Nile waterscapes facilitated the construction of the Giza pyramids during the 3rd millennium BCE.

The pyramids of Giza originally overlooked a now defunct arm of the Nile. This fluvial channel, the Khufu branch, enabled navigation to the Pyramid Harbor complex but its precise environmental history is unclear. To fill this knowledge gap, we use pollen-derived vegetation patterns to reconstruct 8,000 y of fluvial variations on the Giza floodplain. After a high-stand level concomitant with the African Humid Period, our results show that Giza's waterscapes responded to a gradual insolation-driven aridification of East Africa, with the lowest Nile levels recorded at the end of the Dynastic Period. The Khufu branch remained at a high-water level (∼40% of its Holocene maximum) during the reigns of Khufu, Khafre, and Menkaure, facilitating the transportation of construction materials to the Giza Pyramid Complex.

Data-adaptive and pathway-based tests for association studies between somatic mutations and germline variations in human cancers.

Cancer is a disease driven by a combination of inherited genetic variants and somatic mutations. Recently available large-scale sequencing data of cancer genomes have provided an unprecedented opportunity to study the interactions between them. However, previous studies on this topic have been limited by simple, low statistical power tests such as Fisher's exact test. In this paper, we design data-adaptive and pathway-based tests based on the score statistic for association studies between somatic mutations and germline variations. Previous research has shown that two single-nucleotide polymorphism (SNP)-set-based association tests, adaptive sum of powered score (aSPU) and data-adaptive pathway-based (aSPUpath) tests, increase the power in genome-wide association studies (GWASs) with a single disease trait in a case-control study. We extend aSPU and aSPUpath to multi-traits, that is, somatic mutations of multiple genes in a cohort study, allowing extensive information aggregation at both SNP and gene levels. p $p$ -values from different parameters assuming varying genetic architecture are combined to yield data-adaptive tests for somatic mutations and germline variations. Extensive simulations show that, in comparison with some commonly used methods, our data-adaptive somatic mutations/germline variations tests can be applied to multiple germline SNPs/genes/pathways, and generally have much higher statistical powers while maintaining the appropriate type I error. The proposed tests are applied to a large-scale real-world International Cancer Genome Consortium whole genome sequencing data set of 2583 subjects, detecting more significant and biologically relevant associations compared with the other existing methods on both gene and pathway levels. Our study has systematically identified the associations between various germline variations and somatic mutations across different cancer types, which potentially provides valuable utility for cancer risk prediction, prognosis, and therapeutics.

Streptomyces cathayae sp. nov., an endophytic actinobacterium from the root tissue of Cathaya argyrophylla.

An endophytic actinobacterium, designated strain HUAS 5T, was isolated from the root tissue of Cathaya argyrophylla collected in Chenzhou city of Hunan Province, PR China. This strain produced grey aerial mycelium that differentiated into spiral spore chains with spiny-surfaced ellipsoidal spores on Gause's synthetic No. 1 medium. Strain HUAS 5T grew well on Gause's synthetic No. 1, Reasoner'2 and ISP serial media. This strain grew at 15-40 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0) and in presence of 0-5.0% (w/v) NaCl. The predominant cellular fatty acids of strain HUAS 5T (> 5.0%) were iso-C16:0, iso-C14:0, anteiso-C15:0, iso-C15:0, C16:0, iso-C16:1 H and Sum in Feature 3 (C16:1 ω7c/C16:1 ω6c). Sequence analysis of the 16S rRNA gene indicated that this strain belonged to the genus Streptomyces and exhibited highest sequence similarity to Streptomyces hirsutus NRRL B-2713T (97.3%), which is much less than 98.7% cut-off point of species definitions for bacteria and archaea. Phylogenetic analysis of 16S rRNA gene sequence and whole genome indicated that strain HUAS 5T formed an independent lineage, which suggested that it belonged to a potential novel species. Based on the morphological, cultural, physio-biochemical properties and chemotaxonomy, strain HUAS 5T (= MCCC 1K08552T = JCM 36055T) is deemed to represent a novel Streptomyces species, for which we put forward the name Streptomyces cathayae sp. nov.

Tri-frequency simultaneous ultrasound pickling for the acceleration of the NaCl content and quality improvement of pork (longissimus dorsi).

BACKGROUND: The pickling process with NaCl is an essential step for pork preservation. This study aimed to investigate the effect of different ultrasonic intensities of tri-frequency simultaneous ultrasound (TSIU) pickling on the NaCl content and quality of pork (longissimus dorsi). After 30 min pickling, the NaCl content, moisture content, pickling yield, cooking loss, textural properties, color, pH, moisture migration and distribution as well as microstructure of pork were assessed. RESULTS: Results showed that among all the ultrasonic treatment intensities (85-150 W L-1), the NaCl content of the sample pickled by an intensity of 101.3 W L-1 was higher than that of other intensities. TSIU 101.3 W L-1 showed 59.95% higher NaCl content than the control sample. In addition, the sample treated with TSIU of 101.3 W L-1 had higher pickling yield and moisture content, better textural properties of pork (including hardness and chewiness), and less cooking loss. The results of the low-field nuclear magnetic resonance showed that, compared with the control group, the relaxation time T21 of the ultrasound-assisted pickling samples increased, while the proportion of T22 (A22) reduction ranged from 175.0% to 379.9%. The microstructure designated that the ultrasonic treatment could facilitate changes in meat texture. CONCLUSION: Ultrasound marination of different intensities promoted the diffusion of NaCl and affected the quality of pork tenderloins. The TSIU at 101.3 W L-1 could better accelerate NaCl transport and homogeneous distribution on meat, thereby improving the sample quality. © 2024 Society of Chemical Industry.

Proposal of Streptomyces sporoverrucosus Gause et al. 1983 as a later heterotypic synonym of Streptomyces goshikiensis Niida et al. 1966 and an emended description of Streptomyces goshikiensis.

The taxonomic relationship of Streptomyces goshikiensis and Streptomyces sporoverrucosus was re-evaluated using comparative genome analysis. The 16S rRNA gene sequence analysis indicated that S. goshikiensis JCM 4640T and S. sporoverrucosus CGMCC 4.1796T shared 100% sequence similarity. Phylogenetic analysis based on 16S rRNA gene and genomic sequences exhibited that they were closely related to each other. However, the values of average nucleotide identity (ANIb/ANIm) and digital DNA-DNA hybridization (dDDH) between the genomes of two type strains were 98.33%/98.69% and 87.2%, respectively, greater than the two recognized thresholds values of 96.7% ANI and 70% dDDH for species delineation. These results suggested that S. goshikiensis and S. sporoverrucosus should share the same taxonomic position. In addition, this conclusion was further supported by highly similar morphological, cultural, physiological, biochemical and chemotaxonomic characteristics between them. Consequently, it is proposed that S. sporoverrucosus is a later heterotypic synonym of S. goshikiensis.

Two new species of Bacillidium (Microsporidia) from coelomocytes of Branchiura sowerbyi (Oligochaeta: Naididae) in China.

Bacillidium spp. exclusively infect oligochaetes and these microsporidian pathogens are typically characterized by their rod-shaped spores. Seven Bacillidium spp. are presently reported from different organs of oligochaetes. Here, we describe two new Bacillidium species, Bacillidium sinensis n. sp. and Bacillidium branchilis n. sp., from coelomocytes of Branchiura sowerbyi. This is the first report of Bacillidium spp. in oligochaetes from China. Both species of Bacillidium elicit the formations of opaque xenoma-like lesions in coelomocytes of the host. A diplokaryotic nucleus occurs in all life stages of these two new Bacillidium species. Mature spores of B. sinensis are 15.9 ± 0.6 (14.7-17.1) µm long (average ± standard error, range, n = 50) and 2.5 ± 0.1 (2.3-2.7) µm wide in fresh preparations. A new type of exospore (sixteen-layered exospore) is discovered from B. sinensis n. sp. which is distinctly different from B. branchilis n. sp., and other Bacillidium spp. (double-layered exospore) reported previously. These two Bacillidium species are morphologically distinguished from each other and all Bacillidium spp. described previously in terms of hosts, infection sites, spore size, spore wall or polar filament thickness. BLASTn searches indicated that these two new microsporidian parasites are surprisingly most similar to Janacekia tainanus (94.76% for B. sinensis and 90. 2% for B. branchilis) isolated from the fat body of midge larva (Kiefferulus tainanus). Phylogenetic analysis demonstrates that the two novel taxons cluster with J. debaisieuxi, J. tainanus, and Bacillidium sp. within the Jirovecia-Bacillidium-Janacekia clade. Other available 18S rRNA gene sequences for microsporidia that infect oligochaetes include J. sinensis, B. vesiculoformis, Neoflabelliforma aurantiae, and Bacillidium sp., but these do not form a single cluster with B. sinensis and B. branchilis, but are instead dispersed through the clade. Based on the ultrastructural features and molecular characteristics, two new species within the genus Bacillidium, B. sinensis n. sp. and B. branchilis n. sp., are designated.

Distinct vulnerability to oxidative stress determines the ammonia sensitivity of crayfish (Procambarus clarkii) at different developmental stages.

Red swamp crayfish (Procambarus clarkii) has increasingly become a high-value freshwater product in China. During the intensive cultivation, excessive ammonia exposure is an important lethal factor of crayfish. We investigated the toxic effects and mechanisms of ammonia on crayfish at two different developmental stages. A preliminary ammonia stress test showed a 96-h LC50 of 135.10 mg/L and 299.61 mg/L for Stage_1 crayfish (8.47 ± 1.68 g) and Stage_2 crayfish (18.33 ± 2.41 g), respectively. During a prolonged ammonia exposure (up to 96 h), serum acid phosphatase and alkaline phosphatase showed a time-dependent decrease. Histological assessment indicated the degree of hepatopancreatic injury, which was mainly characterized as tubule lumen dilatation, degenerated tubule, vacuolization and dissolved hepatic epithelial cell, increased with exposure time. Enhanced malondialdehyde level and reduced antioxidant capacity of hepatopancreas were also observed. The mRNA expression and activity of catalase and superoxide dismutase showed an initial up-regulation within 24 h, and then gradually down-regulated with the exposure time. In the post-treatment recovery period, the Stage_2 crayfish exerted a stronger antioxidant and detoxification capacity than that of the Stage_1 crayfish, and thus quickly recovered from the ammonia exposure. Our findings provide a further understanding of the adverse effects of ammonia stress and suggest guidelines for water quality management during crayfish farming.

Marine Bromophenol Bis(2,3,6-Tribromo-4,5-Dihydroxybenzyl)ether Inhibits Angiogenesis in Human Umbilical Vein Endothelial Cells and Reduces Vasculogenic Mimicry in Human Lung Cancer A549 Cells.

Angiogenesis, including the growth of new capillary blood vessels from existing ones and the malignant tumors cells formed vasculogenic mimicry, is quite important for the tumor metastasis. Anti-angiogenesis is one of the significant therapies in tumor treatment, while the clinical angiogenesis inhibitors usually exhibit endothelial cells dysfunction and drug resistance. Bis(2,3,6-tribromo-4,5-dihydroxybenzyl)ether (BTDE), a marine algae-derived bromophenol compound, has shown various biological activities, however, its anti-angiogenesis function remains unknown. The present study illustrated that BTDE had anti-angiogenesis effect in vitro through inhibiting human umbilical vein endothelial cells migration, invasion, tube formation, and the activity of matrix metalloproteinases 9 (MMP9), and in vivo BTDE also blocked intersegmental vessel formation in zebrafish embryos. Moreover, BTDE inhibited the migration, invasion, and vasculogenic mimicry formation of lung cancer cell A549. All these results indicated that BTDE could be used as a potential candidate in anti-angiogenesis for the treatment of cancer.

NIR-Light-Triggered Anticancer Strategy for Dual-Modality Imaging-Guided Combination Therapy via a Bioinspired Hybrid PLGA Nanoplatform.

A promising approach toward cancer therapy is expected to integrate imaging and therapeutic agents into a versatile nanocarrier for achieving improved antitumor efficacy and reducing the side effects of conventional chemotherapy. Herein, we designed a poly(d,l-lactic- co-glycolic acid) (PLGA)-based theranostic nanoplatform using the double emulsion solvent evaporation method (W/O/W), which is associated with bovine serum albumin (BSA) modifications, to codeliver indocyanine green (ICG), a widely used near-infrared (NIR) dye, and doxorubicin (Dox), a chemotherapeutic drug, for dual-modality imaging-guided chemo-photothermal combination cancer therapy. The resultant ICG/Dox co-loaded hybrid PLGA nanoparticles (denoted as IDPNs) had a diameter of around 200 nm and exhibited excellent monodispersity, fluorescence/size stability, and biocompatibility. It was confirmed that IDPNs displayed a photothermal effect and that the heat induced faster release of Dox, which led to enhanced drug accumulation in cells and was followed by their efficient escape from the lysosomes into the cytoplasm and drug diffusion into the nucleus, resulting in a chemo-photothermal combinatorial therapeutic effect in vitro. Moreover, the IDPNs exhibited a high ability to accumulate in tumor tissue, owing to the enhanced permeability and retention (EPR) effect, and could realize real-time fluorescence/photoacoustic imaging of solid tumors with a high spatial resolution. In addition, the exposure of tumor regions to NIR irradiation could enhance the tumor penetration ability of IDPNs, almost eradicating subcutaneous tumors. In addition, the inhibition rate of IDPNs used in combination with laser irradiation against EMT-6 tumors in tumor-bearing nude mice (chemo-photothermal therapy) was approximately 95.6%, which was much higher than that for chemo- or photothermal treatment alone. Our study validated the fact that the use of well-defined IDPNs with NIR laser treatment could be a promising strategy for the early diagnosis and passive tumor-targeted chemo-photothermal therapy for cancer.

Divergent transcriptomic responses underlying the ranaviruses-amphibian interaction processes on interspecies infection of Chinese giant salamander.

BACKGROUND: Ranaviruses (family Iridoviridae, nucleocytoplasmic large DNA viruses) have been reported as promiscuous pathogens of cold-blooded vertebrates. Rana grylio virus (RGV, a ranavirus), from diseased frog Rana grylio with a genome of 105.79 kb and Andrias davidianus ranavirus (ADRV), from diseased Chinese giant salamander (CGS) with a genome of 106.73 kb, contains 99% homologous genes. RESULTS: To uncover the differences in virus replication and host responses under interspecies infection, we analyzed transcriptomes of CGS challenged with RGV and ADRV in different time points (1d, 7d) for the first time. A total of 128,533 unigenes were obtained from 820,858,128 clean reads. Transcriptome analysis revealed stronger gene expression of RGV than ADRV at 1 d post infection (dpi), which was supported by infection in vitro. RGV replicated faster and had higher titers than ADRV in cultured CGS cell line. RT-qPCR revealed the RGV genes including the immediate early gene (RGV-89R) had higher expression level than that of ADRV at 1 dpi. It further verified the acute infection of RGV in interspecies infection. The number of differentially expressed genes and enriched pathways from RGV were lower than that from ADRV, which reflected the variant host responses at transcriptional level. No obvious changes of key components in pathway "Antigen processing and presentation" were detected for RGV at 1 dpi. Contrarily, ADRV infection down-regulated the expression levels of MHC I and CD8. The divergent host immune responses revealed the differences between interspecies and natural infection, which may resulted in different fates of the two viruses. Altogether, these results revealed the differences in transcriptome responses among ranavirus interspecies infection of amphibian and new insights in DNA virus-host interactions in interspecies infection. CONCLUSION: The DNA virus (RGV) not only expressed self-genes and replicated quickly after entry into host under interspecies infection, but also avoided the over-activation of host responses. The strategy could gain time for the survival of interspecies pathogen, and may provide opportunity for its adaptive evolution and interspecies transmission.

Fish reovirus GCReV-109 VP33 protein elicits protective immunity in rare minnows.

Grass carp reovirus strain 109 (GCReV-109) was previously isolated from a grass carp (Ctenopharyngodon idellus) with hemorrhagic disease, and its complete genome has been sequenced. However, the infectivity of GCReV-109 has not been studied, and the viral protein VP33, encoded on genome segment S11, had no detectable sequence homology to other known reovirus proteins. In this study, we characterized GCReV-109 infections in vivo and in vitro, as well as the VP33 protein. Infectivity analysis showed that GCReV-109 caused severe hemorrhagic disease and 100% mortality at dilutions up to 10(-4) in rare minnows (Gobiocypris rarus) by 8 days postinfection, but no visible cytopathic effect was observed in GCReV-109-infected subcultured grass carp muscle (GCM) cells. To confirm that GCReV-109 could be propagated in GCM cells, three virus genome segments were detected by RT-PCR, and large numbers of virus particles were observed by transmission electron microscopy in samples from the infected GCM cells. The suspension of GCReV-109-infected GCM cells was pathogenic to rare minnows. VP33 protein was expressed and purified for generation of an anti-VP33 antiserum. In western blot analysis of purified GCReV-109 particles, the antiserum specifically recognized a protein band (approximately 33 kDa). This revealed that VP33 is a major structural protein of GCReV-109 that might have immunogenic properties. The protective efficacy of the anti-VP33 antiserum against GCReV-109 infection was tested. The death of infected fish was delayed and the mortality fell to 10% when fish were treated with the anti-VP33 antiserum, suggesting that it might be useful for the prevention and control of fish reoviral disease.

Complete genome sequence and architecture of crucian carp Carassius auratus herpesvirus (CaHV).

Crucian carp Carassius auratus herpesvirus (CaHV) was isolated from diseased crucian carp with acute gill hemorrhages and high mortality. The CaHV genome was sequenced and analyzed. The data showed that it consists of 275,348 bp and contains 150 predicted ORFs. The architecture of the CaHV genome differs from those of four cyprinid herpesviruses (CyHV1, CyHV2, SY-C1, CyHV3), with insertions, deletions and the absence of a terminal direct repeat. Phylogenetic analysis of the DNA polymerase sequences of 17 strains of Herpesvirales members, and the concatenated 12 core ORFs from 10 strains of alloherpesviruses showed that CaHV clustered together with members of the genus Cyprinivirus, family Alloherpesviridae.

Development and application of monoclonal antibodies for detection and analysis of aquareoviruses.

Monoclonal antibodies (mAbs) play an important role in detection of aquareoviruses. Three mAbs against grass carp reovirus (GCRV) were prepared. Isotyping revealed that all three mAbs were of subclass IgG2b. Western blot assay showed that all three mAbs reacted with GCRV 69 kDa protein (the putative VP5). In addition to the 69 kDa protein of GCRV, mAb 4B6 also recognize a 54 kDa protein. All three mAbs were used for detecting aquareovirus by Western blot assay and indirect immunofluorescence assay (IFA). All of them reacted with GCRV, and mAb 4A3 could also react with turbot Scophthalmus maximus reovirus (SMReV) and largemouth bass Microptererus salmonides reovirus (MsReV). Viral antigens were only observed in the cytoplasm of infected cells. Finally, syncytia formation was observed with light microscopy and fluorescence microscopy using fluorescein labelled 4A3 mAb at various times post-infection. Syncytia were observed at 36 hr post-infection (hpi) by light microscopy and at 12 hpi by fluorescence microscopy. The immunofluorescence based assay allowed earlier detection of virus than observation of virus-induced cytopathic effect (CPE) assay in inoculated cell cultures. The sensitivity and specificity of these mAbs may be useful for diagnosis and monitoring of aquareoviruses.

Establishment of three cell lines from Chinese giant salamander and their sensitivities to the wild-type and recombinant ranavirus.

Known as lethal pathogens, Ranaviruses have been identified in diseased fish, amphibians (including Chinese giant salamander Andrias davidianus, the world's largest amphibian) and reptiles, causing organ necrosis and systemic hemorrhage. Here, three Chinese giant salamander cell lines, thymus cell line (GSTC), spleen cell line (GSSC) and kidney cell line (GSKC) were initially established. Their sensitivities to ranaviruses, wild-type Andrias davidianus ranavirus (ADRV) and recombinant Rana grylio virus carrying EGFP gene (rRGV-EGFP) were tested. Temporal transcription pattern of ranavirus major capsid protein (MCP), fluorescence and electron microscopy observations showed that both the wild-type and recombinant ranavirus could replicate in the cell lines.

Complete genome sequence and comparative analysis of grass carp reovirus strain 109 (GCReV-109) with other grass carp reovirus strains reveals no significant correlation with regional distribution.

A new grass carp reovirus strain, tentatively named GCReV-109, was isolated in Hubei, China, and its complete genome sequence was determined. The genome contained 11 double-stranded RNA segments (S1-S11) covering 24,620 base pairs. All of the segments had conserved terminal nucleotides, with GUAA(U)/CU at the 5' end and UCAUC at the 3' end. Protein sequence comparison showed that GCReV-109 was most closely related to GCRV-GD108 and shared 96.6-99.5 % protein sequence identity but only shared 16.7-46.1 and 15.1-45.4 % identity with GCRV-873 and HGDRV, respectively. Phylogenetic analysis showed that grass carp reovirus strains in China can be divided into three genotypes. Further analysis revealed homology between the GCRV-109 VP56 and HGDRV VP55 proteins, as well as GCReV-109 NS38, GCRV-873 NS38, and HGDRV VP39. The results of these comparisons also indicated that the homology between viruses was not necessarily linked to their geographical distribution. Our study will help in recognizing and understanding the genome structure and genetic diversity of grass carp reovirus.

Zebrafish mutants in egln1 display a hypoxic response and develop polycythemia.

AIMS: Prolyl hydroxylase domain 2 (PHD2), encoded by the Egln1 gene, serves as a pivotal regulator of the hypoxia-inducible factor (HIF) pathway and acts as a cellular oxygen sensor. Somatic inactivation of Phd2 in mice results in polycythemia and congestive heart failure. However, due to the embryonic lethality of Phd2 deficiency, its role in development remains elusive. Here, we investigated the function of two egln1 paralogous genes, egln1a and egln1b, in zebrafish. MAIN METHODS: The egln1 null zebrafish were generated using the CRISPR/Cas9 system. Quantitative real-time PCR assays and Western blot analysis were employed to detect the effect of egln1 deficiency on the hypoxia signaling pathway. The hypoxia response of egln1 mutant zebrafish were assessed by analyzing heart rate, gill agitation frequency, and blood flow velocity. Subsequently, o-dianisidine staining and in situ hybridization were used to investigate the role of egln1 in zebrafish hematopoietic function. KEY FINDINGS: Our data show that the loss of egln1a or egln1b individually has no visible effects on growth rate. However, the egln1a; egln1b double mutant displayed significant growth retardation and elevated mortality at around 2.5 months old. Both egln1a-null and egln1b-null zebrafish embryo exhibited enhanced tolerance to hypoxia, systemic hypoxic response that include hif pathway activation, increased cardiac activity, and polycythemia. SIGNIFICANCE: Our research introduces zebrafish egln1 mutants as the first congenital embryonic viable systemic vertebrate animal model for PHD2, providing novel insights into hypoxic signaling and the progression of PHD2- associated disease.

Evaluation of low-temperature ultrasonic marination of pork meat at various frequencies on physicochemical properties, myoglobin levels, and volatile compounds.

This study aims to evaluate the pork meat quality after ultrasonic brining at different frequencies, thereby providing a more comprehensive understanding of the effects of ultrasound marination on meat. The texture profile analysis showed that ultrasonic curing at various frequencies significantly improved the textural properties of samples, especially at 26.8 kHz, resulting in a reduction of tenderness, hardness, and chewiness values by 44%, 43%, and 44%, respectively. The cooking loss of samples marinated by ultrasound decreased from 27% without ultrasonic treatment to 22%, indicating a significant improvement in water-holding capacity, while the changes in pH had only a subtle impact on pork quality. Meanwhile, the color of pork became more rosy hue due to decreased L⁎ values and increased a⁎ values, which was mainly attributed to an elevated proportion of oxymyoglobin and reduced metmyoglobin content. Additionally, ultrasonic marination did not exert a negative impact on the oxidation of pork protein and lipids. After roasting, samples marinated by ultrasound exhibited a significantly higher abundance of volatile flavor compounds compared to static marinated meat (with an increase of 16 flavor substances) and fresh pork (with an increase of 24 flavor substances), demonstrating the efficacy of ultrasonic marination in enhancing the overall flavor and taste profile of pork. Consequently, the application of ultrasonic technology holds great potential for the "home kitchen type" rapid marination.

Comparison of prediction models for soy protein isolate hydrolysates bitterness built using sensory, spectrofluorometric and chromatographic data from varying enzymes and degree of hydrolysis.

The bitterness of soy protein isolate hydrolysates prepared using five proteases at varying degree of hydrolysis (DH) and its relation to physicochemical properties, i.e., surface hydrophobicity (H0), relative hydrophobicity (RH), and molecular weight (MW), were studied and developed for predictive modelling using machine learning. Bitter scores were collected from sensory analysis and assigned as the target, while the physicochemical properties were assigned as the features. The modelling involved data pre-processing with local outlier factor; model development with support vector machine, linear regression, adaptive boosting, and K-nearest neighbors algorithms; and performance evaluation by 10-fold stratified cross-validation. The results indicated that alcalase hydrolysates were the most bitter, followed by protamex, flavorzyme, papain, and bromelain. Distinctive correlation results were found among the physicochemical properties, influenced by the disparity of each protease. Among the features, the combination of RH-MW fitted various classification models and resulted in the best prediction performance.

Human-like adrenal features in Chinese tree shrews revealed by multi-omics analysis of adrenal cell populations and steroid synthesis.

The Chinese tree shrew ( Tupaia belangeri chinensis) has emerged as a promising model for investigating adrenal steroid synthesis, but it is unclear whether the same cells produce steroid hormones and whether their production is regulated in the same way as in humans. Here, we comprehensively mapped the cell types and pathways of steroid metabolism in the adrenal gland of Chinese tree shrews using single-cell RNA sequencing, spatial transcriptome analysis, mass spectrometry, and immunohistochemistry. We compared the transcriptomes of various adrenal cell types across tree shrews, humans, macaques, and mice. Results showed that tree shrew adrenal glands expressed many of the same key enzymes for steroid synthesis as humans, including CYP11B2, CYP11B1, CYB5A, and CHGA. Biochemical analysis confirmed the production of aldosterone, cortisol, and dehydroepiandrosterone but not dehydroepiandrosterone sulfate in the tree shrew adrenal glands. Furthermore, genes in adrenal cell types in tree shrews were correlated with genetic risk factors for polycystic ovary syndrome, primary aldosteronism, hypertension, and related disorders in humans based on genome-wide association studies. Overall, this study suggests that the adrenal glands of Chinese tree shrews may consist of closely related cell populations with functional similarity to those of the human adrenal gland. Our comprehensive results (publicly available at http://gxmujyzmolab.cn:16245/scAGMap/) should facilitate the advancement of this animal model for the investigation of adrenal gland disorders.

Genome architecture changes and major gene variations of Andrias davidianus ranavirus (ADRV).

Ranaviruses are emerging pathogens that have led to global impact and public concern. As a rarely endangered species and the largest amphibian in the world, the Chinese giant salamander, Andrias davidianus, has recently undergone outbreaks of epidemic diseases with high mortality. In this study, we isolated and identified a novel ranavirus from the Chinese giant salamanders that exhibited systemic hemorrhage and swelling syndrome with high death rate in China during May 2011 to August 2012. The isolate, designated Andrias davidianus ranavirus (ADRV), not only could induce cytopathic effects in different fish cell lines and yield high viral titers, but also caused severely hemorrhagic lesions and resulted in 100% mortality in experimental infections of salamanders. The complete genome of ADRV was sequenced and compared with other sequenced amphibian ranaviruses. Gene content and phylogenetic analyses revealed that ADRV should belong to an amphibian subgroup in genus Ranavirus, and is more closely related to frog ranaviruses than to other salamander ranaviruses. Homologous gene comparisons show that ADRV contains 99%, 97%, 94%, 93% and 85% homologues in RGV, FV3, CMTV, TFV and ATV genomes respectively. In addition, several variable major genes, such as duplicate US22 family-like genes, viral eukaryotic translation initiation factor 2 alpha gene and novel 75L gene with both motifs of nuclear localization signal (NLS) and nuclear export signal (NES), were predicted to contribute to pathogen virulence and host susceptibility. These findings confirm the etiologic role of ADRV in epidemic diseases of Chinese giant salamanders, and broaden our understanding of evolutionary emergence of ranaviruses.