Project description:Abstract Old‐growth forests host a rich diversity of invertebrate assemblages. Among them, saproxylic insects play a fundamental role in the nutrient cycle and ecosystem functioning. In these environments, coevolution between insect and plants have reached a stable equilibrium over millions of years. These delicate ecosystems are threatened mainly by habitat loss and fragmentation, and to date, they have to face the new “plastic threat.” Plastics are widespread in all biomes and ecosystems accumulating throughout the years due to their low degradation rate. Once accumulated, large pieces of plastics can be degraded into smaller particles, the latter representing a great threat to biodiversity and ecosystem health, producing detrimental effects on biota. Since the effects of plastics on terrestrial systems remain largely unexplored, this study aimed at contributing to increasing the knowledge on the interaction between plastics and terrestrial biota. We put our emphasis on the novel and broad topic of plastic degradation by saproxylic beetle larvae, describing how they fragmented macroplastics into microplastics. To investigate whether saproxylic cetonid larvae could degrade expanded polystyrene, we performed an experiment. Thus, we put larvae collected in the field in an expanded polystyrene box. We observed that larvae dug in the thickness of the box fragmenting macroplastics into microplastics and producing a total of 3441 particles. Then, we removed the larvae from the EPS box and isolated them in glass jars filled with natural substrate. The substrate was checked for EPS microplastics previously ingested and now egested by larvae. Additionally, we pointed out that plastics remained attached to cetonid larvae setae, with a mean number of 30.7 ± 12.5 items. Although preliminary, our results highlighted that microplastics attached to saproxylic cetonid larvae might be transported into habitats and transferred along the food web. In conclusion, plastic pollution might affect vulnerable species and ecosystem services representing a risk also for human health. Macroplastics are degraded by abiotic factors (e.g., UV rays, wind, and rain) but also by biotic ones (e.g., larvae). Thus, this fragmentation process originates in microplastics that can be ingested by organisms and remain attached to cetonid larvae setae after digging into plastics. Then, microplastics may be transferred along with the food web when larvae are eaten by predators, such as hole‐nesting birds.
Project description:Neurofibromatosis type 1 (NF1) is an autosomal dominant disease with complete penetrance but high variable expressivity. NF1 is caused by loss-of-function mutations in the NF1 gene, a negative regulator of the RAS-MAPK pathway. The NF1 gene has one of the highest mutation rates in human disorders, which may explain the outbreak of independent de novo variants in the same family. Here, we report the co-occurrence of pathogenic variants in the NF1 and SPRED1 genes in six families with NF1 and Legius syndrome, using next-generation sequencing. In five of these families, we observed the co-occurrence of two independent NF1 variants. All NF1 variants were classified as pathogenic, according to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) guidelines. In the sixth family, one sibling inherited a complete deletion of the NF1 gene from her mother and carried a variant of unknown significance in the SPRED1 gene. This variant was also present in her brother, who was diagnosed with Legius syndrome, a differential diagnosis of NF1. This work illustrates the complexity of molecular diagnosis in a not-so-rare genetic disease.
Project description:Chromosome organization by structural maintenance of chromosomes (SMC) complexes is vital to living organisms. SMC complexes were recently found to be motors that extrude DNA loops. However, it remains unclear what happens when multiple complexes encounter one another in vivo on the same DNA and how interactions help organize an active genome. We created a crash-course track system to study SMC complex encounters in vivo by engineering the Bacillus subtilis chromosome to have defined SMC loading sites. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of never-before-seen chromosome folding patterns. Via 3D polymer simulations and theory, we find that these patterns require SMC complexes to bypass each other in vivo, as recently seen in an in vitro study. We posit that the bypassing activity enables SMC complexes to spatially organize a functional and busy genome.
Project description:New detections of thermophiles in psychrobiotic (i.e., bearing cold-tolerant life forms) marine and terrestrial habitats including Arctic marine sediments, Antarctic accretion ice, permafrost, and elsewhere are continually being reported. These microorganisms present great opportunities for microbial ecologists to examine biogeographical processes for spore-formers and non-spore-formers alike, including dispersal histories connecting warm and cold biospheres. In this review, we examine different examples of thermophiles in cryobiotic locations, and highlight exploration of thermophiles at cold temperatures under laboratory conditions. The survival of thermophiles in psychrobiotic environments provokes novel considerations of physiological and molecular mechanisms underlying natural cryopreservation of microorganisms. Cultures of thermophiles maintained at low temperature may serve as a non-sporulating laboratory model for further exploration of metabolic potential of thermophiles at psychrobiotic temperatures, as well as for elucidating molecular mechanisms behind natural preservation and adaptation to psychrobiotic environments. These investigations are highly relevant for the search for life on other cold and icy planets in the Solar System, such as Mars, Europa and Enceladus.
Project description:Cooperation by generalised reciprocity implies that individuals apply the decision rule "help anyone if helped by someone". This mechanism has been shown to generate evolutionarily stable levels of cooperation, but as yet it is unclear how widely this cooperation mechanism is applied among animals. Dogs (Canis familiaris) are highly social animals with considerable cognitive potential and the ability to differentiate between individual social partners. But although dogs can solve complex problems, they may use simple rules for behavioural decisions. Here we show that dogs trained in an instrumental cooperative task to provide food to a social partner help conspecifics more often after receiving help from a dog before. Remarkably, in so doing they show no distinction between partners that had helped them before and completely unfamiliar conspecifics. Apparently, dogs use the simple decision rule characterizing generalised reciprocity, although they are probably capable of using the more complex decision rule of direct reciprocity: "help someone who has helped you". However, generalized reciprocity involves lower information processing costs and is therefore a cheaper cooperation strategy. Our results imply that generalised reciprocity might be applied more commonly than direct reciprocity also in other mutually cooperating animals.
Project description:Next Generation Sequencing (NGS) using capture or amplicons strategies allows the detection of a large number of mutations increasing the rate of positive diagnosis for the patients. However, most of the detected mutations are Single Nucleotide Variants (SNVs) or small indels. Structural Variants (SVs) are often underdiagnosed in inherited genetic diseases, probably because few user-friendly tools are available for biologists or geneticists to identify them easily. We present here the diagnosis of two brothers presenting a demyelinating motor-sensitive neuropathy: a presumed homozygous c.5744_5745delAT in exon 10 of SACS gene was initially detected, while actually these patients were heterozygous for this mutation and harbored a large deletion of SACS exon 10 in the other allele. This hidden mutation has been detected thanks to the user-friendly CovCopCan software. We recommend to systematically use such a software to screen NGS data in order to detect SVs, such as Copy Number Variations, to improve diagnosis of the patients.
Project description:It is often difficult to determine which of the sequence and structural differences between divergent members of multigene families are functionally important. Here we use a laboratory evolution approach to determine functionally important structural differences between two distantly related disulfide isomerases, DsbC and DsbG from Escherichia coli. Surprisingly, we found single amino acid substitutions in DsbG that were able to complement dsbC in vivo and have more DsbC-like isomerase activity in vitro. Crystal structures of the three strongest point mutants, DsbG K113E, DsbG V216M, and DsbG T200M, reveal changes in highly surface-exposed regions that cause DsbG to more closely resemble the distantly related DsbC. In this case, laboratory evolution appears to have taken a direct route to allow one protein family member to complement another, with single substitutions apparently bypassing much of the need for multiple changes that took place over approximately 0.5 billion years of evolution. Our findings suggest that, for these two proteins at least, regions important in determining functional differences may represent only a tiny fraction of the overall protein structure.
Project description:Abstract: Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. To probe these mechanisms, we perform a forward genetic screen for mutants with enhanced O2 perception in C. elegans. Multiple mutants exhibiting increased responsiveness to O2 concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL chemosensory neurons. We find that ADL’s responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1 and other sensory defective mutants resulting in an enhanced neurosecretion. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling of ADL neurons indicates its acquired O2-evoked neurosecretion is the result of a transcriptional reprogramming that up-regulates neuropeptide signalling. We show that the conserved neuropeptide receptor NPR-22 is necessary and sufficient in ADL to enhance its neurosecretion levels. Sensory loss can thus confer cross-modal plasticity by re-wiring peptidergic circuits.
Project description:Although the anatomical arrangement of brain regions and the functional structures within them are similar across individuals, the representation of neural information, such as recorded brain activity, varies among individuals owing to various factors. Therefore, appropriate conversion and translation of brain information is essential when decoding neural information using a model trained using another person's data or to achieving brain-to-brain communication. We propose a brain representation transfer method that involves transforming a data representation obtained from one person's brain into that obtained from another person's brain, without relying on corresponding label information between the transferred datasets. We defined the requirements to enable such brain representation transfer and developed an algorithm that distills the assumption of common similarity structure across the brain datasets into a rotational and reflectional transformation across low-dimensional hyperspheres using encoders for non-linear dimensional reduction. We first validated our proposed method using data from artificial neural networks as substitute neural activity and examining various experimental factors. We then evaluated the applicability of our method to real brain activity using functional magnetic resonance imaging response data acquired from human participants. The results of these validation experiments showed that our method successfully performed representation transfer and achieved transformations in some cases that were similar to those obtained when using corresponding label information. Additionally, we reconstructed images from individuals' data without training personalized decoders by performing brain representation transfer. The results suggest that our unsupervised transfer method is useful for the reapplication of existing models personalized to specific participants and datasets to decode brain information from other individuals. Our findings also serve as a proof of concept for the methodology, enabling the exchange of the latent properties of neural information representing individuals' sensations.
Project description:Theoretical models of disease dynamics on networks can aid our understanding of how infectious diseases spread through a population. Models that incorporate decision-making mechanisms can furthermore capture how behaviour-driven aspects of transmission such as vaccination choices and the use of non-pharmaceutical interventions (NPIs) interact with disease dynamics. However, these two interventions are usually modelled separately. Here, we construct a simulation model of influenza transmission through a contact network, where individuals can choose whether to become vaccinated and/or practice NPIs. These decisions are based on previous experience with the disease, the current state of infection amongst one's contacts, and the personal and social impacts of the choices they make. We find that the interventions interfere with one another: because of negative feedback between intervention uptake and infection prevalence, it is difficult to simultaneously increase uptake of all interventions by changing utilities or perceived risks. However, on account of vaccine efficacy being higher than NPI efficacy, measures to expand NPI practice have only a small net impact on influenza incidence due to strongly mitigating feedback from vaccinating behaviour, whereas expanding vaccine uptake causes a significant net reduction in influenza incidence, despite the reduction of NPI practice in response. As a result, measures that support expansion of only vaccination (such as reducing vaccine cost), or measures that simultaneously support vaccination and NPIs (such as emphasizing harms of influenza infection, or satisfaction from preventing infection in others through both interventions) can significantly reduce influenza incidence, whereas measures that only support expansion of NPI practice (such as making hand sanitizers more available) have little net impact on influenza incidence. (However, measures that improve NPI efficacy may fare better.) We conclude that the impact of interference on programs relying on multiple interventions should be more carefully studied, for both influenza and other infectious diseases.