Comparative transcriptome analyses reveal the genetic basis underlying the immune function of three amphibians' skin

Improving the Accuracy of Continuous Blood Glucose Measurement Using Personalized Calibration and Machine Learning

Despite tremendous developments in continuous blood glucose measurement (CBGM) sensors, they are still not accurate for all patients with diabetes. As glucose concentration in the blood is <1% of the total blood volume, it is challenging to accurately measure glucose levels in the interstitial fluid using CBGM sensors due to within-patient and between-patient variations. To address this issue, we developed a novel data-driven approach to accurately predict CBGM values using personalized calibration and machine learning. First, we scientifically divided measured blood glucose into smaller groups, namely, hypoglycemia (<80 mg/dL), nondiabetic (81-115 mg/dL), prediabetes (116-150 mg/dL), diabetes (151-181 mg/dL), severe diabetes (181-250 mg/dL), and critical diabetes (>250 mg/dL). Second, we separately trained each group using different machine learning models based on patients' personalized parameters, such as physical activity, posture, heart rate, breath rate, skin temperature, and food intake. Lastly, we used multilayer perceptron (MLP) for the D1NAMO dataset (training to test ratio: 70:30) and grid search for hyperparameter optimization to predict accurate blood glucose concentrations. We successfully applied our proposed approach in nine patients with type 1 diabetes and observed that the mean absolute relative difference (MARD) decreased from 17.8% to 8.3%.

Copper-mediated shifts in transcriptomic responses of intestines in Bufo gargarizans tadpoles to lead stress

The differential transcriptomic responses of intestines in Bufo gargarizans tadpoles to Pb alone or in the presence of Cu were evaluated. Tadpoles were exposed to 30 μg/L Pb individually and in combination with Cu at 16 or 64 μg/L from Gosner stage (Gs) 26 to Gs 38. After de novo assembly, 105,107 unigenes were generated. Compared to the control group, 7387, 6937, and 11139 differentially expressed genes (DEGs) were identified in the treatment of Pb + Cu0, Pb + Cu16, and Pb + Cu64, respectively. In addition, functional annotation and enrichment analysis of DEGs revealed substantial transcriptional reprogramming of diverse molecular and biological pathways were induced in all heavy metal treatments. The relative expression levels of genes associated with intestinal epithelial barrier and bile acids (BAs) metabolism, such as mucin2, claudin5, ZO-1, Asbt, and Ost-β, were validated by qPCR. This study demonstrated that Pb exposure induced transcriptional responses in tadpoles, and the responses could be modulated by Cu.

Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage

Antibiotic resistance is a global health crisis increasing in prevalence every day. To combat this crisis, alternative antimicrobial therapeutics are urgently needed. Antimicrobial peptides (AMPs), a family of short defense proteins, are produced naturally by all organisms and hold great potential as effective alternatives to small molecule antibiotics. Here, we present rAMPage, a scalable bioinformatics discovery platform for identifying AMP sequences from RNA sequencing (RNA-seq) datasets. In our study, we demonstrate the utility and scalability of rAMPage, running it on 84 publicly available RNA-seq datasets from 75 amphibian and insect species—species known to have rich AMP repertoires. Across these datasets, we identified 1137 putative AMPs, 1024 of which were deemed novel by a homology search in cataloged AMPs in public databases. We selected 21 peptide sequences from this set for antimicrobial susceptibility testing against Escherichia coli and Staphylococcus aureus and observed that seven of them have high antimicrobial activity. Our study illustrates how in silico methods such as rAMPage can enable the fast and efficient discovery of novel antimicrobial peptides as an effective first step in the strenuous process of antimicrobial drug development.

Immune and endocrine responses of Cururu toads (Rhinella icterica) in their natural habitat after LPS stimulation

Glucocorticoids and melatonin display immunomodulatory functions, with both immune-stimulatory and suppressor effects, depending on the context. While their immune properties are well-explored in mammals, there are still few studies on this immune-endocrine interaction in an inflammatory context in amphibians, all of them under captivity conditions, which can constitute a stressor for these animals. Evaluating how amphibians react to an immune challenge in the field would reveal relevant information regarding how immune-physiological parameters are modulated in natural conditions. This study aimed to investigate the effects of lipopolysaccharide (LPS) injection in male toads (Rhinella icterica) recently captured in their natural habitat in the Atlantic Forest at two different times of the day. We evaluated: splenic cytokines mRNA (interleukin [IL]-1β, IL-6, IL-10, interferon-γ) and complement system protein (C1s), plasma bacterial killing ability (BKA), plasma corticosterone (CORT), melatonin (MEL), and testosterone (T) levels, and neutrophil to lymphocyte ratio (NLR), two hours post-injections. LPS-injection increased NLR, the gene expression of IL-1β, and less evidently CORT levels independently of the time of the day. These results evidence LPS-induced inflammation, similarly observed in toads in captivity. Saline and LPS-injected toads showed a positive correlation between IL-1β and IL-6, both cytokines with pro-inflammatory effects. Also, CORT was negatively associated with T, suggesting inhibition of the hypothalamus-pituitary-gonadal axis in the LPS-stimulated group. Our results are associated with the first stage of the inflammatory assemblage. Studies evaluating further steps of this process might lead to a better understanding of the immune-endocrine relations in amphibians.

Full-length transcriptome assembly of Andrias davidianus (Amphibia: Caudata) skin via hybrid sequencing

The Chinese giant salamander, Andrias davidianus, is the largest amphibian species in the world; it is thus an economically and ecologically important species. The skin of A. davidianus exhibits complex adaptive structural and functional adaptations to facilitate survival in aquatic and terrestrial ecosystems. Here, we report the first full-length amphibian transcriptome from the dorsal skin of A. davidianus, which was assembled using hybrid sequencing and the PacBio and Illumina platforms. A total of 153,038 transcripts were hybrid assembled (mean length of 2039 bp and N50 of 2172 bp), and 133,794 were annotated in at least one database (nr, Swiss-Prot, KEGG, KOGs, GO, and nt). A total of 58,732, 68,742, and 115,876 transcripts were classified into 24 KOG categories, 1903 GO term categories, and 46 KEGG pathways (level 2), respectively. A total of 207,627 protein-coding regions, 785 transcription factors, 27,237 potential long non-coding RNAs, and 8299 simple sequence repeats were also identified. The hybrid-assembled transcriptome recovered more full-length transcripts, had a higher N50 contig length, and a higher annotation rate of unique genes compared with that assembled in previous studies using next-generation sequencing. The high-quality full-length reference gene set generated in this study will help elucidate the genetic characteristics of A. davidianus skin and aid the identification of functional skin proteins.

Frog Skin Innate Immune Defences: Sensing and Surviving Pathogens

Amphibian skin is a mucosal surface in direct and continuous contact with a microbially diverse and laden aquatic and/or terrestrial environment. As such, frog skin is an important innate immune organ and first line of defence against pathogens in the environment. Critical to the innate immune functions of frog skin are the maintenance of physical, chemical, cellular, and microbiological barriers and the complex network of interactions that occur across all the barriers. Despite the global decline in amphibian populations, largely as a result of emerging infectious diseases, we understand little regarding the cellular and molecular mechanisms that underlie the innate immune function of amphibian skin and defence against pathogens. In this review, we discuss the structure, cell composition and cellular junctions that contribute to the skin physical barrier, the antimicrobial peptide arsenal that, in part, comprises the chemical barrier, the pattern recognition receptors involved in recognizing pathogens and initiating innate immune responses in the skin, and the contribution of commensal microbes on the skin to pathogen defence. We briefly discuss the influence of environmental abiotic factors (natural and anthropogenic) and pathogens on the immunocompetency of frog skin defences. Although some aspects of frog innate immunity, such as antimicrobial peptides are well-studied; other components and how they contribute to the skin innate immune barrier, are lacking. Elucidating the complex network of interactions occurring at the interface of the frog's external and internal environments will yield insight into the crucial role amphibian skin plays in host defence and the environmental factors leading to compromised barrier integrity, disease, and host mortality.