Proteomic studies of bone and skeletal health outcomes.

Bone. 2019 Apr 04;:

Authors: Nielson CM, Jacobs JM, Orwoll ES

Abstract
Proteins are an essential part of essentially all biological processes, and there is enormous variation in protein forms and concentrations that is not reflected in DNA or RNA. Recently there have been rapid advances in the ability to measure protein sequence, modification and concentration, particularly with methods based in mass spectrometry. Global measures of proteins in tissues or in the circulation provide a broad assessment of the proteome that can be extremely useful for discovery, and targeted proteomic measures can yield specific and sensitive assessments of specific peptides and proteins. While most proteomic measures are directed at the detection of consensus peptide sequences, mass spectrometry based proteomic methods also allow a detailed examination of the peptide sequence differences that result from genetic variants and that may have important effects on protein function. In evaluating proteomic data, a number of analytical considerations are important, including an understanding of missing data, the challenge of multiple testing and replication, and the use of rapidly evolving methods in systems biology. While proteomics has not yet had a major impact in skeletal research, interesting recent research has used these approaches in the study of bone cell biology and the discovery of biomarkers of skeletal disorders. Proteomics can be expected to have an increasing influence in the study of bone biology and pathophysiology.

PMID: 30954730 [PubMed - as supplied by publisher]

Strategies for purification of the bacteriophage HK97 small and large terminase subunits that yield pure and homogeneous samples that are functional.

Protein Expr Purif. 2019 Apr 04;:

Authors: Weiditch SA, Seraphim TV, Houry WA, Kanelis V

Abstract
Packaging the viral genome in the head of double-stranded DNA viruses, such as bacteriophages, requires the activity of a terminase. The bacteriophage terminase consists of a small terminase subunit (TerS), which binds the viral DNA, and a large terminase subunit (TerL) that possesses the ATPase and nuclease activities for packaging the DNA in the phage head. Some phages require additional components for DNA packaging, such as the HNH endonuclease gp74 in the bacteriophage HK97. Gp74 enhances the activity of terminase-mediated digestion of the cohesive (cos) site that connects individual genomes in phage concatemeric DNA, a pre-requisite to DNA packaging, and this enhancement requires an intact HNH motif in gp74. Testing of whether gp74 alters the terminase DNA binding or enzymatic activities requires obtaining isolated samples of pure TerS and TerL, which has been challenging owing to the poor solubility of these proteins. To this end, we developed methods to obtain purified TerS and TerL proteins that are active. TerS is expressed solubly in E. coli as a fusion with SUMO, which can be removed during purification to yield a TerS nonamer (TerS9). Homogenous samples of a TerL monomer are also obtained, but the homogeneity of the sample depends on the solution conditions, as seen for other terminases. DNA binding, ATPase, and nuclease assays demonstrate that our preparations of TerS9 and TerL are functional, and that they also function with gp74. Purified TerS9 and TerL enable studies into the molecular basis by which gp74 regulates terminase activity in phage maturation.

PMID: 30954531 [PubMed - as supplied by publisher]

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data.

Cell Syst. 2019 Mar 28;:

Authors: Wolock SL, Lopez R, Klein AM

Abstract
Single-cell RNA-sequencing has become a widely used, powerful approach for studying cell populations. However, these methods often generate multiplet artifacts, where two or more cells receive the same barcode, resulting in a hybrid transcriptome. In most experiments, multiplets account for several percent of transcriptomes and can confound downstream data analysis. Here, we present Single-Cell Remover of Doublets (Scrublet), a framework for predicting the impact of multiplets in a given analysis and identifying problematic multiplets. Scrublet avoids the need for expert knowledge or cell clustering by simulating multiplets from the data and building a nearest neighbor classifier. To demonstrate the utility of this approach, we test Scrublet on several datasets that include independent knowledge of cell multiplets. Scrublet is freely available for download at github.com/AllonKleinLab/scrublet.

PMID: 30954476 [PubMed - as supplied by publisher]

The Phospho-Code Determining Circadian Feedback Loop Closure and Output in Neurospora.

Mol Cell. 2019 Mar 26;:

Authors: Wang B, Kettenbach AN, Zhou X, Loros JJ, Dunlap JC

Abstract
In the negative feedback loop driving fungal and animal circadian oscillators, negative elements (FREQUENCY [FRQ], PERIODS [PERs], and CRYPTOCHROMES [CRYs]) are understood to inhibit their own expression, in part by promoting the phosphorylation of their heterodimeric transcriptional activators (e.g., White Collar-1 [WC-1]-WC-2 [White Collar complex; WCC] and BMAL1/Circadian Locomotor Output Cycles Kaput [CLOCK]). However, correlations between heterodimer activity and phosphorylation are weak, contradictions exist, and mechanistic details are almost wholly lacking. We report mapping of 80 phosphosites on WC-1 and 15 on WC-2 and elucidation of the time-of-day-specific code, requiring both a group of phosphoevents on WC-1 and two distinct clusters on WC-2, that governs circadian repression, leading to feedback loop closure. Combinatorial control via phosphorylation also governs rhythmic WCC binding to the promoters of clock-controlled genes mediating the essential first step in circadian output, a group encoding both transcription factors and signaling proteins. These data provide a basic mechanistic understanding for fundamental events underlying circadian negative feedback and output, key aspects of circadian biology.

PMID: 30954403 [PubMed - as supplied by publisher]

Subdiffusive Dynamics Lead to Depleted Particle Densities near Cellular Borders.

Biophys J. 2019 Feb 28;:

Authors: Holmes WR

Abstract
It has long been known that the complex cellular environment leads to anomalous motion of intracellular particles. At a gross level, this is characterized by mean-squared displacements that deviate from the standard linear profile. Statistical analysis of particle trajectories has helped further elucidate how different characteristics of the cellular environment can introduce different types of anomalousness. A significant majority of this literature has, however, focused on characterizing the properties of trajectories that do not interact with cell borders (e.g., cell membrane or nucleus). Numerous biological processes ranging from protein activation to exocytosis, however, require particles to be near a membrane. This study investigates the consequences of a canonical type of subdiffusive motion, fractional Brownian motion, and its physical analog, generalized Langevin equation dynamics, on the spatial localization of particles near reflecting boundaries. Results show that this type of subdiffusive motion leads to the formation of significant zones of depleted particle density near boundaries and that this effect is independent of the specific model details encoding those dynamics. Rather, these depletion layers are a natural and robust consequence of the anticorrelated nature of motion increments that is at the core of fractional Brownian motion (or alternatively generalized Langevin equation) dynamics. If such depletion zones are present, it would be of profound importance given the wide array of signaling and transport processes that occur near membranes. If not, that would suggest our understanding of this type of anomalous motion may be flawed. Either way, this result points to the need to further investigate the consequences of anomalous particle motions near cell borders from both theoretical and experimental perspectives.

PMID: 30954212 [PubMed - as supplied by publisher]

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"systems biology"

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"systems biology"

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"systems biology"

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35 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/04/02

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Structure-activity relationship studies of (E)-3,4-dihydroxystyryl alkyl sulfones as novel neuroprotective agents based on improved antioxidant, anti-inflammatory activities and BBB permeability.

Eur J Med Chem. 2019 Mar 21;171:420-433

Authors: Chen Y, Wu B, Hao Y, Liu Y, Zhang Z, Tian C, Ning X, Guo Y, Liu J, Wang X

Abstract
(E)-3,4-dihydroxystyryl alkyl sulfones, as new analogues of neurodegenerative agents, were designed and synthesized. The biological results demonstrated that most of the target compounds preserved antioxidant and anti-inflammatory potency in scavenging reactive free radicals, protecting neuronal cells against neurotoxins such as H2O2, 6-hydroxydopamine and inhibiting lipopolysaccharide (LPS)-induced over-production of NO. Among these compounds, 6.22 with cyclopentyl propyl exhibited prominent antioxidant activity at low concentration (2.5 μM) in H2O2 model (cell viability = 94.5%). In addition, 6.22 (IC50 = 1.6 μM) displayed better anti-inflammatory activity than that of lead compound 1 (IC50 = 13.4 μM). In view of the outstanding performance of 6.22, the apoptotic rates of H2O2-damaged PC12 cells were detected by Annexin V-FITC/PI assay. 6.22 showed higher potency in inhibition of apoptosis than 1 at low concentration (2.5 μM), consisting with the antioxidant and anti-inflammatory models. Furthermore, with the predicted CNS (+) blood-brain barrier (BBB) permeability (Pe = 6.84 × 10-6 cm s-1), low cytotoxicity and favorable physiochemical properties based on calculation, compound 6.22 can be further developed as a potential multifunctional neuroprotective agent.

PMID: 30928712 [PubMed - as supplied by publisher]

Stratification of asthma phenotypes by airway proteomic signatures.

J Allergy Clin Immunol. 2019 Mar 27;:

Authors: Schofield JPR, Burg D, Nicholas B, Strazzeri F, Brandsma J, Staykova D, Folisi C, Bansal AT, Xian Y, Guo Y, Rowe A, Corfield J, Wilson S, Ward J, Lutter R, Shaw DE, Bakke PS, Caruso M, Dahlen SE, Fowler SJ, Horváth I, Howarth P, Krug N, Montuschi P, Sanak M, Sandström T, Sun K, Pandis I, Riley J, Auffray C, De Meulder B, Lefaudeux D, Sousa AR, Adcock IM, Chung KF, Sterk PJ, Skipp PJ, Djukanović R, U-BIOPRED Study Group

Abstract
BACKGROUND: Stratification by eosinophil and neutrophil counts increases our understanding of asthma and helps target therapy, but there is room for improvement in our accuracy to predict treatment responses and a need for better understanding of the underlying mechanisms.
OBJECTIVE: Identify molecular sub-phenotypes of asthma defined by proteomic signatures for improved stratification.
METHODS: Unbiased label-free quantitative mass spectrometry and topological data analysis were used to analyse the proteomes of sputum supernatants from 246 participants (206 asthmatics) as a novel means of asthma stratification. Microarray analysis of sputum cells provided transcriptomics data additionally to inform on underlying mechanisms.
RESULTS: Analysis of the sputum proteome resulted in 10 clusters, proteotypes, based on similarity in proteomics features, representing discrete molecular sub-phenotypes of asthma. Overlaying granulocyte counts onto the 10 clusters as metadata further defined three of these as highly eosinophilic, three as highly neutrophilic, and two as highly atopic with relatively low granulocytic inflammation. For each of these three phenotypes, logistic regression analysis identified candidate protein biomarkers, and matched transcriptomic data pointed to differentially activated underlying mechanisms.
CONCLUSION: This study provides further stratification of asthma currently classified by quantifying granulocytic inflammation and gives additional insight into their underlying mechanisms which could become targets for novel therapies.

PMID: 30928653 [PubMed - as supplied by publisher]

Genomic analysis of the origins of extant casein variation in goats.

J Dairy Sci. 2019 Mar 27;:

Authors: Guan D, Mármol-Sánchez E, Cardoso TF, Such X, Landi V, Tawari NR, Amills M

Abstract
The variation in the casein genes has a major impact on the milk composition of goats. Even though many casein polymorphisms have been identified so far, we do not know yet whether they are evolutionarily ancient (i.e., they existed before domestication) or young (i.e., they emerged after domestication). Herewith, we identified casein polymorphisms in a data set of 106 caprine whole-genome sequences corresponding to bezoars (Capra aegagrus, the ancestor of domestic goats) and 4 domestic goat (Capra hircus) populations from Europe, Africa, the Far East, and the Near East. Domestic and wild goat populations shared a substantial number of casein SNP, from 36.1% (CSN2) to 55.1% (CSN1S2). The comparison of casein variation among bezoars and the 4 domestic goat populations demonstrated that more than 50% of the casein SNP are shared by 2 or more populations, and 18 to 44% are shared by all populations. Moreover, the majority of casein alleles reported in domestic goats also segregate in the bezoar, including several alleles displaying significant associations with milk composition (e.g., the A/B alleles of the CSN1S1 and CSN3 genes, the A allele of the CSN2 gene). We conclude that much of the current diversity of the caprine casein genes comes from ancient standing variation segregating in the ancestor of modern domestic goats.

PMID: 30928270 [PubMed - as supplied by publisher]

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation.

Mol Cell. 2019 Mar 21;:

Authors: Baluapuri A, Hofstetter J, Dudvarski Stankovic N, Endres T, Bhandare P, Vos SM, Adhikari B, Schwarz JD, Narain A, Vogt M, Wang SY, Düster R, Jung LA, Vanselow JT, Wiegering A, Geyer M, Maric HM, Gallant P, Walz S, Schlosser A, Cramer P, Eilers M, Wolf E

Abstract
The MYC oncoprotein binds to promoter-proximal regions of virtually all transcribed genes and enhances RNA polymerase II (Pol II) function, but its precise mode of action is poorly understood. Using mass spectrometry of both MYC and Pol II complexes, we show here that MYC controls the assembly of Pol II with a small set of transcription elongation factors that includes SPT5, a subunit of the elongation factor DSIF. MYC directly binds SPT5, recruits SPT5 to promoters, and enables the CDK7-dependent transfer of SPT5 onto Pol II. Consistent with known functions of SPT5, MYC is required for fast and processive transcription elongation. Intriguingly, the high levels of MYC that are expressed in tumors sequester SPT5 into non-functional complexes, thereby decreasing the expression of growth-suppressive genes. Altogether, these results argue that MYC controls the productive assembly of processive Pol II elongation complexes and provide insight into how oncogenic levels of MYC permit uncontrolled cellular growth.

PMID: 30928206 [PubMed - as supplied by publisher]

The human bitter taste receptor TAS2R7 facilitates the detection of bitter salts.

Biochem Biophys Res Commun. 2019 Mar 27;:

Authors: Behrens M, Redel U, Blank K, Meyerhof W

Abstract
The human sense of taste is devoted to the analysis of the chemical composition of food prior to ingestion. Among the five basic taste qualities bitter taste perception is believed to avoid ingestion of potentially toxic substances. The receptors facilitating the detection of hundreds of chemically different bitter compounds belong to the taste 2 receptor (TAS2R) family, which are part of the G protein-coupled superfamily. Although the chemical classes of bitter compounds that have been identified as agonists of one of the 25 potentially functional human bitter taste receptors cover an enormous chemical space, one distinct group of bitter compounds, the bitter salts have not been assigned to any bitter taste receptor. To close this gap, we screened the entire human bitter taste receptor repertoire by functional calcium mobilization assays with the most famous bitter salt, magnesium sulfate, also known as Epsom salt. Although the profound pharmacological activity and the bitter taste of spring water containing magnesium sulfate has been known since 1697, the molecular basis for its taste has not been elucidated until now. Our screening resulted in the identification of a single receptor, the TAS2R7, responding to magnesium sulfate at concentrations humans perceive this salt as bitter. Subsequently, TAS2R7 was stimulated with other salts and it was found that this receptor also responds to manganese2+ and iron2+ ions, but not to potassium ions. Magnesium sulfate is known to exert a number of beneficial effects on the human body and thus, has been used as medicine against premature uterine contractions, as anti-arrhythmic drug and as laxative, however, magnesium sulfate overdosage can result in cardiac arrest and thus have fatal consequences. Therefore, it appears reasonable that nature placed TAS2R7 as sentinel for high concentrations of bitter salts on our tongues.

PMID: 30928101 [PubMed - as supplied by publisher]

Emergent dynamics of coordinated cells with time delays in a tissue.

Chaos. 2019 Mar;29(3):031101

Authors: Pan C, Jiang Y, Zhu Q, Lin W

Abstract
In this article, we investigate the emergence of tissue dynamics with time delays of diffusion. Such emergent dynamics, describing the tissue homeostasis, usually correspond to particular tissue functions, which are attracting a tremendous amount of attention from both communities of mathematical modeling and systems biology. Specifically, in addition to the within-cell genome dynamics and the diffusion among the cells, we consider several types of time delays of diffusion present in the coordinated cells. We establish several generalized versions of the "monotonicity condition" (MC), whose traditional version [I. Rajapakse and S. Smale, Proc. Natl. Acad. Sci. U.S.A. 114, 1462-1467 (2017)] guaranteed the stability of the equilibrium in a system of coordinated cells without time delay. Indeed, we find that one generalized MC we establish still guarantees the stability of the time-delayed system's equilibrium, which corresponds to a formation of tissue functions depending primarily on individual genome dynamics but less on interacting structures and time delays of diffusion. We also find that, when the generalized MC is further relaxed, the system is able to sustain periodic oscillations, whose periods are verified to have delicate dependence with the selected time delays. These produced oscillations usually represent realistic behaviors of "alive" cells. We use several representative examples to demonstrate the usefulness of the established analytical conditions to the understanding of the emergent dynamics observed in computational models and in real systems as well.

PMID: 30927840 [PubMed - in process]

16 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/03/31

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25 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2019/03/30

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