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The age of the Silurian “Lower Red Beds” (LRBs), which occur widely in South China, has long been controversial because of the scarcity of index fossils. Here, we report a fauna with abundant trilobites from the LRBs in Wuhan, Middle Yangtze region, consisting of Aulacopleura (Paraaulacopleura) pijiazhaiensis, ‘Encrinuroides’ yichangensis, Gaotania hubeiensis, Hyrokybe gaotanensis, Japonoscutellum yichangense, Latiproetus latilimbatus, and Ptilillaenus lojopingensis. These trilobites are common in the Leijiatun, upper Xiangshuyuan, Shihniulan, and Lojoping formations in the Upper Yangtze region, and belong to the middle to upper Aeronian Ptilillaenus or ‘Encrinuroides’–Ptilillaenus–Latiproetus assemblages. The discovery of this trilobite assemblage suggests that the LRBs are probably partly of middle–late Aeronian age in the Middle Yangtze region. Thus, the lower boundary of the LRBs is likely diachronous in the Yangtze region, ranging from the middle–late Aeronian to the early Telychian. The discovery of the Ptilillaenus assemblage in the Wuhan LRBs expands the paleogeographic distribution of this assemblage and provides evidence of deeper depositional environment of the LRBs in the study area versus shallow waters in other areas of the Yangtze region.

Polysaccharides were extracted by hot water and alkali in sequence from Dolichos lablab L. hull, and further purified by ion-exchange and gel columns. Hot water extracted D. lablab hull polysaccharide (DLHP) was rich in glucuronoxylan and pectin, and alkali extracted polysaccharide (DLHAP) mostly embraced glucuronoxylan. The structures of purified glucuronoxylans from DLHP and DLHAP were mainly analyzed by HPAEC-PAD, methylation combined with GC–MS, NMR and SEC-MALLS. DLHP-1 was identified as acetylated glucuronoxylan containing →4)-β-Xylp-(1→ backbone with substitution at O-2 site by α-GlcpA/4-O-methyl-α-GlcpA. The molar ratio of β-Xylp to α-GlcpA was 6.9:1, and acetylation was mainly at O-3 site of β-Xylp with acetylation degree of 21.5%. DLHP-1 and DLHP-2 had similar physicochemical properties, except for molecular weight (Mw). DLHAP-1 was the non-methylated glucuronoxylan almost without acetylation, and it had the molar ratio of β-Xylp to α-GlcpA of 5.6:1. Besides, DLHP-1 (Mw of 20.0 × 103 g mol−1) adopted semi-flexible chain, while DLHAP-1 (Mw of 15.4 × 103 g mol−1) showed flexible chain. These results provided a structural basis for study on polysaccharides from D. lablab hull, which was benefit for understanding biological activities and developing functional food or pharmaceuticals of D. lablab.

Bacterial superinfection aggravates the disease of influenza. Streptococcus pneumoniae is the most common bacterial pathogen. Synergistic virulence has been demonstrated between influenza neuraminidase and pneumococcal NanA and NanB. NanC, the other pneumococcal neuraminidase infrequently present in clinical isolates, is not well characterized. In this study, we report that superinfection with a NanC-negative pneumococcus strain suppresses anti-influenza immunity and impairs viral clearance with higher TGF-β activation in mice. Bacterial load in the lungs also increases as the host immunity is suppressed. NanC-positive isogenic mutant reverses wild type S. pneumoniae–mediated immune suppression and facilitates virus clearance. However, it causes more severe disease as the augmented inflammation causes collateral damage. Both virus-mediated damage and immune response–mediated inflammation are important for pathogenesis of severe influenza. Inflammation may be more critical than virus-mediated damage in influenza with bacterial superinfection.

We conducted a retrospective analysis of the clinical characteristics and dynamic variations of immune indexes in nine COVID-19 patients in Zigong, China. We used flow cytometry and enzyme-linked immunosorbent assays to measure the absolute levels of CD4 and CD8 lymphocytes and SARS-CoV-2 antibodies, respectively. We found that CRP, LDH, HBDH, CD4/CD8 and IgE levels were increased in 6/9 patients, while PA and the absolute numbers of CD4 and CD8 lymphocytes decreased in 7/9 patients. From disease onset through 63 days of follow-up, SARS-CoV-2 IgG levels were consistently higher than those of SARS-CoV-2 IgM, reaching peaks on days 28 and 13, respectively. IgM levels decreased to normal 35 days after disease onset, while IgG levels remained elevated through day 63. IgE levels varied similarly to SARS-CoV-2 IgM. Our results suggest that SARS-CoV-2 may elicit allergic immune responses in patients and that the levels of CRP, PA, LDH, and HBDH, as well as the absolute numbers of CD4 and CD8 lymphocytes could be used as early diagnostic markers of SARS-CoV-2 infection. Lastly, the dynamic variation of SARS-CoV-2 antibodies could guide the timing of blood collection for plasma exchange.

Increasing evidence suggests that long non-coding RNAs (lncRNAs) are of vital importance for various biological processes, and dysregulation of lncRNAs is frequently associated with various diseases such as psoriasis. LncRNAs modulate gene expression at the transcriptional, post-transcriptional, and translational levels; however, the specific regulatory mechanisms of lncRNAs in psoriasis remain largely unexplored. This review provides an overview of recent studies investigating mechanisms and functions of lncRNAs in psoriasis, especially focusing on the role of lncRNAs in keratinocytes, T cells, and dendritic cells.

Background Rab40b is an evolutionarily conserved Rab GTPase that plays an important role in intracellular trafficking and is closely related to cancer progression. However, the role and potential molecular mechanism of Rab40b in hepatocellular carcinoma (HCC) have not yet been elucidated. Materials and methods The expression of Rab40b in HCC tissues and peritumour tissues was tested by qRT-PCR, Western blotting and histological analysis. A Kaplan-Meier survival curve was generated based on the expression of Rab40b in the HCC samples. Cell proliferation assays, wound healing assays, and transwell assays are used to examine the effect of Rab40b on HCC cell growth in vitro. The effect of Rab40b on cell cycle was examined by flow cytometry. A xenograft implantation model was used to assess the effect of Rab40b on the development of HCC cells in vivo. Results Rab40b protein expression is upregulated in HCC tissues, and this upregulation is associated with high pathological stage and poor prognosis in HCC patients. Rab40b overexpression promotes the proliferation and metastasis of HCC cells by upregulating cyclin D1, cyclin E1 and matrix metalloproteinase 2 (MMP2) through the PI3K/AKT signalling pathway. Conversely, Rab40b inhibitors can significantly inhibit the proliferation and metastasis of HCC cell lines and induce G0/G1 cell cycle arrest and apoptosis. Studies of a nude mouse xenograft model demonstrated that Rab40b knockdown can significantly inhibit the proliferation and progression of HCC tumours in vivo. Conclusion Overall, this study demonstrates that Rab40b is an important oncoprotein that promotes HCC progression by regulating the expression of cyclin D1, cyclin E1, p21 and MMP2 through the PI3K/AKT signalling pathway.

Background Koelreuteria henryi Dummer is an indigenous plant in Taiwan. The species has been used in traditional folk medicine for the promotion of liver functions and for treating malaria and urethritis. The present study investigated the antioxidant activity of the flower extract of Koelreuteria henryi Dummer. The extraction conditions were optimized by the contents of total phenolic acids and total flavonoids, and antioxidant activity assays. Moreover, an in vitro study for investigating antioxidant activity of K. henryi flower extract was demonstrated by hydrogen peroxide (H2O2)-induced apoptosis. Results K. henryi flower extracted for 150 min showed high contents of total phenolic acids and total flavonoids. In an in vitro model, L929 cells were pretreated with K. henryi flower extract, and then treated with H2O2 to induce oxidative damage. Results demonstrated that H2O2-induced apoptosis was inhibited by the treatment of 200 μg/ml K. henryi flower extract through the mitochondria-mediated pathway and mitogen-activated protein kinase (MAPK) pathway. The caspase 8/9 activity and expression of p-p38 and pERK were repressed by K. henryi flower extract. In addition, the prevention of H2O2-induced apoptosis by K. henryi flower extract activated the nuclear factor-erythroid 2-related factor (Nrf2) stress response pathway to transcript heme oxygenase 1 (HO-1). Also, K. henryi flower extract prevented H2O2-induced apoptosis through HO-1 production, as evident by the use of HO-1 inhibitor. Conclusions The present study demonstrated that K. henryi flower extract could inhibit the H2O2-induced apoptosis in L929 cells through the activation of the Nrf2/HO-1 pathway. How to cite: Tsai WC, Chang HC, Yin HY, et al. The protective ability and cellular mechanism of Koelreuteria henryi Dummer flower extract against hydrogen peroxide-induced cellular oxidative damage. Electron J Biotechnol 2020;47. https://doi.org/10.1016/j.ejbt.2020.07.006 .

Backgrounds The novel coronavirus disease (COVID‐19) poses serious threat to global public health and economics. Serial interval (SI), time between the symptom onsets of a primary case and a second case, is a key epidemiological parameter. We estimated SI of COVID‐19 in Shenzhen, China based on 27 records of transmission chains. Methods We adopted three parametric models: Weibull, Lognormal and Gamma distributions and an interval censored likelihood framework. The three models were compared using the corrected Akaike information criterion (AICc). We also fitted the epidemic curve of COVID‐19 to the exponential growth to estimate the reproduction number. Findings Using a Weibull distribution, we estimated mean SI at 5.9 days (95%CI: 3.9−9.6) and a standard deviation (SD) at 4.8 days (95%CI: 3.1−10.1). Using a logistic growth model, we estimated the basic reproduction number in Shenzhen at 2.6 (95%CI: 2.4−2.8). Conclusion The SI of COVID‐19 is relative shorter than that of SARS and MERS, other two beta coronavirus diseases, which suggests the iteration of the transmission was rapid. It is crucial to isolate close contacts promptly to control the spread of COVID‐19 effectively.

Background Glucomannans (GMs) are a group of hydrophilic polysaccharides, which have been produced from different parts of natural plants. Studies on plant-derived GMs contribute to wide applications of GMs or GMs-added products that have desirable quality and health characteristics. Among those popular GMs, konjac glucomannan (KGM) and acemannan are the most famous ones that have been widely reviewed from various points in recent years. However, there is a lack of a comprehensive review to introduce the sources, extraction and purification methods, structural features, and other aspects of GMs from common natural plants such as Aloe, Dendrobium, Bletilla, and so on. Scope and approach This review firstly presents the extraction and purification technologies of GMs from different plant sources, aiming at optimizing more effective production methods with specific treatments for special plant origins. After that, structural features, biological properties, as well as structure-function relationship are summarized. Key findings and conclusions GMs have been widely isolated from different sectors (leaf, stem, and roots) of many plant resources. A general extraction and purification procedure together with several suggestions is put forward to prepare GMs. Although the β-(1 → 4)-linked main chain has been confirmed, detailed structural characteristics of GMs such as side chain and functional group related properties need further studies. Molecular weights, monosaccharide composition, and acetyl group of GMs are key factors that have been identified to affect plentiful biological properties such as immunomodulatory, anti-tumor, anti-diabetic activities. However, the inherent action mechanisms remain unclear. Several research interests in the future are recommended.

Background Taraxacum species (commonly known as dandelion) used as herbal medicine have been reported to exhibit an antiproliferative effect on hepatoma cells and antitumor activity in non-small-cell lung cancer cells. Although several investigations have demonstrated the safety of Taraxacum officinale, the safety of tissue-cultured plants of T. formosanum has not been assessed so far. Therefore, the present study examines the safety of the water extract of the entire plant of tissue cultured T. formosanum based on acute and subacute toxicity tests in rats, as well as the Ames tests. Results No death or toxicity symptoms were observed in the acute and subacute tests. The results of the acute test revealed that the LD50 (50% of lethal dose) value of the T. formosanum water extract for rats exceeded 5 g/kg bw. No abnormal changes in the body weight, weekly food consumption, organ weight, or hematological, biochemical, and morphological parameters were observed in the subacute toxicity test. Thus, the no observed adverse effect level (NOAEL) of T. formosanum water extract was estimated to be higher than 2.0 g/kg. Finally, the results of the Ames test revealed that T. formosanum water extract was not genotoxic at any tested concentration to any of five Salmonella strains. Conclusions The water extract of tissue-cultured T. formosanum was non-toxic to rats in acute and subacute tests and exhibited no genotoxicity to five Salmonella strains. How to cite: Tsai WC, Chang HC, Tseng YH, et al. Toxicity evaluation of water extract of tissue-cultured Taraxacum formosanum by acute, subacute administration, and Ames test. Electron J Biotechnol 2020;45. https://doi.org/10.1016/j.ejbt.2020.04.001

Thioredoxin-interacting protein (TXNIP) is a multifunctional protein that functions in tumor suppression, oxidative stress, and inflammatory responses. However, how TXNIP functions during microbial infections is rarely reported. In this study, we demonstrate that Brucella infection decreased TXNIP expression to promote its intracellular growth in macrophages by decreasing the production of NO and reactive oxygen species (ROS). Following Brucella abortus infection, TXNIP knockout RAW264.7 cells produced significantly lower levels of NO and ROS, compared with wild-type RAW264.7 cells. Inducible NO synthase (iNOS) inhibitor treatment reduced NO levels, which resulted in a dose-dependent restoration of TXNIP expression, demonstrating that the expression of TXNIP is regulated by NO. In addition, the expression of iNOS and the production of NO were dependent on the type IV secretion system of Brucella. Moreover, Brucella infection reduced TXNIP expression in bone marrow–derived macrophages and mouse lung and spleen. Knocked down of the TXNIP expression in bone marrow–derived macrophages increased intracellular survival of Brucella. These findings revealed the following: 1) TXNIP is a novel molecule to promote Brucella intracellular survival by reducing the production of NO and ROS; 2) a negative feedback–regulation system of NO confers protection against iNOS-mediated antibacterial effects. The elucidation of this mechanism may reveal a novel host surveillance pathway for bacterial intracellular survival.

Aims Hypertension is a leading cause of cerebral small vessel disease (CSVD). Currently, treatments for CSVD are limited. Nicotinamide riboside (NR) can protect against vascular injury and cognitive impairment in neurodegenerative diseases. In this study, the protective effects of NR against angiotensin ‐ (Ang ‐)–induced CSVD were evaluated. Methods To explore the effects of NR in CSVD, C57BL/6 mice were infused with Ang ‐, and NR was added to the food of the mice for 28 days. Then, short‐term memory, blood‐brain barrier (BBB) integrity, and endothelial function were detected. Arteriole injury and glial activation were also evaluated. Results Our data showed that mice infused with Ang ‐ exhibited decreased short‐term memory function and BBB leakage due to decreased claudin‐5 expression and increased caveolae‐mediated endocytosis after 28 days. Furthermore, Ang ‐ decreased the expression of α‐smooth muscle actin (α‐SMA) and increased the expression of proliferating cell nuclear antigen (PCNA) in arterioles and decreased the expression of neurofilament 200 (NF200) and myelin basic protein (MBP) in the white matter. These CSVD‐related damages induced by Ang ‐ were inhibited by NR administration. Moreover, NR administration significantly reduced glial activation around the vessels. Conclusion Our results indicated that NR administration alleviated Ang ‐–induced CSVD by protecting BBB integrity, vascular remodeling, neuroinflammation, and white matter injury (WMI)–associated cognitive impairment.

Acinetobacter baumannii emerged as one of the most important pathogens that causes nosocomial infections due to its increased multidrug resistance. Identifying capsular epidemiology in A. baumannii can aid in the development of effective treatments and preventive measures against this emerging pathogen. Here we established a wzc-based method, and combined it with wzy-PCR to determine capsular types of A. baumannii causing nosocomial bacteraemia collected at two medical centres in Taiwan from 2015 to 2017. Among the 237 patients with A. baumannii bacteraemia, 98 (41.4%) isolates were resistant to carbapenems. Four prevalent capsular types (KL2, KL10, KL22, and KL52) accounted for 84.7% of carbapenem-resistant A. baumannii (CRAB) and 12.2% of non-CRAB. The rate of pneumonia, intensive care unit admission, APACHE II score, and Pitt bacteraemia score were higher in patients with KL2/10/22/52 infection than in those with non-KL2/10/22/52 infection. Patients with KL2/10/22/52 infection and patients with CRAB infection have a higher cumulative incidence of attributable and all-cause in-hospital 30-day mortality. On multivariate analysis, appropriate empirical antimicrobial therapy within 24 h was associated with a lower risk of 30-day attributable mortality in the KL2/10/22/52 isolates (odds ratio = 0.19, 95% CI: 0.06–0.66, p = 0.008) but not in non-KL2/10/22/52 isolates. Early recognition of carbapenem resistance-associated capsular types may help clinicians to promptly implement appropriate antimicrobial therapy for improving the outcomes in patients with CRAB bacteraemia.

The novel coronavirus disease 2019 (COVID-19) infection broke out in December 2019 in Wuhan, and rapidly overspread 31 provinces in mainland China on 31 January 2020. In the face of the increasing number of daily confirmed infected cases, it has become a common concern and worthy of pondering when the infection will appear the turning points, what is the final size and when the infection would be ultimately controlled. Based on the current control measures, we proposed a dynamical transmission model with contact trace and quarantine and predicted the peak time and final size for daily confirmed infected cases by employing Markov Chain Monte Carlo algorithm. We estimate the basic reproductive number of COVID-19 is 5.78 (95%CI: 5.71–5.89). Under the current intervention before 31 January, the number of daily confirmed infected cases is expected to peak on around 11 February 2020 with the size of 4066 (95%CI: 3898–4472). The infection of COVID-19 might be controlled approximately after 18 May 2020. Reducing contact and increasing trace about the risk population are likely to be the present effective measures.

Incidence of invasive pneumococcal disease caused by antimicrobial-resistant Streptococcus pneumoniae types not included in pneumococcal conjugate vaccines has increased, including a penicillin- and meropenem-resistant serotype 15A-ST63 clone in Japan. During 2013-2017, we collected 206 invasive pneumococcal isolates in Taiwan for penicillin and meropenem susceptibility testing. We found serotypes 15B/C-ST83 and 15A-ST63 were the most prevalent penicillin- and meropenem-resistant clones. A transformation study confirmed that penicillin-binding protein (PBP) 2b was the primary meropenem resistance determinant, and PBP1a was essential for high-level resistance. The rate of serotype 15B/C-ST83 increased during the study. All 15B/C-ST83 isolates showed an ermB macrolide resistance genotype. Prediction analysis of recombination sites revealed 12 recombination regions in 15B/C-ST83 compared with the S. pneumoniae Spain23F-ST81 genome. Pneumococcal clones rapidly recombine to acquire survival advantages and undergo local expansion under the selective pressure exerted by vaccines and antimicrobial drugs. The spread of 15B/C-ST83 is alarming for countries with high antimicrobial pressure.

The sequence of the ribosomal RNA gene (rDNA) plays an important role in species identification and phylogenetic analysis. However, the only published full-length sequence of a ribosomal gene of green algae is that of Ulva mutabilis. In this study, we amplified the full-length sequence of each ribosomal gene unit of the ribosomal gene of Blidingia minima. The full-length sequence of the ribosomal gene in Blidingia minima is 8676 bp, including the 1759 bp 18S rDNA, 576 bp internal transcribed spacer (ITS) + 5.8S rDNA, 3282 bp 28S rDNA, and 3059 bp intergenic spacer (IGS) region. We then carried out a series of genetic analyses based on the ITS and IGS sequences, to verify whether IGS sequences are useful for studying the genetic diversity of green algae from different locations. We amplified the IGS sequences of Blidingia minima from 10 different locations in the Yellow Sea. Multiple alignments of the IGS sequences of samples from these 10 different sites revealed varying degrees of base differences, and comparative analysis of the ITS sequences revealed that our amplified species was classified as Blidingia minima and distinct from other green algae. In conclusion, our full-length amplified ribosomal gene provides useful information to enrich the data on green algae ribosomal genes and provides an effective molecular marker for the analysis of the interspecies and intraspecies relationships of Blidingia minima.

The emergence of novel antimicrobial resistance genes conferring resistance to last-resort antimicrobials poses a serious challenge to global public health security. Recently, one plasmid-mediated RND family multidrug resistance efflux pump gene cluster named tmexCD1-toprJ1, which confers resistance to tigecycline, was identified in bacteria of animal and human origins. However, the comprehensive landscape of the genomic epidemiology of this novel resistance determinant remained unclear. To fill this knowledge gap, we isolated 25 tmexCD1-toprJ1-positive bacteria from 682 samples collected along the pork production chain, including swine farms, slaughterhouses, and retail pork, and characterized the positive strains systematically using antimicrobial susceptibility testing, conjugation assays, single-molecule sequencing, and genomic analyses. We found that tmexCD1-toprJ1-positive bacteria were most prevalent in slaughterhouses (7.32%), followed by retail pork (0.72%). Most of the positive strains were Klebsiella pneumoniae (23/25), followed by Proteus mirabilis (2/25). IncFIB(Mar)/IncHI1B hybrid plasmids were mainly vectors for tmexCD1-toprJ1 and dominated the horizontal dissemination of tmexCD1-toprJ1 among K. pneumoniae isolates. However, in this study, we identified the IncR plasmid as a tmexCD1-toprJ1-positive plasmid with a broad host range, which evidenced that the widespread prevalence of tmexCD1-toprJ1 is possible due to such kinds of plasmids in the future. In addition, we found diversity and heterogeneity of translocatable units containing tmexCD1-toprJ1 in the plasmids. We also investigated the genetic features of tmexCD1-toprJ1 in online databases, which led to the proposal of the umuC gene as the potential insertion site of tmexCD1-toprJ1. Collectively, this study enriches the epidemiological and genomic characterization of tmexCD1-toprJ1 and provides a theoretical basis for preventing an increase in tmexCD1-toprJ1 prevalence. IMPORTANCE Tigecycline, the first member of the glycylcycline class of antibacterial agents, is frequently used to treat complicated infections caused by multidrug-resistant Gram-positive and Gram-negative bacteria. The emergence of a novel plasmid-mediated efflux pump, TmexCD1-ToprJ1, conferring resistance to multiple antimicrobials, including tigecycline, poses a huge risk to human health. In this study, we investigated the prevalence of tmexCD1-toprJ1-positive strains along the food production chain and found that tmexCD1-toprJ1 was mainly distributed in IncFIB(Mar)/HI1B hybrid plasmids of K. pneumoniae. We also observed a potential risk of transmission of such plasmids along the pork processing chain, which finally may incur a threat to humans. Furthermore, the IncFIB(Mar)/HI1B tmexCD1-toprJ1-positive plasmids with a limited host range and specific insertion sites of tmexCD1-toprJ1 are strong evidence to prevent a fulminant epidemic of tmexCD1-toprJ1 among diverse pathogens. The mobilization and dissemination of tmexCD1-toprJ1, especially when driven by plasmids, deserve sustained attention and investigations.

Description, A network dependency platform was generated to define a landscape of cancer drug mechanisms in pulmonary hypertension., Cancer therapies are being considered for treating rare noncancerous diseases like pulmonary hypertension (PH), but effective computational screening is lacking. Via transcriptomic differential dependency analyses leveraging parallels between cancer and PH, we mapped a landscape of cancer drug functions dependent upon rewiring of PH gene clusters. Bromodomain and extra-terminal motif (BET) protein inhibitors were predicted to rely upon several gene clusters inclusive of galectin-8 (LGALS8). Correspondingly, LGALS8 was found to mediate the BET inhibitor–dependent control of endothelial apoptosis, an essential role for PH in vivo. Separately, a piperlongumine analog’s actions were predicted to depend upon the iron-sulfur biogenesis gene ISCU. Correspondingly, the analog was found to inhibit ISCU glutathionylation, rescuing oxidative metabolism, decreasing endothelial apoptosis, and improving PH. Thus, we identified crucial drug-gene axes central to endothelial dysfunction and therapeutic priorities for PH. These results establish a wide-ranging, network dependency platform to redefine cancer drugs for use in noncancerous conditions.

Dissemination of multidrug-resistant, particularly tigecycline-resistant, Acinetobacter baumannii is of critical importance, as tigecycline is considered a last-line antibiotic. Acquisition of tet(X), a tigecycline-inactivating enzyme mostly found in strains of animal origin, imparts tigecycline resistance to A. baumannii. Herein, we investigated the presence of tet(X) variants among 228 tigecycline-non-susceptible A. baumannii isolates from patients at a Taiwanese hospital via polymerase chain reaction using a newly designed universal primer pair. Seven strains (3%) carrying tet(X)-like genes were subjected to whole genome sequencing, revealing high DNA identity. Phylogenetic analysis based on the PFGE profile clustered the seven strains in a clade, which were thus considered outbreak strains. These strains, which were found to co-harbor the chromosome-encoded tet(X6) and the plasmid-encoded blaOXA-72 genes, showed a distinct genotype with an uncommon sequence type (Oxford ST793/Pasteur ST723) and a new capsular type (KL129). In conclusion, we identified an outbreak clone co-carrying tet(X6) and blaOXA-72 among a group of clinical A. baumannii isolates in Taiwan. To the best of our knowledge, this is the first description of tet(X6) in humans and the first report of a tet(X)-like gene in Taiwan. These findings identify the risk for the spread of tet(X6)-carrying tigecycline- and carbapenem-resistant A. baumannii in human healthcare settings.

BackgroundStreptococcus pneumoniaeis a common cause of post-influenza secondary bacterial infection, which results in excessive morbidity and mortality. Although 13-valent pneumococcal conjugate vaccine (PCV13) vaccination programs have decreased the incidence of pneumococcal pneumonia, PCV13 failed to prevent serotype 3 pneumococcal disease as effectively as other vaccine serotypes. We aimed to investigate the mechanisms underlying the co-pathogenesis of influenza virus and serotype 3 pneumococci.MethodsWe carried out a genome-wide screening of a serotype 3S. pneumoniaetransposon insertion mutant library in a mouse model of coinfection with influenza A virus (IAV) to identify the bacterial factors required for this synergism.ResultsDirect, high-throughput sequencing of transposon insertion sites identified 24 genes required for both coinfection and bacterial infection alone. Targeted deletion of the putative aminotransferase (PA) gene decreased bacterial growth, which was restored by supplementation with methionine. The bacterial burden in a coinfection with thePAgene deletion mutant and IAV in the lung was lower than that in a coinfection with wild-type pneumococcus and IAV, but was significantly higher than that in an infection with thePAgene deletion mutant alone. These data suggest that IAV infection alters host metabolism to benefit pneumococcal fitness and confer higher susceptibility to pneumococcal infection. We further demonstrated that bacterial growth was increased by supplementation with methionine or IAV-infected mouse lung homogenates.ConclusionsThe data indicates that modulation of host metabolism during IAV infection may serve as a potential therapeutic intervention against secondary bacterial infections caused by serotype 3 pneumococci during IAV outbreaks in the future.

Heritable symbionts play an essential role in many aspects of host ecology in a temperature-dependent manner. However, how temperature impacts the host and their interaction with endosymbionts remains largely unknown. Here, we investigated the impact of moderate (20°C) and high (30 and 35°C) temperatures on symbioses between the spider mite Tetranychus truncatus and two maternally inherited endosymbionts (Wolbachia and Spiroplasma). We found that the thermal tolerance of mites (as measured by survival after heat exposure) was lower for mites that were singly infected with either Wolbachia or Spiroplasma than it was for co-infected or uninfected mites. Although a relatively high temperature (30°C) is thought to promote bacterial replication, rearing at high temperature (35°C) resulted in losses of Wolbachia and particularly Spiroplasma. Exposing the mites to 20°C reduced the density and transmission of Spiroplasma but not Wolbachia. The four spider mite strains tested differed in the numbers of heat shock genes (Hsps) induced under moderate or high temperature exposure. In thermal preference (Tp) assays, the two Wolbachia-infected spider mite strains preferred a lower temperature than strains without Wolbachia. Our results show that endosymbiont-mediated spider mite responses to temperature stress are complex, involving a combination of changing endosymbiont infection patterns, altered thermoregulatory behavior, and transcription responses.

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission1,2. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission and is a key element in safely reopening society. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. We show that SwabSeq can test nasal and oral specimens for SARS-CoV-2 with or without RNA extraction while maintaining analytical sensitivity better than or comparable to that of fluorescence-based RT-qPCR tests. SwabSeq is simple, sensitive, flexible, rapidly scalable, inexpensive enough to test widely and frequently, and can provide a turn around time of 12 to 24 hours.

High intake of dietary fibers was found to be inversely associated with type-2 diabetes (T2D), whereas the difference among different dietary fibers on T2D remains unclear. Therefore, we have investigated the effects of different dietary fibers on T2D. Nine types of dietary fibers were used to investigate and evaluate their effects on type-2 diabetic rats via physiology, genomics, and metabolomics. We found that supplementation with β-glucan, arabinogalactan, guar gum, apple pectin, glucomannan, and arabinoxylan significantly reduced the fasting blood glucose, whereas carrageenan, xylan, and xanthan gum did not affect glycemic control in diabetic rats. Also, bioactive dietary fibers (β-glucan, arabinogalactan, guar gum, and apple pectin) associated with the increased butyric acid level and abundance of beneficial bacteria (Lachnobacterium, Parabacteroides, Faecalibacterium, Akkermansia, and some butyric acid-producing bacteria), as well as improved host metabolism by decreasing 12α-hydroxylated bile acids, acylcarnitines, and amino acids (leucine, phenylalanine, citrulline, etc.), thereby exert beneficial effects on T2D. It was also found that β-glucan might attenuate insulin resistance via downregulation of Prevotella copri-mediated biosynthesis of branched-chain amino acids in T2D. Together, our study uncovered the effects of different dietary fibers on T2D, along with their potential mechanism.

Purpose: Protein kinases are known to play a prominent role in oncogenic progression across multiple cancer subtypes, yet their role in prostate cancer progression remains underexplored. The purpose of this study was to identify kinases that drive prostate cancer progression. Experimental Design: To discover kinases that drive prostate cancer progression, we investigated the association between gene expression of all known kinases and long-term clinical outcomes in tumor samples from 545 patients with high-risk disease. We evaluated the impact of genetic and pharmacologic inhibition of the most significant kinase associated with metastatic progression in vitro and in vivo. Results: DNA-dependent protein kinase (DNAPK) was identified as the most significant kinase associated with metastatic progression in high-risk prostate cancer. Inhibition of DNAPK suppressed the growth of both AR-dependent and AR-independent prostate cancer cells. Gene set enrichment analysis nominated Wnt as the top pathway associated with DNAPK. We found that DNAPK interacts with the Wnt transcription factor LEF1 and is critical for LEF1-mediated transcription. Conclusions: Our data show that DNAPK drives prostate cancer progression through transcriptional regulation of Wnt signaling and is an attractive therapeutic target in aggressive prostate cancer.

Green tide algal blooms occur worldwide, especially in China’s Yellow Sea, and have caused serious damage to local ecological environments and economies. As a dominant agent of green tides, the green macroalga Ulva has caused widespread concern. In this study, phylogenetic clades were constructed among related Ulva species isolated from Pyropia rafts at six sites over 1.5 years based on internal transcribed spacer (ITS) and tufA sequences. In addition, traditional observation ploidy methods and flow cytometry methods were used to analyse continuous change in the biphase and sex ratios of Ulva species and to assess the changes in phase advantages over time. The results showed that the perennial Ulva populations on rafts mainly consisted of Ulva flexuosa and Ulva prolifera, and the biphasic dominance of the attached Ulva populations changed with the seasons: sporophytes were predominant mainly in winter and spring, and gametophytes were predominant mainly in summer and autumn. At the same time, there were some differences in gametophyte and sporophyte frequencies (mainly sporophyte biased) compared to the null model prediction of a √2:1 ratio, while the sex ratio of male and female gametophytes remained 1:1 throughout the year. Our results indicate the presence of both phases of bloom-forming species of Ulva in green tides year round, and that multiple generations coexist and grow continuously.

Peroxiredoxin-5 (Prdx5) is a multifunctional protein involved in oxidative stress, apoptosis and inflammatory responses. However, how Prdx5 functions during microbial infections is rarely reported. In this study, we demonstrate that Brucella infection increased Prdx5 expression to promote its intracellular growth in macrophages. Further study show that B. abortus infection promoted its intracellular growth by decreasing the production of nitric oxide and reactive oxygen species. In addition, the expression of Prdx5 was independent on live Brucella and the type IV secretion system of Brucella. Instead, its expression was regulated by the lipopolysaccharide of Brucella. Moreover, Brucella infection increased Prdx5 expression in primary macrophage and mice. Collectively, these findings demonstrate for the first time that Prdx5 promotes Brucella intracellular growth by decreasing the production of NO and ROS. This finding provides new insights into the evasive strategies of Brucella and will be useful for the development of novel effective therapeutic approaches to treat Brucella infections.

Rehderodendron truongsonense, a new species from Vietnam, is described and illustrated. In the treatment of the Styracaceae for the Flore du Cambodge, du Laos, et du Viêtnam, specimens of this species were recognized as R. macrocarpum Hu. These specimens clearly differ from R. macrocarpum, however, as well as from all other species of Rehderodendron (where these characters are known) by, e.g., an evergreen versus deciduous habit, fewer secondary veins of the leaf blade, shorter inflorescences and corolla lobes, large and conspicuous lowermost bracteoles, the presence of eight ovules per carpel, and a fruit with ca. 10 to 20 ribs that are indistinct. Phylogenetic analysis based on five chloroplast DNA regions (clpP-psbB, ndhD-psaC-ndhE-ndhG, rpl22-rps19, rps18-rpl20, and psbI-trnS-GCU) placed the new species as nested within Rehderodendron and sister to R. gongshanense. This new species is endemic to the Truong Son Mountain Range, from which the epithet is derived, and we assign it an IUCN Red List preliminary status as Near Threatened.

Fishponds are artificial yet dynamic environments. Microbes play a vital role in the conversion and metabolism of organic matter in aquaculture environments such as fishponds. Changes in bacterial community composition in three fishponds over a 5‐month period were investigated by sequencing the 16S rRNA gene through Illumina Miseq. A total of 2,195,879 sequences and 9,975 operational taxonomic units (OTUs) were obtained. Further analysis showed that the dominant phyla in three ponds were similar, including Proteobacteria, and Bacteroidetes. A comprehensive analysis of the diversity, redundancy analysis (RDA) and partial redundancy analysis (pRDA) showed a spatial‐temporal structural pattern in the bacterial communities. The bacterial community composition in the three fishponds was shaped more by spatial variation than by temporal variation. The effect of pond isolation was emphasized by the significant differences observed in the three fishponds. However, the temporal succession of bacterial communities in each pond exhibited a similar trend. Correlation analysis and RDA also indicated that temporal variation was significantly associated with TOC, TN and NO₂⁻. This study would improve our understanding of the assembly mechanisms of a microbial structure in artificial pond ecosystems, and provide useful information for fishpond management.

The subgenomic mRNA (sgRNA) promoter for coat protein (CP) was isolated from the cDNA infectious clone of Odontoglossum ringspot virus Taiwan strain (ORSV-TW), which is a positive single-stranded RNA virus of the Tobamovirus family. The 5′-end deletion analysis of the 290 nucleotides ORSV CP sgRNA promoter was performed to investigate the promoter activity. A series of different ORSV CP sgRNA promoter deletions were characterized by driving the expression of a fused green fluorescent protein (GFP)-β-glucuronidase (GUS) gene using Agrobacterium-mediated infiltration in Phalaenopsis petals and Nicotiana benthamiana leaves. The results of deletion analysis indicated that the region between 24 nucleotides upstream and 18 nucleotides downstream of translation start codon was sufficient for promoter activity. The activity of this minimal promoter was relatively stronger than other promoters with longer length. A minimal ORSV CP sgRNA promoter was found to accumulate high levels of GFP and GUS, suggesting that this sequence might drive the foreign protein expression in heterologous systems.

Microbiota is just beginning to be recognized as an important player in carcinogenesis and the interplay among microbes is greater than expected. Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease for which mortality closely parallels incidence. Early detection would provide the best opportunity to increase survival rates. Specific well-studied oral, gastrointestinal, and intrapancreatic microbes and some kinds of hepatotropic viruses and bactibilia may have potential etiological roles in pancreatic carcinogenesis, or modulating individual responses to oncotherapy. Concrete mechanisms mainly involve perpetuating inflammation, regulating the immune system-microbe-tumor axis, affecting metabolism, and altering the tumor microenvironment. The revolutionary technology of omics has generated insight into cancer microbiomes. A better understanding of the microbiota in PDAC might lead to the establishment of screening or early-stage diagnosis methods, implementation of cancer bacteriotherapy, adjustment of therapeutic efficacy even alleviating the adverse effects, creating new opportunities and fostering hope for desperate PDAC patients.

Plants in Amorphophallus genus are rich in soluble dietary fibres and have long been used as food and traditional medicine in Asian countries. In the present investigation, natural O-acetyl-glucomannans were extracted from tubers of Amorphophallus rivirei (konjac), A. albus and two local types of A. bulbifer (wild type M and wild type B), which were designated as KGM, AGM, MGM, and BGM, successively. Comparative studies were conducted on their physicochemical properties and primary structures. The four AcGMs had about 90% (w/w) neutral sugar, 11% (w/w) moisture, and 1%–2% (w/w) ash. Relatively high contents of acetyl groups (17%–24%, w/w) were detected. Mannose and glucose as the main components existed in molar ratios of 1.41, 1.41, 1.21, and 1.58 for KGM, AGM, MGM, and BGM, respectively. Relative molecular weights of AcGMs increased in the order of: KGM

Aloe barbadensis Miller (Aloe vera) has long been used in food, cosmetic and pharmaceutical industries. The solid wastes such as the spikes and the outer green skins are usually separated from the inner gel and discarded during the process of Aloe vera leaves. Three kinds of polysaccharides (designated as ASP-4N, ASP-6N and ASP-8N) were successfully purified from the leaf skin of Aloe vera in our previous work. The present study aimed to analyze the structural and molecular features of ASP-6N and ASP-8N using methylation and GC-MS, NMR, high performance size-exclusion chromatography coupled with multi-angle laser light scattering (HPSEC-MALLS) and scanning electron microscopy (SEM) techniques. Results showed that ASP-6N and ASP-8N were β-(1→4)-glucomannans with acetyl groups, which may attach to O-2, O-3 or O-6 of mannopyranosyl residues in the backbone as mono-, di-, or tri-acetylated forms. HPSEC-MALLS analysis indicated that the polysaccharide fractions from Aloe leaf skin adopted various conformations in the aqueous solution depending on their molecular mass. The polysaccharides had fibrous, ribbon-like and spherical morphology by SEM observation.

Aloe barbadensis Miller (Aloe vera) is a kind of popular medicinal and horticultural crops widely cultivated around the world. Polysaccharides with different structural features and bioactivities have been isolated from the pulp of Aloe vera. In the current study, a novel polysaccharide fraction (AGP40) isolated and purified from gel juice of Aloe vera was subjected to structural and conformational analysis. AGP40 had a backbone consisting of major →4)-β-Manp-(1 → residues and minor →3)-β-Manp-(1 → and →4)-β-Glcp-(1 → residues. Low degree of branches distributed at O-6 of 4-linked mannose in the main chain. The acetyl groups in AGP40 presented as mono- or di-substituents (O-2, O-3, O-6, O-2,3, O-2,6 and O-3,6). AGP40 performed as random coil conformation in 0.1 M NaNO3 solution, and had fibrous filaments and irregular spherical structures in solid state. Detailed structural and conformational analysis of AGP40 in the present study may greatly improve the bioactive function investigation and mechanism explanation of acetyl glucomannans in the future.

Macrolepiota albuminosa (Berk.) Pegler is abundant in active polysaccharides, but little is known about their structures and solution properties. In this study, water-extracted polysaccharides from M. albuminosa (MAWP) were purified into three fractions with structural heterogeneity, which was attributed to the diversity in molecular weight, monosaccharide composition and linkage patterns, further affecting their solution properties. Methylation and NMR analysis revealed MAWP-60p and MAWP-70 were a 3-O-methylated glucomannogalactan and a previously unreported glucomannogalactan, whereas MAWP-80 was elucidated as a branched galactoglucan. Besides, three fractions exhibited random coil conformation in aqueous solution, while MAWP-60p had the highest viscosity due to its highest molecular weight, mean square radius of gyration (Rg) and O-methyl group attached to the backbone. The molecular weight, monosaccharide composition and glycosidic linkages might be the major contributors to the flexibility, molecular size and stereochemistry of mushroom polysaccharide chains.

Acinetobacter baumannii is the main cause of nosocomial infections, and the treatment of such infections has become more difficult due to the emergence of carbapenem resistance. This study focused on major carbapenemase genes and explored the association between carbapenemase genes, sequence types (ST types), and capsular types (K types). A total of 98 carbapenem-resistant A. baumannii (CRAB) strains were collected from two hospitals, the Chang Gung Memorial Hospital-Lin Kou branch (LCGMH) in northern Taiwan and the CGMH-Kaohsiung branch (KCGMH) in southern Taiwan, from 2015–2017. Major carbapenemase genes of class A, B, and D β-lactamases were detected by polymerase chain reaction. All strains except 1 were positive for blaOXA-51-like, 76 strains (77.6%) carried blaOXA-23-like, and 25 strains (25.5%) carried blaOXA-24-like. The regional distribution showed that blaOXA-23-like was more predominant than blaOXA-24-like in both hospitals (85.3% and 60% in LCGMH and KCGMH, respectively); however, blaOXA-24-like displayed a much higher percentage in KCGMH (46.7%) than in LCGMH (16.2%). Oxford multilocus sequence typing and global optimal eBURST analysis were conducted for 59 strains. We revealed the association between blaOXA gene patterns, ST types, and K types and demonstrated that four major K types, KL2, KL10, KL22, and KL52, which were associated with specific ST types, were mainly clustered into clonal complexes CC208 and CC549 (a unique clonal complex found in Taiwan). These findings provide important information for monitoring the epidemiology and dissemination of this pathogen.

Increasing evidence has indicated that long noncoding RNAs (lncRNAs) are involved in the progression of laryngeal squamous cell carcinoma (LSCC). Here, we aimed to disclose the role of MNX1-AS1 in LSCC progression, and explore whether MNX1-AS1 participates in LSCC progression via targeting miR-744-5p to active BCL9/β-catenin signaling. Sixty-five human LSCC tissues and the paracancerous normal tissues were recruited to determine the levels of MNX1-AS1, miR-744-5p and BCL9 using qRT-PCR. The interaction of miR-744-5p and MNX1-AS1/BCL9 was determined by using the RNA immunoprecipitation (RIP) assay and/or luciferase gene reporter assay. Cell viability, in vivo tumor formation, invasion and migration abilities were detected by MTT, Xenograft models and Transwell assays. MNX1-AS1 level was increased significantly in human LSCC tissues as compared with the normal tissues, which showed a positive correlation with BCL9 level while a negative correlation with miR-744-5p level. High level of MNX1-AS1 predicted a poor prognosis and an advanced clinical process in LSCC patients. miR-744-5p targeted upregulation weakened the luciferase activity of MNX1-AS1 and /BCL9, and downregulated their expression levels-wt, while showed no effect when the binding sites were mutated. Knockdown of MNX1-AS1 markedly weakened cell viability, migration, and invasion abilities, while BCL9 overexpression abolished these tendencies. In addition, MNX1-AS1 downregulation induced decreases in tumor volumes and weights in vivo, accompanied by reductions in BCL9, Ki-67 and β-catenin expression and an increase in miR-744-5p expression. Collectively, this study reveals that MNX1-AS1 contributes to cell growth and migration by regulating miR-744-5p/BCL9/β-catenin axis in LSCC.

Glycolysis inhibitors are promising therapeutic drugs for tumor treatment, which target the uniquely elevated glucose metabolism of cancer cells. Butyrate is a critical product of beneficial microbes in the colon, which exerts extraordinary anti-cancer activities. In particular, butyrate shows biased inhibitory effects on the cell growth of cancerous colonocytes, whereas it is the major energy source for normal colonocytes. Besides its roles as the histone deacetylases (HDACs) inhibitor and the ligand for G-protein coupled receptor (GPR) 109a, the influence of butyrate on the glucose metabolism of cancerous colonocytes and the underlying molecular mechanism are not fully understood. Here, we show that butyrate markedly inhibited glucose transport and glycolysis of colorectal cancer cells, through reducing the abundance of membrane GLUT1 and cytoplasmic G6PD, which was regulated by the GPR109a-AKT signaling pathway. Moreover, butyrate significantly promoted the chemotherapeutical efficacy of 5-fluorouracil (5-FU) on cancerous colonocytes, with exacerbated impairment of DNA synthesis efficiency. Our findings provide useful information to better understand the molecular basis for the impact of butyrate on the glucose metabolism of colorectal cancer cells, which would promote the development of beneficial metabolites of gut microbiota as therapeutical or adjuvant anti-cancer drugs.

Type 2 diabetes (T2D) is a worldwide epidemic associated with metabolic disorders and intestinal microbiota alterations. Polysaccharides have been considered to be beneficial to the prevention and alleviation of T2D. In the present study, ultra-performance liquid chromatography-triple-time-of-flight-based metabolomics and proteomics and 16S rRNA sequencing methods were employed to evaluate the effects of glucomannans from Dendrobium officinale stem, konjac, and Aloe vera leaves on host metabolism and intestinal microbiota regulation in type 2 diabetic rats and potential mechanisms. The metabolism of amino acids was significantly disturbed in the type 2 diabetic rats, especially the upregulated branched-chain amino acid (BCAA) metabolism. Host-derived BCAA metabolism was significantly decreased in type 2 diabetic rats. However, the levels of BCAAs in host circulation and gene abundance of BCAA biosynthesis in gut microbiota were significantly increased in diabetic rats, which suggested that the disturbed intestinal microbiota might be responsible for the increased circulation of BCAAs in T2D. Glucomannan treatment decreased the abundance of microbial BCAA biosynthesis-related genes and ameliorated the host BCAA metabolism. Also, glucomannan with a higher molecular weight and a lower ratio of mannose/glucose possessed better antidiabetic effects. In summary, the antidiabetic effects of glucomannans might be associated with the amelioration of BCAA metabolism by modulating intestinal microbiota.

BACKGROUND Gastric cancer (GC) is one of the leading causes of cancer-related mortality worldwide. We aimed to identify differentially expressed genes (DEGs) and their potential mechanisms associated with the prognosis of GC patients. MATERIAL AND METHODS This study was based on gene profiling information for 37 paired samples of GC and adjacent normal tissues from the GSE118916, GSE79973, and GSE19826 datasets in the Gene Expression Omnibus database. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to investigate the biological role of the DEGs. The protein-protein interaction (PPI) network was constructed by Cytoscape, and the Kaplan-Meier plotter was used for prognostic analysis. RESULTS We identified 119 DEGs, including 21 upregulated and 98 downregulated genes, in GC. The 21 upregulated genes were mainly enriched in extracellular matrix-receptor interaction, focal adhesion, and transforming growth factor-s signaling, while the 98 downregulated genes were significantly associated with gastric acid secretion, retinol metabolism, and metabolism of xenobiotics by cytochrome P450. Thirty hub DEGs were obtained for further analysis. Twenty-five of the 30 hub DEGs were significantly associated with the prognosis of GC, and 21 of the 25 hub DEGs showed consistent expression trends within the 3 profile datasets. KEGG reanalysis of these 21 hub DEGs showed that COL1A1, COL1A2, COL2A1, COL11A1, THBS2, and SPP1 were mainly enriched in the extracellular matrix-receptor interaction pathways. CONCLUSIONS We identified 6 genes that were significantly related to the prognosis of GC patients. These genes and pathways could serve as potential prognostic markers and be used to develop treatments for GC patients.

Background Changshun green-shell laying hens are unique to Guizhou Province, China, and have high egg quality. Improving egg production performance has become an important breeding task, and in recent years, the development of high-throughput sequencing technology provides a fast and exact method for genetic selection. Therefore, we aimed to use this technology to analyze the differences between the ovarian mRNA transcriptome of low and high-yield Changshun green-shell layer hens, identify critical pathways and candidate genes involved in controlling the egg production rate, and provide basic data for layer breeding. Results The egg production rates of the low egg production group (LP) and the high egg production group (HP) were 68.00 ± 5.56 % and 93.67 ± 7.09 %, with significant differences between the groups (p p Gallus gallus genome. Further analysis identified 142 differentially expressed genes (DEGs), and among them, 55 were upregulated and 87 were downregulated in the ovaries. KEGG pathway enrichment analysis identified 9 significantly enriched pathways, with the neuroactive ligand-receptor interaction pathway being the most enriched. GO enrichment analysis indicated that the GO term transmembrane receptor protein tyrosine kinase activity, and the DEGs identified in this GO term, including PRLR, NRP1, IL15, BANK1, NTRK1, CCK, and HGF may be associated with crucial roles in the regulation of egg production. Conclusions The above-mentioned DEGs may be relevant for the molecular breeding of Changshun green-shell laying hens. Moreover, enrichment analysis indicated that the neuroactive ligand-receptor interaction pathway and receptor protein tyrosine kinases may play crucial roles in the regulation of ovarian function and egg production.

The study of DNA damage repair response (DDR) in prostate cancer is restricted by the limited number of prostate cancer cell lines and lack of surrogates for heterogeneity in clinical samples. Here, we sought to leverage our experience with patient derived explants (PDEs) cultured ex vivo to study dynamics of DDR in primary tumors following application of clinically relevant doses of ionizing radiation (IR) to tumor cells in their native 3-dimensional microenvironment. We compared DDR dynamics between prostate cancer cell lines, PDEs and xenograft derived explants (XDEs) following treatment with IR (2Gy) either alone or in combination with pharmacological modulators of DDR. We have shown that following treatment with 2Gy, DDR can be consistently detected in PDEs from multiple solid tumors, including prostate, kidney, testes, lung and breast, as evidenced by γ-H2AX, 53BP1, phospho-ATM and phospho-DNA-PKcs foci. By examining kinetics of resolution of IR-induced foci, we have shown that DDR in prostate PDEs (complete resolution in 8 h) is much faster than in prostate cancer cell lines (, Highlights • IR induces distinct DNA damage repair kinetics in prostate cancer PDEs and cell lines. • IR induces a distinct transcriptional program in prostate cancer PDE and cell lines. • DNA-PKcs inhibition blocks IR-induced DDR in prostate cancer PDE. • Inhibition of AR impairs NHEJ in prostate cancer PDEs.

Background The comparative evolutionary genomics analysis was used to study the functions of novel Ka/Ks-predicted human exons in a zebrafish model. The Yulink (MIOS, Entrez Gene: 54,468), a conserved gene from zebrafish to human with WD40 repeats at N-terminus, was identified and found to encode an 875 amino acid in human. The biological function of this Yulink gene in cardiomyocytes remains unexplored. The purpose of this study is to determine the involvement of Yulink in the functions of cardiomyocytes and to investigate its molecular regulatory mechanism. Methods Knockdown of Yulink was performed using morpholino or shRNA in zebrafish, mouse HL-1 cardiomyocytes, and human iPSC-derived cardiomyocytes. The expression levels of mRNA and protein were quantified by qPCR and western blots. Other methods including DNA binding, ligand uptake, agonists treatment and Ca2+ imaging assays were used to study the molecular regulatory mechanism by Yulink. Statistical data were shown as mean ± SD or mean ± standard error. Results The knockdown of yulink with three specific morpholinos in zebrafish resulted in cardiac dysfunctions with pericardial edema, decreased heart beats and cardiac output. The Yulink knockdown in mouse HL-1 cardiomyocytes disrupted Ca2+ cycling, reduced DNA binding activity of PPARγ (peroxisome proliferator-activated receptor gamma) and resulted in a reduction of Serca2 (sarcoplasmic reticulum Ca2+ ATPase 2) expression. Expression of Serca2 was up-regulated by PPARγ agonists and down-regulated by PPARγ-shRNA knockdown, suggesting that Yulink regulates SERCA2 expression through PPARγ in mouse HL-1 cardiomyocytes. On the other hand, YULINK, PPARγ or SERCA2 over-expression rescued the phenotypes of Yulink KD cells. In addition, knockdown of YULINK in human iPSC-derived cardiomyocytes also disrupted Ca2+ cycling via decreased SERCA2 expression. Conclusions Overall, our data showed that Yulink is an evolutionarily conserved gene from zebrafish to human. Mechanistically Yulink regulated Serca2 expression in cardiomyocytes, presumably mediated through PPARγ nuclear entry. Deficiency of Yulink in mouse and human cardiomyocytes resulted in irregular Ca2+ cycling, which may contribute to arrhythmogenesis.

Mitotic crossovers have the potential to cause large-scale genome rearrangements. Here, we describe high-throughput, single-cell, whole-genome sequencing methods for mapping crossovers genome-wide at scale. The methods are generalizable to various eukaryotes and to other end points requiring high-throughput, high-coverage single cell sequencing.

Brucella vaccination is one of the most important strategies for controlling brucellosis in livestock. The A19 strain was the effective vaccine used to control brucellosis in China. However, the characteristics of physiological and attenuated virulence of the A19 strain are not investigated in detail. In this study, we compared the phenotypic characteristics of the A19 to the wild-type strain S2308. Virulence test showed that the A19 was significantly attenuated at chronic infection stage in infected mouse model. In growth analysis, the A19 exhibited a quick growth at exponential phase and premature at stationary phase. The inflammatory response of macrophages infected by the A19 was detected using TaqMan qPCR assay, indicating that the inflammatory level of the A19-infected macrophages was higher than that of the S2308 infection. Cell death analysis showed that the A19 was not cytotoxic for macrophages. Cell infection showed that the A19 reduced its ability to invade, survive and traffic within host cells, and the intracellular A19 hardly excludes lysosome-associated marker LAMP-1, suggesting that the A19 can't escape the lysosome degradation within host cells. In further study, the sensitivity test exhibited that the A19 is more sensitive to stress and bactericidal factors than the S2308 strain, Western blot and silver staining analysis exhibited that the A19 has a different expression pattern of OMPs and reduces LPS O-antigen expression relative to the S2308 strain. Those data give us a more detailed understanding about the A19 vaccine strain, which will be beneficial for improvement of current Brucella vaccine and overcoming its defects.

Background Cognitive impairment is a well-defined complication of chronic kidney disease (CKD), but the neural mechanisms are largely unknown. Objectives The study aimed to assess white matter (WM) microstructure changes and their relationship with cognitive impairment development during CKD progression. Methods Diffusion tensor imaging (DTI) datasets were acquired from 38 patients with CKD (19 patients were at stage 3; 19 patients were at stage 4) and 22 healthy controls (HCs). Tract-based spatial statistics (TBSS) was implemented to assess the differences in WM integrity among the three groups. The associations between abnormal WM integrity and clinical indicators (digit symbol test scores, the type A number connection test scores, hemoglobin, serum urea, serum creatinine, serum calcium, and serum potassium levels) were also computed. Results Compared with patients with CKD at stage 3 and HCs, patients with CKD at stage 4 showed significantly lower fractional anisotropy (FA) and higher mean diffusivity (MD) in the corpus callosum (CC), anterior thalamic radiation, inferior fronto-occipital fasciculus, and inferior longitudinal fasciculus. Correlation analysis showed that the MD in the genu of CC was negatively associated with the digit symbol test scores (r = -0.61, p = 0.01), and the FA in the left anterior thalamic radiation was positively associated with the level of serum calcium (r = 0.58, p = 0.01). Conclusion Patients with non-end-stage CKD have multiple abnormalities in WM regions. DTI metrics change with the progression of CKD and are primarily associated with cognitive impairment. The reduced integrity of WM tracts may be related to a low level of blood calcium.

Osteosarcoma (OS) has high heterogeneity and poor prognosis. In order to explore the molecular mechanism of OS and the tumor micro-environment (TME) on OS, we employed single-cell RNA-sequencing (scRNA-seq) on 110,745 individual cells from OS primary lesion, recurrent focal and metastatic tissues. We identified 5 main malignant subpopulations of OS cells, 3 clusters of osteoclast(OC) and 2 types of cancer-associated fibroblasts (CAFs). Further we found that the progenitor OC and, antigen presenting CAF (apCAF) were lower in lung metastatic and recurrent tumor tissues than in primary tumor tissue. M2-like macrophages were predominant in the TME myeloid cells. Inactivation state of tumor-infiltrating T cells, mainly the CD4-/CD8-T and Treg cells, existed in lung metastatic tissues. T-cell immunoreceptor with Ig and ITIM domains (TIGIT) expressed in 11 samples. We then blocked TIGIT which significantly enhancd the cytotoxic effects of primary T cells on OS cell lines. Our report represents the first use of scRNA-seq for the transcriptomic profiling of OS cells. Thus, the findings in this study will serve as a valuable resource for deciphering the intra-tumoral heterogeneity in OS and provide potential therapeutic strategies for OS in clinic.

Campylobacter is one of the most important foodborne pathogens worldwide, and poultry is regarded as the main reservoir of Campylobacter. The contamination of Campylobacter in broiler chickens at the farm level is closely related to the transmission of Campylobacter in the poultry production chain. This study identified 464 Campylobacter isolates from 1,534 samples from broiler rearing period and slaughtering process including 233 Campylobacter jejuni isolates and 231 Campylobacter coli isolates. We have observed a dynamic distribution of Campylobacter during broiler chicken production, that 66.3% of Campylobacter isolates were C. jejuni during broiler rearing period, while C. coli occupied 60.4% of Campylobacter isolates during the broiler slaughtering process. A tag-label method allowed us to track the dynamic of Campylobacter in each broiler chicken from 31-day age at rearing to the partition step in the slaughterhouse. At the 31-day during rearing, 150 broiler chicken were labeled, and was tracked for Campylobacter positive from rearing period to slaughtering process. Among the labeled broiler, 11 of the tracking broiler samples were able to detect Campylobacter from rearing period to slaughtering. All Campylobacter isolates from the 11 tracking samples were sequenced and analyzed. C. jejuni isolates were divided into four STs and C. coli isolates were divided into six STs. Isolates with identical core genome were observed from the same tag-labeled samples at different stages indicating a vertical transmission of Campylobacter in the early broiler meat production. Meanwhile, the core genome analysis elucidated the cross-contamination of Campylobacter during the rearing period and the slaughtering process. The virulotyping analysis revealed that all C. jejuni isolates shared the same virulotypes, while C. coli isolates were divided into three different virulotypes. The antimicrobial resistance gene analysis demonstrated that all Campylobacter isolates contained at least two antibiotic resistance genes (ARGs), and the ARG profiles were well-corresponding to each ST type. Our study observed a high prevalence of Campylobacter during the early chicken meat production, and further studies will be needed to investigate the diversity and transmission of Campylobacter in the poultry production chain.

Myeloid cells, such as neutrophils, are produced in the bone marrow in high quantities and are important in the pathogenesis of vascular diseases such as pulmonary hypertension (PH). Although neutrophil recruitment into sites of inflammation has been well studied, the mechanisms of neutrophil egress from the bone marrow are not well understood. Using computational flow cytometry, we observed increased neutrophils in the lungs of patients and mice with PH. Moreover, we found elevated levels ofIL-6 in the blood and lungs of patients and mice with PH. We observed that transgenic mice overexpressingIl-6 in the lungs displayed elevated neutrophil egress from the bone marrow and exaggerated neutrophil recruitment to the lungs, resulting in exacerbated pulmonary vascular remodeling, and dysfunctional hemodynamics. Mechanistically, we found that IL-6-induced neutrophil egress from the bone marrow was dependent on interferon regulatory factor 4 (IRF-4)-mediated CX3CR1 expression in neutrophils. Consequently, Cx3cr1 genetic deficiency in hematopoietic cells in Il-6-transgenic mice significantly reduced neutrophil egress from bone marrow and decreased neutrophil counts in the lungs, thus ameliorating pulmonary remodeling and hemodynamics. In summary, these findings define a novel mechanism of IL-6-induced neutrophil egress from the bone marrow and reveal a new therapeutic target to curtail neutrophil-mediated inflammation in pulmonary vascular disease.