Flow cytometric chromosome sorting in plants: The next generation

Genome analysis in many plant species is hampered by large genome size and by sequence redundancy due to the presence of repetitive DNA and polyploidy. One solution is to reduce the sample complexity by dissecting the genomes to single chromosomes. This can be realized by flow cytometric sorting, which enables purification of chromosomes in large numbers. Coupling the chromosome sorting technology with next generation sequencing provides a targeted and cost effective way to tackle complex genomes. The methods outlined in this article describe a procedure for preparation of chromosomal DNA suitable for next-generation sequencing.     

Immunology for the next generation

Immunologists need to establish a vibrant dialogue with young people. This is not only important for the continuation and progress of biomedical research, but it can also contribute to the fight against diseases such as HIV/AIDS and can help young people to make informed decisions about lifestyle, medical treatment and ethical issues. Good communication skills are crucial to any scientific career, and the lessons learned from talking with non-scientists can also be useful when writing scientific papers and grants. This article is a personal account of one scientist's experience of communicating biomedical science to young people.     

Adaptation genomics: the next generation

Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?     

The next generation of exoskeletons: lighter, cheaper devices are in the works

Many researchers and engineers are busy in their laboratories working on devices that will bring mobility to people who have lost function in the lower body due to an accident, stroke, multiple sclerosis, or other disorders. "Several pretty sophisticated exoskeletons are already on the market now, and they are all similar to each other in terms of technologies, but we're not ready to replace the wheelchair yet," said exoskeleton developer Homayoon Kaz Kazerooni, Ph.D., professor of mechanical engineering at the University of California (UC) at Berkeley. "Eventually, we will have devices that are used by individuals on a daily basis to replace wheelchairs but not with the existing technology. We're at the beginning of a much bigger era in exoskeletons."     

Vascular tissue engineering: the next generation

It is the ultimate goal of tissue engineering: an autologous tissue engineered vascular graft (TEVG) that is immunologically compatible, nonthrombogenic, and can grow and remodel. Currently, native vessels are the preferred vascular conduit for procedures such as coronary artery bypass (CABG) or peripheral bypass surgery. However, in many cases these are damaged, have already been harvested, or are simply unusable. The use of synthetic conduits is severely limited in smaller diameter vessels due to increased incidence of thrombosis, infection, and graft failure. Current research has therefore energetically pursued the development of a TEVG that can incorporate into a patient's circulatory system, mimic the vasoreactivity and biomechanics of the native vasculature, and maintain long-term patency.     

Hallmarks of cancer: the next generation

The hallmarks of cancer comprise six biological capabilities acquired during the multistep development of human tumors. The hallmarks constitute an organizing principle for rationalizing the complexities of neoplastic disease. They include sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis. Underlying these hallmarks are genome instability, which generates the genetic diversity that expedites their acquisition, and inflammation, which fosters multiple hallmark functions. Conceptual progress in the last decade has added two emerging hallmarks of potential generality to this list-reprogramming of energy metabolism and evading immune destruction. In addition to cancer cells, tumors exhibit another dimension of complexity: they contain a repertoire of recruited, ostensibly normal cells that contribute to the acquisition of hallmark traits by creating the "tumor microenvironment." Recognition of the widespread applicability of these concepts will increasingly affect the development of new means to treat human cancer.     

Bead-based microfluidic immunoassays: the next generation

Microfluidic devices possess many advantages like high throughput, short analysis time, small volume and high sensitivity that fulfill all the important criteria of an immunoassay used for clinical diagnoses, environmental analyses and biochemical studies. These devices can be made from a few different materials, with polymers presently emerging as the most popular choice. Other than being optically clear, non-toxic and cheap, polymers can also be easily fabricated with a variety of techniques. In addition, there are many polymer surface modification methods available to improve the efficiency of these devices. Unfortunately, current microfluidic immunoassays have limited multiplexing capability compared to flow cytometric assays. Flow cytometry employ the use of encoded microbeads in contrast with normal or paramagnetic microbeads applied in current microfluidic devices. The encoded microbead is the key in providing multiplexing capability to the assay by allowing multi-analyte analysis. Using several unique sets of code, different analytes can be detected in a single assay by tracing the identity of individual beads. The same principle could be applied to microfluidic immunoassays in order to retain all the advantages of a fluidic device and significantly improve multiplexing capability.     

Development of a low bias method for characterizing viral populations using next generation sequencing technology

Background

With an estimated 38 million people worldwide currently infected with human immunodeficiency virus (HIV), and an additional 4.1 million people becoming infected each year, it is important to understand how this virus mutates and develops resistance in order to design successful therapies.

Methodology/Principal Findings

We report a novel experimental method for amplifying full-length HIV genomes without the use of sequence-specific primers for high throughput DNA sequencing, followed by assembly of full length viral genome sequences from the resulting large dataset. Illumina was chosen for sequencing due to its ability to provide greater coverage of the HIV genome compared to prior methods, allowing for more comprehensive characterization of the heterogeneity present in the HIV samples analyzed. Our novel amplification method in combination with Illumina sequencing was used to analyze two HIV populations: a homogenous HIV population based on the canonical NL4-3 strain and a heterogeneous viral population obtained from a HIV patient''s infected T cells. In addition, the resulting sequence was analyzed using a new computational approach to obtain a consensus sequence and several metrics of diversity.

Significance

This study demonstrates how a lower bias amplification method in combination with next generation DNA sequencing provides in-depth, complete coverage of the HIV genome, enabling a stronger characterization of the quasispecies present in a clinically relevant HIV population as well as future study of how HIV mutates in response to a selective pressure.     

Alterations in membrane transport properties by freezing injury in herbaceous plants:

Leakage of ions from a thawed tissue is a common phenomenon of freezing injury. This leakage is usually assumed to be due to loss of membrane semipermeability or membrane rupture by freezing injury. Freeze injured, yet living, onion (Allium cepa L.) epidermal cells were used to study alterations in cell membranes that result in leakage of ions. In spite of a large efflux of ions, freeze injured cells could be plasmolysed and they remained plasmolysed for several days just like the unfrozen control cells. Injured cells also exhibited protoplasmic streaming. Passive transport of KCl, urea and methyl urea across the cell membranes of injured and control cells was also studied. No difference could be detected for the transport rates of urea and methyl urea between control and injured cells. However, a dramatic increase in the transport rate of KCl was found for the injured cells. Depending upon the extent of initial freezing injury, an increase or a decrease in injury symptoms was found in the post-thaw period. During the progress of freezing injury, 10 days after thawing, a swelling of the protoplasm was seen in the irreversibly injured cells. In spite of this swelling, these cells could be plasmolysed. It appears that the high amount of K⁺ that leaks out into the extracellular water, due to freezing injury, causes protoplasmic swelling by replacing Ca²⁺ in the plasma membrane. We conclude that protoplasmic swelling is a sign of secondary injury. The results presented in this study show that membrane semipermeability is not completely lost and membrane rupture does not occur during the initial stage of freezing injury. In fact, the cells have the ability to repair damage depending upon the degree of injury. Our results show there are specific alterations in membrane semipermeability (e.g., transport of K⁺) which could be repaired completely depending on the degree of injury. These findings suggest that ion leakage due to freezing injury is due to alteration in the membrane proteins and not in the membrane lipids.     

Prebiotics and synbiotics: towards the next generation

Recent research in the area of prebiotic oligosaccharides and synbiotic combinations with probiotics is leading towards a more targeted development of functional food ingredients. Improved molecular techniques for analysis of the gut microflora, new manufacturing biotechnologies, and increased understanding of the metabolism of oligosaccharides by probiotics are facilitating development. Such developments are leading us to the time when we will be able to rationally develop prebiotics and synbiotics for specific functional properties and health outcomes.     

Mitochondria: the next (neurode)generation

Adult-onset neurodegenerative disorders are disabling and often fatal diseases of the nervous system whose underlying mechanisms of cell death remain unknown. Defects in mitochondrial respiration had previously been proposed to contribute to the occurrence of many, if not all, of the most common neurodegenerative disorders. However, the discovery of genes mutated in hereditary forms of these enigmatic diseases has additionally suggested defects in mitochondrial dynamics. Such disturbances can lead to changes in mitochondrial trafficking, in interorganellar communication, and in mitochondrial quality control. These new mechanisms by which mitochondria may also be linked to neurodegeneration will likely have far-reaching implications for our understanding of the pathophysiology and treatment of adult-onset neurodegenerative disorders.     

Bio-electrosprays: the next generation of electrified jets

Biological electrosprays are rapidly becoming a robust means by which to engineer living organisms for applications ranging from tissue repair to developmental biology. We previously reported the ability to electrospray living organisms without compromising their viability, but found it challenging to achieve stability in the jetting of these organisms as a result of the chemical properties of the living cellular suspensions. Jet stability is required for the generation of a near-mono distribution of droplets, which is necessary for the development of electrospray technology as a "drop and place" biotechnique. Recently, we determined the conditions needed to achieve jet stability and were able to generate droplets with a near-mono distribution (<50 microm). In this communication, we elucidate the relationship between jet behaviour and droplet size under stable jetting conditions, with a view to further reducing the droplet size to deposit a single living cell within a droplet. We believe that this level of resolution will make electrospray jetting superior amongst the jet-based biotechnologies presently being developed for the engineering of biological architectures comprised of living cells.     

Defrosting the digital library: bibliographic tools for the next generation web

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.     

Tests for the diagnosis of Clostridium difficile infection: the next generation

Clostridium difficile (C. difficile) causes 25-30% of cases of antibiotic associated diarrhea and most cases of pseudomembranous colitis. Patients presenting with diarrhea after hospitalization for 3 or more days should be tested for C. difficile. There are many options available for testing, each of which has inherent advantages and disadvantages. Most laboratories perform toxin testing using an enzyme immunoassay method. In general these tests have sensitivities ranging from 60 to 70% and specificities of 98%. When using these methods, symptomatic patients with negative tests should be tested by another more sensitive method. Until recently, cell culture cytotoxicity neutralization assays (CCNAs) were considered the gold standard in the U.S. A two-step algorithm using an EIA for glutamate dehydrogenase detection followed by testing positives using CCNA, offered an improved alternative until the availability of molecular assays. Although early studies that compared the GDH assay to CCNA demonstrated high sensitivity and negative predictive values, more recent comparisons to toxigenic culture and PCR have shown the sensitivity to be in the mid to high 80's. When testing using a sensitive assay, repeat testing is not cost-effective. Outbreaks caused by a toxin variant epidemic strain have renewed interest in bacterial culture. Toxigenic culture has emerged as the new gold standard against which newer assays should be compared. However, there is no agreed upon standard method for culture performance. At least 4 FDA cleared nucleic acid amplification assays are available to clinical laboratories and several of these have been well evaluated in the literature. Because these assays detect a gene that encodes toxin and not the toxin itself it is important that laboratories test only patients with diarrhea. These molecular assays have been shown to be superior to toxin EIAs, CCNA and 2-step algorithms, but not to toxigenic culture. More studies are needed to assess the impact of molecular tests on treatment and nosocomial spread of Clostridium difficile infections.     

Revisiting microbial keratinases: next generation proteases for sustainable biotechnology

Keratinases are special proteases which attack the highly recalcitrant keratin substrates. They stand apart from the conventional proteases due to their broad substrate specificity towards a variety of insoluble keratin rich substrates like feather, wool, nail, hair. Owing to this ability, keratinases find immense applications in various environmental and biotechnological sectors. The current boost in keratinase research has come up with the discovery of the ability of keratinases to address the challenging issue of prion decontamination. Here we present a comprehensive review on microbial keratinases giving an account of chronological progress of research along with the major milestones. Major focus has been on the key characteristics of keratinases, such as substrate specificity, keratin degradation mechanisms, molecular properties, and their role in prion decontamination along with other pharmaceutical applications. We conclude by critically evaluating the present state of the keratinases discussing their commercial status along with future research directions.     

Wake-promoting agents: search for next generation modafinil: part II

In search of a next generation molecule to modafinil, a novel wake promoting agent, we previously disclosed bi-phenyl derived racemate compound (±)-2 as a new generation of wake-promoting agent. Here we describe the profiles of the individual enantiomers (-)-2 and (+)-2, respectively.     

Wake-promoting agents: search for next generation modafinil: part I

In search of a next generation molecule to the novel wake promoting agent modafinil, a series of bi-phenyl derived wakefulness enhancing agents (in rat) was developed. From this work, compound 17 has been selected for additional studies.