Characterizing activity-dependent processes with a piecewise exponential model

The response of some biological processes is dependent on the frequency of stimulation. With first-order processes, the response is driven exponentially to an equilibrium determined by the value of the driving function. When the stimulus or driving function is viewed as switching between constant values the resulting response is piecewise exponential. With periodic excitation, the time course of a point fixed in time relative to the initiation time of each stimulus is shown to be exponential with a rate and steady state that are linearly dependent on the rates and equilibria associated with each component exponential. This linearity can be exploited and leads to a simple estimation procedure for the apparent state-dependent rates.     

Sex bias and omission exists in Batten disease research: Systematic review of the use of animal disease models

Batten disease, also known as the neuronal ceroid lipofuscinoses (NCL), is a group of inherited neurodegenerative disorders mainly affecting children. NCL are characterised by seizures, loss of vision, and progressive motor and cognitive decline, and are the most common form of childhood dementia. At least one type of Batten disease and three types of mouse disease models show sex differences in their severity and progression. Scientific research has a recognised prevalent omission of female animals when using model organisms for basic and preclinical research. Sex bias and omission in research using animal models of Batten disease may affect understanding and treatment development. We conducted a systematic review of research publications since the first identification of NCL genes in 1995, identifying those using animal models. We found that <10 % of these papers considered sex as a biological variable. There was consistent omission of female model organisms in studies. This varied over the period but is improving; one third of papers considered sex as a biological variable in the last decade, and there is a noticeable increase in the last 5 years. The wide-ranging reasons for this published sex bias are discussed, including misunderstanding regarding oestrogen, impact on sample size, and the underrepresentation of female scientists. Their implications for Batten disease and future research are considered. Recommendations going forward support requirements by funders for consideration of sex in all stages of experimental design and implementation, and a role for publishers, families and others with a particular interest in Batten disease.     

Nitric oxide signaling is disrupted in the yeast model for Batten disease

The juvenile form of neuronal ceroid lipofuscinoses (JNCLs), or Batten disease, results from mutations in the CLN3 gene, and it is characterized by the accumulation of lipopigments in the lysosomes of several cell types and by extensive neuronal death. We report that the yeast model for JNCL (btn1-Delta) that lacks BTN1, the homologue to human CLN3, has increased resistance to menadione-generated oxidative stress. Expression of human CLN3 complemented the btn1-Delta phenotype, and equivalent Btn1p/Cln3 mutations correlated with JNCL severity. We show that the previously reported decreased levels of L-arginine in btn1-Delta limit the synthesis of nitric oxide (.NO) in both physiological and oxidative stress conditions. This defect in .NO synthesis seems to suppress the signaling required for yeast menadione-induced apoptosis, thus explaining btn1-Delta phenotype of increased resistance. We propose that in JNCL, a limited capacity to synthesize .NO directly caused by the absence of Cln3 function may contribute to the pathology of the disease.     

Cellular models of Batten disease

The Neuronal Ceroid Lipofuscinoses (NCL), otherwise known as Batten disease, are a group of neurodegenerative diseases caused by mutations in 13 known genes. All except one NCL is autosomal recessive in inheritance, with similar aetiology and characterised by the accumulation of autofluorescent storage material in the lysosomes of cells. Age of onset and the rate of progression vary between the NCLs. They are collectively one of the most common lysosomal storage diseases, but the enigma remains of how genetically distinct diseases result in such remarkably similar pathogenesis. Much has been learnt from cellular studies about the function of the proteins encoded by the affected genes. Such research has utilised primitive unicellular models such as yeast and amoeba containing gene orthologues, cells derived from naturally occurring (sheep) and genetically engineered (mouse) animal models or patient-derived cells. Most recently, patient-derived induced pluripotent stem cell (iPSC) lines have been differentiated into neural cell-types to study molecular pathogenesis in the cells most profoundly affected by disease. Here, we review how cell models have informed much of the biochemical understanding of the NCLs and how more complex models are being used to further this understanding and potentially act as platforms for therapeutic efficacy studies in the future.     

A foliar disease model for use in wheat disease management decision support systems

A model of winter wheat foliar disease is described, parameterised and tested for Septoria tritici (leaf blotch), Puccinia striiformis (yellow rust), Erysiphe graminis (powdery mildew) and Puccinia triticina (brown rust). The model estimates disease‐induced green area loss, and can be coupled with a wheat canopy model, in order to estimate remaining light‐intercepting green tissue and hence the capacity for resource capture. The model differs from those reported by other workers in three respects. First, variables (such as weather, host resistance and inoculum pressure) that affect disease risk are integrated in their effect on disease progress. The agronomic and meteorological data called for are restricted to those commonly available to growers by their own observations and from meteorological service networks. Second, field observations during the growing season can be used both to correct current estimates of disease severity and to modify parameters that determine predicted severity. Third, pathogen growth and symptom expression are modelled to allow the effects of fungicides to be accounted for as protectant activity (reducing infections that occur postapplication) and eradicant activity (reducing growth of presymptomatic infections). The model was tested against data from a wide range of sites and varieties and was shown to predict the expected level of disease sufficiently accurately to support fungicide treatment decisions.     

Cell death pathways in juvenile Batten disease

Apoptosis, Golgi fragmentation and elevated ceramide levels occur in Juvenile Neuronal Ceroid Lipofuscinosis (JNCL) neurons, lymphoblasts and fibroblasts. Our purpose was to examine whether apoptosis is the mechanism of cell death in JNCL. This was tested by analyzing caspase-dependent/independent pathways and autophagy, and caspase effects on ceramide and Golgi fragmentation. zVAD prevented caspase activation, but not all cell death. Inhibiting caspase-8 suppressed caspases more than inhibition of any other caspase. Inhibiting caspase-8/6 was synergistic. zVAD suppressed autophagy. 3-methyladenine suppressed caspase activation less than zVAD did. Blocking autophagy/caspase-8/or-6 was synergistic. Blocking autophagy/caspase-3/or-9 was not. Inhibiting caspase-9/3 suppressed autophagy. Golgi fragmentation was suppressed by zVAD, and blocked by CLN3. CLN3, not zVAD, prevented ceramide elevation. In conclusion: caspase-dependent/independent apoptosis and autophagy occur caspase-dependent pathways initiate autophagy Golgi fragmentation results from apoptosis ceramide elevation is independent of caspases, and CLN3 blocks all cell death, prevents Golgi fragmentation and elevation of ceramide in JNCL.     

On the cusp of cures: Breakthroughs in Batten disease research

Batten disease is a family of rare, lysosomal disorders caused by mutations in one of at least 13 genes, which encode a diverse set of lysosomal and extralysosomal proteins. Despite decades of research, the development of effective therapies has remained intractable. But now, the field is experiencing rapid, unprecedented progress on multiple fronts. New tools are providing insights into previously unsolvable problems, with molecular functions now known for nine Batten disease proteins. Protein interactome data are uncovering potential functional overlap between several Batten disease proteins, providing long-sought links between seemingly disparate proteins. Understanding of cellular etiology is elucidating contributions from and interactions between various CNS cell types. Collectively, this explosion in insight is hastening an unparalleled period of therapeutic breakthroughs, with multiple therapies showing great promise in preclinical and clinical studies. The coming years will provide a continuation of this rapid progress, with the promise of effective treatments giving patients hope.     

A wheat canopy model for use in disease management decision support systems

A model is described which predicts those aspects of wheat canopy development and growth which are influential in determining the development of epidemics of foliar pathogens, the efficacy of foliar applied fungicides and the impact of disease on yield; specifically the emergence, expansion and senescence of upper culm leaves in relation to anthesis date. This focus on upper leaves allowed prediction of leaf emergence dates by reference to anthesis, rather than sowing. This avoided the step changes in flag leaf emergence date with temperature, reported with earlier models, without the additional complexity of a stochastic approach. The model is designed to be coupled to models of foliar disease, where the primary effect on yield is via reduction in green canopy area and hence interception of photosynthetically active radiation. Mechanisms were incorporated to allow observations of crop development during the growing season to update state variables and adjust parameters affecting future predictions. The model was calibrated using experimental data, and validated against independent observations of crop development on four wheat cultivars across seven contrasting sites in the UK. Anthesis date and upper culm leaf emergence were always predicted within one week of their observed dates.     

Mixed cultures of eukaryotic cells: Cytotoxic processes

The results of studies of mixed eukaryotic cell cultures are reviewed. Such cultures allowin vitro modeling of a broad spectrum of processes happening in a living organism, such as maintenance of homeostasis, differentiation during embryogenesis and ontogeny, different forms of pathology, interaction between normal and transformed cells, and establishment of immunity. Special attention is paid to cytotoxic processes arising in cocultures.     

Cell cycle arrest in Batten disease lymphoblast cells

Batten disease is an inherited neurodegenerative disorder caused by a CLN3 gene mutation. Batten disease is characterized by blindness, seizures, cognitive decline, and early death. Although apoptotic cell death is one of the pathological hallmarks of Batten disease, little is known about the regulatory mechanism of apoptosis in this disease. Since the CLN3 gene is suggested to be involved in the cell cycle in a yeast model, we investigated the cell cycle profile and its regulatory factors in lymphoblast cells from Batten disease patients. We found G1/G0 cell cycle arrest in Batten disease cells, with overexpression of p21, sphingosine, glucosylceramide, and sulfatide as possible cell cycle regulators.     

Phosphate transport processes in eukaryotic cells

Conclusion Much more work has been done on P_i transport processes, even in the last five years, than we have been able to mention in the space available. We have restricted our discussion to studies on mechanisms of transport or transport regulation, identification of transport proteins and their essential amino acids, and isolation, purification, and reconstitution of P_i transport systems. Many valuable studies on the physiology of P_i transport and its regulation and P_i transport in nonepithelial cells have also been conducted. Transport of P_i into and out of organelles other than the mitochondrion is gaining well-deserved attention, as are transport processes in fungi and plants. It is hoped that in another five years many P_i transport processes will be understood in true molecular terms and that this will increase our knowledge of cellular bioenergetics and metabolism.     

Cln3 function is linked to osmoregulation in a Dictyostelium model of Batten disease

Mutations in CLN3 cause a juvenile form of neuronal ceroid lipofuscinosis (NCL), commonly known as Batten disease. Currently, there is no cure for NCL and the mechanisms underlying the disease are not well understood. In the social amoeba Dictyostelium discoideum, the CLN3 homolog, Cln3, localizes predominantly to the contractile vacuole (CV) system. This dynamic organelle functions in osmoregulation, and intriguingly, osmoregulatory defects have been observed in mammalian cell models of CLN3 disease. Therefore, we used Dictyostelium to further study the involvement of CLN3 in this conserved cellular process. First, we assessed the localization of GFP-Cln3 during mitosis and cytokinesis, where CV system function is essential. GFP-Cln3 localized to the CV system during mitosis and cln3^? cells displayed defects in cytokinesis. The recovery of cln3^? cells from hypotonic stress and their progression through multicellular development was delayed and these effects were exaggerated when cells were treated with ammonium chloride. In addition, Cln3-deficiency reduced the viability of cells during hypotonic stress and impaired the integrity of spores. During hypertonic stress, Cln3-deficiency reduced cell viability and inhibited development. We then performed RNA sequencing to gain insight into the molecular pathways underlying the sensitivity of cln3^? cells to osmotic stress. This analysis revealed that cln3-deficiency upregulated the expression of tpp1A, the Dictyostelium homolog of human TPP1/CLN2. We used this information to show a correlated increase in Tpp1 enzymatic activity in cln3^? cells. In total, our study provides new insight in the mechanisms underlying the role of CLN3 in osmoregulation and neurodegeneration.