The scope and infringement of patents claiming strains of bacteria.

Increasing numbers of patents directed to bacteria and bacterial products are being filed and granted, many of which claim specific deposited strains of bacteria. However, there remains significant uncertainty regarding exactly what scope patent claims limited to deposited strains might have. A claim limited to a specific deposited strain could be interpreted extremely narrowly, extending only to descendants of that deposit. However, a review of the available guidance from courts across the globe suggests that in practice such claims are likely to be infringed by competitor products. The commercial value of patent claims to bacteria depends on the regulatory and competitive landscape, and can be strengthened by appropriate details in patent applications.

Semi-automated camera trap image processing for the detection of ungulate fence crossing events.

Remote cameras are an increasingly important tool for ecological research. While remote camera traps collect field data with minimal human attention, the images they collect require post-processing and characterization before it can be ecologically and statistically analyzed, requiring the input of substantial time and money from researchers. The need for post-processing is due, in part, to a high incidence of non-target images. We developed a stand-alone semi-automated computer program to aid in image processing, categorization, and data reduction by employing background subtraction and histogram rules. Unlike previous work that uses video as input, our program uses still camera trap images. The program was developed for an ungulate fence crossing project and tested against an image dataset which had been previously processed by a human operator. Our program placed images into categories representing the confidence of a particular sequence of images containing a fence crossing event. This resulted in a reduction of 54.8% of images that required further human operator characterization while retaining 72.6% of the known fence crossing events. This program can provide researchers using remote camera data the ability to reduce the time and cost required for image post-processing and characterization. Further, we discuss how this procedure might be generalized to situations not specifically related to animal use of linear features.

A Sterile 20 Family Kinase and Its Co-factor CCM-3 Regulate Contractile Ring Proteins on Germline Intercellular Bridges.

Germ cells in most animals are connected by intercellular bridges, actin-based rings that form stable cytoplasmic connections between cells promoting communication and coordination [1]. Moreover, these connections are required for fertility [1, 2]. Intercellular bridges are proposed to arise from stabilization of the cytokinetic ring during incomplete cytokinesis [1]. Paradoxically, proteins that promote closure of cytokinetic rings are enriched on stably open intercellular bridges [1, 3, 4]. Given this inconsistency, the mechanism of intercellular bridge stabilization is unclear. Here, we used the C. elegans germline as a model for identifying molecular mechanisms regulating intercellular bridges. We report that bridges are actually highly dynamic, changing size at precise times during germ cell development. We focused on the regulation of bridge stability by anillins, key regulators of cytokinetic rings and cytoplasmic bridges [1, 4-7]. We identified GCK-1, a conserved serine/threonine kinase [8], as a putative novel anillin interactor. GCK-1 works together with CCM-3, a known binding partner [9], to promote intercellular bridge stability and limit localization of both canonical anillin and non-muscle myosin II (NMM-II) to intercellular bridges. Additionally, we found that a shorter anillin, known to stabilize bridges [4, 7], also regulates NMM-II levels at bridges. Consistent with these results, negative regulators of NMM-II stabilize intercellular bridges in the Drosophila egg chamber [10, 11]. Together with our findings, this suggests that tuning of myosin levels is a conserved mechanism for the stabilization of intercellular bridges that can occur by diverse molecular mechanisms.

BioGPS and MyGene.info: organizing online, gene-centric information.

Fast-evolving technologies have enabled researchers to easily generate data at genome scale, and using these technologies to compare biological states typically results in a list of candidate genes. Researchers are then faced with the daunting task of prioritizing these candidate genes for follow-up studies. There are hundreds, possibly even thousands, of web-based gene annotation resources available, but it quickly becomes impractical to manually access and review all of these sites for each gene in a candidate gene list. BioGPS (http://biogps.org) was created as a centralized gene portal for aggregating distributed gene annotation resources, emphasizing community extensibility and user customizability. BioGPS serves as a convenient tool for users to access known gene-centric resources, as well as a mechanism to discover new resources that were previously unknown to the user. This article describes updates to BioGPS made after its initial release in 2008. We summarize recent additions of features and data, as well as the robust user activity that underlies this community intelligence application. Finally, we describe MyGene.info (http://mygene.info) and related web services that provide programmatic access to BioGPS.

Prosthetic rehabilitation of an individual papillary unit: a clinical report.

This article is a clinical and technical report to illustrate the prosthetic correction of an individual interdental papilla, which had been lost due to periodontal disease. The patient presented with localised aggressive periodontitis and was successfully treated non-surgically. As a result of the periodontal disease and its management, the interdental papilla between the 11 and 21 were lost and prosthetically replaced. The clinical details of the case and the technical procedures are fully illustrated within this article.

Methods and models in neurodegenerative and systemic protein aggregation diseases.

Protein misfolding and aggregation are implicated in a wide range of increasingly prevalent human diseases ranging from dementia to diabetes. In this review we discuss the current experimental strategies that are being employed in the investigation of the pathogenesis of three important protein misfolding disorders. The first, Alzheimer's disease (AD), is the most prevalent neurodegenerative disease and is thought to be initiated by the aggregation of a natively unstructured peptide called amyloid beta (Abeta). We discuss methods for the characterization of the aggregation properties of Abeta in vitro and how the results of such experiments can be correlated with data from animal models of disease. We then consider another form of amyloidosis, where a systemic distribution of amyloid deposit is caused by aggregation and deposition of mutational variants of lysozyme. We describe how experiments in vitro, and more recently in vivo, have provided insights into the origins of this disease. Finally we outline the varied paradigms that have been employed in the study of the serpinopathies, and in particular, a dementia caused by neuroserpin polymerization.

Endoplasmic reticulum-associated degradation (ERAD) and autophagy cooperate to degrade polymerogenic mutant serpins.

The serpinopathies are a family of diseases characterized by the accumulation of ordered polymers of mutant protein within the endoplasmic reticulum. They are a diverse group including alpha(1)-antitrypsin deficiency and the inherited dementia familial encephalopathy with neuroserpin inclusion bodies or FENIB. We have used transient transfection of COS7 cells and mouse embryonic fibroblasts, PC12 cell lines that conditionally express wild type and mutant neuroserpin and fly models of FENIB to assess the cellular handling of wild type and mutant serpins. By using a polymer-specific monoclonal antibody, we show that mutant neuroserpin forms polymers after a delay of at least 30 min and that polymers can be cleared in PC12 cell lines and from the brain in a fly model of FENIB. At steady state, the fractions of intracellular polymerogenic G392E mutant neuroserpin in the monomeric and polymeric states are comparable. Inhibition of the proteasome with MG132 reveals that both mutant neuroserpin and alpha(1)-antitrypsin are degraded predominantly by endoplasmic reticulum-associated degradation (ERAD). Pharmacological and genetic inhibitions demonstrate that autophagy is responsible for bulk turnover of wild type and mutant serpins, but can be stimulated by rapamycin to compensate for proteasome inhibition. The significance of these findings to the treatment of serpinopathies is discussed.

alpha1-Antitrypsin deficiency, chronic obstructive pulmonary disease and the serpinopathies.

alpha1-Antitrypsin is the prototypical member of the serine proteinase inhibitor or serpin superfamily of proteins. The family includes alpha1-antichymotrypsin, C1 inhibitor, antithrombin and neuroserpin, which are all linked by a common molecular structure and the same suicidal mechanism for inhibiting their target enzymes. Point mutations result in an aberrant conformational transition and the formation of polymers that are retained within the cell of synthesis. The intracellular accumulation of polymers of mutant alpha1-antitrypsin and neuroserpin results in a toxic gain-of-function phenotype associated with cirrhosis and dementia respectively. The lack of important inhibitors results in overactivity of proteolytic cascades and diseases such as COPD (chronic obstructive pulmonary disease) (alpha1-antitrypsin and alpha1-antichymotrypsin), thrombosis (antithrombin) and angio-oedema (C1 inhibitor). We have grouped these conditions that share the same underlying disease mechanism together as the serpinopathies. In the present review, the molecular and pathophysiological basis of alpha1-antitrypsin deficiency and other serpinopathies are considered, and we show how understanding this unusual mechanism of disease has resulted in the development of novel therapeutic strategies.

The intracellular accumulation of polymeric neuroserpin explains the severity of the dementia FENIB.

Familial encephalopathy with neuroserpin inclusion bodies (FENIB) is an autosomal dominant dementia that is characterized by the retention of polymers of neuroserpin as inclusions within the endoplasmic reticulum (ER) of neurons. We have developed monoclonal antibodies that detect polymerized neuroserpin and have used COS-7 cells, stably transfected PC12 cell lines and transgenic Drosophila melanogaster to characterize the cellular handling of all four mutant forms of neuroserpin that cause FENIB. We show a direct correlation between the severity of the disease-causing mutation and the accumulation of neuroserpin polymers in cell and fly models of the disease. Moreover, mutant neuroserpin causes locomotor deficits in the fly allowing us to demonstrate a direct link between polymer accumulation and neuronal toxicity.

The C. elegans RSA complex localizes protein phosphatase 2A to centrosomes and regulates mitotic spindle assembly.

Microtubule behavior changes during the cell cycle and during spindle assembly. However, it remains unclear how these changes are regulated and coordinated. We describe a complex that targets the Protein Phosphatase 2A holoenzyme (PP2A) to centrosomes in C. elegans embryos. This complex includes Regulator of Spindle Assembly 1 (RSA-1), a targeting subunit for PP2A, and RSA-2, a protein that binds and recruits RSA-1 to centrosomes. In contrast to the multiple functions of the PP2A catalytic subunit, RSA-1 and RSA-2 are specifically required for microtubule outgrowth from centrosomes and for spindle assembly. The centrosomally localized RSA-PP2A complex mediates these functions in part by regulating two critical mitotic effectors: the microtubule destabilizer KLP-7 and the C. elegans regulator of spindle assembly TPXL-1. By regulating a subset of PP2A functions at the centrosome, the RSA complex could therefore provide a means of coordinating microtubule outgrowth from centrosomes and kinetochore microtubule stability during mitotic spindle assembly.

TRB3 links the E3 ubiquitin ligase COP1 to lipid metabolism.

During fasting, increased concentrations of circulating catecholamines promote the mobilization of lipid stores from adipose tissue in part by phosphorylating and inactivating acetyl-coenzyme A carboxylase (ACC), the rate-limiting enzyme in fatty acid synthesis. Here, we describe a parallel pathway, in which the pseudokinase Tribbles 3 (TRB3), whose abundance is increased during fasting, stimulates lipolysis by triggering the degradation of ACC in adipose tissue. TRB3 promoted ACC ubiquitination through an association with the E3 ubiquitin ligase constitutive photomorphogenic protein 1 (COP1). Indeed, adipocytes deficient in TRB3 accumulated larger amounts of ACC protein than did wild-type cells. Because transgenic mice expressing TRB3 in adipose tissue are protected from diet-induced obesity due to enhanced fatty acid oxidation, these results demonstrate how phosphorylation and ubiquitination pathways converge on a key regulator of lipid metabolism to maintain energy homeostasis.

The CENP-F-like proteins HCP-1 and HCP-2 target CLASP to kinetochores to mediate chromosome segregation.

During chromosome segregation, kinetochores form dynamic connections with spindle microtubules. In vertebrates, these attachments require the activities of a number of outer kinetochore proteins, including CENP-F [1, 2] and the widely conserved microtubule-associated protein CLASP [3]. Here, we investigate the functional relationship between HCP-1/2, two redundant CENP-F-like proteins, and CLASP(CLS-2) in Caenorhabditis elegans. HCP-1/2 and CLASP(CLS-2) localize transiently to mitotic C. elegans kinetochores with nearly identical kinetic profiles, and biochemical purifications demonstrate that they also associate physically. In embryos depleted of HCP-1/2, CLASP(CLS-2) no longer localizes to chromosomes, whereas CLASP(CLS-2) depletion does not prevent HCP-1/2 targeting. Consistent with the localization dependency and biochemical association, depletion of HCP-1/2 or CLASP(CLS-2) resulted in virtually identical defects in mitotic chromosome segregation characterized by a failure of sister-chromatid biorientation. This phenotype could be partially suppressed by disrupting the astral forces that pull spindle poles apart in the 1 cell embryo, indicating that CLASP(CLS-2) is required for biorientation when chromosome-spindle attachments are subjected to poleward force. Our results establish that the key role of HCP-1/2 is to target CLASP(CLS-2) to kinetochores, and they support the recently proposed model that CLASP functions to promote the polymerization of kinetochore bound microtubules [4].