A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ~20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

Genome-wide association study in a rat model of temperament identifies multiple loci for exploratory locomotion and anxiety-like traits.

Common genetic factors likely contribute to multiple psychiatric diseases including mood and substance use disorders. Certain stable, heritable traits reflecting temperament, termed externalizing or internalizing, play a large role in modulating vulnerability to these disorders. To model these heritable tendencies, we selectively bred rats for high and low exploration in a novel environment [bred High Responders (bHR) vs. Low Responders (bLR)]. To identify genes underlying the response to selection, we phenotyped and genotyped 538 rats from an F2 cross between bHR and bLR. Several behavioral traits show high heritability, including the selection trait: exploratory locomotion (EL) in a novel environment. There were significant phenotypic and genetic correlations between tests that capture facets of EL and anxiety. There were also correlations with Pavlovian conditioned approach (PavCA) behavior despite the lower heritability of that trait. Ten significant and conditionally independent loci for six behavioral traits were identified. Five of the six traits reflect different facets of EL that were captured by three behavioral tests. Distance traveled measures from the open field and the elevated plus maze map onto different loci, thus may represent different aspects of novelty-induced locomotor activity. The sixth behavioral trait, number of fecal boli, is the only anxiety-related trait mapping to a significant locus on chromosome 18 within which the Pik3c3 gene is located. There were no significant loci for PavCA. We identified a missense variant in the Plekhf1 gene on the chromosome 1:95 Mb QTL and Fancf and Gas2 as potential candidate genes that may drive the chromosome 1:107 Mb QTL for EL traits. The identification of a locomotor activity-related QTL on chromosome 7 encompassing the Pkhd1l1 and Trhr genes is consistent with our previous finding of these genes being differentially expressed in the hippocampus of bHR vs. bLR rats. The strong heritability coupled with identification of several loci associated with exploratory locomotion and emotionality provide compelling support for this selectively bred rat model in discovering relatively large effect causal variants tied to elements of internalizing and externalizing behaviors inherent to psychiatric and substance use disorders.

Geographic Differences on Clinical Manifestations of COVID-19 Infection Between Overseas Chinese and Local Chinese Patients.

INTRODUCTION: The novel coronavirus (COVID-19) has become a global pandemic with sharp rises in the number of confirmed cases and rapid spread across the world. Here, we looked at the effects of geographic differences on clinical manifestations of SARS-CoV-2 infected patients. METHODS: A total of 114 confirmed COVID-19 patients were included in this study. The epidemiological, demographic, clinical, as well as laboratory findings were extracted from the electronic medical records of these patients. RESULTS: We report the observation that patients from overseas residents diagnosed with COVID-19 were mildly symptomatic with cough and presented with lower inflammatory response and attenuated virus clearance rate, as well as correspondingly prolonged days of hospital stay than local Chinese patients. Moreover, the receiver-operating characteristic (ROC) analysis, performed to provide a measure of the difference between two groups, showed that serum albumin had the highest area under the curve value (0.81, p < 0.001). DISCUSSION: Our results suggested that blood albumin level acted as a predictive value in distinguishing clinical features between local and overseas Chinese. This work underscores the need to identify distinguishably prognostic factors of geographical dissimilarity in COVID-19 patients.

Immunological Evaluation on Potential Treatment Window for Hospitalized COVID-19 Patients.

PURPOSE: Novel coronavirus disease has become such an escalating epidemic that the exponential growth of infected patients has overloaded the health-care systems in many countries. Determination of early assessments for patients with a risk of clinical deterioration would benefit the management of COVID-19 outbreaks. PATIENTS AND METHODS: A total of 214 confirmed COVID-19 patients were enrolled from January 11th to February 11th 2020. Medical records including laboratory parameters, clinical outcomes and other characteristics of the admitted patients were analyzed retrospectively. RESULTS: The critical patients experienced a significantly prolonged onset-admission interval and presented with lymphopenia (r=-0.547, p=0.015) and lower albumin level (p<0.001) 6 days after symptom onset. Early admission of critical patients significantly reduced the duration of hormone therapy. Starting from 9 days of hospital stay, the reduced lymphocyte counts exhibited linear growth. Furthermore, on days 9 and 12, significant correlations were demonstrated between immunological manifestations and duration of hormone therapy in critical patients, and length of hospital stay in severe patients. In addition, the virus negative conversion rate was more significantly correlated with increased lymphocytes in critical patients. CONCLUSION: Early intervention, within 6 days of symptom onset, benefited patients' recovery from critical illness. The 9-12 days of hospital care represented a valuable window during which to evaluate the therapeutic effects on physical recovery and virus clearance.

Polymerase Chain Reaction Assays Reverted to Positive in 25 Discharged Patients With COVID-19.

We report the observation that 14.5% of COVID-19 patients had positive RT-PCR testing again after discharge. We describe correlations between laboratory parameters and treatment duration (P = .002) and time to virus recrudescence (P = .008), suggesting the need for additional measures to confirm illness resolution in COVID-19 patients.

The correlation between viral clearance and biochemical outcomes of 94 COVID-19 infected discharged patients.

OBJECTIVE: This study aims to evaluate the correlation between viral clearance and blood biochemical index of 94 discharged patients with COVID-19 infection in Shenzhen Third People's Hospital, enrolled from Jan 5 to Feb 13, 2020. METHODS: The clinical and laboratory findings were extracted from the electronic medical records of the patients. The data were analysed and reviewed by a trained team of physicians. Information on clinical signs and symptoms, medical treatment, virus clearance, and laboratory parameters including interleukin 6 (IL-6) and C-reactive protein were collected. RESULTS: COVID-19 mRNA clearance ratio was identified significantly correlated with the decline of serum creatine kinase (CK) and lactate dehydrogenase (LDH) levels. Furthermore, COVID-19 mRNA clearance time was positively correlated with the length of hospital stay in patients treated with either IFN-α + lopinavir/ritonavir or IFN-α + lopinavir/ritonavir + ribavirin. CONCLUSIONS: Therapeutic regimens of IFN-α + lopinavir/ritonavir and IFN-α + lopinavir/ritonavir + ribavirin might be beneficial for treatment of COVID-19. Serum LDH or CK decline may predict a favorable response to treatment of COVID-19 infection.

Combination of saikosaponin c and telbivudine synergistically enhances the anti-HBV activity.

OBJECTIVE: The present study was undertaken to obtain data using the combination of SSc and lamivudine (LAM), entecavir (ETV) or telbivudine (LdT) in HepG2.2.15 cells to explore whether SSc acts as a potent adjuvant of nucleoside analogues in anti-HBV treatment. METHODS: HepG2.2.15 cells were incubated with either SSc combined with any one of three nucleoside analogues (NAs) LAM, ETV, LdT or only one of them for 48 h. The expression profiles of HBV DNA, HBsAg, HBeAg, and HBcAg were examined by real-time quantitative PCR, ELISA, and western blot. RESULTS: Compared with mono-drug treatment, the combination of SSc and any of the three nucleoside analogues significantly promoted additional reduction on HBV DNA level. Declined levels of HBsAg, HBeAg, and HBcAg were observed in SSc and LdT combination group. CONCLUSION: These in vitro results indicated that SSc acted as a promising nucleoside analogue adjuvant, especially for telbivudine in the therapeutic strategies against HBV infection.

Saikosaponin C exerts anti-HBV effects by attenuating HNF1α and HNF4α expression to suppress HBV pgRNA synthesis.

OBJECTIVE: Saikosaponin c (SSc), a compound purified from the traditional Chinese herb of Radix Bupleuri was previously identified to exhibit anti-HBV replication activity. However, the mechanism through which SSc acts against HBV remains unknown. In this study, we investigated the mechanism of SSc mediated anti-HBV activity. METHODS: HepG2.2.15 cells were cultured at 37 â„ƒ in the presence of 1-40 µg/mL of SSc or DMSO as a control. The expression profile of HBV markers, cytokines, HNF1α and HNF4α were investigated by real-time quantitative PCR, Elisa, Western blot and Dot blotting. Knockdown of HNF1α or HNF4α in HepG2.2.15 cells was mediated by two small siRNAs specifically targeting HNF1α or HNF4α. RESULTS: We found that SSc stimulates IL-6 expression, leading to attenuated HNF1α and HNF4α expression, which further mediates suppression of HBV pgRNA synthesis. Knockdown of HNF1α or HNF4α in HepG2.2.15 cells by RNA interference abrogates SSc's anti-HBV role. Moreover, SSc is effective to both wild-type and drug-resistant HBV mutants. CONCLUSION: SSc inhibits pgRNA synthesis by targeting HNF1α and HNF4α. These results indicate that SSc acts as a promising compound for modulating pgRNA transcription in the therapeutic strategies against HBV infection.

Molecular analysis of a large novel deletion causing α+-thalassemia.

BACKGROUND: α-thalassaemia is an inherited blood disorder caused by mutations in the α-globin gene cluster. Recognizing the pathogenic α-globin gene mutations associated with α-Thalassemia is of significant importance to thalassaemia's diagnosis and management. METHODS: A family with α-thalassaemia from Fujian, China was recruited for this study. The phenotype was confirmed through haematological analysis. Commercially available Gap-PCR genotypic methods were employed to identify the known deletions causing α-thalassemia. MLPA analysis was used to study the novel mutations; this was then confirmed through DNA sequencing and bioinformatics analysis. RESULTS: The proband of the family belonged to Southeast Asian type (--SEA) thalassaemia. None of the known mutations associated with α-thalassaemia were detected in this family's genetics, whereas a novel 6.9 kb deletion (16p13.3 g.29,785-36,746) covering the α2 gene on the globin gene cluster was identified with MLPA and confirmed through Sanger Sequencing. This data led us to propose a novel pathogenic deletion associated with α-thalassemia: -α6.9 /--SEA. CONCLUSIONS: A novel α-thalassaemia deletion was identified in members of a Chinese family and subsequently analyzed. This finding has helped broaden the spectrum of pathogenic mutations leading to the development of α-thalassaemia, paving the way for improved disease diagnosis and management.

Hydrophilic Porous Poly(l-Lactic Acid) Nanomembranes: Self-Assembly, and Anti-Biofouling and Anti-Thrombosis Effects.

Hydrophilic PEGylated porous self-assembled nanomembranes (PSANMs) with average thickness and pore diameter of ca. 10 and 20-24 nm were successfully prepared by an emulsification-induced programmable self-assembly strategy. The hydrophilicity, anti-biofouling, and anti-thrombosis properties of PEGylated PSANMs were largely improved in comparison with the nonfunctionalized PSANMs, which could transform into hydrophilic (PEGylated PSANMs, minimum water contact angle: 38.8°) from hydrophobic units (PSANMs, maximum water contact angle: 137.5°) with increasing PEG density and length. The total protein adsorption of PEGylated PSANMs was about six times lower than that of the PSANMs, while the thrombosis of the PEGylated PSANMs (maximum R-time: 5.37 min) was also greatly relieved in comparison with the PSANMs (minimum R-time: 2.93 min). Such PEG-modified PSANMs may have applications in drug delivery and tissue and organ repair in vivo.

Folate Receptor-Mediated Renal-Targeting Nanoplatform for the Specific Delivery of Triptolide to Treat Renal Ischemia/Reperfusion Injury.

Triptolide (TP) has been widely used in clinical medicine; however, it has created a dilemma due to its toxicity and nonspecificity. Here, we reported a biocompatible and high-efficiency renal-targeting nanoplatform for renal ischemia/reperfusion injury (IRI) therapy, in which the toxic drug of TP was encapsulated into folate (FA)-modified Pluronic F127/P123 nanoparticles (FPNPs). The TP-loaded FPNPs (TP-FPNPs) had good stability and could effectively reduce the cytotoxicity of TP. Compared with the Pluronic nanoparticles (PNPs) group, cellular uptake ability of FPNPs significantly improved because of folate receptor-mediated endocytosis effect. Ex vivo organ imaging and pharmacokinetic results indicated that FPNPs possessed high kidney selectivity and long retention time. The therapeutic effect of TP-FPNPs on renal IRI was more superior to that of free TP, such as lower acute tubular injury index (2.9-fold), renal function indexes of serum creatinine (4.3-fold), urea nitrogen (2.0-fold), and Western blotting (2.4-fold). Systemic toxicity assay suggested that TP-FPNPs had much lower nephrotoxicity, hepatotoxicity, and genital system toxicity than free TP. Thus, renal-targeting FPNPs will be a potential delivery platform of hydrophobic drugs for treatment of renal diseases.

Resveratrol Exerts Antioxidant Effects by Activating SIRT2 To Deacetylate Prx1.

Resveratrol is a promising chemical agent that treats multiple aging-related diseases and improves life span. While reactive oxygen species undoubtedly play ubiquitous roles in the aging process and resveratrol has been shown to be an effective antioxidant, the mechanism through which resveratrol acts against oxidative stress remains unknown. Here we show that resveratrol activates SIRT2 to deacetylate Prx1, leading to an increased H2O2 reduction activity and a decreased cellular H2O2 concentration. Knockdown of SIRT2 or Prx1 by RNA interference abrogates resveratrol's ability to reduce the H2O2 level in HepG2 cells. Using purified SIRT2 and a Prx1 mutant harboring acetyllysine at position 27 (Prx1-27AcK), we show that resveratrol enhances SIRT2's activity to deacetylate Prx1-27AcK, resulting in a significantly increased H2O2 reducing activity. Thus, SIRT2 and Prx1 are targets for modulating intracellular redox status in the therapeutic strategies for the treatment of aging-related disorders.

Significant enhancement of hPrx1 chaperone activity through lysine acetylation.

The reversible acetylation of proteins plays a key role in regulating biological processes, including chromatin remodeling, progression of the cell cycle, and actin nucleation. Human peroxiredoxin 1(hPrx1), one of the most abundant proteins in the cytoplasm, has been shown to be acetylated in human liver-carcinoma tissues. However, little is known about what function(s) the acetylation serves for hPrx1. Herein, using the method of genetic code expansion, we incorporated N(ε)-acetyllysine (AcK) site-specifically into hPrx1. Our data showed that acetylation the K(27) residue promotes oligomerization of hPrx1 at low concentrations. In addition, K(27)-acetylated hPrx1(hPrx1-AcK27) exhibited greatly enhanced chaperone activity (e.g. protecting the protein malate dehydrogenase (MDH) from thermally induced aggregation and assisting the refolding of denatured citrate synthase (CS)). These findings suggest that the site-specific acetylation of hPrx1 may change its biological role in response to environmental changes.

Genetically encoded cyclopropene directs rapid, photoclick-chemistry-mediated protein labeling in mammalian cells.

We just click: Genetic incorporation of a cyclopropene amino acid CpK (see scheme) site-specifically into proteins in E. coli and mammalian cells was achieved using an orthogonal aminoacyl-tRNA synthetase/tRNA(CUA) pair (CpKRS/MbtRNA(CUA)). Cyclopropene exhibited fast reaction kinetics in the photoclick reaction and allowed rapid (ca. 2 min) labeling of proteins.