Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies

Background  

All polypeptide backbones have the potential to form amyloid fibrils, which are associated with a number of degenerative disorders. However, the likelihood that amyloidosis would actually occur under physiological conditions depends largely on the amino acid composition of a protein. We explore using a naive Bayesian classifier and a weighted decision tree for predicting the amyloidogenicity of immunoglobulin sequences.     

Flying over water: how “On bird species diversity” influenced aquatic ecology

Habitat complexity has long been known to influence animal community structure by increasing the number of available habitats. Fifty years have passed since MacArthur brothers published the seminal paper “On bird species diversity”, which revolutionized studies of habitat structure. This paper first evidenced and quantified the relationship between species diversity (birds) and habitat structural complexity (the number of stratified layers of landscape vegetation). In this article, we aim to pay homage to R. H. MacArthur’s contribution and to briefly analyze the citation history and influence of “On bird species diversity”, focusing primarily on aquatic studies. We searched for all papers that cited “On bird species diversity” on Thomson Reuters (ISI—Web of Knowledge) and analyzed them for temporal citation trends. In addition, considering only aquatic papers, we explored whether and how habitat complexity was measured, as well as the ecological organization level, attributes of organisms, taxonomic groups and study design (observational or experimental). “On bird species diversity” citations increased over time, but this paper was less cited by limnologists compared to terrestrial and marine scientists. The majority of investigations in aquatic ecosystems quantified habitat complexity, but few used mathematical modeling. The high number of citations, which continues to increase, shows the great influence of “On bird species diversity” on ecological studies and typifies it as a classic in the ecological literature. However, the low citation frequency found in papers devoted to freshwater ecosystems indicates that limnologists in general neglect this original contribution in studies of habitat complexity.     

Soil seed bank in a patchy vegetation of coastal sandy plains in southeastern Brazil

Large seed banks have been found in tropical dry forests and also in habitats with high seasonality in rainfall. However, patchily structured vegetation could induce great spatial variation in the seed bank. We characterized the seed bank in a patchy vegetation of restinga, a common type of coastal vegetation found in the Atlantic forest biome. We also evaluated whether there is any spatial variation between the litter and soil layer, bare sand, and the edge and center of vegetation patches with distinct species dominance. We found 104 seeds/m² in the seed bank using a 5‐cm‐depth sampling. Seven out of 16 species found in the restinga seed bank germinated; two of these were found in the early stages of vegetation patches. We found a higher number of seeds at the edge than in the center of vegetation patches. However, there were no significant differences in the number of seeds in the seed bank between the litter and soil layer, and between vegetation patches with distinct species dominance. Bare sandy soils had lower seed bank densities than vegetation patches. A small seed bank size might be explained by the low proportion of seeds from herbaceous and woody species, which are pioneers in the Atlantic forest. However, seed bank might play an important role in the early stages of the successional process, due to the occurrence of the few species that are able to colonize new young vegetation patches.     

Localization of GABA- and glutamate-like immunoreactivity in the cardiac ganglion of the lobster Panulirus argus

Wholemount immunohistochemical methods were used to examine the localization of γ-aminobutyric acid (GABA) and glutamate within the cardiac system of the Caribbean spiny lobster Panulirus argus. All of the GABA-like immunoreactivity (GABAi) in the cardiac ganglion originated from a single bilateral pair of fibers that entered the heart via the two dorsal nerves. Each GABAi axon bifurcated upon entering the ganglion and gave rise to varicose fibers that surrounded the somata and initial segments of the five large motor neurons. The four small posterior cells did not appear to receive somatic contacts. Double-labeling experiments in which individual motor neurons were injected with Neurobiotin showed that their dendritic processes, which project to muscle bundles adjacent to the ganglion and are thought to respond to stretch, were also accompanied by branches of the GABAi fibers. Glutamate-like immunoreactivity (GLUi) was present in each of the motor neuron cell bodies. In some preparations, GLUi was also detected in large caliber fibers in the major ganglionic nerves. These fibers gave rise to more slender branches that innervated the cardiac muscle bundles. GLUi was also found in the small cell bodies and in fibers surrounding motor neuron somata. Taken together, these findings support previous electrophysiological, pharmacological and anatomical studies indicating that GABA mediates extrinsic inhibition and that glutamate acts as a neuromuscular and intraganglionic transmitter in this system. While axosomatic contacts may play a major role in both transmitter systems, the GABAergic inhibition also appears to involve substantial axodendritic synaptic signaling.     

Alarm scent-marking during predatory attempts in the Cabrera vole (Microtus cabrerae Thomas, 1906)

The alarm pheromones often released by animals under stressful situations seem to elicit behavioral changes in conspecifics, which in the appropriate context can be viewed as anti-predatory responses. However, the releasing of alarm pheromones associated with predatory events has not been demonstrated in mammals. In the current study with wild-caught Cabrera voles, we carried out experiments in the laboratory and in the field to assess the release of alarm pheromones in scent-marks during simulated predatory events and disclose their effects on conspecifics. We first conducted an assay wherein voles where let to scent-mark a clean substrate in the absence of disturbance (control) and under the simulation of predatory events. Contrarily to the control, no fecal boli were released and the area marked with urine was significantly larger during the predatory simulation. In a subsequent assay, we assessed the voles’ preference between urine-marks released under predatory simulation and in control conditions. Voles showed a significant preference by control substrates. Finally, a third assay was carried out in the vole’s habitat wherein the individual activity was monitored by radio-tracking before and after placement of urine-marks obtained during the conditions described above. The vole’s activity was only reduced near the urine-marks released during the simulated predatory events. The results suggest that: (1) during predatory attempts, Cabrera voles release an alarm pheromone in their urine-marks; (2) the putative alarm pheromone reduces the voles’ activity in the surroundings of the marked area; (3) the putative alarm pheromone persists in the field affecting conspecifics’ activity for several days.     

Cryptophytes: An emerging algal group in the rapidly changing Antarctic Peninsula marine environments

The western Antarctic Peninsula (WAP) is a climatically sensitive region where foundational changes at the basis of the food web have been recorded; cryptophytes are gradually outgrowing diatoms together with a decreased size spectrum of the phytoplankton community. Based on a 11-year (2008–2018) in-situ dataset, we demonstrate a strong coupling between biomass accumulation of cryptophytes, summer upper ocean stability, and the mixed layer depth. Our results shed light on the environmental conditions favoring the cryptophyte success in coastal regions of the WAP, especially during situations of shallower mixed layers associated with lower diatom biomass, which evidences a clear competition or niche segregation between diatoms and cryptophytes. We also unravel the cryptophyte photo-physiological niche by exploring its capacity to thrive under high light stress normally found in confined stratified upper layers. Such conditions are becoming more frequent in the Antarctic coastal waters and will likely have significant future implications at various levels of the marine food web. The competitive advantage of cryptophytes in environments with significant light level fluctuations was supported by laboratory experiments that revealed a high flexibility of cryptophytes to grow in different light conditions driven by a fast photo-regulating response. All tested physiological parameters support the hypothesis that cryptophytes are highly flexible regarding their growing light conditions and extremely efficient in rapidly photo-regulating changes to environmental light levels. This plasticity would give them a competitive advantage in exploiting an ecological niche where light levels fluctuate quickly. These findings provide new insights on niche separation between diatoms and cryptophytes, which is vital for a thorough understanding of the WAP marine ecosystem.