Ubiquitinomics: History,methods, and applications in basic research and drug discovery

The ubiquitin-proteasome system (UPS) was discovered about 40 years ago and is known to regulate a multitude of cellular processes including protein homeostasis. Ubiquitylated proteins are recognized by downstream effectors, resulting in alterations of protein abundance, activity, or localization. Not surprisingly, the ubiquitylation machinery is dysregulated in numerous diseases, including cancers and neurodegeneration. Mass spectrometry (MS)-based proteomics has emerged as a transformative technology for characterizing protein ubiquitylation in an unbiased fashion. Here, we provide an overview of the different MS-based approaches for studying protein ubiquitylation. We review various methods for enriching and quantifying ubiquitin modifications at the peptide or protein level, outline MS acquisition, and data processing approaches and discuss key challenges. Finally, we examine how MS-based ubiquitinomics can aid both basic biology and drug discovery research.     

History, challenges and perspectives of cell microencapsulation

Cell microencapsulation continues to hold significant promise for biotechnology and medicine. The controlled, and continuous, delivery of therapeutic products to the host by immunoisolated cells is a potentially cost-effective method to treat a wide range of diseases. Although there are several issues that need to be addressed, including capsule manufacture, properties and performance, in the past few years, a stepwise analysis on the essential obstacles and limitations has brought the whole technology closer to a realistic proposal for clinical application. This paper summarizes the current situation in the cell encapsulation field and discusses the main events that have occurred along the way.     

Pyocyanin: production,applications, challenges and new insights

Pseudomonas aeruginosa is an opportunistic, Gram-negative bacterium and is one of the most commercially and biotechnologically valuable microorganisms. Strains of P. aeruginosa secrete a variety of redox-active phenazine compounds, the most well studied being pyocyanin. Pyocyanin is responsible for the blue-green colour characteristic of Pseudomonas spp. It is considered both as a virulence factor and a quorum sensing signalling molecule for P. aeruginosa. Pyocyanin is an electrochemically active metabolite, involved in a variety of significant biological activities including gene expression, maintaining fitness of bacterial cells and biofilm formation. It is also recognised as an electron shuttle for bacterial respiration and as an antibacterial and antifungal agent. This review summarises recent advances of pyocyanin production from P. aeruginosa with special attention to antagonistic property and bio-control activity. The review also covers the challenges and new insights into pyocyanin from P. aeruginosa.     

G-estimation and artificial censoring: problems, challenges, and applications

In principle, G-estimation is an attractive approach for dealing with confounding by variables affected by treatment. It has rarely been applied for estimation of the effects of treatment on failure-time outcomes. Part of this is due to artificial censoring, an analytic device which considers some subjects who actually were observed to fail as if they were censored. Artificial censoring leads to a lack of smoothness in the estimating function, which can pose problems in variance estimation and in optimization. It also can lead to failure to have solutions to the usual estimating functions, which then raises questions about the appropriate criteria for optimization. To improve performance of the optimization procedures, we consider approaches for reducing the amount of artificial censoring, propose the substitution of smooth for indicator functions, and propose the use of estimating functions scaled to a measure of the information in the data; we evaluate performance of these approaches using simulation. We also consider appropriate optimization criteria in the presence of information loss due to artificial censoring. We motivate and illustrate our approaches using observational data on the effect of erythropoietin on mortality among subjects on hemodialysis.     

Targets,models and challenges in osteoarthritis research

Osteoarthritis is a chronic degenerative disorder of the joint and represents one of the most common diseases worldwide. Its prevalence and severity are increasing owing to aging of the population, but treatment options remain largely limited to painkillers and anti-inflammatory drugs, which only provide symptomatic relief. In the late stages of the disease, surgical interventions are often necessary to partially restore joint function. Although the focus of osteoarthritis research has been originally on the articular cartilage, novel findings are now pointing to osteoarthritis as a disease of the whole joint, in which failure of different joint components can occur. In this Review, we summarize recent progress in the field, including data from novel ‘omics’ technologies and from a number of preclinical and clinical trials. We describe different in vitro and in vivo systems that can be used to study molecules, pathways and cells that are involved in osteoarthritis. We illustrate that a comprehensive and multisystem approach is necessary to understand the complexity and heterogeneity of the disease and to better guide the development of novel therapeutic strategies for osteoarthritis.KEY WORDS: Osteoarthritis, Cartilage, Bone, Animal models     

The challenges of modelling antibody repertoire dynamics in HIV infection

Antibody affinity maturation by somatic hypermutation of B-cell immunoglobulin variable region genes has been studied for decades in various model systems using well-defined antigens. While much is known about the molecular details of the process, our understanding of the selective forces that generate affinity maturation are less well developed, particularly in the case of a co-evolving pathogen such as HIV. Despite this gap in understanding, high-throughput antibody sequence data are increasingly being collected to investigate the evolutionary trajectories of antibody lineages in HIV-infected individuals. Here, we review what is known in controlled experimental systems about the mechanisms underlying antibody selection and compare this to the observed temporal patterns of antibody evolution in HIV infection. We describe how our current understanding of antibody selection mechanisms leaves questions about antibody dynamics in HIV infection unanswered. Without a mechanistic understanding of antibody selection in the context of a co-evolving viral population, modelling and analysis of antibody sequences in HIV-infected individuals will be limited in their interpretation and predictive ability.     

Single-cell metagenomics: challenges and applications

With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simultaneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.     

Antigen-driven T-cell repertoire selection during adaptive immune responses

Protective immunity against a variety of infections depends on the amplification and differentiation of rare na?ve antigen-specific CD4 and CD8 T cells. Recent evidence indicates that the clonotypic composition of the responding T-cell compartment has a critical role in the immune defense against pathogens. The present review compares and contrasts how naive CD4 and CD8 T cells recognize their cognate antigen, and discusses the factors that regulate the genesis and maintenance of the CD4 and CD8 T-cell receptor repertoire diversity.     

Genetic control of the immune repertoire in nematode infections

Mammals vary considerably, both within and between species, in the way in which their innate and adaptive immune systems respond to infections. An understanding of the processes involved in such variability will not only contribute to explaining heterogeneity in susceptibility and pathology, but will also be relevant to vaccination. This will be particularly important for the new generation of vaccines that are likely to be composed of one or a few cloned or synthesized antigens. For helminth infections, this could have particular relevance to hypersensitivity responses. The adaptive immune response is fundamentally constrained by the genetic constitution of an individual, and the need to avoid reactivity to self. This will have important implications for the dynamic relationship between host defences and parasite evasion mechanisms at both physiological and evolutionary levels. In this review, Malcolm Kennedy examines the genetic control of the specificity of the immune response to nematode infections, and in particular, the role of the major histocompatibility complex.     

If the immune repertoire evolved to be large,random, and somatically generated,then..

The evolution of the somatically generated random combining site repertoire of the "adaptive" immune system depended on the concurrent appearance of a somatic process that sorted the repertoire into anti-self and anti-nonself. Unlike the germline-selected sorting process characteristic of "innate" defense mechanisms, somatic sorting of the repertoire requires that antigens be classified based on their behavior, not on their physical or chemical properties. As specific recognitive combining sites (paratopes) define antigenic determinants (epitopes), the sorting of the repertoire operates epitope-by-epitope. By contrast, the coupling of the paratope to effector function must operate antigen-by-antigen because the response to each epitope on the antigen must be in the same effector class (i.e., coherent). This distinction resolves a long standing debate and provides a basis for analyzing the various models.     

Microbial gene expression in soil: methods, applications and challenges

About 99% of soil microorganisms are unculturable. However, advances in molecular biology techniques allow for the analysis of living microorganisms. With the advent of new technologies and the optimization of previous methods, various approaches to studying gene expression are expanding the field of microbiology and molecular biology. Methods used for RNA extraction, DNA microarrays, real-time PCR, competitive RT-PCR, stable isotope probing and the use of reporter genes provide methods for detecting and quantifying gene expression. Through the use of these methods, researchers can study the influence of soil environmental factors such as nutrients, oxygen status, pH, pollutants, agro-chemicals, moisture and temperature on gene expression and some of the mechanisms involved in the responses of cells to their environment. This review will also address information gaps in bacterial gene expression in soil and possible future research to develop an understanding of microbial activities in soil environments.     

Analysis of the human immune repertoire using human monoclonal antibodies

The investigations of the human immune response to cancer and other diseases have been hampered by the difficulty in determining the specificity of low-titered antibodies in serum, and the inability to define the specificity of individual lymphocytes. In order to study these issues, we developed the hybridoma technology so that human monoclonal antibodies (hM Ab) could be reliably and reproducibly obtained. Using a variety of fusion partners of both mouse and human origin, a large number of human immunoglobulin-secreting hybrids have been generated. We have found that 5 to 10% of the hybridomas produced secrete hM Ab reactive with antigens (Ag) expressed by human cells. Specificity analysis and cellular localization studies of the Ag have been performed for a large number of these hM Ab, and several general points have emerged from our study: (A) A significant proportion of the evaluable B-cell repertoire is directed to the production of antibodies reactive with Ags expressed by human cells. (B) The great majority of these Ags have an intracellular location, and are broadly distributed, being expressed by both normal and malignant cells. (C) Intracellular and cell surface differentiation Ags and other Ags with restricted distribution have been defined by hM Ab, including a series of cell surface and intracellular Ags not detected on normal cells. (D) The relationship of these findings to cancer is unclear as hM Ab showing distinctive distributions have been generated from the lymphocytes of normal individuals as well as tumor-bearing patients. (E) hM Ab with distributions distinct from any known mouse monoclonal antibodies (mM Ab) have been obtained.(ABSTRACT TRUNCATED AT 250 WORDS)