminuria is not the perfect marker for the early detection of DN. The present article provides an overview of the literature reporting some relevant biomarkers that have been found to be associated with DN and that potentially may be used to predict the onset and/or monitor the progression of nephropathy. In particular, biomarkers of renal damage, inflammation, and oxidative stress may be useful tools for detection at an early stage or prediction of DN. Proteomic-based biomarker discovery represents a novel strategy to improve diagnosis, prognosis and treatment of DN; however, proteomics-based approaches are not yet available in most of the clinical chemistry laboratories. The use of a panel with a combination of biomarkers instead of urinary albumin alone seems to be an interesting approach for early detection of DN, including markers of glomerular damage (e.g., albumin), tubular damage (e.g., NAG and KIM-1), inflammation (e.g., TNF-α) and oxidative stress (e.g., 8-OHdG) because these mechanisms contribute to the development and outcomes of this disease.
► An overview of the literature reporting some relevant biomarkers associated with DN ► Biomarkers of renal damage, inflammation, and oxidative stress for detection of DN ► Proteomics analysis represents a novel strategy to improve diagnosis of DN.
A recessive phenotype called spin (spontaneous inflammation) was induced by N-ethyl-N-nitrosourea (ENU) mutagenesis in C57BL/6J mice. Homozygotes display chronic inflammatory lesions affecting the ...feet, salivary glands and lungs, and antichromatin antibodies. They are immunocompetent and show enhanced resistance to infection by Listeria monocytogenes. TLR-induced TNF and IL-1 production are normal in macrophages derived from spin mice. The autoinflammatory phenotype of spin mice is fully suppressed by compound homozygosity for Myd88poc, Irak4otiose, and Il1r1-null mutations, but not Ticam1Lps², Stat1m¹Btlr, or Tnf-null mutations. Both autoimmune and autoinflammatory phenotypes are suppressed when spin homozygotes are derived into a germ-free environment. The spin phenotype was ascribed to a viable hypomorphic allele of Ptpn6, which encodes the tyrosine phosphatase SHP1, mutated in mice with the classical motheaten alleles me and me-v. Inflammation and autoimmunity caused by SHP1 deficiency are thus conditional. The SHP1-deficient phenotype is driven by microbes, which activate TLR signaling pathways to elicit IL-1 production. IL-1 signaling via MyD88 elicits inflammatory disease.
Quorum sensing (QS) is a bacterial communication mechanism in which secreted signaling molecules impact population function and gene expression. QS-like phenomena have been reported in eukaryotes ...with largely unknown contributing molecules, functions, and mechanisms. We identify Qsp1, a secreted peptide, as a central signaling molecule that regulates virulence in the fungal pathogen Cryptococcus neoformans. QSP1 is a direct target of three transcription factors required for virulence, and qsp1Δ mutants exhibit attenuated infection, slowed tissue accumulation, and greater control by primary macrophages. Qsp1 mediates autoregulatory signaling that modulates secreted protease activity and promotes cell wall function at high cell densities. Peptide production requires release from a secreted precursor, proQsp1, by a cell-associated protease, Pqp1. Qsp1 sensing requires an oligopeptide transporter, Opt1, and remarkably, cytoplasmic expression of mature Qsp1 complements multiple phenotypes of qsp1Δ. Thus, C. neoformans produces an autoregulatory peptide that matures extracellularly but functions intracellularly to regulate virulence.
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•Qsp1 is an autoregulatory signaling peptide required for fungal virulence•Qsp1 controls intracellular growth, cell wall, and protease activities•Opt1 is a peptide transporter required for Qsp1 action in receiving cells•Intracellular expression of mature Qsp1 complements qsp1Δ phenotypes
Bacterial quorum sensing (QS) often controls virulence. Homer et al. reveal a peptide-based QS system in the fungal pathogen C. neoformans. This system requires signaling mechanisms in which the exported peptide is imported and acts intracellularly to control aspects of virulence, including growth, cell surface properties, and secreted protease activities.
The relationship between deforestation and malaria is a spatiotemporal process of variation in Plasmodium incidence in human-dominated Amazonian rural environments. The present study aimed to assess ...the underlying mechanisms of malarial exposure risk at a fine scale in 5-km
sites across the Brazilian Amazon, using field-collected data with a longitudinal spatiotemporally structured approach. Anopheline mosquitoes were sampled from 80 sites to investigate the Plasmodium infection rate in mosquito communities and to estimate the malaria exposure risk in rural landscapes. The remaining amount of forest cover (accumulated deforestation) and the deforestation timeline were estimated in each site to represent the main parameters of both the frontier malaria hypothesis and an alternate scenario, the deforestation-malaria hypothesis, proposed herein. The maximum frequency of pathogenic sites occurred at the intermediate forest cover level (50% of accumulated deforestation) at two temporal deforestation peaks, e.g., 10 and 35 years after the beginning of the organization of a settlement. The incidence density of infected anophelines in sites where the original forest cover decreased by more than 50% in the first 25 years of settlement development was at least twice as high as the incidence density calculated for the other sites studied (adjusted incidence density ratio = 2.25; 95% CI, 1.38-3.68; p = 0.001). The results of this study support the frontier malaria as a unifying hypothesis for explaining malaria emergence and for designing specific control interventions in the Brazilian Amazon.
Activated microglia have been implicated in the pathogenesis of age-related macular degeneration (AMD), diabetic retinopathy, and other neurodegenerative and neuroinflammatory disorders, but our ...understanding of the mechanisms behind their activation is in infant stages. With the goal of identifying novel genes associated with microglial activation in the retina, we applied a semiquantitative fundus spot scoring scale to an unbiased, state-of-the-science mouse forward genetics pipeline. A mutation in the gene encoding the E3 ubiquitin ligase Herc3 led to prominent accumulation of fundus spots. CRISPR mutagenesis was used to generate Herc3
mice, which developed prominent accumulation of fundus spots and corresponding activated Iba1 + /CD16 + subretinal microglia, retinal thinning on OCT and histology, and functional deficits by Optomotory and electrophysiology. Bulk RNA sequencing identified activation of inflammatory pathways and differentially expressed genes involved in the modulation of microglial activation. Thus, despite the known expression of multiple E3 ubiquitin ligases in the retina, we identified a non-redundant role for Herc3 in retinal homeostasis. Our findings are significant given that a dysregulated ubiquitin-proteasome system (UPS) is important in prevalent retinal diseases, in which activated microglia appear to play a role. This association between Herc3 deficiency, retinal microglial activation and retinal degeneration merits further study.
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