Cyclic AMP modulation and its effects on chemo-resistant colon cancer cell proliferation and survival

One of the major problems associated with colorectal cancer is resistance to cytotoxic chemotherapeutic agents. New strategies are therefore required to inhibit colon cancer proliferation and survival. Here I use modulators of cAMP pathways, including inhibitors of phosphodiesterase 4 (PDE4) enzymes, which are under clinical development for other disease states, to inhibit the breakdown of cAMP and to assess the effects of raising intracellular cAMP on colon cancer proliferation and survival. I found that some chemo-resistant cancer cells are addicted to keeping low cAMP in PDE4 regulated compartments, and modulation of this pool causes G1/S-phase arrest and apoptosis. I also show that PDE4 controlled cAMP negatively regulates the PI 3-Kinase/Akt pathway, which some cells are addicted to for survival. Furthermore, I investigated the expression and role of PDE4 enzymes in metastatic colon cancer cells and assessed the effects of modulating their expression on survival. Also, I used a clinically relevant analogue of forskolin, an agonist of adenylyl cyclase, to examine the general effect on growth of epithelial cancer cell lines. This work might provide new strategies for the treatment of advanced colon cancer

User guide to seed regulatory framework analysis and implications for vegetatively propagated crops. RTB User Guide

Farmers who grow vegetatively propagated crops (VPC) face certain limitations in access to seed. Some of these constraints are related to policy, institutions and markets. This user guide describes a tool for conducting seed regulatory framework analysis for VPCs. It addresses quality assurance models (e.g. seed certification) and other regulations that can increase availability and access to quality VPC seed for smallholders. The methods used to collect and analyze the data include literature reviews, analysis of regulatory documents, focus group discussions and validation workshops. Stakeholder consultations through standardized key informant interviews are especially important. The resulting analysis is used to advise policy makers and regulatory bodies

The locus for an inherited cataract in sheep maps to ovine chromosome 6

Purpose: Cataracts are an important cause of blindness in humans but there are few large animal models available. One of these animal models is Ovine Heritable Cataract, a bilateral cortical cataract which develops after birth. This cataract has been used as a model for human cataracts in drug trials, but the gene responsible for the cataract trait is unknown. A genetic test for cataract would improve the efficiency of the model by predicting which animals would develop cataracts. Identifying the genetic basis of the cataract would indicate its relevance to human cataract. Methods: A genome scan was performed on 20 sheep chromosomes, representing 86% of the genome, to determine the position of the cataract locus. Additional microsatellite markers were tested on chromosome 6 using a larger pedigree. Fine mapping was performed using a breakpoint panel of 36 animals and novel microsatellite markers taken from the bovine genome assembly. All exons of the candidate gene nudix (nucleoside diphosphate linked moiety X)-type motif 9 (NUDT9) were sequenced in normal and affected sheep. Results: Significant linkage was found between cataract status and markers on chromosome 6. Linkage analysis on the larger pedigree showed the most likely position of the cataract locus was between 112.3 and 132.9 cM from the centromere. During fine mapping, NUDT9 was considered as a positional candidate for the cataract gene because it was located within the linked interval and is expressed in the lens. The gene was ruled out as the cataract gene after extensive genotype analysis, but a single nucleotide polymorphism (SNP) inside it provided a useful restriction fragment length polymorphism (RFLP) marker for further fine mapping. Twelve new markers were found and used to map the cataract locus to between 131.1 and 131.8 cM from the centromere. Conclusions: A region of ovine chromosome 6 strongly linked to cataract has been identified, and a genetic test for cataract based on a SNP within this region has been developed. The best candidate gene within this region is AF4/FMR2 family, member 1 (AFF1), the mouse equivalent of which is associated with an inherited cataract.This research was supported by the New Zealand Foundation for Research, Science, and Technology, grant number LINX0205

The endolysosomal adaptor PLEKHM1 is a direct target for both mTOR and MAPK pathways

The lysosome is a cellular signalling hub at the point of convergence of endocytic and autophagic pathways, where the contents are degraded and recycled. Pleckstrin homology domain-containing family member 1 (PLEKHM1) acts as an adaptor to facilitate the fusion of endocytic and autophagic vesicles with the lysosome. However, it is unclear how PLEKHM1 function at the lysosome is controlled. Herein, we show that PLEKHM1 co-precipitates with, and is directly phosphorylated by, mTOR. Using a phospho-specific antibody against Ser432/S435 of PLEKHM1, we show that the same motif is a direct target for ERK2-mediated phosphorylation in a growth factor-dependent manner. This dual regulation of PLEKHM1 at a highly conserved region points to a convergence of both growth factor- and amino acid-sensing pathways, placing PLEKHM1 at a critical juncture of cellular metabolism

Regulatory Options to Improve Seed Systems for Vegetatively Propagated Crops in Developing Countries

In many developing countries, smallholder farmers cultivating vegetatively propagated crops (VPCs) have limited access to quality planting material. This constraint can limit both the yield of and returns on VPC cultivation. Yet policy and regulatory initiatives designed to strengthen access to quality VPC planting materials have been relatively unsuccessful to date. Part of the problem is the unique biological and economic characteristics of vegetative propagation and its distinctness from cereal crops, which dominate narratives on seed system reforms. Drawing on qualitative analysis of policy and practice, this study examines reform options related to quality assurance regulations in four crop-country combinations: cassava in Nigeria and Vietnam, and potato in Kenya and Vietnam. The study highlights theory and evidence on existing models of regulation; alternative models that may better incentivize cost-effective multiplication and distribution; and recommendations for policy, regulation, and investment in VPC seed markets. Findings indicate that regulations designed around strict and centralized quality control systems tend to limit market size, while more localized production systems are limited by both capacity and reach. These findings suggest the need for alternatives that balance a permissive regulatory regime with decentralized production systems, grassroots capacity development, market surveillance, and systems that integrate internal (producer-level) quality assurance with external (regulatory) quality assurance

Structural and Functional analysis of the GABARAP interaction motif (GIM)

© 2017 The Authors. Published under the terms of the CC BY 4.0 license. Through the canonical LC3 interaction motif (LIR), [W/F/Y]-X 1 -X 2 -[I/L/V], protein complexes are recruited to autophagosomes to perform their functions as either autophagy adaptors or receptors. How these adaptors/receptors selectively interact with either LC3 or GABARAP families remains unclear. Herein, we determine the range of selectivity of 30 known core LIR motifs towards individual LC3s and GABARAPs. From these, we define a GABARAP Interaction Motif (GIM) sequence ([W/F] -[V/I]-X 2 -V) that the adaptor protein PLEKHM1 tightly conforms to. Using biophysical and structural approaches, we show that the PLEKHM1-LIR is indeed 11-fold more specific for GABARAP than LC3B. Selective mutation of the X 1 and X 2 positions either completely abolished the interaction with all LC3 and GABARAPs or increased PLEKHM1-GIM selectivity 20-fold towards LC3B. Finally, we show that conversion of p62/SQSTM1, FUNDC1 and FIP200 LIRs into our newly defined GIM, by introducing two valine residues, enhances their interaction with endogenous GABARAP over LC3B. The identification of a GABARAP-specific interaction motif will aid the identification and characterization of the expanding array of autophagy receptor and adaptor proteins and their in vivo functions

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability

The Lingering Effects of an Artificial Blind Spot

BACKGROUND: When steady fixation is maintained on the centre of a large patch of texture, holes in the periphery of the texture rapidly fade from awareness, producing artificial scotomata (i.e., invisible areas of reduced vision, like the natural ‘blind spot’). There has been considerable controversy about whether this apparent ‘filling in’ depends on a low-level or high-level visual process. Evidence for an active process is that when the texture around the scotomata is suddenly removed, phantasms of the texture appear within the previous scotomata. METHODOLOGY: To see if these phantasms were equivalent to real low-level signals, we measured contrast discrimination for real dynamic texture patches presented on top of the phantasms. PRINCIPAL FINDINGS: Phantasm intensity varied with adapting contrast. Contrast discrimination depended on both (real) pedestal contrast and phantasm intensity, in a manner indicative of a common sensory threshold. The phantasms showed inter-ocular transfer, proving that their effects are cortical rather than retinal. CONCLUSIONS: We show that this effect is consistent with a tonic spreading of the adapting texture into the scotomata, coupled with some overall loss of sensitivity. Our results support the view that ‘filling in’ happens at an early stage of visual processing, quite possibly in primary visual cortex (V1)

LRRK2 phosphorylation status and kinase activity regulate (macro)autophagy in a Rab8a/Rab10-dependent manner

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most common genetic cause of Parkinson’s disease (PD), with growing importance also for Crohn’s disease and cancer. LRRK2 is a large and complex protein possessing both GTPase and kinase activity. Moreover, LRRK2 activity and function can be influenced by its phosphorylation status. In this regard, many LRRK2 PD-associated mutants display decreased phosphorylation of the constitutive phosphorylation cluster S910/S935/S955/S973, but the role of these changes in phosphorylation status with respect to LRRK2 physiological functions remains unknown. Here, we propose that the S910/S935/S955/S973 phosphorylation sites act as key regulators of LRRK2-mediated autophagy under both basal and starvation conditions. We show that quadruple LRRK2 phosphomutant cells (4xSA; S910A/S935A/S955A/S973A) have impaired lysosomal functionality and fail to induce and proceed with autophagy during starvation. In contrast, treatment with the specific LRRK2 kinase inhibitors MLi-2 (100 nM) or PF-06447475 (150 nM), which also led to decreased LRRK2 phosphorylation of S910/S935/S955/S973, did not affect autophagy. In explanation, we demonstrate that the autophagy impairment due to the 4xSA LRRK2 phospho-dead mutant is driven by its enhanced LRRK2 kinase activity. We show mechanistically that this involves increased phosphorylation of LRRK2 downstream targets Rab8a and Rab10, as the autophagy impairment in 4xSA LRRK2 cells is counteracted by expression of phosphorylation-deficient mutants T72A Rab8a and T73A Rab10. Similarly, reduced autophagy and decreased LRRK2 phosphorylation at the constitutive sites were observed in cells expressing the pathological R1441C LRRK2 PD mutant, which also displays increased kinase activity. These data underscore the relation between LRRK2 phosphorylation at its constitutive sites and the importance of increased LRRK2 kinase activity in autophagy regulation and PD pathology