A practical guide to interpreting and generating bottom-up proteomics data visualizations

Mass-spectrometry based bottom-up proteomics is the main method to analyze proteomes comprehensively and the rapid evolution of instrumentation and data analysis has made the technology widely available. Data visualization is an integral part of the analysis process and it is crucial for the communication of results. This is a major challenge due to the immense complexity of MS data. In this review, we provide an overview of commonly used visualizations, starting with raw data of traditional and novel MS technologies, then basic peptide and protein level analyses, and finally visualization of highly complex datasets and networks. We specifically provide guidance on how to critically interpret and discuss the multitude of different proteomics data visualizations. Furthermore, we highlight Python-based libraries and other open science tools that can be applied for independent and transparent generation of customized visualizations. To further encourage programmatic data visualization, we provide the Python code used to generate all data figures in this review on GitHub ().DATA AVAILABILITY STATEMENT Proteomics data from the following ProteomeExchange repositories were reused to generate Figures in this study: PXD012867, PXD017703, PXD010697, PXD010103

Communication Technology of Audience Activation on Local TV

Currently, there are many kinds of communicative relations between the broadcasters and the audience. Departing from the tradition of simply delivering the information, TV, especially local, now activates the audience, inviting it to participate in the creative process. Communication technologies include: gaming techniques (television quizzes, raffles, contests); providing the audience with the opportunity to express its views and wishes on air; inviting ordinary viewers to participate in the program; special television projects with the participation of the ordinary representatives and others. The article substantiates the prospects of development of the system of local television on the basis of the definition of modern technologies of interaction with the audience.В настоящее время существуют множество видов коммуникативных отношений телекомпаний с аудиторией. Отходя от традиционного простого донесения информации, ТВ, особенно местное, сегодня активизирует аудиторию, приглашая ее к участию в творческом процессе. К коммуникативным технологиям относятся: игровые приемы (телевизионные викторины, розыгрыши, конкурсы); предоставление возможности высказать свое мнение и пожелание в эфире; приглашением обычных телезрителей к участию в программе; специальные телевизионные проекты с участием представителей «из народа» и др. В статье дано обоснование перспектив развития системы местного телевидения на базе определения современных технологий взаимодействия с аудиторией

Bone Tissue Engineering: Scalability and Optimization of Densified Collagen-Fibril Bone Graft Substitute Materials

Over 240 million people missing teeth worldwide experience lingering problems such as difficulty speaking and eating, undesirable aesthetics, and resorption of bone supporting neighboring teeth. The gold standard of treatment utilizes grafts to attach a function-restoring implant to supporting bone. Current graft materials suffer from problems including autologous donor site morbidity, long resorption time, incomplete integration with the maxillae or mandible, and structural weakness. Patient-specific, cellularized bone grafts may be a solution to these issues by accelerating and improving the quality of regenerated bone. Recently, encapsulation of mesenchymal stem cells within self-assembling type I collagen oligomer matrices has been shown to support rapid mineralization of small-scale bone constructs (cylinders with diameter and height of 6mm and 1mm, respectively) in vitro. However, this method’s volume and geometric constraints for nutrient transport and cell viability are still unknown. In this study, the effects of construct size and medium formulation on mineralization were investigated using conventional static culture methods. To create constructs, human adipose stem cells (hASCs) were embedded in oligomer matrices, allowed to polymerize, and compressed to final cell and fibril densities of 3x107 cells/mL and 50 mg/mL, respectively. Varying construct sizes (maximum diameter and thickness of 11 mm and 0.81 mm) were cultured for 1 week in growth medium or osteogenic medium with varying calcium concentrations. Alizarin red staining was used to detect calcium deposits indicative of cell-induced mineralization. Preliminary data suggests that culture in osteogenic medium supplemented with both 8 mM and 16 mM calcium may induce rapid, uniform mineralization across all sizes tested, and 16 mM calcium supplementation induces greater mineralization. However, additional validation by direct measurement of cell viability and osteogenic differentiation will be needed to better compare bone regeneration as a function of scale

Injectable Highly Tunable Oligomeric Collagen Matrices for Dental Tissue Regeneration

Current stem cell transplantation approaches lack efficacy, because they limit cell survival and retention and, more importantly, lack a suitable cellular niche to modulate lineage-specific differentiation. Here, we evaluate the intrinsic ability of type I oligomeric collagen matrices to modulate dental pulp stem cells (DPSCs) endothelial and odontogenic differentiation as a potential stem cell-based therapy for regenerative endodontics. DPSCs were encapsulated in low-stiffness (235 Pa) and high-stiffness (800 Pa) oligomeric collagen matrices and then evaluated for long-term cell survival, as well as endothelial and odontogenic differentiation following in vitro cell culture. Moreover, the effect of growth factor incorporation, i.e., vascular endothelial growth factor (VEGF) into 235 Pa oligomeric collagen or bone morphogenetic protein (BMP2) into the 800 Pa oligomeric collagen counterpart on endothelial or odontogenic differentiation of encapsulated DPSCs was investigated. DPSCs-laden oligomeric collagen matrices allowed long-term cell survival. Real time polymerase chain reaction (RT-PCR) data showed that the DPSCs cultured in 235 Pa matrices demonstrated an increased expression of endothelial markers after 28 days, and the effect was enhanced upon VEGF incorporation. There was a significant increase in alkaline phosphatase (ALP) activity at Day 14 in the 800 Pa DPSCs-laden oligomeric collagen matrices, regardless of BMP2 incorporation. However, Alizarin S data demonstrated higher mineralization by Day 21 and the effect was amplified in BMP2-modified matrices. Herein, we present key data that strongly support future research aimed at clinical translation of an injectable oligomeric collagen system for delivery and fate regulation of DPSCs to enable pulp and dentin regeneration at specific locations of the root canal system

Amine functionalization of cholecyst-derived extracellular matrix with generation 1 PAMAM dendrimer

This document is the unedited author's version of a Submitted Work that was subsequently accepted for publication in Biomacromolecules, copyright © American Chemical Society after peer review. To access the final edited and published work, see http://pubs.acs.org/doi/pdf/10.1021/bm701055k.A method to functionalize cholecyst-derived extracellular matrix (CEM) with free amine groups was established in an attempt to improve its potential for tethering of bioactive molecules. CEM was incorporated with Generation-1 polyamidoamine (G1 PAMAM) dendrimer by using N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide and N-hydroxysuccinimide cross-linking system. The nature of incorporation of PAMAM dendrimer was evaluated using shrink temperature measurements, Fourier transform infrared (FTIR) assessment, ninhydrin assay, and swellability. The effects of PAMAM incorporation on mechanical and degradation properties of CEM were evaluated using a uniaxial mechanical test and collagenase degradation assay, respectively. Ninhydrin assay and FTIR assessment confirmed the presence of increasing free amine groups with increasing quantity of PAMAM in dendrimer-incorporated CEM (DENCEM) scaffolds. The amount of dendrimer used was found to be critical in controlling scaffold degradation, shrink temperature, and free amine content. Cell culture studies showed that fibroblasts seeded on DENCEM maintained their metabolic activity and ability to proliferate in vitro. In addition, fluorescence cell staining and scanning electron microscopy analysis of cell-seeded DENCEM showed preservation of normal fibroblast morphology and phenotype

Opportunities for organoids as new models of aging.

The biology of aging is challenging to study, particularly in humans. As a result, model organisms are used to approximate the physiological context of aging in humans. However, the best model organisms remain expensive and time-consuming to use. More importantly, they may not reflect directly on the process of aging in people. Human cell culture provides an alternative, but many functional signs of aging occur at the level of tissues rather than cells and are therefore not readily apparent in traditional cell culture models. Organoids have the potential to effectively balance between the strengths and weaknesses of traditional models of aging. They have sufficient complexity to capture relevant signs of aging at the molecular, cellular, and tissue levels, while presenting an experimentally tractable alternative to animal studies. Organoid systems have been developed to model many human tissues and diseases. Here we provide a perspective on the potential for organoids to serve as models for aging and describe how current organoid techniques could be applied to aging research

In vitro Anticancer Screening of 24 Locally Used Nigerian Medicinal Plants

Background: Plants that are used as traditional medicine represent a relevant pool for selecting plant candidates that may have anticancer properties. In this study, the ethnomedicinal approach was used to select several medicinal plants native to Nigeria, on the basis of their local or traditional uses. The collected plants were then evaluated for cytoxicity. Methods: The antitumor activity of methanolic extracts obtained from 24 of the selected plants, were evaluated in vitro on five human cancer cell lines. Results: Results obtained from the plants screened indicate that 18 plant extracts of folk medicine exhibited promising cytotoxic activity against human carcinoma cell lines. Erythrophleum suaveolens (Guill. & Perr.) Brenan was found to demonstrate potent anti-cancer activity in this study exhibiting IC50 = 0.2-1.3 $\mu$g/ml. Conclusions: Based on the significantly potent activity of some plants extracts reported here, further studies aimed at mechanism elucidation and bio-guided isolation of active anticancer compounds is currently underway.Chemistry and Chemical Biolog

Quantitative Analysis of the Effect of Cancer Invasiveness and Collagen Concentration on 3D Matrix Remodeling

Extracellular matrix (ECM) remodeling is a key component of cell migration and tumor metastasis, and has been associated with cancer progression. Despite the importance of matrix remodeling, systematic and quantitative studies on the process have largely been lacking. Furthermore, it remains unclear if the disrupted tensional homeostasis characteristic of malignancy is due to initially altered ECM and tissue properties, or to the alteration of the tissue by tumor cells. To explore these questions, we studied matrix remodeling by two different prostate cancer cell lines in a three-dimensional collagen system. Over one week, we monitored structural changes in gels of varying collagen content using confocal reflection microscopy and quantitative image analysis, tracking metrics of fibril fraction, pore size, and fiber length and diameter. Gels that were seeded with no cells (control), LNCaP cells, and DU-145 cells were quantitatively compared. Gels with higher collagen content initially had smaller pore sizes and higher fibril fractions, as expected. However, over time, LNCaP- and DU-145-populated matrices showed different structural properties compared both to each other and to the control gels, with LNCaP cells appearing to favor microenvironments with lower collagen fiber fractions and larger pores than DU-145 cells. We posit that the DU-145 cells' preference for denser matrices is due to their higher invasiveness and proteolytic capabilities. Inhibition of matrix proteases resulted in reduced fibril fractions for high concentration gels seeded with either cell type, supporting our hypothesis. Our novel quantitative results probe the dynamics of gel remodeling in three dimensions and suggest that prostate cancer cells remodel their ECM in a synergistic manner that is dependent on both initial matrix properties as well as their invasiveness

Microgenomic Analysis in Skeletal Muscle: Expression Signatures of Individual Fast and Slow Myofibers

BACKGROUND: Skeletal muscle is a complex, versatile tissue composed of a variety of functionally diverse fiber types. Although the biochemical, structural and functional properties of myofibers have been the subject of intense investigation for the last decades, understanding molecular processes regulating fiber type diversity is still complicated by the heterogeneity of cell types present in the whole muscle organ. METHODOLOGY/PRINCIPAL FINDINGS: We have produced a first catalogue of genes expressed in mouse slow-oxidative (type 1) and fast-glycolytic (type 2B) fibers through transcriptome analysis at the single fiber level (microgenomics). Individual fibers were obtained from murine soleus and EDL muscles and initially classified by myosin heavy chain isoform content. Gene expression profiling on high density DNA oligonucleotide microarrays showed that both qualitative and quantitative improvements were achieved, compared to results with standard muscle homogenate. First, myofiber profiles were virtually free from non-muscle transcriptional activity. Second, thousands of muscle-specific genes were identified, leading to a better definition of gene signatures in the two fiber types as well as the detection of metabolic and signaling pathways that are differentially activated in specific fiber types. Several regulatory proteins showed preferential expression in slow myofibers. Discriminant analysis revealed novel genes that could be useful for fiber type functional classification. CONCLUSIONS/SIGNIFICANCE: As gene expression analyses at the single fiber level significantly increased the resolution power, this innovative approach would allow a better understanding of the adaptive transcriptomic transitions occurring in myofibers under physiological and pathological condition

Functional tissue engineering of ligament healing

Ligaments and tendons are dense connective tissues that are important in transmitting forces and facilitate joint articulation in the musculoskeletal system. Their injury frequency is high especially for those that are functional important, like the anterior cruciate ligament (ACL) and medial collateral ligament (MCL) of the knee as well as the glenohumeral ligaments and the rotator cuff tendons of the shoulder. Because the healing responses are different in these ligaments and tendons after injury, the consequences and treatments are tissue- and site-specific. In this review, we will elaborate on the injuries of the knee ligaments as well as using functional tissue engineering (FTE) approaches to improve their healing. Specifically, the ACL of knee has limited capability to heal, and results of non-surgical management of its midsubstance rupture have been poor. Consequently, surgical reconstruction of the ACL is regularly performed to gain knee stability. However, the long-term results are not satisfactory besides the numerous complications accompanied with the surgeries. With the rapid development of FTE, there is a renewed interest in revisiting ACL healing. Approaches such as using growth factors, stem cells and scaffolds have been widely investigated. In this article, the biology of normal and healing ligaments is first reviewed, followed by a discussion on the issues related to the treatment of ACL injuries. Afterwards, current promising FTE methods are presented for the treatment of ligament injuries, including the use of growth factors, gene delivery, and cell therapy with a particular emphasis on the use of ECM bioscaffolds. The challenging areas are listed in the future direction that suggests where collection of energy could be placed in order to restore the injured ligaments and tendons structurally and functionally