Ulcerative keratitis caused by Acanthamoeba

This article describes first, aspects of the general biology of Acanthamoeba and second, the incidence, pathogenesis, symptoms, diagnosis and treatment of Acanthamoeba keratitis.

Elements of molecular neurobiology

The 1980s have seen spectacular advances in our understanding of the molecular bases of neurobiology. Biological membranes, channel proteins, cytoskeletal elements, and neuroactive peptides have all been illuminated by the molecular approach. The operation of synapses can be seen to be far more subtle and complex than has previously been imagined, and the development of the brain and physical basis of memory have both been illuminated by this new understanding. In addition, some of the ways in which the brain may go wrong can be traced to malfunction at the molecular level. This study attemps a synthesis of this new knowledge, to provide an indication of how an understanding at the molecular level can help towards a theory of the brain in health and disease. The text will be of benefit to undergraduate students of biochemistry, medical science, pharmacy, pharmacology and general biology.

Demographic effects of thatch harvest and implications for sustainable use of irapai palm (Lepidocaryum tenue, Mart.), by riverine communities in the Peruvian Amazon

Lepidocaryum tenue Mart. (Arecaceae) is a small, understory palm of terra firme forests of the western and central Amazon basin. Known as irapai, it is used for roof thatch by Amazonian peoples who collect its leaves from the wild and generate income from its fronds and articles fabricated from them. Increasing demand has caused local concern that populations are declining. Cultivation attempts have been unsuccessful. The purpose of this study was to investigate market conditions and quantify population dynamics and demographic responses of harvested and unharvested irapai growing near Iquitos, Peru. ^ Ethnobotanical research included participant surveys to determine movement of thatch tiles, called crisnejas, through Moronacocha Port. I also conducted a seed germination trial, and for four years studied five populations growing in communities with similar topography and soils but different land tenure and management strategies. Stage, survival, leaf production, and reproductive transitions were used to calculate ramet demographic rates and develop population projection matrices. ^ Weavers made an average of 20–30 crisnejas per day (90–130 leaves each), and earned US$0.09 to 0.70 each (US$1.80 to 21.00 per day). Average crisnejas per month sold per vendor was 2,955 with a profit range of US$0.05 to 0.32 per crisneja. Wholesalers worked with capital outlay from US$100 to 400, and an estimated ten to twenty vendors could be found at a given time. Consumers paid between US$0.23 to 1.20 per crisneja. Although differences in demographic rates by location existed, most were not significant enough to attribute to management. ^ After 60 months, mean seed germination rate was 19.5% in all media (37.9% in peat). Seedling survival was less than two percent after twelve months. Annual palm mortality was three percent, and occurred disproportionately in small (<50 cm) palms. Small palms grew more in height. Unharvested palms grew less than harvested palms. Large palms (≥50 cm) produced more leaves, were more likely to reproduce, and collectors harvested them more frequently. Reproductive potentials (sexual and asexual) were low. Population growth rates were greater than or not significantly different from 1.0, indicating populations maintained or increased in size. Current levels of irapai harvest appear sustainable. DNA analysis of stems and recruits is recommended to understand population composition and stage-specific asexual fecundity. ^

Glycogen Synthase Kinase 3 influences cell motility and chemotaxis by regulating phosphatidylinositol 3 kinase localization in Dictyostelium discoideum

Glycogen Synthase Kinase 3 (GSK3), a serine/threonine kinase initially characterized in the context of glycogen metabolism, has been repeatedly realized as a multitasking protein that can regulate numerous cellular events in both metazoa and protozoa. I recently found GSK3 plays a role in regulating chemotaxis, a guided cell movement in response to an external chemical gradient, in one of the best studied model systems for chemotaxis - Dictyostelium discoideum. ^ It was initially found that comparing to wild type cells, gsk3 - cells showed aberrant chemotaxis with a significant decrease in both speed and chemotactic indices. In Dictyostelium, phosphatidylinositol 3,4,5-triphosphate (PIP3) signaling is one of the best characterized pathways that regulate chemotaxis. Molecular analysis uncovered that gsk3- cells suffer from high basal level of PIP3, the product of PI3K. Upon chemoattractant cAMP stimulation, wild type cells displayed a transient increase in the level of PIP3. In contrast, gsk3- cells exhibited neither significant increase nor adaptation. On the other hand, no aberrant dynamic of phosphatase and tensin homolog (PTEN), which antagonizes PI3K function, was observed. Upon membrane localization of PI3K, PI3K become activated by Ras, which will in turn further facilitate membrane localization of PI3K in an F-Actin dependent manner. The gsk3- cells treated with F-Actin inhibitor Latrunculin-A showed no significant difference in the PIP3 level. ^ I also showed GSK3 affected the phosphorylation level of the localization domain of PI3K1 (PI3K1-LD). PI3K1-LD proteins from gsk3- cells displayed less phosphorylation on serine residues compared to that from wild type cells. When the potential GSK3 phosphorylation sites of PI3K1-LD were substituted with aspartic acids (Phosphomimetic substitution), its membrane localization was suppressed in gsk3- cells. When these serine residues of PI3K1-LD were substituted with alanine, aberrantly high level of membrane localization of the PI3K1-LD was monitored in wild type cells. Wild type, phosphomimetic, and alanine substitution of PI3K1-LD fused with GFP proteins also displayed identical localization behavior as suggested by the cell fraction studies. Lastly, I identified that all three potential GSK3 phosphorylation sites on PI3K1-LD could be phosphorylated in vitro by GSK3.^

Mutation at the Human D1S80 Minisatellite Locus

Little is known about the general biology of minisatellites. The purpose of this study is to examine repeat mutations from the D1S80 minisatellite locus by sequence analysis to elucidate the mutational process at this locus. This is a highly polymorphic minisatellite locus, located in the subtelomeric region of chromosome 1. We have analyzed 90,000 human germline transmission events and found seven (7) mutations at this locus. The D1S80 alleles of the parentage trio, the child, mother, and the alleged father were sequenced and the origin of the mutation was determined. Using American Association of Blood Banks (AABB) guidelines, we found a male mutation rate of 1 . 0 4 × 1 0− 4 and a female mutation rate of 5 . 1 8 × 1 0− 5 with an overall mutation rate of approximately 7 . 7 7 × 1 0− 5. Also, in this study, we found that the identified mutations are in close proximity to the center of the repeat array rather than at the ends of the repeat array. Several studies have examined the mutational mechanisms of the minisatellites according to infinite allele model (IAM) and the one-step stepwise mutation model (SMM). In this study, we found that this locus fits into the one-step mutation model (SMM) mechanism in six out of seven instances similar to STR loci.

Vidéos contre lectures: Une évaluation de l'utilisation de vidéos pour accomplir la construction initiale de connaissances

Abstract : The goal of this study was to determine whether providing videos for students to watch before class would be more effective than assigning readings. The study took place within a flipped classroom: a methodology designed to engage students in the initial construction of knowledge before class, freeing up classroom time for active learning pedagogies. Preparing for class by watching videos should require less of the students’ time than doing readings, and they should respond better to videos than to readings because these more closely mimic this generation’s interactions with information and media. Consequently, flipped classroom students provided with videos should perceive a lower workload, which could translate into more positive learning outcomes. From an instructor’s perspective, however, developing and organizing videos is extremely time consuming. Thus, a teacher giving consideration to flipping their class would likely want to know whether videos would lead to positive outcomes for their students before actually committing to developing these. However, no research to date was identified which has examined the question of whether flipped class videos would be more effective than readings. The hypotheses for the study were that videos would result in measurable learning gains for the students, and would lead to lower time demands and perceived workloads, as well as more positive attitudes. These were tested using a quasi-experimental design involving a convenience sample of two small college General Biology 1 courses taught by the same teacher. One group had videos to watch before class for the first 1/3 of the course (treatment; Class A), during which the other was assigned readings (control; Class B). Following this, both groups were provided with videos. Student scores were compared on pre-instruction and in-class quizzes, activities, four unit tests, and a final exam. Further, students completed a 44 item survey as well as a demographic questionnaire. Results suggest greater learning gains for students provided with videos. Certainly, students from Class B improved significantly when provided with videos, especially as compared to Class A, whose improvement over the same time span was marginal. However, conclusions based on these results are somewhat tentative, as Class A performed rather poorly on all summative assessments, and this could have driven the patterns observed, at least partially. From the surveys, Class B students reported that they spent more time preparing for class, were less likely to do the necessary preparations, and generally perceived their effort and workload levels to be higher. These factors were significant enough that they contributed to four students from Class B (10% of the class) dropping the course over the semester. In addition, students from both groups also reported more positive attitudes towards videos than readings, although they did not necessarily feel that videos were (or would be) a more effective study and learning tool. The results of this study suggest that any effort on the part of an instructor to prepare or organize videos as pre-class instructional tools would likely be well spent. However, even outside of the context of a flipped classroom, this study provides an indication that assigned readings can place heavy workload requirements on students, which should give cause for any instructor employing mandatory readings to reassess their approach. Finally, since both groups were statistically equivalent across all measured demographic variables, it appears that some of the observed disparities in assessment scores may have been driven by differences in group dynamics. Consequently, the suggestion is made that an instrument to measure classroom climate should be incorporated into any research design comparing two or more interacting groups of students, as group dynamics have the potential to play a key role in any outcomes.||Résumé : L'objectif de cette étude était de déterminer si fournir des vidéos aux étudiants avant une classe serait plus efficace comme méthode d’apprentissage individuel que de leur donner une liste de lectures à compléter. L'étude a eu lieu dans une classe renversée – une stratégie plus reconnu sous le nom de «classroom flipping» – ce qui ce trouve à être une méthodologie qui vise à obliger les élèves d’accomplir le transfert de connaissances initial avant la classe, en vue de libérer du temps de classe pour des activités pédagogiques plus approfondie. En théorie, pour les élèves, se préparer pour une classe renversé en regardant des vidéos devrait exiger moins de temps que d’être obligé à apprendre le matériel en lisant. En plus, présenter le matériel d’un cours avec des vidéos imite de plus près les genres d’interactions qu’on les étudiants de cette génération avec de l'information et les médias, ce qui devrait faciliter leur tâche. Par conséquent, les élèves d’une classe renversée fournies avec des vidéos devraient percevoir une charge de travail moins élevée, et ceci pourrait se traduire en bilans d'apprentissage plus positifs. Cependant, du point de vue du professeur, avoir à développer et organiser des vidéos se présente comme un gros défi, surtout en vue du temps et de l’effort qui sont requis. Ainsi, un enseignant qui songe à renversée sa classe voudrait probablement savoir si le fait d’offrir des vidéos mène à des résultats positifs avant de réellement s'engager dans le développement de ces derniers. Par contre, lors de l’écriture de ce texte, aucune étude n’a été identifié qui répond à cette question, et aucune publication compare la performance des étudiants lorsqu’ils ont des vidéos à regarder avec lorsqu’ils sont obligés de faire de la lecture pour se préparer. Alors, les hypothèses de l'étude étaient que des étudiants ayant accès à des vidéos démontreraient des gains d’apprentissages évidents, qu’ils apercevraient des requêtes de temps moins encombrantes et une charge de travail plus faible, et, en vue de ces derniers, que les étudiants auraient des attitudes plus positives envers le cours et le matériel. Les hypothèses ont été testés à l'aide d'un modèle quasi-expérimental, avec comme échantillon deux classes collégiales de Biologie générale 1, tout les deux enseignés par le même professeur. Un de ces groupes avaient accès à des vidéos pour se préparer pour chaque classe lors du premier tiers du cours, alors que l’autre groupe étaient obligé de faire de la lecture. Après le premier tiers du cours, ce qui fut 10 des 30 classes du semestre, les deux groupes ont été fournis avec des vidéos pour le restant du cours. Des notes ont été ramassées et comparées sur des mini-examens préparatoires avant et durant les classes, sur des activités complétées en classe, sur quatre examens en classe, et un examen final. En outre, les étudiants ont rempli un questionnaire composé de 44 items, ainsi qu’un autre questionnaire démographique. Les résultats de l’étude suggèrent qu’une décision d’offrir des vidéos aux élèves peut mener à des gains d'apprentissage plus élevés comparativement à l’option lecture. En particulier, les élèves du groupe initial de lecture se sont considérablement améliorées lorsqu'ils ont été fournis avec des vidéos, surtout par rapport au groupe initial de vidéos, dont l’amélioration durant la même période était marginale. Cependant, ces conclusions sont un peu incertaines, parce que la performance du groupe initial de vidéos était globalement médiocre, ce qui aurait pu mener aux résultats observés. Par contre, les résultats obtenus des questionnaires étaient moins incertains, et indiquent que les élèves qui se sont vues attribués des lectures passaient plus de temps pour préparer leurs classes, étaient plus aptes à ne pas faire les préparatifs nécessaires, et ont aperçus leurs niveaux d'efforts et leurs charges de travails comme étant plus élevés. Ces facteurs étaient suffisamment importants qu'ils ont contribué au fait que quatre étudiants du groupe de lecture, soit 10% de la classe, ont abandonnés le cours durant le premier tiers du semestre. Finalement, les élèves ont démontrés des attitudes plus positives envers les vidéos, bien qu'ils ne trouvaient pas nécessairement que ceux-ci étaient plus efficaces que les lectures lorsqu’ils voulaient étudier pour les examens. Basé sur ces résultats, il est possible de conclure que tout effort de la part d'un instructeur pour préparer ou organiser des vidéos pédagogiques serait probablement un bon investissement. En plus, et même en dehors du contexte d'une classe renversée, cette étude offre une indication qu’une stratégie pédagogique qui oblige les étudiants à faire beaucoup de lecture peut imposer des exigences et une charge de travail très élevée pour les étudiants, ce qui devrait donner cause à tout instructeur qui attribue des lectures à réévaluer leur approche. Enfin, puisque les deux groupes étaient équivalents d’un point de vue statistique sur toutes les mesures démographiques, il semble que certaines disparités entre les deux groupes dans les notes d'évaluation et d’examens peuvent possiblement avoir été entraînées par des différentes dynamiques dans chaque group. Par conséquent, il est suggéré que des mesures de relations entre étudiants et de dynamiques de groupes devraient être incorporé dans n’importe qu’elle recherche comparant deux ou plusieurs groupes d’étudiants, et surtout quand ces étudiants sont en interaction, parce-que en toute apparence les dynamiques de groupes ont le potentiel de jouer un rôle clé dans les résultats obtenus.

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

A text-book of biology for students in general, medical and technical courses,

Mode of access: Internet.

General cytology; a textbook of cellular structure and function for students of biology and medicine,

Bibliography at end of most of the sections.

Aspects of the biology of the yabby Trypea australiensis (Dana) (Decapoda : Thalassinidea) and the potential of burrow counts as an indirect measure of population density

The thalassinidean shrimp Trypea australiensis (the yabby) commonly occurs on intertidal sandflats and subtidal regions of sheltered embayments and estuaries along the east coast of Australia and is harvested commercially and recreationally for use as bait by anglers. The potential for counts of burrow openings to provide a reliable indirect estimate of the abundance of yabbies was examined on intertidal sandflats on North Stradbroke Island (Queensland, Australia). The relationship between the number of burrow openings and the abundance of yabbies was generally poor and also varied significantly through time, casting doubt on previous estimates of abundance for this species based on unvalidated hole counts. Spatial and temporal variation in population density, the size at maturity and the reproductive period of the yabby were also assessed. Except for an initial peak in abundance as a result of recruitment, the density of yabbies was constant throughout the study but considerably less than that estimated from a previous study in the same area. Ovigerous females were recorded at 3 mm carapace length (CL) which is smaller than previously recorded for this species and thalassinideans in general. Small ovigerous females were found throughout the study, including the summer months, which is unusual for thalassinideans in the intertidal zone. It was hypothesised that in the intertidal zone, small female yabbies may be able to balance the metabolic demands of reproduction and respiration at higher temperatures than can larger females allowing them to reproduce in the warmer months.

The cell biology of atherosclerosis - new developments

In the development of atherosclerotic lesions, three basic processes occur: 1) invasion of the artery wall by leucocytes, particularly monocytes and T-lymphocytes; 2) smooth muscle phenotypic modulation, proliferation, and synthesis of extracellular matrix; and 3) intracellular (macrophage and smooth muscle) lipoprotein uptake and lipid accumulation. Invasion of the vessel wall by leucocytes is mediated through the expression of adhesion molecules on both leucocytes and the endothelium making them 'sticky'. The adhesion molecules are induced by high serum cholesterol levels or complement fragments. Leucocytes which have adhered to the endothelium are chemo-attracted into the vessel wall by cytokines produced by early arriving leucocytes or by low density lipoprotein which has passively passed into the wall, in the process being trapped and oxidised. The oxidised low density lipoprotein is taken up by scavenger receptors (which are not subject to down-regulation) on both macrophages and smooth muscle cells. The overaccumulation of lipid is toxic to the cells and they die contributing to the central necrotic core. The macrophages and T-lymphocytes produce substances which induce smooth muscle cells of the artery wall to change from a 'contractile' (high volume fraction of myofilaments [V(v)myo]) to a 'synthetic' (low V(v)myo) phenotype. In this altered state they respond to growth factors released from macrophages, platelets, regenerating endothelial cells and smooth muscle cells; produce large amounts of matrix; express lipoprotein scavenger receptors; express adhesion molecules for leucocytes; and express HLA-DR following exposure to the T-lymphocyte product, IFN-delta, suggesting that they can become involved in a generalised immune reaction.

APOE polymorphism is associated with lipid profile, but not with arterial stiffness in the general population

Background: Cardiovascular diseases (CVD) are the main cause of death and disability in developed countries. In most cases, the progress of CVD is influenced by environmental factors and multifactorial inheritance. The purpose of this study was to investigate the association between APOE genotypes, cardiovascular risk factors, and a noninvasive measure of arterial stiffness in the Brazilian population. Methods: A total of 1493 urban Brazilian individuals were randomly selected from the general population of the Vitoria City Metropolitan area. Genetic analysis of the APOE polymorphism was conducted by PCR-RFLP and pulse wave velocity analyzed with a noninvasive automatic device. Results: Age, gender, body mass index, triglycerides, creatinine, uric acid, blood glucose, blood pressure phenotypes were no different between epsilon 2, epsilon 3 and epsilon 4 alleles. The epsilon 4 allele was associated with higher total-cholesterol (p < 0.001), LDL-C (p < 0.001), total-cholesterol/HDL-C ratio (p < 0.001), LDL/HDL-C ratio (p < 0.001), lower HDL-C values (p < 0.001) and higher risk to obesity (OR = 1.358, 95% CI = 1.019-1.811) and hyperuricemia (OR = 1.748, 95% CI = 1.170-2.611). Nevertheless, pulse wave velocity (p = 0.66) measures were no different between genotypes. The significant association between APOE genotypes and lipid levels persisted after a 5-year follow-up interval, but no interaction between time and genotype was observed for lipids longitudinal behavior. Conclusion: The epsilon 4 allele of the APOE gene is associated with a worse lipid profile in the Brazilian urban population. In our relatively young sample, the observed effect of APOE genotype on lipid levels was not translated into significant effects in arterial wall stiffness.

A general model for host plant selection in phytophagous insects

We develop a general theoretical framework for exploring the host plant selection behaviour of herbivorous insects. This model can be used to address a number of questions, including the evolution of specialists, generalists, preference hierarchies, and learning. We use our model to: (i) demonstrate the consequences of the extent to which the reproductive success of a foraging female is limited by the rate at which they find host plants (host limitation) or the number of eggs they carry (egg limitation); (ii) emphasize the different consequences of variation in behaviour before and after landing on (locating) a host (termed pre- and post-alighting, respectively); (iii) show that, in contrast to previous predictions, learning can be favoured in post-alighting behaviour-in particular, individuals can be selected to concentrate oviposition on an abundant low-quality host, whilst ignoring a rare higher-quality host; (iv) emphasize the importance of interactions between mechanisms in favouring specialization or learning. (C) 2002 Elsevier Science Ltd.