Recombinase polymerase amplification combined with Pyrococcus furiosus Argonaute for fast Salmonella spp. testing in food safety

Foodborne illness caused by Salmonella spp. is one of the most prevalent public health problems globally, which have brought immeasurable economic burden and social impact to countries around the world. Neither current nucleic acid amplification detection method nor standard culture method (2-3 days) are suitable for field detection in areas with a heavy burden of Salmonella spp. Here, we developed a highly sensitive and accurate assay for Salmonella spp. detection in less than 40 min. Specifically, the invA gene of Salmonella spp. was amplified by recombinase polymerase amplification (RPA), followed by Pyrococcus furiosus Argonaute (PfAgo)-based target sequence cleavage, which could be observed by a fluorescence reader or the naked eye. The assay offered the lowest detectable concentration of 1.05 × 101 colony forming units/mL (CFU/mL). This assay had strong specificity and high sensitivity for the detection of Salmonella spp. in field samples, which indicated the feasibility of this assay.

AI is a viable alternative to high throughput screening: a 318-target study

High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.

Implementation of micelle-enabled C(sp2)-C(sp3) cross-electrophile coupling in pharmaceutical synthesis

A sustainable C(sp2)-C(sp3) cross-electrophile coupling was developed between readily available 5-bromophthalide and 1-benzyl-4-iodopiperidine under micellar conditions, leading to a key intermediate of one of our development compounds. Copper was found to play a crucial role as a co-catalyst in this dual catalysis system. The chemistry and process were successfully demonstrated in a kilo scale to deliver sufficient drug substance to the clinical campaigns. This is the first reported scale-up of such a challenging cross-electrophilic coupling that uses an aqueous medium, and not undesirable reprotoxic polar aprotic solvents (e.g. DMF, DMAc, and NMP).

Regulation of nuclear transcription by mitochondrial RNA in endothelial cells

Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, thus termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.

Cross-species comparison illuminates the importance of iron homeostasis for splenic anti-immunosenescence

Although immunosenescence may result in increased morbidity and mortality, many mammals have evolved effective immune coping strategies to extend their lifespans. Thus, the immune systems of long-lived mammals present unique models to study healthy longevity. To identify the molecular clues of anti-immunosenescence, we first built high-quality reference genome for a long-lived myotis bat, and then compared three long-lived mammals (i.e., bat, naked mole rat, and human) versus the short-lived mammal, mouse, in splenic immune cells at single-cell resolution. A close relationship between B:T cell ratio and immunosenescence was detected, as B:T cell ratio was much higher in mouse than long-lived mammals and significantly increased during aging. Importantly, we identified several iron-related genes that could resist immunosenescence changes, especially the iron chaperon, PCBP1, which was upregulated in long-lived mammals but dramatically downregulated during aging in all splenic immune cell types. Supportively, immune cells of mouse spleens contained more free iron than those of bat spleens, suggesting higher level of ROS-induced damage in mouse. PCBP1 downregulation during aging was also detected in hepatic but not pulmonary immune cells, which is consistent with the crucial roles of spleen and liver in organismal iron recycling. Furthermore, PCBP1 perturbation in immune cell lines would result in cellular iron dyshomeostasis and senescence. Finally, we identified two transcription factors that could regulate PCBP1 during aging. Together, our findings highlight the importance of iron homeostasis in splenic anti-immunosenescence, and provide unique insight for improving human healthspan.

First Dark Matter Search Results from the LUX-ZEPLIN (LZ) Experiment

The LUX-ZEPLIN experiment is a dark matter detector centered on a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility in Lead, South Dakota, USA. This Letter reports results from LUX-ZEPLIN's first search for weakly interacting massive particles (WIMPs) with an exposure of 60 live days using a fiducial mass of 5.5 t. A profile-likelihood ratio analysis shows the data to be consistent with a background-only hypothesis, setting new limits on spin-independent WIMP-nucleon, spin-dependent WIMP-neutron, and spin-dependent WIMP-proton cross sections for WIMP masses above 9  GeV/c^{2}. The most stringent limit is set for spin-independent scattering at 36  GeV/c^{2}, rejecting cross sections above 9.2×10^{-48}  cm at the 90% confidence level.

Human Post-Translational SUMOylation Modification of SARS-CoV-2 Nucleocapsid Protein Enhances Its Interaction Affinity with Itself and Plays a Critical Role in Its Nuclear Translocation

Viruses, such as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infect hosts and take advantage of host cellular machinery for genome replication and new virion production. Identifying and elucidating host pathways for viral infection is critical for understanding the development of the viral life cycle and novel therapeutics. The SARS-CoV-2 N protein is critical for viral RNA (vRNA) genome packaging in new virion formation. Using our quantitative Förster energy transfer/Mass spectrometry (qFRET/MS) coupled method and immunofluorescence imaging, we identified three SUMOylation sites of the SARS-CoV-2 N protein. We found that (1) Small Ubiquitin-like modifier (SUMO) modification in Nucleocapsid (N) protein interaction affinity increased, leading to enhanced oligomerization of the N protein; (2) one of the identified SUMOylation sites, K65, is critical for its nuclear translocation. These results suggest that the host human SUMOylation pathway may be critical for N protein functions in viral replication and pathology in vivo. Thus, blocking essential host pathways could provide a novel strategy for future anti-viral therapeutics development, such as for SARS-CoV-2 and other viruses.

Predicting Drug Treatment Outcomes in Childrens with Tuberous Sclerosis Complex-Related Epilepsy: A Clinical Radiomics Study

BACKGROUND AND PURPOSE

Highly predictive markers of drug treatment outcomes of tuberous sclerosis complex-related epilepsy are a key unmet clinical need. The objective of this study was to identify meaningful clinical and radiomic predictors of outcomes of epilepsy drug treatment in patients with tuberous sclerosis complex.

MATERIALS AND METHODS

A total of 105 children with tuberous sclerosis complex-related epilepsy were enrolled in this retrospective study. The pretreatment baseline predictors that were used to predict drug treatment outcomes included patient demographic and clinical information, gene data, electroencephalogram data, and radiomic features that were extracted from pretreatment MR imaging scans. The Spearman correlation coefficient and least absolute shrinkage and selection operator were calculated to select the most relevant features for the drug treatment outcome to build a comprehensive model with radiomic and clinical features for clinical application.

RESULTS

Four MR imaging-based radiomic features and 5 key clinical features were selected to predict the drug treatment outcome. Good discriminative performances were achieved in testing cohorts (area under the curve = 0.85, accuracy = 80.0%, sensitivity = 0.75, and specificity = 0.83) for the epilepsy drug treatment outcome. The model of radiomic and clinical features resulted in favorable calibration curves in all cohorts.

CONCLUSIONS

Our results suggested that the radiomic and clinical features model may predict the epilepsy drug treatment outcome. Age of onset, infantile spasms, antiseizure medication numbers, epileptiform discharge in left parieto-occipital area of electroencephalography, and gene mutation type are the key clinical factors to predict the epilepsy drug treatment outcome. The texture and first-order statistic features are the most valuable radiomic features for predicting drug treatment outcomes.

Spatially resolved expression landscape and gene-regulatory network of human gastric corpus epithelium

Molecular knowledge of human gastric corpus epithelium remains incomplete. Here, by integrated analyses using single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) techniques, we uncovered the spatially resolved expression landscape and gene-regulatory network of human gastric corpus epithelium. Specifically, we identified a stem/progenitor cell population in the isthmus of human gastric corpus, where EGF and WNT signaling pathways were activated. Meanwhile, LGR4, but not LGR5, was responsible for the activation of WNT signaling pathway. Importantly, FABP5 and NME1 were identified and validated as crucial for both normal gastric stem/progenitor cells and gastric cancer cells. Finally, we explored the epigenetic regulation of critical genes for gastric corpus epithelium at chromatin state level, and identified several important cell-type-specific transcription factors. In summary, our work provides novel insights to systematically understand the cellular diversity and homeostasis of human gastric corpus epithelium in vivo.

Learning from real world data about combinatorial treatment selection for COVID-19

COVID-19 is an unprecedented global pandemic with a serious negative impact on virtually every part of the world. Although much progress has been made in preventing and treating the disease, much remains to be learned about how best to treat the disease while considering patient and disease characteristics. This paper reports a case study of combinatorial treatment selection for COVID-19 based on real-world data from a large hospital in Southern China. In this observational study, 417 confirmed COVID-19 patients were treated with various combinations of drugs and followed for four weeks after discharge (or until death). Treatment failure is defined as death during hospitalization or recurrence of COVID-19 within four weeks of discharge. Using a virtual multiple matching method to adjust for confounding, we estimate and compare the failure rates of different combinatorial treatments, both in the whole study population and in subpopulations defined by baseline characteristics. Our analysis reveals that treatment effects are substantial and heterogeneous, and that the optimal combinatorial treatment may depend on baseline age, systolic blood pressure, and c-reactive protein level. Using these three variables to stratify the study population leads to a stratified treatment strategy that involves several different combinations of drugs (for patients in different strata). Our findings are exploratory and require further validation.

A Rapid Antimicrobial Resistance Diagnostic Platform for Staphylococcus aureus Using Recombinase Polymerase Amplification

Antimicrobial resistance (AMR) has posed a global threat to public health. The Staphylococcus aureus strains have especially developed AMR to practically all antimicrobial medications. There is an unmet need for rapid and accurate detection of the S. aureus AMR. In this study, we developed two versions of recombinase polymerase amplification (RPA), the fluorescent signal monitoring and lateral flow dipstick, for detecting the clinically relevant AMR genes retained by S. aureus isolates and simultaneously identifying such isolates at the species level. The sensitivity and specificity were validated with clinical samples. Our results showed that this RPA tool was able to detect antibiotic resistance for all the 54 collected S. aureus isolates with high sensitivity, specificity, and accuracy (all higher than 92%). Moreover, results of the RPA tool are 100% consistent with that of PCR. In sum, we successfully developed a rapid and accurate AMR diagnostic platform for S. aureus. The RPA might be used as an effective diagnostic test in clinical microbiology laboratories to improve the design and application of antibiotic therapy. IMPORTANCE Staphylococcus aureus is a species of Staphylococcus and belongs to Gram-positive. Meanwhile, S. aureus remains one of the most common nosocomial and community-acquired infections, causing blood flow, skin, soft tissue, and lower respiratory tract infections. The identification of the particular nuc gene and the other eight genes of drug-resistant S. aureus can reliably and quickly diagnose the illness, allowing doctors to prescribe treatment regimens sooner. The detection target in this work is a particular gene of S. aureus, and a POCT is built to simultaneously recognize S. aureus and analyze genes representing four common antibiotic families. We developed and assessed a rapid and on-site diagnostic platform for the specific and sensitive detection of S. aureus. This method allows the determination of S. aureus infection and 10 different AMR genes representing four different families of antibiotics within 40 min. It was easily adaptable in low-resource circumstances and professional-lacking circumstances. It should be supported in overcoming the continuous difficulty of drug-resistant S. aureus infections, which is a shortage of diagnostic tools that can swiftly detect infectious bacteria and numerous antibiotic resistance indicators.

Integrated analysis of long non-coding RNAs and mRNA expression profiles identified potential interactions regulating melanogenesis in chicken skin

1. Long non-coding RNAs (lncRNAs) play important roles in various physiological functions. However, the mechanisms underlying the regulation of lncRNAs in melanogenesis remain unclear. To determine the molecular mechanisms involved in skin melanogenesis, the present study depicted the expression profiles of lncRNAs and messenger RNAs (mRNAs) in black- (B group) and white- (W group) skinned chickens using RNA sequencing.2. In total, 373 differentially expressed lncRNAs (DELs; 203 up-regulated and 170 down-regulated) and 253 differentially expressed genes (DEGs; 152 up-regulated and 101 down-regulated) were identified between the B and W groups. A total of eight known melanogenesis-related genes were identified (KIT, TYRP1, DCT (TYRP2), SLC45A2, OCA2, EDNRB2, TRPM1 and RAB38).3. Functional annotation of the co-expressed DEGs and DELs was performed using Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses. The co-expressed DEGs were mainly involved in melanogenesis and the co-expressed genes of 117 and 108 DELs were significantly enriched in the melanogenesis and tyrosine metabolism pathways, respectively.4. The DEL-DEG interaction network revealed that three lncRNAs (XR_003072387.1, XR_003075112.1, and XR_003077033.1) and DCT genes may have key roles in regulating melanogenesis in chicken skin. This data provides the groundwork for studying the lncRNA regulatory mechanisms of skin melanogenesis and suggested a new perspective on the modulation of melanogenesis in chicken skin based on a lncRNA-mRNA causal regulatory network.

[Application of robot-assisted laparoscopic sentinel lymph node tracing in treating endometrial carcinoma]

Objective: To investigate the value of robot-assisted laparoscopic indocyanine green sentinel lymph node (SLN) tracing in treating endometrial carcinoma. Methods: Thirty-two patients with early-staging endometrial carcinoma were operated with laparoscopic comprehensive staging laparotomy from January 2019 to December 2021. At the same time, the SLN detection was performed by near-infrared fluorescence imaging tracer technology, in which the tracer was indocyanine green. Sixteen cases were injected with indocyanine green before laparoscopic surgery, and 16 cases were injected with indocyanine green before robot-assisted laparoscopic surgery. The operation index, postoperative complications, prognosis, and lymph node dissection were compared between the two groups. Results: (1) The mean age of patients in the robot group was (54.7±8.1) years old, and was (54.9±8.8) years old in the laparoscopic group. There were no significant difference between the two groups (t=0.06, P=0.951). (2) Intraoperative blood loss [(131±40) vs (169±57) ml], hemoglobin difference before and after surgery [(11.2±5.4) vs (15.5±5.7) g/L], the length of stay after operation [(6.2±1.3) vs (8.6±1.4) days] between the robot group and the laparoscopic group were compared, and the differences were statistically significant (all P<0.05). (3) SLNs were detected in all 16 patients in the robotic group, and a total of 41 SLNs were detected. SLNs were detected in 15 of the 16 patients in the laparoscopy group, and a total of 40 SLNs were detected. Compared with the laparoscopic group (15/16), the total detection rate of SLN in the robotic group (16/16), there were no statistical significance (χ²=1.03, P=0.310). Compared with the laparoscopic group (7/15), the SLN bilateral detection rate in the robotic group (10/16), there were also no significant difference (χ²=0.78, P=0.376). The number of lymph nodes detected in surgery group (16.6±4.1) were lower than those in the laparoscopy surgery group (21.0±7.1), while there were no statistically difference between the two groups (χ²=2.01, P=0.054). There was no tumor metastasis in the resected lymph nodes and SLN between the two groups. The false negative rate of SLN in diagnosing endometrial cancer postoperative lymph node metastasis was 0, and the negative predictive value was 100%. (4) The pelvic and retroperitoneal lymph nodes were divided into five regions, which were the left pelvis, the right pelvis, the presacral region, the deep inguinal region, and the abdominal aorta. The numbers of SLN of unilateral detection and bilateral pelvic detection between two groups showed no significant differences (all P>0.05). The left pelvis had the most SLN imaging in both groups, followed by the right pelvis, para-aortic, and deep groin. (5) There was one patient in both robotic group and laparoscopic group with postoperative complications, which were urinary retention and pelvic lymph node cyst respectively. There were no significant differences in the incidence of complications between the two groups (χ²=0.97, P=1.000). The median follow-up time after operation was 14 months (range 6-24 months). During the follow-up period, no local recurrence or distant metastasis was found between the two groups of endometrial cancer patients. Conclusions: Compared with the laparoscopic group, the robot group has less intraoperative blood loss and shorter postoperative hospital stay. The bilateral detection rate of SLN in the group was better than that of laparoscopy.

Antimony release and volatilization from rice paddy soils: Field and microcosm study

The fate of antimony (Sb) in submerged soils and the impact of common agricultural practices (e.g., manuring) on Sb release and volatilization is understudied. We investigated porewater Sb release and volatilization in the field and laboratory for three rice paddy soils. In the field study, the porewater Sb concentration (up to 107.1 μg L^-1) was associated with iron (Fe) at two sites, and with pH, Fe, manganese (Mn), and sulfate (SO₄^2-) at one site. The surface water Sb concentrations (up to 495.3 ± 113.7 μg L^-1) were up to 99 times higher than the regulatory values indicating a potential risk to aquaculture and rice agriculture. For the first time, volatile Sb was detected in rice paddy fields using a validated quantitative method (18.1 ± 5.2 to 217.9 ± 160.7 mg ha^-1 y^-1). We also investigated the influence of two common rice agriculture practices (flooding and manuring) on Sb release and volatilization in a 56-day microcosm experiment using the same soils from the field campaign. Flooding induced an immediate, but temporary, Sb release into the porewater that declined with SO₄^2-, indicating that SO₄^2- reduction may reduce porewater Sb concentrations. A secondary Sb release, corresponding to Fe reduction in the porewater, was observed in some of the microcosms. Our results suggest flooding-induced Sb release into rice paddy porewaters is temporary but relevant. Manuring the soils did not impact the porewater Sb concentration but did enhance Sb volatilization. Volatile Sb (159.6 ± 108.4 to 2237.5 ± 679.7 ng kg^-1 y^-1) was detected in most of the treatments and was correlated with the surface water Sb concentration. Our study indicates that Sb volatilization could be occurring at the soil-water interface or directly in the surface water and highlights that future works should investigate this potentially relevant mechanism.

Duck CD8+ T Cell Response to H5N1 Highly Pathogenic Avian Influenza Virus Infection In Vivo and In Vitro

Domestic ducks are the important host for H5N1 highly pathogenic avian influenza virus (HPAIV) infection and epidemiology, but little is known about the duck T cell response to H5N1 AIV infection. In infection experiments of mallard ducks, we detected significantly increased CD8+ cells and augmented expression of cytotoxicity-associated genes, including granzyme A and IFN-γ, in PBMCs from 5 to 9 d postinfection when the virus shedding was clearly decreased, which suggested the importance of the duck cytotoxic T cell response in eliminating H5N1 infection in vivo. Intriguingly, we found that a CD8high+ population of PBMCs was clearly upregulated in infected ducks from 7 to 9 d postinfection compared with uninfected ducks. Next, we used Smart-Seq2 technology to investigate the heterogeneity and transcriptional differences of the duck CD8+ cells. Thus, CD8high+ cells were likely to be more responsive to H5N1 AIV infection, based on the high level of expression of genes involved in T cell responses, activation, and proliferation, including MALT1, ITK, LCK, CD3E, CD247, CFLAR, IL-18R1, and IL-18RAP. More importantly, we have also successfully cultured H5N1 AIV-specific duck T cells in vitro, to our knowledge, for the first time, and demonstrated that the CD8high+ population was increased with the duck T cell activation and response in vitro, which was consistent with results in vivo. Thus, the duck CD8high+ cells represent a potentially effective immune response to H5N1 AIV infection in vivo and in vitro. These findings provide novel insights and direction for developing effective H5N1 AIV vaccines.

[Transcriptomic analysis of the ΔPaLoc mutant of Clostridioides difficile and verification of its toxicity]

Objective: Comparative analyses of wild-type Clostridioides difficile 630 (Cd630) strain and pathogenicity locus (PaLoc) knockout mutant (ΔPaLoc) by using RNA-seq technology. Analysis of differential expression of Cd630 wild-type strain and ΔPaLoc mutant strain and measurement of its cellular virulence changes. Lay the foundation for the construction of an toxin-attenuated vaccine strain against Clostridioides difficile. Methods: Analysis of Cd630 and ΔPaLoc mutant strains using high-throughput sequencing (RNA-seq). Clustering differentially expressed genes and screening differentially expressed genes by DESeq software. Further analysis of differential genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Finally, cytotoxicity assays of ΔPaLoc and Cd630 strains were performed in the African monkey kidney epithelial cell (Vero) and the human colonic cell (Caco-2) lines. Results: The transcriptome data showed that the ΔPaLoc mutant toxin genes tcdA and tcdB were not transcribed. Compared to the wild-type strain, CD630_36010, CD630_020910,CD630_02080 and cel genes upregulated 17.92,11.40,8.93 and 7.55 fold, respectively. Whereas the hom2 (high serine dehydrogenase), the CD630_15810 (spore-forming protein), CD630_23230 (zinc-binding dehydrogenase) and CD630_23240 (galactitol 1-phosphate 5-dehydrogenase) genes were down-regulated by 0.06, 0.075, 0.133 and 0.183 fold, respectively. The GO and KEGG enrichment analyses showed that the differentially transcribed genes in ΔPaLoc were enriched in the density-sensing system, ABC transport system, two-component system, phosphotransferase (PTS) system, and sugar metabolism pathway, as well as vancomycin resistance-related pathways. Cytotoxicity assays showed that the ΔPaLoc mutant strain lost its virulence to Vero and Caco-2 cells compared to the wild-type Cd630 strain. Conclusion: Transcriptional sequencing analysis of the Cd630 and ΔPaLoc mutant strains showed that the toxin genes were not transcribed. Those other differential genes could provide a reference for further studies on the physiological and biochemical properties of the ΔPaLoc mutant strain. Cytotoxicity assays confirmed that the ΔPaLoc mutant lost virulence to Vero and Caco-2 cells, thus laying the foundation for constructing an toxin-attenuated vaccine strain against C. difficile.

Effect of a genetically engineered interferon-alpha versus traditional interferon-alpha in the treatment of moderate-to-severe COVID-19: a randomised clinical trial

BACKGROUND

There are few effective therapies for coronavirus disease 2019 (COVID-19) upon the outbreak of the pandemic. To compare the effectiveness of a novel genetically engineered recombinant super-compound interferon (rSIFN-co) with traditional interferon-alpha added to baseline antiviral agents (lopinavir-ritonavir or umifenovir) for the treatment of moderate-to-severe COVID-19.

METHOD

In this multicenter randomized (1:1) trial, patients hospitalized with moderate-to-severe COVID-19 received either rSIFN-co nebulization or interferon-alpha nebulization added to baseline antiviral agents for no more than 28 days. The primary endpoint was the time to clinical improvement. Secondary endpoints included the overall rate of clinical improvement assessed on day 28, the time to radiological improvement and virus nucleic acid negative conversion.

RESULTS

A total of 94 patients were included in the safety set (46 patients assigned to rSIFN-co group, 48 to interferon-alpha group). The time to clinical improvement was 11.5 days versus 14.0 days (95% CI 1.10 to 2.81, p = .019); the overall rate of clinical improvement on day 28 was 93.5% versus 77.1% (difference, 16.4%; 95% CI 3% to 30%); the time to radiological improvement was 8.0 days versus 10.0 days (p = .002), the time to virus nucleic acid negative conversion was 7.0 days versus 10.0 days (p = .018) in the rSIFN-co and interferon alpha arms, respectively. Adverse events were balanced with no deaths among groups.

CONCLUSIONS AND RELEVANCE

rSIFN-co was associated with a shorter time of clinical improvement than traditional interferon-alpha in the treatment of moderate-to-severe COVID-19 when combined with baseline antiviral agents. rSIFN-co therapy alone or combined with other antiviral therapy is worth to be further studied.Key messagesThere are few effective therapies for coronavirus disease 2019 (COVID-19) upon the outbreak of the pandemic. Interferon alphas, by inducing both innate and adaptive immune responses, have shown clinical efficacy in treating severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus.In this multicenter, head-to-head, randomized, clinical trial which included 94 participants with moderate-to-severe COVID-19, the rSIFN-co plus antiviral agents (lopinavir-ritonavir or umifenovir) was associated with a shorter time of clinical improvement than interferon-alpha plus antiviral agents.

Product inhibition kinetics determinations - Substrate interaction affinity and enzymatic kinetics using one quantitative FRET assay

Product inhibition is a common phenomenon during enzyme-catalyzed reactions. Almost all product molecules of an enzyme reaction should have some structural similarities to the substrate, and can thus still have affinities to the active site of the enzyme as product inhibitor. Currently, the characterizations of product inhibition are generally carried out by different methods to determine product binding affinity to the enzyme and the enzyme kinetics parameters, and then these parameters are combined to determine product inhibition. However, due to different sensitivity and variations, kinetics parameters determined from different methods are often not compatible, resulting in not accurate measurement. Here, we report a novel method that determines the two different classes of kinetics parameters, IC₅₀ and K_i(or K_D), K_cat and K_M, using one single assay method-quantitative FRET(qFRET) assay for characterizing the product inhibition of pre-SUMO1's maturation by its protease SENP1. One method to determine all kinetics parameters provides, for the first time, not only a convenient method to determine all kinetics parameters, but more importantly, a novel approach to combine different measurements with mutually compatible results and errors.

Quantitative FRET (qFRET) Technology for the Determination of Protein-Protein Interaction Affinity in Solution

Protein-protein interactions play pivotal roles in life, and the protein interaction affinity confers specific protein interaction events in physiology or pathology. Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research to detect molecular interactions in vitro and in vivo. The FRET assay provides very high sensitivity and efficiency. Several attempts have been made to develop the FRET assay into a quantitative measurement for protein-protein interaction affinity in the past. However, the progress has been slow due to complicated procedures or because of challenges in differentiating the FRET signal from other direct emission signals from donor and receptor. This review focuses on recent developments of the quantitative FRET analysis and its application in the determination of protein-protein interaction affinity (K_D), either through FRET acceptor emission or donor quenching methods. This paper mainly reviews novel theatrical developments and experimental procedures rather than specific experimental results. The FRET-based approach for protein interaction affinity determination provides several advantages, including high sensitivity, high accuracy, low cost, and high-throughput assay. The FRET-based methodology holds excellent potential for those difficult-to-be expressed proteins and for protein interactions in living cells.

[Analysis on the imported Coronavirus Disease 2019 related cluster epidemic in rural areas of Chengdu]

An epidemiological investigation was carried out on a local cluster of outbreak caused by imported cases of Coronavirus Disease 2019 (COVID-19) in rural areas of Chengdu in December 2020, to find out the source of infection and the chain of transmission. According to Prevention and Control Protocol for COVID-19 (Version 7), field epidemiological investigation was adopted, combined with big data technology, video image investigation, gene sequencing and other methods to carry out investigation into COVID-19 cases and infections source tracing, analyze the epidemiological association, and map the chain of transmission. From December 7 to 17, 2020, 13 local COVID-19 confirmed cases and 1 asymptomatic case were diagnosed in Chengdu, of which 12 cases (85.71%) had a history of residence and activity in the village courtyard of Taiping (TP), Pidu (P) District, Chengdu. From November 8, 2020 to November 28, 2020, a group of inbound people form Nepal were transferred to the designated entry personnel quarantine hotel of P District which was adjacent to the TP village. During quarantine, there were 5 cases who tested positive for COVID-19. Through gene sequencing alignment, genes of local cases and Nepalese imported cases from the same period are homologous, all belong to the lineage of L2.2.3 (B.1.36 according to Pangolin lineage typing method). According to the results of field epidemiological investigation and gene sequencing analysis, the index case was most likely infected by contact with household waste of quarantine site. Under the situation of normalization prevention and control of COVID-19, sentinel monitoring of fever clinics in primary medical institutions is the key to early detection of the epidemic. The multi-department joint epidemiological investigation and the application of gene technology are the core links of the investigation and traceability of modern infectious diseases. The allocation of public health resources in rural areas needs to be strengthened. We need to improve the capacity for early surveillance and early warning of the epidemic in rural areas.

Dual-target one-step nested PCR for sensitive detection of SARS-CoV-2 nucleic acids

The Corona Virus Disease reported in 2019 (COVID-19) poses a significant threat to human and public health. Its early and accurate detection can reduce the spread and recurrence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Real-time reverse transcription fluorescent quantitative polymerase chain reaction (RT-qPCR) is the "gold standard" for detecting the nucleic acid of SARS-CoV-2. This study developed and tested a dual-target (ORF1ab and N gene) one-step nested RT-qPCR (DTO-N-PCR) to detect SARS-CoV-2. Ten-fold serial dilutions of mixed synthetic DNA from SARS-CoV-2 ORF1ab and N gene were used as templates to test the sensitivity of DTO-N-PCR. Its specificity was subsequently tested using throat swab specimens from 10 COVID-19 patients and 35 healthy participants. DTO-N-PCR was more sensitive and specific than conventional RT-qPCR. It has unique features, including a dual-target (ORF1ab and N gene), rapid one-step operation of reverse transcription and PCR, four pairs of inner and outer primers, and specific probes. These features aid in its rapid, accurate, and efficient detection of SARS-CoV-2 RNA.

A meta-analysis comparing the efficacy and safety of gemcitabine plus cisplatin induction chemotherapy in patients with locoregionally advanced NPC

PURPOSE

Nasopharyngeal carcinoma (NPC) is a malignant tumor endangering human health. Gemcitabine or cisplatin chemotherapy has been regarded as effective treatment for patients with locoregionally advanced NPC. However, the effect of gemcitabine plus cisplatin concurrent chemoradiotherapy (CCRT) remained controversial among the studies. Therefore, we conducted this meta-analysis to assess the efficacy and safety of induction chemotherapy by gemcitabine and cisplatin (GP regimen) in patients with locoregionally advanced NPC.

METHODS

A systematic literature search was performed using PubMed, Web of Science, and Embase to evaluate the survival benefit and toxicity profiles of patients with locoregionally advanced NPC who were treated with CCRT. A random-effects model or a fixed-effects model was used to pool the data according to the heterogeneity among the included studies.

RESULTS

A total of five studies with 1286 patients met the inclusion criteria and were included in this meta-analysis. Pooled estimate showed that GP regimen was associated with significant improvements in OS (HR = 0.57, 95% CI 0.45, 0.73; P < 0.001), DFS (HR = 0.56, 95% CI 0.47, 0.66; P < 0.001), and DRFS (HR = 0.51, 95% CI 0.36, 0.73; P < 0.001), but not in LRFS (HR = 0.54, 95% CI 0.25, 1.19; P = 0.126) and ORR (RR = 1.30, 95% CI 0.54, 3.09; P = 0.556). Moreover, the incidence of adverse events of all grades (RR = 1.15, 95%CI 0.11, 1.38; P = 0.063) or grade 3-4 (RR = 0.96, 95%CI 0.57, 1.29; P = 0.385), was comparable between GP regimen and control treatments.

CONCLUSION

Our meta-analysis indicated that the patients with locoregionally advanced NPC could benefit from the regimen of gemcitabine plus cisplatin induction chemotherapy.

Intense 2.1-4.2 µm broadband emission of Co/Er:PbF2 mid-infrared laser crystal

A novel mid-infrared (MIR) laser crystal Co/Er:PbF₂ was successfully grown. The use of Er³⁺ ion co-doping to sensitize a Co²⁺ ion and enhance the 2.1-4.2 µm broadband MIR emission of the Co²⁺ ion in a PbF₂ crystal was studied for the first time, to the best of our knowledge. The Er³⁺ ion was demonstrated to be an effective sensitizer of the Co²⁺ ion, making the Co/Er:PbF₂ crystal propitious to be pumped by commercialized laser diodes. Furthermore, with Er³⁺ ion co-doping, the local symmetry of Co²⁺ and Er³⁺ ions was seriously distorted, thereby enhancing the 2.1-4.2 µm MIR emissions. This study provides a path for designing MIR laser materials with optimal performance.

P–547 Single-cell RNA sequencing identifies molecular regulations associated with poor maturation performance on rescue in vitro matured oocytes

Study question

What is the transcriptome signature associated with rescuein vitro matured (rIVM) oocytes?

Summary answer

GATA–1/CREB1/WNT signaling axis was repressed in rIVM oocytes of poor quality.

What is known already

rIVM aims to produce mature oocytes (MII) for in vitro fertilization (IVF) through IVM of immature oocytes collected from stimulated ovaries. It is less popular due to limited success rate in infertility treatment. Genetic aberrations, cellular stress, and the absence of cumulus cell support in oocytes could account for the failure of rIVM.

Study design, size, duration

We applied single-cell RNA sequencing (scRNA-seq) to capture the transcriptomes of human in vivo (IVO) oocytes (n = 10) from 7 donors and rIVM oocytes (n = 10) from 10 donors, followed by studying the maternal age effect and ovarian responses on rIVM oocyte transcriptomes.

Participants/materials, setting, methods

Human oocytes were collected from donors aged 28–41 years with a body mass index of &lt; 30. RNA extraction, cDNA generation, library construction and sequencing were performed in one preparation. scRNA-seq data were then processed and analyzed. Selected genes in therIVM vs. IVO comparison were validated by quantitative real-time PCR.

Main results and the role of chance

The transcriptome profiles of rIVM/IVO showed distinctive differences. A total of 1559 differentially expressed genes (DEGs, genes with at least two-fold change and adjusted p &lt; 0.05) were found to be enriched in metabolic processes, biosynthesis, and oxidative phosphorylation. Among these DEGs, we identified a repression of WNT/β-catenin signaling in rIVM when compared with IVO oocytes. We found that estradiol level exhibited a significant age-independent correlation with the IVO mature oocyte ratio (MII ratio). rIVM oocytes with higher MII ratio showed over-represented cellular processes such as anti-apoptosis. To further identify targets that contribute to the poor outcomes of rIVM, we compared oocytes collected from young donors with high MII ratio versus donors of advanced maternal age and revealed CREB1was an important regulator in rIVM. Our study identified GATA–1/CREB1/WNT signaling was repressed in both rIVM condition and rIVM oocytes of low-quality.

Limitations, reasons for caution

In the rIVM oocytes of high- and low-quality comparison, the number of samples was limited after data filtering with stringent selection criteria. For the oocyte stage identification, we were unable to predict the presence of oocyte spindle so polar body extrusion was the only indicator.

Wider implications of the findings: This study showed that GATA–1/CREB1/WNT signaling and antioxidant actions were repressed in rIVM condition and was further downregulated in rIVM oocytes of low-quality, providing us the foundation of subsequent follow-up research on human subjects.

Trial registration number

Not applicable

Single-cell RNA sequencing identifies molecular targets associated with poor in vitro maturation performance of oocytes collected from ovarian stimulation

STUDY QUESTION

What is the transcriptome signature associated with poor performance of rescue IVM (rIVM) oocytes and how can we rejuvenate them?

SUMMARY ANSWER

The GATA-1/CREB1/WNT signalling axis was repressed in rIVM oocytes, particularly those of poor quality; restoration of this axis may produce more usable rIVM oocytes.

WHAT IS KNOWN ALREADY

rIVM aims to produce mature oocytes (MII) for IVF through IVM of immature oocytes collected from stimulated ovaries. It is not popular due to limited success rate in infertility treatment. Genetic aberrations, cellular stress and the absence of cumulus cell support in oocytes could account for the failure of rIVM.

STUDY DESIGN, SIZE, DURATION

We applied single-cell RNA sequencing (scRNA-seq) to capture the transcriptomes of human in vivo oocytes (IVO) (n = 10) from 7 donors and rIVM oocytes (n = 10) from 10 donors. The effects of maternal age and ovarian responses on rIVM oocyte transcriptomes were also studied. In parallel, we studied the effect of gallic acid on the maturation rate of mouse oocytes cultured in IVM medium with (n = 84) and without (n = 85) gallic acid.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Human oocytes were collected from donors aged 28-41 years with a body mass index of <30. RNA extraction, cDNA generation, library construction and sequencing were performed in one preparation. scRNA-seq data were then processed and analysed. Selected genes in the rIVM versus IVO comparison were validated by quantitative real-time PCR. For the gallic acid study, we collected immature oocytes from 5-month-old mice and studied the effect of 10-μM gallic acid on their maturation rate.

MAIN RESULTS AND THE ROLE OF CHANCE

The transcriptome profiles of rIVM/IVO oocytes showed distinctive differences. A total of 1559 differentially expressed genes (DEGs, genes with at least 2-fold change and adjusted P < 0.05) were found to be enriched in metabolic processes, biosynthesis and oxidative phosphorylation. Among these DEGs, we identified a repression of WNT/β-catenin signalling in rIVM when compared with IVO oocytes. We found that oestradiol levels exhibited a significant age-independent correlation with the IVO mature oocyte ratio (MII ratio) for each donor. rIVM oocytes from women with a high MII ratio were found to have over-represented cellular processes such as anti-apoptosis. To further identify targets that contribute to the poor clinical outcomes of rIVM, we compared oocytes collected from young donors with a high MII ratio with oocytes from donors of advanced maternal age and lower MII ratio, and revealed that CREB1 is an important regulator. Thus, our study identified that GATA-1/CREB1/WNT signalling was repressed in both rIVM oocytes versus IVO oocytes and in rIVM oocytes of lower versus higher quality. Consequently we investigated gallic acid, as a potential antioxidant substrate in human rIVM medium, and found that it increased the mouse oocyte maturation rate by 31.1%.

LARGE SCALE DATA

Raw data from this study can be accessed through GSE158539.

LIMITATIONS, REASONS FOR CAUTION

In the rIVM oocytes of the high- and low-quality comparison, the number of samples was limited after data filtering with stringent selection criteria. For the oocyte stage identification, we were unable to predict the presence of oocyte spindle, so polar body extrusion was the only indicator.

WIDER IMPLICATIONS OF THE FINDINGS

This study showed that GATA-1/CREB1/WNT signalling was repressed in rIVM oocytes compared with IVO oocytes and was further downregulated in low-quality rIVM oocytes, providing us the foundation of subsequent follow-up research on human oocytes and raising safety concerns about the clinical use of rescued oocytes.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by the Collaborative Research Fund, Research Grants Council, C4054-16G, and Research Committee Funding (Research Sustainability of Major RGC Funding Schemes), The Chinese University of Hong Kong. The authors have no conflicts of interest to declare.

Asymmetric expression patterns of B- and C-class MADS-box genes correspond to the asymmetrically specified androecial identities of Canna indica

Canna indica is a common ornamental plant with asymmetric flowers having colourful petaloid staminodes. The only fertile stamen comprises a one-theca anther and a petaloid appendage and represents the lowest stamen number in the order Zingiberales. The molecular mechanism for the asymmetric androecial petaloidy remains poorly understood. Here, we studied the identity specification in Canna stamen. We observed four types of abnormal flower in terms of androecium identity transformation and analysed the corresponding floral symmetry changes. We further tested the expression patterns of B- and C-class MADS-box genes using in situ hybridization in normal Canna stamen. Homeotic conversions in the androecium were accompanied by floral symmetry changes, and the asymmetric stamen is key in contributing to the floral asymmetry. Both B- and C-class genes exhibited higher expression levels in the anther primordium than in other androecial parts. This asymmetric expression pattern precisely corresponded to the asymmetric identities of the Canna androecium. We identified C. indica as a model species for studying androecial organ identity and floral symmetry synthetically in Zingiberales. We hypothesized that homeotic genes specify floral organ identity in a putative dose-dependent manner. The results add to the current understanding of organ identity-related floral symmetry.

Multi-omics longitudinal analyses in stages I to III CRC patients: Surveillance liquid biopsy test to predict early recurrence and enable risk-stratified postoperative CRC management

3613

Background: One-third of colorectal cancer (CRC) recurs following curative surgery and chemotherapy. Accordingly, novel methods are needed to predict recurrence to enable clinical course mitigating strategies. Serial monitoring of plasma by mass spectrometry (MS) and multi-omics modeling (MMO) of CRC relapse chronology provide the framework for liquid biopsy test development to supersede existing imaging modalities such as CT scans according to relapse related pathologies. We hypothesized that plasma MS and MMO analysis of relapse related pathologies can deconvolute high risk stratification for CRC recurrence within the cancer continuum of care pre/post-surgery and/or pre/post adjuvant chemotherapy (ACT). Methods: 189 CRC patients (Stage I-III) underwent one of three treatment modalities: Modality 1 (Surgery followed by ACT), Modality 2 (Surgery only), Modality 3 (Neoadjuvant chemotherapy followed by surgery and ACT). Plasma samples (n = 441) were collected from patients before surgery, 30 days post-op, and every 3 months until death or month 24 whichever came first. The MMO approach was used to analyze biological features encompassing native peptides, proteins, metabolites, lipids, and ceramides. MMO panels were developed comprising the significantly perturbed features as per the treatment modalities. These panels were used to predict relapse from plasma collected pre-op, 30-day post-op or after adjuvant chemotherapy. CEA levels were monitored in parallel. Results: Follow-up data was available for 135 patients (Stage I-III) and 25/135 had evidence of radiological recurrence. Irrespective of the treatment modality, longitudinal follow-up using the MMO panel was able to predict disease recurrence greater than 7 months before clinical progression was confirmed by CT scan. There was no significant correlation between longitudinal CEA levels and recurrence status, hence CEA levels alone did not provide any lead time advantage over the MMO panel or radiological surveillance. Kaplan-Meier (KM) survival analysis revealed that patients that were MMO panel positive had a poor survival irrespective of treatment modalities used: Modality 1 (HR = 6.2, p value = 0.003, test immediately post-surgery and immediately before ACT; HR = 31.6, p value = 0.01, test immediately after ACT); Modality 2 (HR = 11.2; p value = 0.01, test immediately after-surgery); Modality 3 (HR > 40, p value = 0.08, test immediately after neo-ACT and before-surgery; HR > 40, p value = 0.004, test immediately after-surgery). Conclusions: The MMO panel predicts CRC recurrence several months prior to detection by conventional CT scans, thus providing opportunity for alternative therapeutic strategies much earlier in the disease course.

[CRISPR/Cas9-mediated TEAD1 knockout induces phenotypic modulation of corpus cavernosum smooth muscle cells in diabetic rats with erectile dysfunction]

OBJECTIVE

To construct a corpus cavemosum smooth muscle cell (CCSMCs) line with TEAD1 knockout from diabetic rats with erectile dysfunction (ED) using CRISPR/Cas9 technology and explore the role of TEAD1 in phenotypic modulation of CCSMCs in diabetic rats with ED.

OBJECTIVE

Models of diabetic ED were established in male Sprague-Dawley rats by intraperitoneal injection of streptozotocin. CCSMCs from the rat models were primarily cultured and identified with immunofluorescence assay. Three sgRNAs (sgRNA-1, sgRNA-2 and sgRNA-3) were transfected via lentiviral vectors into 293T cells to prepare the sgRNA-Cas9 lentivirus. CCSMCs from diabetic rats with ED were infected by the lentivirus, and the cellular expression of TEAD1 protein was detected using Western blotting. In CCSMCs infected with the sgRNA-Cas9 lentivirus (CCSMCs-sgRNA-2), or the empty lentiviral vector (CCSMCs-sgRNA-NC) and the blank control cells (CCSMCs-CK), the expressions of cellular phenotypic markers SMMHC, calponin and PCNA at the mRNA and protein levels were detected using real-time fluorescence quantitative RT-PCR (qRT-PCR) and Western blotting, respectively.

OBJECTIVE

The primarily cultured CCSMCs from diabetic rats with ED showed a high α-SMA-positive rate of over 95%. The recombinant lentivirus of TEAD1-sgRNA was successfully packaged, and stable TEAD1-deficient CCSMC lines derived from diabetic rat with ED were obtained. Western blotting confirmed that the protein expression of TEAD1 in TEAD1-sgRNA-2 group was the lowest (P < 0.05), and this cell line was used in subsequent experiment. The results of qRT-PCR and Western blotting showed significantly up-regulated expressions of SMMHC and calponin (all P < 0.05) and down-regulated expression of PCNA (all P < 0.05) at both the mRNA and protein levels in TEAD1-deficient CCSMCs from diabetic rats with ED.

OBJECTIVE

We successfully constructed a stable CCSMCs line with CRISPR/Cas9-mediated TEAD1 knockout from diabetic rats with ED. TEAD1 gene knockout can induce phenotype transformation of the CCSMCs from diabetic rats with ED from the synthetic to the contractile type.

Isopeptidase Kinetics Determination by a Real Time and Sensitive qFRET Approach

Isopeptidase activity of proteases plays critical roles in physiological and pathological processes in living organisms, such as protein stability in cancers and protein activity in infectious diseases. However, the kinetics of protease isopeptidase activity has not been explored before due to a lack of methodology. Here, we report the development of novel qFRET-based protease assay for characterizing the isopeptidase kinetics of SENP1. The reversible process of SUMOylation in vivo requires an enzymatic cascade that includes E1, E2, and E3 enzymes and Sentrin/SUMO-specific proteases (SENPs), which can act either as endopeptidases that process the pre-SUMO before its conjugation, or as isopeptidases to deconjugate SUMO from its target substrate. We first produced the isopeptidase substrate of CyPet-SUMO1/YPet-RanGAP1c by SUMOylation reaction in the presence of SUMO E1 and E2 enzymes. Then a qFRET analyses of real-time FRET signal reduction of the conjugated substrate of CyPet-SUMO1/YPet-RanGAP1c to free CyPet-SUMO1 and YPet-RanGAP1c by the SENP1 were able to obtain the kinetic parameters, K_cat, K_M, and catalytic efficiency (K_cat/K_M) of SENP1. This represents a pioneer effort in isopeptidase kinetics determination. Importantly, the general methodology of qFRET-based protease isopeptidase kinetic determination can also be applied to other proteases.

Efficacy and tolerability of immunotherapy in advanced nasopharyngeal carcinoma with or without chemotherapy: a meta-analysis

INTRODUCTION

Evidence of programmed death-1 inhibitors in nasopharyngeal carcinoma has been accumulated. However, previous clinical studies were basically small sample size.

OBJECTIVE

This study aimed to summarize existing studies to comprehensively compare programmed death-1 inhibitors in nasopharyngeal carcinoma with or without chemotherapy.

METHODS

Different databases were searched for full-text publications with a programmed death-1 inhibitor with or without chemotherapy. No study-to-study heterogeneity was detected, and fixed-effect models were applied to synthesize data.

RESULTS

Seven studies were included. The mean progression-free survival duration of programmed death-1 inhibitors treatment was 4.66 months. The 6 month progression-free survival rate was 50%, however, the12 month progression-free survival rate fell to 27%. Comparing with programmed death-1 inhibitor monotherapy, the objective response rate was higher in combination therapy (pooled RR=2.90, 95% CI: 2.07-4.08). The partial response rate was higher in patients receiving programmed death-1 in association with chemotherapy (pooled RR=3.09, 95% CI: 2.15-4.46), In contrast, the progressive disease rate was lower in combination therapy group (pooled RR=0.06, 95% CI: 0.01-0.31). Stable disease condition was comparable (pooled RR=0.90, 95% CI: 0.50-1.64) with or without chemotherapy. Programmed death-1 single use or combined with chemotherapy did not influence the total adverse events occurrence (pooled RR=0.99, 95% CI: 0.93-1.05). However, combination therapy could increase the risk of serious adverse events such as anemia, thrombocytopenia, and neutropenia.

CONCLUSION

The present study summarized the efficacy and safety of programmed death-1 inhibitors in nasopharyngeal carcinoma. Combination therapy showed higher anti-tumor activity except for higher risk of myelosuppression.

A functional mutation in the AMPD1 promoter region affects promoter activity and breast meat freshness in chicken

Freshness is an important index to determine the quality deterioration (protein degradation and changes in appearance) of chilled chicken meat and is a primary consideration of consumers. Adenosine monophosphate deaminase 1 (AMPD1) catalyzes the deamination of adenosine monophosphate to inosine monophosphate in skeletal muscle and is the rate-limiting step in the purine nucleotide cycle. Inosine monophosphate is regarded as an important indicator of meat freshness in chicken. This study investigated the association of polymorphisms in the chicken AMPD1 promoter region with meat freshness during freezing storage. An SNP (c. -905G>A) was found to be associated with the freshness (K-value) of chicken breast meat. Chickens with the AA genotype had significantly lower K-values than those with GG and AG genotypes (P < 0.01). Individuals with the AA genotype also had higher breast meat AMPD1 mRNA levels than did those with the GG and AG genotypes (P < 0.01, P < 0.05). A luciferase assay revealed that genotype AA had greater transcriptional activity than genotype GG. Transcription factor binding site analysis identified distinct putative transcription factor binding sites in the two alleles of mutation site c. -905. In summary, we identified an SNP (c. -905G>A) in the promoter region of the AMPD1 gene that may modulate the binding affinity of different transcription factors to control AMPD1 expression and affect the freshness K-value of chicken meat.

Kinetics of SARS-CoV-2 positivity of infected and recovered patients from a single center

Recurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive detection in infected but recovered individuals has been reported. Patients who have recovered from coronavirus disease 2019 (COVID-19) could profoundly impact the health care system. We sought to define the kinetics and relevance of PCR-positive recurrence during recovery from acute COVID-19 to better understand risks for prolonged infectivity and reinfection. A series of 414 patients with confirmed SARS-Cov-2 infection, at The Second Affiliated Hospital of Southern University of Science and Technology in Shenzhen, China from January 11 to April 23, 2020. Statistical analyses were performed of the clinical, laboratory, radiologic image, medical treatment, and clinical course of admission/quarantine/readmission data, and a recurrence predictive algorithm was developed. 16.7% recovered patients with PCR positive recurring one to three times, despite being in strict quarantine. Younger patients with mild pulmonary respiratory syndrome had higher risk of PCR positivity recurrence. The recurrence prediction model had an area under the ROC curve of 0.786. This case series provides characteristics of patients with recurrent SARS-CoV-2 positivity. Use of a prediction algorithm may identify patients at high risk of recurrent SARS-CoV-2 positivity and help to establish protocols for health policy.

Comparative analysis of key immune protection factors in H9N2 avian influenza viruses infected and immunized specific pathogen-free chicken

H9N2 avian influenza viruses (AIV) continue to circulate in vaccinated chicken flocks in China, which prompted us to investigate the differential immune protection factors induced by H9N2 AIV infection and immunization for analyzing the reason of protection deficiency of H9N2 AIV inactivated vaccine. In this study, we firstly explored virus-induced optimal immune responses in chicken after H9N2 AIV infection. And, we found that H9N2 hemagglutination inhibition (HI) antibody level, antiviral interferon-stimulated genes including 2′,5’-oligoadenylate synthetase-like and myxovirus resistance 1, CD8⁺ T cell response in peripheral blood lymphocytes (PBL) accompanied by the cytotoxicity-associated genes, including poly (ADP-ribose) polymerase and IFN-r play important roles in defending against H9N2 infection. Besides, we observed that vaccine immunization triggered the similar H9N2 HI antibody level as viral infection, the increase of CD4⁺ T cell percentage instead of CD8⁺ T cell percentage in PBL. Moreover, we further made a comparative analysis of immune-related gene expression profile in PBL and lung after H9N2 AIV infection and immunization, respectively. The results showed that vaccine immunization contributed to the up-regulation of Th2 cytokine. But the deficiency of cytotoxicity-associated genes induced by H9N2 AIV inactivated vaccine may be the potential key reason of protection deficiency. These findings provide evidence and direction for developing effective H9N2 AIV vaccines.

Linc00261 suppresses growth and metastasis of non-small cell lung cancer via repressing epithelial-mesenchymal transition

OBJECTIVE

Long non-coding RNAs (lncRNAs) have been identified to participate in the development and progression of various types of cancers, including non-small cell lung cancer (NSCLC). However, the expression and function of linc00261 in NSCLC has not been studied yet. We aim to explore the role and potential of linc00261 in NSCLC tumorigenesis.

PATIENTS AND METHODS

The expression level of linc00261 in 71 paired of NSCLC tissues and matched normal tissues, was detected using quantitative Real-time polymerase chain reaction (qRT-PCR). Linc00261 expression in NSCLC cells was also measured. NSCLC cells were transfected with pcDNA3.1 or siRNA linc00261 to upregulate or downregulate linc00261 expression, respectively. MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay and colony formation assay were utilized for examining the proliferative ability of NSCLC cells. Wound-healing and transwell assays were performed for detecting the metastatic ability of NSCLC cells. Protein levels of epithelial-mesenchymal transition markers were detected by Western blot. Furthermore, in vivo function of linc00261 was evaluated using the nude mice.

RESULTS

Linc00261 expressed significantly lower in NSCLC tissues and cell lines than that in the adjacent normal tissues or control cell line. Over-expression of linc00261 significantly inhibited proliferation, invasion and migration of NSCLC cells. On the contrast, knockdown of linc00261 promoted cell growth and metastasis of NSCLC cells. Furthermore, linc00261 inhibited the epithelial-mesenchymal transition of NSCLC via downregulating Snail. Linc00261 could slow down the growth of xenograft of NSCLC in vivo.

CONCLUSIONS

We demonstrated that linc00261 was lowly expressed in NSCLC tissues and cells. It inhibited cell proliferation and metastasis by downregulating Snail expression via EMT. This might provide a novel sight for the biological treatment for NSCLC.

A novel SUMOylation site in the influenza a virus NS1 protein identified with a highly sensitive FRET assay

Nonstructural protein 1 (NS1) of the influenza A virus is a major contributor to the virulence of the seasonal influenza A viruses, in part because it interferes with host viral defense mechanisms. SUMOylation regulates NS1 activity, and several residues of NS1 have been identified with traditional biochemical approaches as acceptor sites for SUMOylation. In this study, we developed a novel FRET assay to assess SUMOylation. Using this assay, we demonstrated that the lysine residue K131 in the effector domain of NS1 is a previously unidentified SUMO acceptor site. A recombinant H1N1 influenza A virus (A/PR/8/34) expressing a K131 SUMOylation-deficient NS1 had a significantly lower growth rate than the wild-type virus. These results suggest that NS1 SUMOylation at K131 is required for the rapid replication of H1N1 influenza viruses. The interaction between the NS1 protein and the host SUMOylation components may serve as a novel target for the development of anti-influenza A drugs.

Identification of differentially expressed genes associated with egg production in black-boned chicken

1. Muchuan black-bone chicken is well known in China for its meat quality and medicinal properties; however, its egg-laying performance is not ideal. To better understand the molecular mechanisms of black-boned chicken egg-laying, high-throughput RNA sequencing was performed to compare differences in the pituitary transcriptome between three high-rate (group H) and three low-rate (group L) egg production chickens. 2. In total, 171 differentially expressed genes (DEGs) were identified between the two groups, of which 113 were upregulated and 58 were downregulated in group L. Some of these genes are known to be related to hormone secretion or the regulation of reproductive processes; these include prolactin-releasing hormone (PRLH), distal-less homeobox 6 (DLX6), interferon regulatory factor 4 (IRF4), and cilia and flagella associated protein 69 (CFAP69). Notably, expression pattern analysis indicated that both PRLH and DLX6 may influence egg-laying performance. 3. The dataset provided a foundation for discovering important genes and pathways involved in the chicken egg-laying process, and may help to improve understanding of the molecular mechanisms of chicken reproduction.