Unveiling CRESS DNA Virus Diversity in Oysters by Virome.

Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study's findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment.

Deep learning enables automatic adult age estimation based on CT reconstruction images of the costal cartilage.

OBJECTIVE: Adult age estimation (AAE) is a challenging task. Deep learning (DL) could be a supportive tool. This study aimed to develop DL models for AAE based on CT images and compare their performance to the manual visual scoring method. METHODS: Chest CT were reconstructed using volume rendering (VR) and maximum intensity projection (MIP) separately. Retrospective data of 2500 patients aged 20.00-69.99 years were obtained. The cohort was split into training (80%) and validation (20%) sets. Additional independent data from 200 patients were used as the test set and external validation set. Different modality DL models were developed accordingly. Comparisons were hierarchically performed by VR versus MIP, single-modality versus multi-modality, and DL versus manual method. Mean absolute error (MAE) was the primary parameter of comparison. RESULTS: A total of 2700 patients (mean age = 45.24 years ± 14.03 [SD]) were evaluated. Of single-modality models, MAEs yielded by VR were lower than MIP. Multi-modality models generally yielded lower MAEs than the optimal single-modality model. The best-performing multi-modality model obtained the lowest MAEs of 3.78 in males and 3.40 in females. On the test set, DL achieved MAEs of 3.78 in males and 3.92 in females, which were far better than the MAEs of 8.90 and 6.42 respectively, for the manual method. For the external validation, MAEs were 6.05 in males and 6.68 in females for DL, and 6.93 and 8.28 for the manual method. CONCLUSIONS: DL demonstrated better performance than the manual method in AAE based on CT reconstruction of the costal cartilage. CLINICAL RELEVANCE STATEMENT: Aging leads to diseases, functional performance deterioration, and both physical and physiological damage over time. Accurate AAE may aid in diagnosing the personalization of aging processes. KEY POINTS: • VR-based DL models outperformed MIP-based models with lower MAEs and higher R2 values. • All multi-modality DL models showed better performance than single-modality models in adult age estimation. • DL models achieved a better performance than expert assessments.

A discussion of RNA virus taxonomy based on the 2020 International Committee on Taxonomy of Viruses report.

RNA viruses have a higher mutation rate than DNA viruses; however, RNA viruses are insufficiently studied outside disease settings. The International Committee on Taxonomy of Viruses (ICTV) is an organization set up by virologists to standardize virus classification. To better understand ICTV taxonomy and the characteristics and rules of different RNA virus families, we analyzed the 3,529 RNA viruses included in the 2020 ICTV report using five widely used metrics: length, host, GC content, number of predicted ORFs, and sequence similarity. The results show that host type has a significant influence on viral genome length and GC content. The genome lengths of virus members within the same genus are quite similar: 98.28% of the genome length differences within any particular genus are less than 20%. The species within those genera containing segmented viruses also have a similar length and number of segments. The number of predicted ORFs in the RNA viral genomes also shows a strong, statistically significant correlation with genome length. We suggest that due to the high mutation rate of RNA virus genomes, current RNA virus classification should mainly rely on protein similarities rather than nucleic acid similarities.

Forensic age prediction and age classification for critical age thresholds via 3.0T magnetic resonance imaging of the knee in the Chinese Han population.

OBJECTIVES: To assess the performance of knee MRI for forensic age prediction and classification for 12-, 14-, 16-, and 18-year thresholds. METHODS: The ossification stages of distal femoral epiphyses and proximal tibial epiphyses were assessed using an integrated staging system by Schmeling et al. and Kellinghaus et al. for knee 3.0T MRI with T1-weighted turbo spin-echo (T1-TSE) in sagittal orientation among 852 Chinese Han individuals (483 males and 369 females) aged 7-30 years. Regression models for age prediction were constructed and their performances were evaluated based on mean absolute deviation (MAD) values. In addition, the performances of age classification were assessed using receiver operating characteristic (ROC) analyses. RESULTS: The intra- and inter-observer agreement levels were very good (κ > 0.80). The complete fusion of those two types of epiphyses took place before 18.0 years in our study participants. The minimum MAD values were 2.51 years (distal femur) and 2.69 years (proximal tibia) in males, and 2.75 years (distal femur) and 2.87 years (proximal tibia) in females. The specificity values of constructed prediction models were all above 90% for the 12-, 14-, and 16-year thresholds, compared to the 74.8-84.6% for the 18-year threshold. Better performances of age prediction and classification were observed in males by distal femoral epiphyses. CONCLUSIONS: Ossification stages via 3.0T MRI of the knee with T1-TSE sequence using an integrated staging system could be a reliable noninvasive method for age prediction or for age classification for 12-, 14-, and 16-year thresholds, especially in males by distal femoral epiphyses. However, assessments based on the full bony fusion of the distal femoral epiphysis and proximal tibial epiphysis seemed not reliable for age classification for the 18-year threshold in the Chinese Han population.

Novel RNA viruses in oysters revealed by virome.

Eighteen novel RNA viruses were found in Crassostrea hongkongensis. Phylogenic analysis shows evidence of recombination between major genes of viruses. Picobirnaviruses are ubiquitous and abundant in oysters.

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system.

An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, Haliotis diversicolor, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone), producers (algae or a substrate), and the environment (water). DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems modeling.

Structural insights into the inhibition of type VI effector Tae3 by its immunity protein Tai3.

The recently described T6SS (type VI secretion system) acts as a needle that punctures the membrane of the target cells to deliver effector proteins. Type VI amidase effectors can be classified into four divergent families (Tae1-Tae4). These effectors are secreted into the periplasmic space of neighbouring cells via the T6SS and subsequently rupture peptidoglycan. However, the donor cells are protected from damage because of the presence of their cognate immunity proteins [Tai1 (type VI amidase immunity 1)-Tai4]. In the present paper, we describe the structure of Tae3 in complex with Tai3. The Tae3-Tai3 complex exists as a stable heterohexamer, which is composed of two Tae3 molecules and two Tai3 homodimers (Tae3-Tai34-Tae3). Tae3 shares a common NlpC/P60 fold, which consists of N-terminal and C-terminal subdomains. Structural analysis indicates that two unique loops around the catalytic cleft adopt a closed conformation, resulting in a narrow and extended groove involved in the binding of the substrate. The inhibition of Tae3 is attributed to the insertion of the Ω-loop (loop of α3-α4) of Tai3 into the catalytic groove. Furthermore, a cell viability assay confirmed that a conserved motif (Gln-Asp-Xaa) in Tai3 members may play a key role in the inhibition process. Taken together, the present study has revealed a novel inhibition mechanism and provides insights into the role played by T6SS in interspecific competition.

Structure of the type VI effector-immunity complex (Tae4-Tai4) provides novel insights into the inhibition mechanism of the effector by its immunity protein.

The type VI secretion system (T6SS), a multisubunit needle-like apparatus, has recently been found to play a role in interspecies interactions. The gram-negative bacteria harboring T6SS (donor) deliver the effectors into their neighboring cells (recipient) to kill them. Meanwhile, the cognate immunity proteins were employed to protect the donor cells against the toxic effectors. Tae4 (type VI amidase effector 4) and Tai4 (type VI amidase immunity 4) are newly identified T6SS effector-immunity pairs. Here, we report the crystal structures of Tae4 from Enterobacter cloacae and Tae4-Tai4 complexes from both E. cloacae and Salmonella typhimurium. Tae4 acts as a DL-endopeptidase and displays a typical N1pC/P60 domain. Unlike Tsi1 (type VI secretion immunity 1), Tai4 is an all-helical protein and forms a dimer in solution. The small angle x-ray scattering study combined with the analytical ultracentrifugation reveal that the Tae4-Tai4 complex is a compact heterotetramer that consists of a Tai4 dimer and two Tae4 molecules in solution. Structure-based mutational analysis of the Tae4-Tai4 interface shows that a helix (α3) of one subunit in dimeric Tai4 plays a major role in binding of Tae4, whereas a protruding loop (L4) in the other subunit is mainly responsible for inhibiting Tae4 activity. The inhibition process requires collaboration between the Tai4 dimer. These results reveal a novel and unique inhibition mechanism in effector-immunity pairs and suggest a new strategy to develop antipathogen drugs.

Insights into the catalytic mechanism of 16S rRNA methyltransferase RsmE (m³U1498) from crystal and solution structures.

RsmE is the founding member of a new RNA methyltransferase (MTase) family responsible for methylation of U1498 in 16S ribosomal RNA in Escherichia coli. It is well conserved across bacteria and plants and may play an important role in ribosomal intersubunit communication. The crystal structure in monomer showed that it consists of two distinct but structurally related domains: the PUA (pseudouridine synthases and archaeosine-specific transglycosylases)-like RNA recognition and binding domain and the conserved MTase domain with a deep trefoil knot. Analysis of small-angle X-ray scattering data revealed that RsmE forms a flexible dimeric conformation that may be essential for substrate binding. The S-adenosyl-l-methionine (AdoMet)-binding characteristic determined by isothermal titration calorimetry suggested that there is only one AdoMet molecule bound in the subunit of the homodimer. In vitro methylation assay of the mutants based on the RsmE-AdoMet-uridylic acid complex model showed key residues involved in substrate binding and catalysis. Comprehensive comparisons of RsmE with closely related MTases, combined with the biochemical experiments, indicated that the MTase domain of one subunit in dimeric RsmE is responsible for binding of one AdoMet molecule and catalytic process while the PUA-like domain in the other subunit is mainly responsible for recognition of one substrate molecule (the ribosomal RNA fragment and ribosomal protein complex). The methylation process is required by collaboration of both subunits, and dimerization is functionally critical for catalysis. In general, our study provides new information on the structure-function relationship of RsmE and thereby suggests a novel catalytic mechanism.

Structural insights into the function of 23S rRNA methyltransferase RlmG (m²G1835) from Escherichia coli.

RlmG is a specific AdoMet-dependent methyltransferase (MTase) responsible for N²-methylation of G1835 in 23S rRNA of Escherichia coli. Methylation of m²G1835 specifically enhances association of ribosomal subunits and provides a significant advantage for bacteria in osmotic and oxidative stress. Here, the crystal structure of RlmG in complex with AdoMet and its structure in solution were determined. The structure of RlmG is similar to that of the MTase RsmC, consisting of two homologous domains: the N-terminal domain (NTD) in the recognition and binding of the substrate, and the C-terminal domain (CTD) in AdoMet-binding and the catalytic process. However, there are distinct positively charged protuberances and a distribution of conserved residues contributing to the charged surface patch, especially in the NTD of RlmG for direct binding of protein-free rRNA. The RNA-binding properties of the NTD and CTD characterized by both gel electrophoresis mobility shift assays and isothermal titration calorimetry showed that NTD could bind RNA independently and RNA binding was achieved by the NTD, accomplished by a coordinating role of the CTD. The model of the RlmG-AdoMet-RNA complex suggested that RlmG may unfold its substrate RNA in the positively charged cleft between the NTD and CTD, and then G1835 disengages from its Watson-Crick pairing with C1905 and flips out to insert into the active site. Our structure and biochemical studies provide novel insights into the catalytic mechanism of G1835 methylation.

Structural and SAXS analysis of the budding yeast SHU-complex proteins.

In Saccharomyces cerevisiae, four proteins, Shu1, Shu2, Psy3 and Csm2, form a stable SHU-complex both in vivo and in vitro. These proteins are involved in the early stages of the homologous recombination DNA damage repair process. In this paper, the crystal structure of the Psy3-Csm2 sub-complex is presented at 1.8Å resolution and successfully fitted into our small angle X-ray scattering (SAXS) data of the SHU-complex. Taken together with our electrophoretic mobility shift assay (EMSA) results, a model is proposed for the SHU-protein complex coupled with DNA.

Nested PCR detection of abalone shriveling syndrome-associated virus in China.

Haliotis diversicolor (small abalone) is an economic seafood found off the Southern coast of China. Since 1999, the cultured abalone yields in China have been affected severely by continual outbreaks of a fatal epidemic disease caused by abalone shriveling syndrome associated virus (AbSV), a double-stranded DNA virus. Although the pathogenicity and genome of AbSV have been ascertained, the epidemiology of AbSV infection remains to be investigated. In the present study, four pairs of AbSV-specific primers were designed on the basis of open reading frame (ORF)24 and ORF25 sequences in the AbSV genome. Two nested PCR detection methods were established by optimization of the annealing temperatures of primers. The results showed that the specificity of primers for AbSV detection could not be interfered with by the host genome and other aquaculture species or viruses. The detection limits of the two methods were about 10 copies of recombinant plasmid containing AbSV genes in 20µL reaction mixture. The results of detection of the AbSV epidemic showed that AbSV was still present in juvenile abalones in some farms along the Southern coast of China (Fujian and Guangdong).

Quantitative PCR detection for abalone shriveling syndrome-associated virus.

Haliotis diversicolor (small abalone) is an important seafood found along the southern coast of China. Since 1999, the yields of cultured abalone in China have been severely affected by an epidemic of continuous outbreaks of a fatal disease. A novel double-stranded DNA virus, abalone shriveling syndrome-associated virus (AbSV), was proven to be one of the main causative agent. Although the pathogenicity and genome of AbSV has been ascertained, the epidemiology of AbSV remains to be investigated. In this study, four pairs of AbSV-specific primers were designed on the basis of the AbSV genome, and were tested for their specificities and sensitivities in quantitative real-time PCRs (qPCRs) after optimization of the annealing temperature. The 3F3/3B3 primer pair was finally chosen with a good specificity and high efficiency of amplification, with a detection limit of about 10 copies of recombinant plasmid containing AbSV genes in a 20-µL reaction mixture. In the detection of AbSV in abalone samples along the southern coast of China, most of the diseased samples had more than 80 virus copies in 1ng host genome DNA. AbSV was also demonstrated in mature hybrid (LY) and juvenile (JH) abalones from assays of healthy animals collected in recent years.

The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6.

The COP9 signalosome (CSN) is a multiprotein complex containing eight subunits and is highly conserved from fungi to human. CSN is proposed to widely participate in many physiological processes, including protein degradation, DNA damage response and signal transduction. Among those subunits, only CSN5 and CSN6 belong to JAMM family. CSN5 possesses isopeptidase activity, but CSN6 lacks this ability. Here we report the 2.5Å crystal structure of MPN domain from Drosophila melanogaster CSN6. Structural comparison with other MPN domains, along with bioinformation analysis, suggests that MPN domain from CSN6 may serve as a scaffold instead of a metalloprotease.

[Experimental research of small-incision Descemet's stripping endothelial keratoplasty].

OBJECTIVE: To investigate the surgical procedure, clinical efficacy, complications, density of endothelial cells and histological changes after Descemet's stripping endothelial keratoplasty (DSEK) surgery. METHODS: It was a experimental study. Twenty four New Zealand rabbits were divided into 3 groups, 8 rabbits per group. Donor grafts were dissected from 16 New Zealand rabbit eyes. Group A was experimental group, a 5 mm limbal tunnel incision was made. Descemet's membrane was striped off at 10 mm diameter, then the same diameter donor cornea (including Descemet's membrane and endothelium with a little of posterior stroma) was inserted into the recipient's anterior chamber. Air was injected into the anterior chamber to press the graft up against the recipient cornea. Group B was the control group, only striped the Descemet's membrane at the recipient cornea. Group C was the experiment control group, the procedure was similar to the group A, but the donor graft was without endothelial cells. RESULTS: All corneas of group A were transparent, and the mean density of the endothelial cells was (2195 +/- 77)/mm2 (t = 12.455, P < 0.001). Endothelial grafts attached to the recipients well and no scar formation between them under histological observation. The corneas were severe edema in groups B and C one month after surgery. CONCLUSIONS: DSEK is a safe surgery, can be recovered rapidly with little damages, and without interface scar formation after surgery. DSEK may be the first choice for the treatment of bullous keratopathy.

[Effects of abrupt salinity stress on osmoregulation of juvenile Rachycentron canadum].

Rachycentron canadum is a thriving mariculture species for offshore cage in southern Mainland and Taiwan of China, due to its rapid growth rate and high quality flesh. In this paper, the gill Na(+)-K+ ATPase (NKA) activity and iono- and osmoregulation of juvenile R. canadum were investigated in a 12 h stress of ambient salinities (0-45), and the results showed that after an abrupt transfer to the salinities of 0, 5, 15, 25, 37 (control) and 45, the death of juvenile R. canadum only occurred in salinity 0, with a mortality of 100% by the end of the experiment. In all treatments, the gill NKA activity and serum osmolality fluctuated in first 3 h, and then changed smoothly. The NKA activity varied with salinity grade in U shape, being significantly (P < 0.05) higher in salinity 5 and the lowest in salinity 15 in 12 h, while the serum osmolality (ranged 293-399 mOsmol x kg(-1)) presented a positive correlation with salinity. Serum [Na+] and [Cl-] concentration slightly increased with salinity within the period of 3-12 h, while serum [K+] displayed a reverse pattern. The isosmotic point was estimated as 328.2 mOsm x kg(-1) and corresponded to salinity 11.48. The isoionic points for serum [Na+], [K+] and [Cl-] were estimated as 155.2, 6.16, and 137.1 mmol x L(-1), which corresponded to the salinities of 10.68, 20.44 and 8.41, respectively. It was concluded that R. canadum could be characterized physiologically as a "higher-NKA-in-hyposmotic media" marine euryhaline teleost with the capability of rapid and effective hyper/hypo iono- and osmoregulation.