Search

Simple Summary: It is widely accepted that climate change is a rapidly increasing threat to the aquaculture industry, with the biggest issue being a slow but continuous rise in water temperature and an associated decrease in dissolved oxygen in some areas. In New Zealand fish farms, during the hottest period of the year (January/February), increased water temperatures have been shown to be detrimental to Chinook salmon performance and are associated with mortalities. We report on the responses of Chinook salmon to a chronic, long-term increase in temperature and decrease in oxygen over a three-month period. We also identified, characterised, and developed relevant biomarkers for Chinook salmon and applied them to monitor responses to changes in the fish's environment. This paper provides evidence on how the use of molecular tools, alongside general health and haematological parameters, have the potential to better inform the aquaculture industry of stock health status, thereby enhancing resilience, efficiency, and productivity. In New Zealand, during the hottest periods of the year, some salmon farms in the Marlborough Sounds reach water temperatures above the optimal range for Chinook salmon. High levels of mortality are recorded during these periods, emphasising the importance of understanding thermal stress in this species. In this study, the responses of Chinook salmon (Oncorhynchus tshawytscha) to chronic, long-term changes in temperature and dissolved oxygen were investigated. This is a unique investigation due to the duration of the stress events the fish were exposed to. Health and haematological parameters were analysed alongside gene expression results to determine the effects of thermal stress on Chinook salmon. Six copies of heat shock protein 90 (HSP90) were discovered and characterised: HSP90AA1.1a, HSP90AA1.2a, HSP90AA1.1b, HSP90AA1.2b, HSP90AB1a and HSP90AB1b, as well as two copies of SOD1, named SOD1a and SOD1b. The amino acid sequences contained features similar to those found in other vertebrate HSP90 and SOD1 sequences, and the phylogenetic tree and synteny analysis provided conclusive evidence of their relationship to other vertebrate HSP90 and SOD1 genes. Primers were designed for qPCR to enable the expression of all copies of HSP90 and SOD1 to be analysed. The expression studies showed that HSP90 and SOD1 were downregulated in the liver and spleen in response to longer term exposure to high temperatures and lower dissolved oxygen. HSP90 was also downregulated in the gill; however, the results for SOD1 expression in the gill were not conclusive. This study provides important insights into the physiological and genetic responses of Chinook salmon to temperature and oxygen stress, which are critical for developing sustainable fish aquaculture in an era of changing global climates. [ABSTRACT FROM AUTHOR]

Simple Summary: As COVID-19 shifts from pandemic to endemic, emerging variants may be more or less virulent. Predicting whether an emerging COVID-19 variant has of high risk of causing severe disease is needed to plan for potential burdens on hospital capacity and protecting vulnerable populations. However, it takes time to do laboratory and animal experiments to determine whether a new genetic variant might be more severe, and the results may not be representative of when the virus infects humans. By the time there is epidemiological data on the severity of disease associated with a new variant, it can be too late for designing an optimal public health response. There is a critical need for computer models that can predict severe disease risk from genetic sequence data, which can be obtained from just the first few infections in a potential incoming wave. Two key challenges make computer modeling difficult: (1) sequence changes are complex, and (2) using historical data to predict future disease requires accounting for the confounding effects of changing patient demographics, improving therapeutics, and increased vaccination. In this paper, we introduce a novel interpretable deep learning architecture to solve this problem, demonstrating that it can make robust predictions for emerging variants. Through the COVID-19 pandemic, SARS-CoV-2 has gained and lost multiple mutations in novel or unexpected combinations. Predicting how complex mutations affect COVID-19 disease severity is critical in planning public health responses as the virus continues to evolve. This paper presents a novel computational framework to complement conventional lineage classification and applies it to predict the severe disease potential of viral genetic variation. The transformer-based neural network model architecture has additional layers that provide sample embeddings and sequence-wide attention for interpretation and visualization. First, training a model to predict SARS-CoV-2 taxonomy validates the architecture's interpretability. Second, an interpretable predictive model of disease severity is trained on spike protein sequence and patient metadata from GISAID. Confounding effects of changing patient demographics, increasing vaccination rates, and improving treatment over time are addressed by including demographics and case date as independent input to the neural network model. The resulting model can be interpreted to identify potentially significant virus mutations and proves to be a robust predctive tool. Although trained on sequence data obtained entirely before the availability of empirical data for Omicron, the model can predict the Omicron's reduced risk of severe disease, in accord with epidemiological and experimental data. [ABSTRACT FROM AUTHOR]

Simple Summary: This article is mainly about that molecular characterization and expression pattern of leptin in yellow cheek carp (Elopichthys bambusa) and its transcriptional changes in response to fasting and refeeding. In this study, the authors used PCR to clone the CDS of leptin in yellow cheek carp, and analyzed the sequence differences of the gene with other species, constructed the phylogenetic tree, used real-time PCR for analyzing the expression of leptin in different tissues, including the expression of leptin in the brain and liver after fasting–refeeding of yellow cheek carp. This paper found that the full-length cDNA sequence of Eblep was 1140 bp and the length of the open reading frame (ORF), which can encode a protein of 174 amino acids, was 525 bp. The Eblep mRNA transcript was detected in all tested tissues, with the highest expression in the liver and lowest expression in the spleen. It was found that the change in the mRNA expression of EbLep may be an adaptive strategy for different energy levels by studying the expression of EbLep mRNA in the brain and liver under fasting and refeeding. Leptin, a secretory protein encoded by obese genes, plays an important role in regulating feeding and energy metabolism in fish. To study the structure and function of the Leptin gene in yellow cheek carp (Elopichthys bambusa), the full-length cDNA sequence of leptin was cloned, named EbLep. The full-length cDNA of Eblep was 1140 bp, and the length of the open reading frame (ORF), which can encode a protein of 174 amino acids, was 525 bp. The signal peptide was predicted to contain 33 amino acids. Sequence alignment showed that the amino acid sequence of Leptin was conserved in cyprinid fish. Despite large differences between primary structures, the tertiary structure of the EbLep protein was similar to that of the human protein and had four α-helices. The EbLep mRNA transcript was detected in all tested tissues, with the highest expression in the liver and lowest expression in the spleen. In this study, short-term fasting significantly increased the mRNA expression of EbLep in the liver, which returned to a normal level after 6 days of refeeding and was significantly lower than the normal level after 28 days of refeeding. In the brain, the mRNA expression of EbLep significantly decreased during short-term fasting and significantly increased to a higher value than the control group after 1 h of refeeding. It then rapidly decreased to a lower value than the control group after 6 h of refeeding, returning to the normal level after 1 day of refeeding, and significantly decreasing to a lower value than the control group after 28 days of refeeding. To sum up, the change in the mRNA expression of EbLep in the brain and liver may be an adaptive strategy for different energy levels. [ABSTRACT FROM AUTHOR]

Simple Summary: Accurate identification of potential targets for drugs to interact with can accelerate drug development. The identification of drug–target interactions can provide insights into hidden drug efficacy. This paper presents a prediction model based on feature similarity fusion that can identify crucial features of drugs and targets to help predict drug–target interactions. The key to drug discovery is the identification of a target and a corresponding drug compound. Effective identification of drug–target interactions facilitates the development of drug discovery. In this paper, drug similarity and target similarity are considered, and graphical representations are used to extract internal structural information and intermolecular interaction information about drugs and targets. First, drug similarity and target similarity are fused using the similarity network fusion (SNF) method. Then, the graph isomorphic network (GIN) is used to extract the features with information about the internal structure of drug molecules. For target proteins, feature extraction is carried out using TextCNN to efficiently capture the features of target protein sequences. Three different divisions (CVD, CVP, CVT) are used on the standard dataset, and experiments are carried out separately to validate the performance of the model for drug–target interaction prediction. The experimental results show that our method achieves better results on AUC and AUPR. The docking results also show the superiority of the proposed model in predicting drug–target interactions. [ABSTRACT FROM AUTHOR]

Simple Summary: Conotoxins are small, structured components found in the venom of predatory cone snails. They were proven to be valuable probes and models for drug discovery and protein evolution studies. Conotoxins present an opportunity to study protein divergence and discover potential human therapeutic landscapes. Although there is considerable literature on conotoxin evolution and activity, what pushed conotoxin divergence remains unclear. Hence, in this paper, we conducted a two-phase study that investigated conotoxin evolution in terms of divergence, followed by structural analysis to determine the relevant structural elements. By understanding the evolution of conotoxins, we identified patterns that account for their superior specificity. The results revealed similarities based on the cone snail's diet preference. The structural elements are in synch with their target prey preference as if cone snails evolved to fine-tune their conopeptide armory to respond to evolutionary pressures by producing conotoxins selective for their prey of choice. We identified several structural elements that account for this specificity. Conservation patterns are observed within diet subgroups but are divergent from other groups. Predatory cone snails (Conus) developed a sophisticated neuropharmacological mechanism to capture prey, escape against other predators, and deter competitors. Their venom's remarkable specificity for various ion channels and receptors is an evolutionary feat attributable to the venom's variety of peptide components (conotoxins). However, what caused conotoxin divergence remains unclear and may be related to the role of prey shift. Principal component analysis revealed clustering events within diet subgroups indicating peptide sequence similarity patterns based on the prey they subdue. Molecular analyses using multiple sequence alignment and structural element analysis were conducted to observe the events at the molecular level that caused the subgrouping. Three distinct subgroups were identified. Results showed homologous regions and conserved residues within diet subgroups but divergent between other groups. We specified that these structural elements caused subgrouping in alpha conotoxins that may play a role in function specificity. In each diet subgroup, amino acid character, length of intervening amino acids between cysteine residues, and polypeptide length influenced subgrouping. This study provides molecular insights into the role of prey shift, specifically diet preference, in conotoxin divergence. [ABSTRACT FROM AUTHOR]

Simple Summary: Rho family of proteins are involved in cytoskeletal organization, cell mobility and polarity, and are implicated in cancer morphogenesis. The structure and function of the Rho homologs from higher-level organisms are well studied, but not from the lower-level organisms. Such as over 95% of the known structures of Rho GTPases are from higher-order mammalian organisms, with only three structures of Rho homologs reported to date from lower-level, single-celled organisms. In this paper we report the crystal structure of Rho1 from Schizosaccharomyces pombe, also called fission yeast (SpRho1), in complex with GDP in the presence of Mg2+ at 2.63-Å resolution, to broaden our understanding of Rho homologs in lower-level organisms. Although the overall structure is similar to that of known Rho homologs, we observed subtle differences at the Switch I and II regions, in β2 and β3, and in the Rho insert domain and loop from Phe107 to Pro112. Combined with literature and sequence analyses, we suggest that the Switch regions and Rho insert domain may contribute to downstream kinase activation in different species through their interactions with different effectors and regulators; and the conservation and divergence of Rho GTPases among difference species and provide evolutionary insight for SpRho1. While many studies have reported the evolutionary development of Rho GTPases based on their amino acid sequences, the present study, for the first time, explores these evolutionary aspects based on structure. Our analysis indicates that SpRho is evolutionarily closer to HsRhoC than HsRhoA, as previously believed. The Rho protein, a homolog of Ras, is a member of the Ras superfamily of small GTPases. Rho family proteins are involved in cytoskeletal organization, cell mobility, and polarity, and are implicated in cancer morphogenesis. Although Rho homologs from higher-order mammalian organisms are well studied, there are few studies examining Rho proteins in lower-level single-celled organisms. Here, we report on the crystal structure of Rho1 from Schizosaccharomyces pombe (SpRho1) in complex with GDP in the presence of Mg2+ at a 2.78 Å resolution. The overall structure is similar to that of known Rho homologs, including human RhoA, human RhoC, and Aspergillus fumigatus Rho1 (AfRho1), with some exceptions. We observed subtle differences at the Switch I and II regions, in β2 and β3, and in the Rho insert domain and loop from Phe107 to Pro112. Our analysis suggests that SpRho is evolutionarily closer to HsRhoC than HsRhoA, as previously believed. [ABSTRACT FROM AUTHOR]

Simple Summary: Due to most traditional high-throughput experiments are tedious and laborious in identifying potential protein–protein interaction. To better improve accuracy prediction in protein–protein interactions. We proposed a novel computational method that can identify unknown protein–protein interaction efficiently and hope this method can provide a helpful idea and tool for proteomics research. Protein–protein interactions (PPIs) play an essential role in many biological cellular functions. However, it is still tedious and time-consuming to identify protein–protein interactions through traditional experimental methods. For this reason, it is imperative and necessary to develop a computational method for predicting PPIs efficiently. This paper explores a novel computational method for detecting PPIs from protein sequence, the approach which mainly adopts the feature extraction method: Locality Preserving Projections (LPP) and classifier: Rotation Forest (RF). Specifically, we first employ the Position Specific Scoring Matrix (PSSM), which can remain evolutionary information of biological for representing protein sequence efficiently. Then, the LPP descriptor is applied to extract feature vectors from PSSM. The feature vectors are fed into the RF to obtain the final results. The proposed method is applied to two datasets: Yeast and H. pylori, and obtained an average accuracy of 92.81% and 92.56%, respectively. We also compare it with K nearest neighbors (KNN) and support vector machine (SVM) to better evaluate the performance of the proposed method. In summary, all experimental results indicate that the proposed approach is stable and robust for predicting PPIs and promising to be a useful tool for proteomics research. [ABSTRACT FROM AUTHOR]

Simple Summary: The family of coronaviruses comprises a diverse set of strains and variants which cause diseases from the common cold to COVID-19. Moreover, they infect a wide array of hosts from bats, camels, birds, to humans. Studying coronaviruses through the lens of host specificity provides a unique perspective to understanding the evolution, diversity and dynamics of this family. In particular, this can reveal groups of different hosts infected by similar strains, giving clues on strains which were more likely to have evolved to jump from one host to another. In this work, we frame host specificity as a classification task, in designing a very compact numerical representation of the spike sequences of different coronaviruses. Based on this numerical representation, classification methods are able to detect the target host with high accuracy. Such an approach can used to efficiently scale to large volumes of sequences, in order to unveil trends in the host specificity of different coronavirus strains. The study of host specificity has important connections to the question about the origin of SARS-CoV-2 in humans which led to the COVID-19 pandemic—an important open question. There are speculations that bats are a possible origin. Likewise, there are many closely related (corona)viruses, such as SARS, which was found to be transmitted through civets. The study of the different hosts which can be potential carriers and transmitters of deadly viruses to humans is crucial to understanding, mitigating, and preventing current and future pandemics. In coronaviruses, the surface (S) protein, or spike protein, is important in determining host specificity, since it is the point of contact between the virus and the host cell membrane. In this paper, we classify the hosts of over five thousand coronaviruses from their spike protein sequences, segregating them into clusters of distinct hosts among birds, bats, camels, swine, humans, and weasels, to name a few. We propose a feature embedding based on the well-known position weight matrix (PWM), which we call PWM2Vec, and we use it to generate feature vectors from the spike protein sequences of these coronaviruses. While our embedding is inspired by the success of PWMs in biological applications, such as determining protein function and identifying transcription factor binding sites, we are the first (to the best of our knowledge) to use PWMs from viral sequences to generate fixed-length feature vector representations, and use them in the context of host classification. The results on real world data show that when using PWM2Vec, machine learning classifiers are able to perform comparably to the baseline models in terms of predictive performance and runtime—in some cases, the performance is better. We also measure the importance of different amino acids using information gain to show the amino acids which are important for predicting the host of a given coronavirus. Finally, we perform some statistical analyses on these results to show that our embedding is more compact than the embeddings of the baseline models. [ABSTRACT FROM AUTHOR]