Issues In Biological Sciences Research Articles

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding

Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail problem, with a large number of GO families containing few annotated proteins. Herein, an innovative strategy named AnnoPRO was therefore constructed by enabling sequence-based multi-scale protein representation, dual-path protein encoding using pre-training, and function annotation by long short-term memory-based decoding. A variety of case studies based on different benchmarks were conducted, which confirmed the superior performance of AnnoPRO among available methods. Source code and models have been made freely available at: https://github.com/idrblab/AnnoPRO and https://zenodo.org/records/10012272

Evolutionary processes driving spatial patterns of intraspecific genetic diversity in river ecosystems.

Describing, understanding and predicting the spatial distribution of genetic diversity is a central issue in biological sciences. In river landscapes, it is generally predicted that neutral genetic diversity should increase downstream, but there have been few attempts to test and validate this assumption across taxonomic groups. Moreover, it is still unclear what are the evolutionary processes that may generate this apparent spatial pattern of diversity. Here, we quantitatively synthesized published results from diverse taxa living in river ecosystems, and we performed a meta-analysis to show that a downstream increase in intraspecific genetic diversity (DIGD) actually constitutes a general spatial pattern of biodiversity that is repeatable across taxa. We further demonstrated that DIGD was stronger for strictly waterborne dispersing than for overland dispersing species. However, for a restricted data set focusing on fishes, there was no evidence that DIGD was related to particular species traits. We then searched for general processes underlying DIGD by simulating genetic data in dendritic-like river systems. Simulations revealed that the three processes we considered (downstream-biased dispersal, increase in habitat availability downstream and upstream-directed colonization) might generate DIGD. Using random forest models, we identified from simulations a set of highly informative summary statistics allowing discriminating among the processes causing DIGD. Finally, combining these discriminant statistics and approximate Bayesian computations on a set of twelve empirical case studies, we hypothesized that DIGD were most likely due to the interaction of two of these three processes and that contrary to expectation, they were not solely caused by downstream-biased dispersal.

‘Engaging in an argumentative discourse’- narratives from biology classrooms

The present paper delves into the classroom dynamics of Biology classrooms taking into account teaching learning processes associated with some of the ethical issues in Biological Sciences. Argumentation and debate appear to be the major transactional approaches adopted by teachers for dealing with these issues. The classroom discourses emanating from teacher student conversations have been analysed on four planes, viz., ethical, social context, interactional context and personal agency of the teacher. Toulmin’s method of argument analysis has been used in order to analyse the level of arguments of both teachers and their students. The findings reveal significant differences on all the four planes at K‐12 and Undergraduate levels and, have implications for building upon teachers’ pedagogical content knowledge (PCK) with respect to ethical issues.

Editorial: Lipid Rafts and Amyloidogenesis

Lipid Rafts and Amyloidogenesis Lipid rafts are the membrane microdomains enriched in cholesterol and sphingolipids, which play important roles in such cellular processes as protein sorting and signal transduction. Lipid rafts have recently received significant attention as they have been shown to be important regions for the generation and accumulation of β-amyloid peptide (Aβ), the main culprit in the pathogenesis of Alzheimer’s disease. For instance, the proteases responsible for the production of Aβ are localized to lipid rafts, and rafts appear to be involved in the pathological aggregation of Aβ. Thus, the relationship between lipid rafts and amyloidogenesis is considered a critical issue to be investigated. In addition, modulation of lipid rafts is an interesting issue in biological sciences. In this special issue, the first two articles by Wataru Araki and Madepalli K. Lakshmana focus on the relation between lipid rafts and the mechanisms of Aβ generation, and the third article by Gunter P. Eckert mainly deals with the manipulation of lipid rafts in neuronal cells. I hope that this special issue provides informative unique collection of minireviews which highlight the significance of lipid rafts in amyloidogenesis.

Editorial: Lipid Rafts and Amyloidogenesis

Lipid Rafts and Amyloidogenesis Lipid rafts are the membrane microdomains enriched in cholesterol and sphingolipids, which play important roles in such cellular processes as protein sorting and signal transduction. Lipid rafts have recently received significant attention as they have been shown to be important regions for the generation and accumulation of β-amyloid peptide (Aβ), the main culprit in the pathogenesis of Alzheimer’s disease. For instance, the proteases responsible for the production of Aβ are localized to lipid rafts, and rafts appear to be involved in the pathological aggregation of Aβ. Thus, the relationship between lipid rafts and amyloidogenesis is considered a critical issue to be investigated. In addition, modulation of lipid rafts is an interesting issue in biological sciences. In this special issue, the first two articles by Wataru Araki and Madepalli K. Lakshmana focus on the relation between lipid rafts and the mechanisms of Aβ generation, and the third article by Gunter P. Eckert mainly deals with the manipulation of lipid rafts in neuronal cells. I hope that this special issue provides informative unique collection of minireviews which highlight the significance of lipid rafts in amyloidogenesis.