Abstract Polysaccharide-degrading bacteria are key participants in the global carbon cycle and algal biomass recycling. Herein, a polysaccharide lyase-producing strain HB226069 was isolated from Sargassum sp. from QingGe Port, Hainan, China. Results of the phylogenetic of 16S rRNA gene and genotypic analysis clearly indicate that the isolate should be classified as Microbulbifer thermotolerans. The whole genome is a 4,021,337 bp circular chromosome with the G + C content of 56.5%. Analysis of the predicted genes indicates that strain HB226069 encodes 161 CAZymes, and abundant putative enzymes involved in polysaccharide degradation were predicted, including alginate lyase, fucosidase, agarase, xylanase, cellulase, pectate lyase, amylase, and chitinase. Three of the putative polysaccharide lyases from PL7 and PL17 families were involved in alginate degradation. The alginate lyases of strain HB226069 showed the maximum activity 117.4 U/mL at 50°C, pH 7.0 and 0.05 M FeCl3, while exhibited the best stability at 30°C and pH 7.0. The thin layer chromatography (TLC) and Electrospray Ionization Mass Spectrometry (ESI-MS) analysis indicated that the alginate oligosaccharide degraded by the partially purified alginate lyases contained oligosaccharides of DP2-DP5 and monosaccharide while reacting for 36 h. The complete genome of M. thermotolerans HB226069 enriches our understanding of the mechanism of polysaccharide lyase production and provides support for its potential application in polysaccharide degradation.

Circular RNA (circRNA), one of the important non-coding RNA molecules with a closed-loop structure, plays a key regulatory role in cell processing. In this study, circRNAs of Epinephelus coioides, an important marine cultured fish in China, were isolated and characterized, and the network of circRNAs and mRNA was explored during Singapore grouper iridovirus (SGIV) infection, one of the most important double stranded DNA virus pathogens of marine fish. 10 g of raw data was obtained by high-throughput sequencing, and 2599 circRNAs were classified. During SGIV infection, 123 and 37 circRNAs occurred differential expression in spleen and spleen cells, indicating that circRNAs would be involved in the viral infection. GO annotation and KEGG demonstrated that circRNAs could target E. coioides genes to regulate cell activity and the activation of immune factors. The results provide some insights into the circRNAs mediated immune regulatory network during bony fish virus infection.

AbstractFor viruses in the familyPotyviridae(potyvirids), three virus-encoded proteins (P3N-PIPO, CI and CP) and several host components are known to coordinately regulate viral cell-to-cell movement. Here, we found that HCPro2 encoded by areca palm necrotic ring spot virus is involved in the intercellular movement, which could be functionally complemented by its counterpart HCPro from a potyvirus. The affinity purification and mass spectrum analysis identified several viral factors (including CI and CP) and a variety of host proteins that physically associate with HCPro2. We demonstrated that HCPro2 interacts with either CI or CPin planta, and the three form plasmodesmata (PD)-localized interactive complex in viral infection. Further, we screened HCPro2-associating host proteins, and identified a common host protein RbCS that mediates the interactions of HCPro2-CI, HCPro2-CP and CI-CP among the complex. Knockdown ofNbRbCSsimultaneously impairs the interactions of HCPro2-CI, HCPro2-CP and CI-CP, and significantly attenuates the intercellular movement and systemic infection for ANRSV and other three tested potyvirids. This study highlights that a nucleus-encoded chloroplast-targeted protein is hijacked by potyvirids as the scaffold protein to mediate the assembly of viral intercellular movement complex to promote viral infection.

Hexavalent chromium (Cr (VI)) is widely distributed in the marine environment of Hainan Province, China and poses a potential threat to its mangrove ecosystems. However, the mechanisms underlying Cr-induced stress and reproductive toxicity in clams remain largely unknown. In this study, the clams, Geloina erosa, were exposed to 4.34, 8.69, 17.38 and 34.76 mg/L Cr (VI) for 24, 48 and 72 h. The gonad-somatic index (GSI) was determined and histological alterations of the ovaries were quantified by light microscopy. The micronucleus test was performed which quantifies the genotoxic presence of small cytoplasmic bodies in eukaryotic cells. Enzymatic assays for catalase (CAT), glutathione reductase (GR), and malondialdehyde (MDA) activities were done. Quantitative real-time PCR (qRT-PCR) was used to quantify the expression of glutathione-S-transferase (GST), heat shock protein 70 (HSP70) and vitellogenin (Vtg) in ovaries of G. erosa. The results showed that the micronucleus frequency was significantly increased when clams were exposed to Cr (VI). Cr (VI) exposure induced the accumulation of MDA and affected CAT and GR enzyme activities. The high Cr (VI) concentration of 34.76 mg/L significantly increased the levels of GR activity, GST expression and HSP70 expression and inhibited Vtg expression and CAT activity. MDA content was significantly increased after 72 h at the high Cr (VI) exposure (34.76 mg/L). Therefore, Cr (VI) exposure may be toxic to the development of ovaries of G. erosa.

Breast cancer is a vital disease that seriously threatens women's health. Fluorescence In Situ Hybridization (FISH) is an effective method to detect breast cancer and can assist in utilizing effective targeted therapies. However, manual and computer vision-based methods have shortcomings in accuracy and real-time performance in post-processing screening samples for breast cancer detection by FISH. We obtain highly accurate cell contour polygons using our original method, called Bio-Snake. Specifically, we first apply B-channel Topology Analysis on breast cancer FISH samples based on boundary tracking algorithm in order to automatically determine the initial cell contour. Afterwards, we apply Adaptive LSTM Alignment method on cell contour optimization in order to more accurately utilize the local contours information. The Weighted Loss is used to train the cell contour segmentation model. Finally, we propose HER2 & Chromosome 17 copy number cell attribution model to assist in sample statistics. Our experimental results demonstrate that our proposed Bio-Snake achieves 51.4 average precision (AP) and 34.0 Mask-AP on the standard benchmarks with an inference speed of 11.1 FPS, which is 34% higher and 14% faster than the current state-of-the-art method.

A 90-day experiment was conducted to explore the effects of creatine on growth performance, liver health status, metabolites, and gut microbiota in Megalobrama amblycephala. There were 6 treatments as follows: control (CD, 29.41% carbohydrates), high carbohydrate (HCD, 38.14% carbohydrates), betaine (BET, 1.2% betaine + 39.76% carbohydrates), creatine 1 (CRE1, 0.5% creatine + 1.2% betaine + 39.29% carbohydrates), creatine 2 (CRE2, 1% creatine + 1.2% betaine + 39.50% carbohydrates), and creatine 3 (CRE3, 2% creatine + 1.2% betaine + 39.44% carbohydrates). The results showed that supplementing creatine and betaine together reduced the feed conversion ratio significantly (P < 0.05, compared to CD and HCD) and improved liver health (compared to HCD). Compared with the BET group, dietary creatine significantly increased the abundances of Firmicutes, Bacteroidota, ZOR0006, and Bacteroides and decreased the abundances of Proteobacteria, Fusobacteriota, Vibrio, Crenobacter, and Shewanella in the CRE1 group. Dietary creatine increased the content of taurine, arginine, ornithine, γ-aminobutyric acid (g-ABA), and creatine (CRE1 vs. BET group) and the expression of creatine kinase (ck), sulfinoalanine decarboxylase (csad), guanidinoacetate N-methyltransferase (gamt), glycine amidinotransferase (gatm), agmatinase (agmat), diamine oxidase1 (aoc1), and glutamate decarboxylase (gad) in the CRE1 group. Overall, these results suggested that dietary supplementation of creatine (0.5-2%) did not affect the growth performance, but it altered the gut microbial composition at the phylum and genus levels, which might be beneficial to the gut health of M. amblycephala; dietary creatine also increased the serum content of taurine by enhancing the expressions of ck and csad and increased the serum content of g-ABA by enhancing the arginine content and the expressions of gatm, agmat, gad, and aoc1.

Compared with other types of breast cancer, triple-negative breast cancer (TNBC) has the characteristics of a high degree of malignancy and poor prognosis. Early diagnosis of TNBC through biological markers and timely development of effective treatment methods can reduce its mortality. Many Research experiments have confirmed that some specific miRNA expression profiles in TNBC can used as markers for early diagnosis. However, detecting the expression profiles of multiple groups of miRNAs according to traditional detection methods is complicated and consumes many samples. To address this issue, we developed a method for high-throughput, high-sensitivity quantitative detection of multiple sets of miRNAs (including miR-16, miR-21, miR-92, miR-199, and miR-342) specifically expressed in TNBC by rolling circle amplification (RCA) on fluorescence-encoded microspheres. Through the optimization of reaction system conditions, the developed method showed an extensive linear dynamic range and high sensitivity for all five miRNAs with the lowest limit of detection of 2 fmol/L. Meanwhile, this high-throughput detection method also appeared reasonable specificity. Only in the presence of a specific target miRNA, the fluorescence signal on the correspondingly encoded microspheres is significantly increased, while the fluorescence signal on other non-correspondingly encoded microspheres is almost negligible. Furthermore, this process exhibited good recovery and reproducibility in serum. The advantages of this method allow us to more conveniently obtain the expression profiles of multiple groups of TNBC-associated miRNAs, which is beneficial for the early detection of TNBC.

Abstract Long non-coding RNAs (lncRNAs) participate in the biological processes of plants under biotic and abiotic stresses. However, little is known about the function and regulation mechanism of the pathogen-related lncRNAs at a molecular level. A banana lncRNA, namely Malnc2310, is greatly induced by Fusarium oxysporum f. sp. cubense TR4 strain (VCG01213/16) in roots. In this study, we indicate the nuclear localization of Malnc2310 by fluorescence in situ hybridization (FISH). We illustrate that Malnc2310 interacts with several proteins that are related to phenylpropanoid pathway, pathogen response and programmed cell death. Overexpression of Malnc2310 confers higher susceptibility to stresses, such as Fusarium crude extracts, salinity and cold in transgenic Arabidopsis. Furthermore, the Malnc2310 transgenic Arabidopsis accumulated more anthocyanin under Fusarium crude extracts and cold treatments. The Malnc2310 overexpression up-regulated the expression of several key genes that are related to the development of lateral roots and those involved in the anthocyanin biosynthesis pathway. Malnc2310 also enhanced the activity of phenylalanine ammonia lyase (PAL) in transgenic Arabidopsis. Based on our findings, we propose that Malnc2310 binds to PAL to participate in the flavonoid metabolism under stresses. This study provides new insights into the role of Malnc2310 in mediating plants to stress adaptation.

Abstract A Gram-stain-negative, rod-shaped bacterium, designated HB171785T, was isolated from soil sample collected from Qishui Bay, Hainan, China. The strain grew optimally at pH 7–8, 40–45°C and with NaCl 3–4%. The predominant isoprenoid quinone was found to be Q-8 and the major fatty acids were C16:0, C16:1 ω7c / C16:1 ω6c, C18:1 ω7c / C18:1 ω6c and C12:0 3OH. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The size of the draft genome was 4.32 Mbp with G + C content 49.7%. Phylogenetic analysis of 16S rRNA gene sequence indicated that strain HB171785T belonged to the order Alteromonadales, and the closest phylogenetically related species were Neiella marina j221T, “Neiella holothuriorum” 126 and Echinimonas agarilytica LMG2520T with the similarities of 98.2, 96.0 and 95.0%, respectively. The phylogenetic tree based on 16S rRNA genes and phylogenomic tree based on core genomes showed that strain HB171785T clustered together with N. marina j221T, with the highest values of average nucleotide identity (82.9%) and digital DNA-DNA hybridization (25.4%). The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB171785T represents a novel species of the genus Neiella, for which the name Neiella litorisoli sp. nov. is proposed. The type strain is HB171785T (= MCCC 1K04625T = KCTC 82319T).