Epidemiological impact of a large number of false negative SARS-CoV-2 test results in South West England during September and October 2021

During September and October 2021, a substantial number of Polymerase Chain Reaction (PCR) tests in England processed at a single laboratory were incorrectly reported as negative. We estimate the number of false negative test results issued and investigate the epidemiological impact of this incident. We estimate the number of COVID-19 cases that would have been reported had the sensitivity of the laboratory test procedure not dropped for the period 2 September to 12 October. In addition, by making comparisons between the most affected local areas and comparator populations, we estimate the number of additional infections, cases, hospitalisations and deaths that could have occurred as a result of increased transmission due to false negative test results.We estimate that around 39,000 tests may have been false negatives during this period and, as a direct result of this incident, the most affected areas in the South-West of England could have experienced between 6000 and 34,000 additional reportable cases, with a central estimate of around 24,000 additional reportable cases. Using modelled relationships between key variables, we estimate that this central estimate could have translated to approximately 55,000 additional infections.Each false negative likely led to around 1.5 additional infections. The incident is likely to have had a measurable impact on cases and infections in the affected areas in the South-West of England. IMPACT STATEMENT: These results indicate the significant negative impact of incorrect testing on COVID outcomes; and make a substantial contribution to understanding the impact of testing systems and the need to ensure high accuracy in testing and reporting of results.

Mitogenomic architecture and evolution of the soil ciliates Colpoda

Colpoda are cosmopolitan unicellular eukaryotes primarily inhabiting soil and benefiting plant growth, but they remain one of the least understood taxa in genetics and genomics within the realm of ciliated protozoa. Here, we investigate the architecture of de novo assembled mitogenomes of six Colpoda species, using long-read sequencing and involving 36 newly isolated natural strains in total. The mitogenome sizes span from 43 to 63 kbp and typically contain 28-33 protein-coding genes. They possess a linear structure with variable telomeres and central repeats, with one Colpoda elliotti strain isolated from Tibet harboring the longest telomeres among all studied ciliates. Phylogenomic analyses reveal that Colpoda species started to diverge more than 326 million years ago, eventually evolving into two distinct groups. Collinearity analyses also reveal significant genomic divergences and a lack of long collinear blocks. One of the most notable features is the exceptionally high level of gene rearrangements between mitochondrial genomes of different Colpoda species, dominated by gene loss events. Population-level mitogenomic analysis on natural strains also demonstrates high sequence divergence, regardless of geographic distance, but the gene order remains highly conserved within species, offering a new species identification criterion for Colpoda species. Furthermore, we identified underlying heteroplasmic sites in the majority of strains of three Colpoda species, albeit without a discernible recombination signal to account for this heteroplasmy. This comprehensive study systematically unveils the mitogenomic structure and evolution of these ancient and ecologically significant Colpoda ciliates, thus laying the groundwork for a deeper understanding of the evolution of unicellular eukaryotes.IMPORTANCEColpoda, one of the most widespread ciliated protozoa in soil, are poorly understood in regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by gene loss events, potentially leading to the streamlining of Colpoda mitogenomes. Surprisingly, while interspecific rearrangements abound, our population-level mitogenomic study revealed a conserved gene order within species, offering a potential new identification criterion. Phylogenomic analysis traced their lineage over 326 million years, revealing two distinct groups. Substantial genomic divergence might be associated with the lack of extended collinear blocks and relaxed purifying selection. This study systematically reveals Colpoda ciliate mitogenome structures and evolution, providing insights into the survival and evolution of these vital soil microorganisms.

[The mechanism of NRF2 inhibiting ROS induced autophagy to reduce ovarian granulosa cells damage]

This study explores the effects and possible mechanisms of nuclear factor E2 related factor 2 (NRF2) on ovarian granulosa cells, providing a scientific basis to prevent premature ovarian failure. An ovarian cell injury model was constructed by treating human ovarian granulosa cell (KGN cell) with 4-Vinylcyclohexene dioxide (VCD). Firstly, KGN cells were treated with different concentrations of VCD, and cell counting kit 8 (CCK-8) was used to detect ovarian cell proliferation. After determining IC50 by CCK8, the levels of estradiol and progesterone in the cell supernatant were detected using enzyme-linked immunosorbent assay (ELISA), reactive oxygen species (ROS) assay kit was used to detect the content of ROS in ovarian cells, real-time fluorescence quantitative polymerase chain reaction (qRT PCR) was used to detect the mRNA expression level of NRF2, and Western blot was used to detect the protein expression level of NRF2. Further, NRF2 silence (siNRF2) and overexpression (NRF2-OE) cell models were constructed through lentivirus transfection, and the effects of regulating NRF2 on VCD treated cell models were investigated by detecting hormone levels, oxidative stress indicators (ROS, SOD, GSH-Px), and autophagy (LC3B level). The results showed that VCD intervention inhibited the proliferation of ovarian granulosa cells in a time-dependent and dose-dependent manner (F>100, P<0.05), with an IC50 of 1.2 mmol/L at 24 hours. After VCD treatment, the level of estradiol in the cell supernatant decreased from (56.32±10.18) ng/ml to (24.59±8.75) ng/ml (t=5.78, P<0.05). Progesterone decreased from (50.25±7.03) ng/ml to (25.13±6.67) ng/ml (t=6.54, P<0.05). After VCD treatment, the SOD of cells decreased from (44.47±7.71) ng/ml to (30.92±4.97) ng/ml (t=3.61, P<0.05). GSH-Px decreased from (68.51±10.17) ng/ml to (35.19±6.59) ng/ml (t=5.73, P<0.05). Simultaneously accompanied by an increase in autophagy and a decrease in NRF2. This study successfully constructed KGN cell models that silenced NRF2 and overexpressed NRF2. Subsequently, this study treated each group of cells with VCD and found that the cell proliferation activity of the siNRF2 group was significantly reduced (t=8.37, P<0.05), while NRF2-OE could reverse the cell activity damage caused by VCD (t=3.37, P<0.05). The siNRF2 group had the lowest level of estradiol (t=5.78, P<0.05), while NRF2-OE could reverse the decrease in cellular estradiol levels caused by VCD (t=5.58, P<0.05). The siNRF2 group had the lowest progesterone levels (t=3.02, P<0.05), while NRF2-OE could reverse the decrease in cellular progesterone levels caused by VCD (t=2.41, P<0.05). The ROS level in the siNRF2 group was the highest (t=2.86, P<0.05), NRF2-OE could reverse the increase in ROS caused by VCD (t=3.14, P<0.05), the SOD enzyme content in the siNRF2 group was the lowest (t=2.98, P<0.05), and NRF2-OE could reverse the decrease in SOD enzyme content caused by VCD (t=4.72, P<0.05). The GSH-Px enzyme content in the siNRF2 group was the lowest (t=3.67, P<0.05), and NRF2-OE could reverse the decrease in antioxidant enzyme content caused by VCD (t=2.71, P<0.05). The LC3B level was highest in the siNRF2 group (t=2.45, P<0.05), and NRF2-OE was able to reverse the LC3B elevation caused by VCD (t=9.64, P<0.05). In conclusion, NRF2 inhibits ROS induced autophagy, thereby playing a role in reducing ovarian granulosa cell damage, which may be a potential target for premature ovarian failure.

Paramecium Genetics, Genomics, and Evolution

The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently been made in the area of comparative and population genomics. Paramecium species combine some of the lowest known mutation rates with some of the largest known effective populations, along with likely very high recombination rates, thereby harboring a population-genetic environment that promotes an exceptionally efficient capacity for selection. As a consequence, the genomes are extraordinarily streamlined, with very small intergenic regions combined with small numbers of tiny introns. The subject of the bulk of Paramecium research, the ancient Paramecium aurelia species complex, is descended from two whole-genome duplication events that retain high degrees of synteny, thereby providing an exceptional platform for studying the fates of duplicate genes. Despite having a common ancestor dating to several hundred million years ago, the known descendant species are morphologically indistinguishable, raising significant questions about the common view that gene duplications lead to the origins of evolutionary novelties.

An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data

High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures, greatly promoting biological studies involving large amounts of complex samples, especially those involving environmental and pathogen-monitoring ones. Commercial library preparation kits for amplicon sequencing, which generally require multiple steps, including adapter ligation and indexing, are expensive and time-consuming, especially for applications at a large scale. To overcome these limitations, a "one-step PCR approach" has been previously proposed for constructions of amplicon libraries using long fusion primers. However, efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed. To tackle these, we present an integrative protocol for one-step PCR amplicon library construction (OSPALC). High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples. With this protocol, the amplicon library is constructed through one regular PCR with long primers, and the total cost per DNA/cDNA sample decreases to just 7% of the typical cost via the multi-step PCR approach. Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study. Tools to design primers targeting at any genomic regions are also presented. In principle, OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples, and will facilitate research in numerous fields.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00182-1.

Contribution of the SOS response and the DNA repair systems to norfloxacin induced mutations in E. coli

Antibiotic-resistant bacteria severely threaten human health. Besides spontaneous mutations generated by endogenous factors, the resistance might also originate from mutations induced by certain antibiotics, such as the fluoroquinolones. Such antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair systems. However, the relative contributions of these molecular mechanisms remain unclear, hindering understanding of the generation of resistant pathogens. Here, using newly-accumulated mutations of wild-type and SOS-uninducible Escherichia coli strains, as well as those of the strains deficient for the mismatch repair (MMR) and the oxidative damage repair pathways, we find that the SOS response is the major mutagenesis contributor in mutation elevation, responsible for ~ 30-50% of the total base-pair substitution (BPS) mutation-rate elevation upon treatment with sublethal levels of norfloxacin (0 ~ 50 ng/mL). We further estimate the significance of the effects on other mutational features of these mechanisms (i.e., transversions, structural variations, and mutation spectrum) in E. coli using linear models. The SOS response plays a positive role in all three mutational features (mutation rates of BPSs, transversions, structural variations) and affects the mutational spectrum. The repair systems significantly reduce the BPS mutation rate and the transversion rate, regardless of whether antibiotics are present, while significantly increasing the structural variation rate in E. coli. Our results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00185-y.

The divergence of mutation rates and spectra across the Tree of Life

Owing to advances in genome sequencing, genome stability has become one of the most scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological, the mutation rate (per nucleotide site per generation) ranges over three orders of magnitude among species and several-fold within individual phylogenetic lineages. Within all major organismal groups, mutation rates scale negatively with the effective population size of a species and with the amount of functional DNA in the genome. This relationship is most parsimoniously explained by the drift-barrier hypothesis, which postulates that natural selection typically operates to reduce mutation rates until further improvement is thwarted by the power of random genetic drift. Despite this constraint, the molecular mechanisms underlying DNA replication fidelity and repair are free to wander, provided the performance of the entire system is maintained at the prevailing level. The evolutionary flexibility of the mutation rate bears on the resolution of several prior conundrums in phylogenetic and population-genetic analysis and raises challenges for future applications in these areas.

Efficacy and safety of atropine in myopic children: A meta-analysis of randomized controlled trials

PURPOSE

To evaluate the safety and efficacy of atropine for childhood myopia and further explore the optimal concentration of atropine, so as to provide more reference for clinical application.

METHODS

PubMed, Embase, Cochrane Library and ClinicalTrials.gov were comprehensively searched for randomized controlled trials (RCTs) up to October 14, 2021. The efficacy outcomes were progression of spherical equivalent (SE) and axial length (AL). The safety outcomes included accommodation amplitude, pupil size and adverse effects. The meta-analysis was performed using Review Manager 5.3.

RESULTS

Eighteen RCTs involving 3002 eyes were included. The results showed that at 6-36 months of treatment, atropine was effective in slowing the progression of myopia in children. At 12 months, the WMD of SE and AL of low-dose atropine was 0.25 diopters (D) and 0.1 millimeter (mm), moderate-dose atropine was 0.44 D and 0.16mm, high-dose atropine was 1.21 D and 0.82mm, respectively, compared with the control group. Similarly, at 24 months, low-dose atropine was 0.22 D and 0.14mm, moderate-dose atropine was 0.60 D, high-dose atropine was 0.66 D and 0.24mm, respectively. Interestingly, we also found that there was no significant difference in the effects of low-dose atropine on accommodation amplitude and photopic pupil size compared with the control group, and the rate of photophobia, allergy, blurred vision and other side effects was similar between the low-dose atropine group and the control group. In addition, atropine appears to be more effective in myopic children in China than in other countries.

CONCLUSIONS

Atropine in various concentrations can effectively slow myopia progression in children, and its effect is dose-dependent, while low-dose atropine (0.01% atropine) appears to be safer.

Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA

Adenosine-to-inosine tRNA-editing enzyme has been identified for more than two decades, but the study on its DNA editing activity is rather scarce. We show that amphioxus (Branchiostoma japonicum) ADAT2 (BjADAT2) contains the active site 'HxE-PCxxC' and the key residues for target-base-binding, and amphioxus ADAT3 (BjADAT3) harbors both the N-terminal positively charged region and the C-terminal pseudo-catalytic domain important for recognition of substrates. The sequencing of BjADAT2-transformed Escherichia coli genome suggests that BjADAT2 has the potential to target E. coli DNA and can deaminate at TCG and GAA sites in the E. coli genome. Biochemical analyses further demonstrate that BjADAT2, in complex with BjADAT3, can perform A-to-I editing of tRNA and convert C-to-U and A-to-I deamination of DNA. We also show that BjADAT2 preferentially deaminates adenosines and cytidines in the loop of DNA hairpin structures of substrates, and BjADAT3 also affects the type of DNA substrate targeted by BjADAT2. Finally, we find that C89, N113, C148 and Y156 play critical roles in the DNA editing activity of BjADAT2. Collectively, our study indicates that BjADAT2/3 is the sole naturally occurring deaminase with both tRNA and DNA editing capacity identified so far in Metazoa.

de novo structural variations of Escherichia coli detected by Nanopore long-read sequencing

Spontaneous mutations power evolution, while large-scale structural variations (SVs) remain poorly studied, primarily because of the lack of long-read sequencing techniques and powerful analytical tools. Here, we explore the SVs of Escherichia coli by running 67 wild-type (WT) and 37 MMR-deficient (ΔmutS) mutation accumulation lines, each experiencing more than 4000 cell divisions, by applying Nanopore long-read sequencing and Illumina PE150 sequencing, and verifying the results by Sanger sequencing. In addition to precisely repeating previous mutation rates of base-pair substitutions and indels mutation rates, we do find significant improvement in insertion and deletion detection using long-read sequencing. The long-read sequencing and corresponding softwares can particularly detect bacterial SVs in both simulated and real datasets with high accuracy. These lead to SV rates of 2.77 × 10-4 (WT) and 5.26 × 10-4 (MMR-deficient) per cell division per genome, which is comparable with previous reports. This study provides the SV rates of E. coli by applying long-read sequencing and SV-detection programs, revealing a broader and more accurate picture of spontaneous mutations in bacteria.

Silver nanoparticles elevate mutagenesis of eukaryotic genomes

Metal nanoparticles, especially silver, have been used in various medical scenarios, due to their excellent antimicrobial effects. Recent studies have shown that AgNPs do not exert mutagenic effects on target bacteria, but the degree to which they compromise eukaryotic genomes remains unclear. To study this, we evaluated the mutagenic effects of AgNPs on the fission yeast Schizosaccharomyces pombe ATCC-16979, of which ∼23% genes are homologous to human ones, at single-nucleotide resolution, and whole-genome scale by running 283 mutation accumulation lines for ∼260,000 cell divisions in total. We also explored the action and mutagenesis mechanisms using differential gene-expression analysis based on RNAseq. Upon AgNPs treatment, the genomic base-substitution mutation rate of S. pombe at four-fold degenerate sites increased by 3.46×, and small indels were prone to occur in genomic regions that are not simple sequence repeats. The G:C → T:A transversion rate was also significantly increased, likely mostly from oxidative damage. Thus, in addition to their antimicrobial potency, AgNPs might pose slight genotoxicity threats to eukaryotic and possibly human genomes, though at a low magnitude.

Mutagenesis and Resistance Development of Bacteria Challenged by Silver Nanoparticles

Because of their extremely broad spectrum and strong biocidal power, nanoparticles of metals, especially silver (AgNPs), have been widely applied as effective antimicrobial agents against bacteria, fungi, and so on. However, the mutagenic effects of AgNPs and resistance mechanisms of target cells remain controversial. In this study, we discover that AgNPs do not speed up resistance mutation generation by accelerating genome-wide mutation rate of the target bacterium Escherichia coli. AgNPs-treated bacteria also show decreased expression in quorum sensing (QS), one of the major mechanisms leading to population-level drug resistance in microbes. Nonetheless, these nanomaterials are not immune to resistance development by bacteria. Gene expression analysis, experimental evolution in response to sublethal or bactericidal AgNPs treatments, and gene editing reveal that bacteria acquire resistance mainly through two-component regulatory systems, especially those involved in metal detoxification, osmoregulation, and energy metabolism. Although these findings imply low mutagenic risks of nanomaterial-based antimicrobial agents, they also highlight the capacity for bacteria to evolve resistance.

Hypoxia is fine-tuned by Hif-1α and regulates mesendoderm differentiation through the Wnt/β-Catenin pathway

Background

Hypoxia naturally happens in embryogenesis and thus serves as an important environmental factor affecting embryo development. Hif-1α, an essential hypoxia response factor, was mostly considered to mediate or synergistically regulate the effect of hypoxia on stem cells. However, the function and relationship of hypoxia and Hif-1α in regulating mesendoderm differentiation remains controversial.

Results

We here discovered that hypoxia dramatically suppressed the mesendoderm differentiation and promoted the ectoderm differentiation of mouse embryonic stem cells (mESCs). However, hypoxia treatment after mesendoderm was established promoted the downstream differentiation of mesendoderm-derived lineages. These effects of hypoxia were mediated by the repression of the Wnt/β-Catenin pathway and the Wnt/β-Catenin pathway was at least partially regulated by the Akt/Gsk3β axis. Blocking the Wnt/β-Catenin pathway under normoxia using IWP2 mimicked the effects of hypoxia while activating the Wnt/β-Catenin pathway with CHIR99021 fully rescued the mesendoderm differentiation suppression caused by hypoxia. Unexpectedly, Hif-1α overexpression, in contrast to hypoxia, promoted mesendoderm differentiation and suppressed ectoderm differentiation. Knockdown of Hif-1α under normoxia and hypoxia both inhibited the mesendoderm differentiation. Moreover, hypoxia even suppressed the mesendoderm differentiation of Hif-1α knockdown mESCs, further implying that the effects of hypoxia on the mesendoderm differentiation were Hif-1α independent. Consistently, the Wnt/β-Catenin pathway was enhanced by Hif-1α overexpression and inhibited by Hif-1α knockdown. As shown by RNA-seq, unlike hypoxia, the effect of Hif-1α was relatively mild and selectively regulated part of hypoxia response genes, which fine-tuned the effect of hypoxia on mESC differentiation.

Conclusions

This study revealed that hypoxia is fine-tuned by Hif-1α and regulates the mesendoderm and ectoderm differentiation by manipulating the Wnt/β-Catenin pathway, which contributed to the understanding of hypoxia-mediated regulation of development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01423-y.

Who are the real high-risk patients with pathological T2N0M0 non-small-cell lung cancer that can benefit from adjuvant chemotherapy?

Background

Methods

Results

Conclusions

•

ACT could not improve long-term survival in pT2N0M0 NSCLC in general.

•

ACT could only improve OS and DFS in pT2N0M0 NSCLC >4 cm.

•

ACT could not improve CSS in any subgroup of pT2N0M0 NSCLC.

•

For patients with other high-risk factors, ACT failed to improve long-term survival.

Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica

Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.

[Prevention and treatment of mucocutaneous adverse reactions associated with epidermal growth factor receptor inhibitors]

The epidermal growth factor receptor (EGFR) signaling is aberrantly overexpressed in many solid malignancies, making it an important target for anti-cancer biologic agents. Among them, epidermal growth factor receptor inhibitors (EGFRIs), which have been widely used in clinical practice, include anti-EGFR monoclonal antibodies and tyrosine kinase inhibitors. A proportion of patients treated with EGFRIs develop specific, dose-dependent skin toxicity such as papulopustular rash, paronychia, xerosis and itch. These side effects can cause physical and psychosocial discomfort that may result in dose reduction, discontinuance, or replacement of the current EGFRIs treatment. Correct diagnosis and treatment of these skin and mucosal adverse effects associated with EGFRIs is of great significance for the tertiary prevention of malignant tumors. A review on EGFRI-related mucocutaneous adverse reactions is presented here, focusing on the pathogenesis, the various clinical manifestations, the strategies for prevention and treatment of these conditions.

Modified anterior midline approach to treat hyperextension bicondylar tibial plateau fractures: Surgical technique and clinical experience with 18 cases

BACKGROUND

We evaluated the modified anterior midline approach and its efficacy for hyperextension bicondylar tibial plateau (HEBTP) fractures.

METHODS

From 2015 to 2019, 18 patients with HEBTP fractures with just little posterior cortical displacement were treated using the modified anterior midline approach. The operative protocols are fully described in this article, and the following parameters: articular step-off height (ASH), posterior tibial slope angle (pTSA), and medial tibial plateau angle (mTPA) were measured perioperatively and at the final follow-up. We also recorded the Rasmussen score and range of motion (ROM) to assess knee joint function at the final follow-up.

RESULTS

No complications, such as percutaneous nerve damage, infection, skin necrosis, and internal fixation breakage or loosening occurred perioperatively. The mean time for bony union was 13.7 weeks, and the mean preoperative ASH of the anterior cortex was 4.49 mm; this was restored to its normal height after surgery. The mean preoperative pTSA and mTPA were - 5.89° and 81.69°, respectively, compared with 3.89° and 87.91°, respectively, postoperatively. Comparing the postoperative and final follow-up radiographs, there were no significant differences in ASH, pTSA, and mTPA (P < 0.05). The average Rasmussen score was 27.2 (range, 23-29) at the final follow-up. Excellent results were achieved in 14 (77.8%) patients and good in 4 (22.2%) patients. The mean ROM in flexion was 123.2° and 2.9° in extension at the final follow-up.

CONCLUSIONS

This study suggested that the modified anterior midline approach is a reasonable alternative for HEBTP fracture repair.

Erratum: Azimuthal Anisotropy of K_{S}^{0} and Λ+Λ[over ¯] Production at Midrapidity from Au+Au Collisions at sqrt[s]_{NN}=130 GeV [Phys. Rev. Lett. 89, 132301 (2002)]

This corrects the article DOI: 10.1103/PhysRevLett.89.132301.

Erratum: Azimuthal Anisotropy at the Relativistic Heavy Ion Collider: The First and Fourth Harmonics [Phys. Rev. Lett. 92, 062301 (2004)]

This corrects the article DOI: 10.1103/PhysRevLett.92.062301.

Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains

Microbial strains with high genomic stability are particularly sought after for testing the quality of commercial microbiological products, such as biological media and antibiotics. Yet, using mutation-accumulation experiments and de novo assembled complete genomes based on Nanopore long-read sequencing, we find that the widely used quality-control strain Shewanella putrefaciens ATCC-8071, also a facultative pathogen, is a hypermutator, with a base-pair substitution mutation rate of 2.42 × 10-8 per nucleotide site per cell division, ∼146-fold greater than that of the wild-type strain CGMCC-1.6515. Using complementation experiments, we confirm that mutL dysfunction, which was a recent evolutionary event, is the cause for the high mutation rate of ATCC-8071. Further analyses also give insight into possible relationships between mutation and genome evolution in this important bacterium. This discovery of a well-known strain being a hypermutator necessitates screening the mutation rate of bacterial strains before any quality control or experiments.

[Exenatide promotes cholesterol efflux in pancreatic tissue of obese diabetic rats]

OBJECTIVE

To study the effect of exenatide on the expression of ABCA1 and cholesterol metabolism in the pancreas of obese diabetic rats.

OBJECTIVE

Twenty-four normal male SD rats and 18 obese diabetic rats (induced by high-fat feeding and STZ injection) were both divided equally into 2 groups for injections of saline or exenatide. After treatment for a week, the expression of ABCA1, cholesterol metabolism, and islet function of the rats were examined using real-time PCR, Western blotting, oil red O staining, cholesterol content determination, and HE staining.

OBJECTIVE

The expressions of ABCA1 at both mRNA and protein levels in pancreatic tissue were significantly lower in obese diabetic rats than in normal SD rats. The obese diabetic rats showed obvious lipid deposition and increased cholesterol content in the pancreatic tissue with significantly reduced islet volume and structural changes (P < 0.05); exenatide treatment of the diabetic rats significantly up-regulated ABCA1 expression, reduced lipid deposition and cholesterol content in pancreatic tissue, and increased number and volume of the islets, which presented with more orderly alignment (P < 0.05).

OBJECTIVE

Obese diabetic rats have lowered ABCA1 expression, cholesterol efflux block, and cholesterol accumulation in the pancreatic tissue. Exenatide can up-regulate ABCA1 expression and promote cholesterol efflux to reduce cholesterol content in the pancreatic tissue and improve islet function in obese diabetic rats.

LncRNA HOTTIP promotes proliferation and inhibits apoptosis of gastric carcinoma cells via adsorbing miR-615-3p

OBJECTIVE

To explore the role of long-noncoding ribonucleic acid HOXA transcript at the distal tip (lncRNA HOTTIP) in the proliferation and apoptosis of gastric carcinoma cells.

MATERIALS AND METHODS

The expressions of lncRNA HOTTIP in gastric carcinoma cell lines MGC-803, HGC-27, SNU-1, and SGC-7901 and normal gastric mucosa cell line RGM-1 were detected by real-time fluorescence quantitative polymerase chain reaction (PCR) and compared. The effects of lncRNA HOTTIP on proliferation and apoptosis of gastric carcinoma cells were detected by cell counting kit-8 (CCK-8), colony formation assay, and flow cytometry, respectively. StarBase v2.0 website was adopted to predict the relationship between lncRNA HOTTIP and target miRNAs. Dual-Luciferase reporter assay was performed to verify the sponge effect of lncRNA HOTTIP on miR-615-3p. CCK-8 experiment was conducted to detect its effect on proliferation of gastric carcinoma cells after co-silencing lncRNA HOTTIP and miR-615-3p.

RESULTS

LncRNA HOTTIP was highly expressed in gastric carcinoma cell lines MGC-803, HGC-27, SNU-1, and SGC-7901 than in normal gastric mucosa cell line RGM-1. After knockdown of lncRNA HOTTIP, the proliferation function of gastric carcinoma cells was markedly weakened, and the proportion of apoptotic cells increased. LncRNA HOTTIP was able to adsorb miR-615-3p via a sponge effect. Notably, knockdown of miR-615-3p restored the effect of silenced lncRNA HOTTIP on the proliferation function of gastric carcinoma cells.

CONCLUSIONS

LncRNA HOTTIP is highly expressed in gastric carcinoma cells. It affects cell proliferation and apoptosis in gastric carcinoma by adsorbing miR-615-3p via a sponge effect.

Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast

Mutation and recombination are the primary sources of genetic variation. To better understand the evolution of genetic variation, it is crucial to comprehensively investigate the processes involving mutation accumulation and recombination. In this study, we performed mutation accumulation experiments on four heterozygous diploid yeast species in the Saccharomycodaceae family to determine spontaneous mutation rates, mutation spectra, and losses of heterozygosity (LOH). We observed substantial variation in mutation rates and mutation spectra. We also observed high LOH rates (1.65-11.07×10-6 events per heterozygous site per cell division). Biases in spontaneous mutation and LOH together with selection ultimately shape the variable genome-wide nucleotide landscape in yeast species.

The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria

Mutation is a primary source of genetic variation that is used to power evolution. Many studies, however, have shown that most mutations are deleterious and, as a result, extremely low mutation rates might be beneficial for survival. Using a mutation accumulation experiment, an unbiased method for mutation study, we found an extremely low base-substitution mutation rate of 5.94 × 10^-11 per nucleotide site per cell division (95% Poisson confidence intervals: 4.65 × 10^-11, 7.48 × 10^-11) and indel mutation rate of 8.25 × 10^-12 per site per cell division (95% confidence intervals: 3.96 × 10^-12, 1.52 × 10^-11) in the bacterium Photorhabdus luminescens ATCC29999. The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction. It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the effective population size (drift-barrier hypothesis) and we found that the effective population size of this bacterium is significantly greater than most other bacteria. This finding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fidelity can evolve within organisms that maintain large effective population sizes.

Treatment outcomes of percutaneous radiofrequency ablation versus adrenalectomy for adrenal metastases: a retrospective comparative study

PURPOSE

To retrospectively evaluate the clinical outcomes of percutaneous ultrasound (US)-guided radiofrequency ablation (RFA) in treatment of adrenal metastasis (AM), and to compare with adrenalectomy (Adx).

METHODS

From June 2008 to August 2018, a total of 60 patients with AM treated at our hospital were retrospectively reviewed, of whom 29 treated by RFA (RFA group) and 31 by Adx (Adx group). The technical success, local tumor progression (LTP) and overall survival (OS) after the treatment were evaluated and compared.

RESULTS

In RFA group, the first technical success was 72.4% and the second technical success was 86.2%. In Adx group, all the AMs were successfully resected. After 24.5 ± 19.1 months follow-up period, a total of 8 patients (6 in RFA group and 2 in Adx group) were detected LTP. The 1-, 2- and 3- LTP rates after treatment were 17.1%, 30.9% and 44.7% in RFA group, and 6.5%, 6.5% and 6.5% in Adx group, respectively (P = 0.028). However, for AM ≤ 5 cm, the LTP between the two groups were comparable (P = 0.068). The 1-, 2- and 3- OS rates after treatment for AM were 85.0%, 42.4% and 27.8% in RFA group, and 93.0%, 66.1% and 52.3% in Adx group, respectively (P = 0.057). RFA offered shorter treatment time (23.6 ± 16.9 vs. 155.6 ± 58.8 min, P < 0.001), shorter hospital stay (7.8 ± 3.9 vs. 15.0 ± 4.9 days, P < 0.001), and lower hospital cost ($3405.7 ± 1067.8 vs. $5248.0 ± 2261.3, P = 0.003) than Adx.

CONCLUSION

In comparison with Adx, percutaneous US-guided RFA, as an alternative treatment, is feasible and effective in controlling AM, especially in AM ≤ 5 cm in diameter.

CGRP Modulates Orofacial Pain through Mediating Neuron-Glia Crosstalk

Calcitonin gene-related peptide (CGRP) plays a crucial role in the modulation of orofacial pain, and we hypothesized that CGRP mediated a neuron-glia crosstalk in orofacial pain. The objective of this study was to elucidate the mechanisms whereby CGRP mediated trigeminal neuron-glia crosstalk in modulating orofacial pain. Orofacial pain was elicited by ligating closed-coil springs between incisors and molars. Trigeminal neurons and satellite glial cells (SGCs) were cultured for mechanistic exploration. Gene and protein expression were determined through immunostaining, polymerase chain reaction, and Western blot. Orofacial pain was evaluated through the rat grimace scale. Our results revealed that the expressions of CGRP were elevated in both trigeminal neurons and SGCs following the induction of orofacial pain. Intraganglionic administration of CGRP and olcegepant exacerbated and alleviated orofacial pain, respectively. The knockdown of CGRP through viral vector-mediated RNA interference was able to downregulate CGRP expressions in both neurons and SGCs and to alleviate orofacial pain. CGRP upregulated the expression of inducible nitric oxide synthase through the p38 signaling pathway in cultured SGCs. In turn, L-arginine (nitric oxide donor) was able to enhance orofacial pain by upregulating CGRP expressions in vivo. In cultured trigeminal neurons, L-arginine upregulated the expression of CGRP, and this effect was diminished by cilnidipine (N-type calcium channel blocker) while not by mibefradil (L-type calcium channel blocker). In conclusion, CGRP modulated orofacial pain through upregulating the expression of nitric oxide through the p38 signaling pathway in SGCs, and the resulting nitric oxide in turn stimulated CGRP expression through N-type calcium channel in neurons, building a CGRP-mediated positive-feedback neuron-glia crosstalk.

Identification of Vibrio alginolyticus virulent strain-specific DNA regions by suppression subtractive hybridization and PCR

AIMS

Vibrio alginolyticus was frequently isolated from diseased farmed fish in the coaster waters of Hainan Island over the past two decades. In this study, we attempted to identify candidates of virulent strain-specific DNA regions for this pathogen.

METHODS AND RESULTS

Suppression subtractive hybridization (SSH) and PCR were successively performed between the typical virulent strain and avirulent strain of V. alginolyticus, in which they shared 99·54% homology of 16S rDNAs. Out of 2873 subtracted clones, nine clones were finally indicated to harbour virulent strain-specific DNA fragments. The receivable functions of the major fragments in the nine clones were believed to encode methyl-accepting chemotaxis protein (n = 1), type VI secretion system-associated FHA domain protein TagH (n = 1), diguanylate cyclase (n = 1), AraC family transcriptional regulator (n = 1), ABC-type uncharacterized transport system permease component (n = 1) and hypothetical proteins (n = 4). Two hypothetical proteins contain several disordered regions.

CONCLUSIONS

Some specific DNA regions existed in the virulent strain of V. alginolyticus, and the SSH assay could be a highly sensitive method for identifying virulent regions in pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This report is the first to describe the identification of virulent strain-specific DNA regions in the V. alginolyticus genome, which is helpful in developing virulent strain-specific rapid detection methods and is a pivotal precondition for clarifying the molecular virulence mechanism of V. alginolyticus.

Protecting medical staff from skin injury/disease caused by personal protective equipment during epidemic period of COVID-19: experience from China

Linked articles: COVID‐19 SPECIAL FORUM. J Eur Acad Dermatol Venereol 2020; 34: e210–e216.

Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics

Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large group of unicellular eukaryotes with extremely long evolutionary history and genome diversity. With recent publications of multiple ciliate genomes, we start to get a chance to explore perfect SSRs with motif size 1-100 bp and at least three motif repeats in nine species of two ciliate classes, Oligohymenophorea and Spirotrichea. We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in Tetrahymena. Micronuclear SSRs are universally more abundant than the macronuclear ones of the same motif-size, except for the 8-bp-motif SSRs in extensively fragmented chromosomes. Both the abundance and A/T content of SSRs decrease as motif-size increases, while the abundance is positively correlated with the A/T content of the genome. Also, smaller genomes have lower proportions of coding SSRs out of all SSRs in Paramecium species. This genome-wide and cross-species analysis reveals the high diversity of SSRs and reflects the rapid evolution of these simple repetitive elements in ciliate genomes.

Association between rs12742784 polymorphism and hip fracture, bone mineral density, and EPHB2 mRNA expression levels in elderly Chinese women

Objective: This study aimed to determine the association between rs12742784 polymorphism in the non-coding area and hip fracture, bone mineral density (BMD), and EPHB2 mRNA expression levels in elderly Chinese women.Methods: We investigated 250 Chinese women (mean age: 63.5 ± 8.3 years) including 123 hip fracture patients and 127 non-fracture controls. All participants underwent clinical examination to meet the inclusion criteria. Lumbar and hip BMD were detected by dual-energy X-ray absorptiometry. rs12742784 polymorphism was determined by restriction fragment length polymorphism and EPHB2 mRNA expression levels were measured by real-time polymerase chain reaction.Results: Distribution of rs12742784 genotypes agreed with Hardy-Weinberg equilibrium. The frequency of the CT + TT genotype was significantly associated with decreased risk of hip fracture (adjusted odds ratio = 0.57, p < 0.01) after adjusting for age and body mass index, and with increased BMD and EPHB2 mRNA expression levels. The T allele of the rs12742784 single nucleotide polymorphism (SNP) was a protective factor for hip fracture (adjusted odds ratio = 0.56, p < 0.01).Conclusion: rs12742784 polymorphism was associated with EPHB2 mRNA expression levels, BMD, and hip fracture in Chinese women. The T allele of the rs12742784 SNP was a protective factor for osteoporosis and hip fracture.

Specificity of the DNA Mismatch Repair System (MMR) and Mutagenesis Bias in Bacteria

The mutation rate of an organism is influenced by the interaction of evolutionary forces such as natural selection and genetic drift. However, the mutation spectrum (i.e., the frequency distribution of different types of mutations) can be heavily influenced by DNA repair. Using mutation-accumulation lines of the extremophile bacterium Deinococcus radiodurans ΔmutS1 and the model soil bacterium Pseudomonas fluorescens wild-type and MMR- (Methyl-dependent Mismatch Repair-deficient) strains, we report the mutational features of these two important bacteria. We find that P. fluorescens has one of the highest MMR repair efficiencies among tested bacteria. We also discover that MMR of D. radiodurans preferentially repairs deletions, contrary to all other bacteria examined. We then, for the first time, quantify genome-wide efficiency and specificity of MMR in repairing different genomic regions and mutation types, by evaluating the P. fluorescens and D. radiodurans mutation data sets, along with previously reported ones of Bacillus subtilis subsp. subtilis, Escherichia coli, Vibrio cholerae, and V. fischeri. MMR in all six bacteria shares two general features: 1) repair efficiency is influenced by the neighboring base composition for both transitions and transversions, not limited to transversions as previously reported; and 2) MMR only recognizes indels <4 bp in length. This study demonstrates the power of mutation accumulation lines in quantifying DNA repair and mutagenesis patterns.

A Novel SCN9A Mutation (F826Y) in Primary Erythromelalgia Alters the Excitability of Nav1.7

BACKGROUND

Primary erythromelalgia (PE) is a dominant inherited disorder characterized by recurrent pain, redness, and warmth of the extremities that is caused by gain-of-function mutations in Nav1.7 encoding gene SCN9A. Most of the PE-causing mutations of Nav1.7 have been shown to be able to render Nav1.7-expressing cells hyperexcitable, however in most PE cases the symptoms are refractory to treatment with sodium channel blockers and the mechanism underlying the intractability has not been clearly clarified.

OBJECTIVE

To identify the mutation of SCN9A in a Chinese Han family with typical symptoms of PE and study the electrophysiological effect of the identified mutation.

METHODS

A Chinese Han family with typical symptoms of PE was collected and the proband's response to treatment was recorded. All the exons and flanking intronic sequences of SCN9A were amplified with PCR and sequenced. Several online programs were used to predict the damaging effect of variants. The functional effect of variants was studied by voltage-clamp analysis in CHO-K1 cells.

RESULTS

The PE symptoms of the proband are refractory to all kinds of reported medications. Sequence analysis of SCN9A showed that a novel c.2477T>A (p. F826Y) mutation co-segregated with the disease phenotype. Several online programs predicted that the F826Y mutation has a deleterious effect on the gene product. Voltage-clamp analysis showed that while compared with the wild-type channel, activation of the F826Y mutant channel was shifted by 7.7 mV in a hyperpolarizing direction, whereas steadystate inactivation was shifted by 4.3 mV in a depolarizing direction.

CONCLUSION

A novel disease-causing SCN9A Mutation (F826Y) was identified in a Chinese family with typical PE symptoms refractory to treatment. F826Y of Nav1.7 could render DRG neurons hyperexcitable, contributing to the pathogenesis of PE.

Thermodynamic method for establishment of relationship between icephobicity/superhydrophobicity and microstructure-Based on computing for adhesion work

Superhydrophobic surfaces (SHS) have potential in solving the icing of aircraft, high-voltage overhead transmission lines, and other power network devices exposed to the air. For this reason, we wish to establish the relationship between microstructure and the adhesion work by thermodynamic method, also for analysis of the relationship between the hydrophobicity and icephobicity (or anti-icing). Therefore, respectively considering Cassie-Baxter and Wenzel states, such relationship was theoretically established based on one/two-step surface model, enlightened by natural and artificial SHS. Among it, how to obtain the adhesion work of icing per unit ice-solid interface is the key to this study. Followed by it, hydrothermal experiment, chemical deposition, and etching methods were performed to verify our theoretical results.

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How to model for the SHS based on the natural and artificial SHS;

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Computation for adhesion work (w_aw) per unit area of a water droplet–SHS interface;

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Computation for adhesion work (w_ai) per unit area of a frozen water droplet–SHS interface;

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Computation for reduced adhesion work (w_a2) after icing;

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Hydrothermal experiment, chemical deposition and etching methods were used for validation of modeling.

The earliest human occupation of the high-altitude Tibetan Plateau 40 thousand to 30 thousand years ago

The Tibetan Plateau is the highest and one of the most demanding environments ever inhabited by humans. We investigated the timing and mechanisms of its initial colonization at the Nwya Devu site, located nearly 4600 meters above sea level. This site, dating from 40,000 to 30,000 years ago, is the highest Paleolithic archaeological site yet identified globally. Nwya Devu has yielded an abundant blade tool assemblage, indicating hitherto-unknown capacities for the survival of modern humans who camped in this environment. This site deepens the history of the peopling of the "roof of the world" and the antiquity of human high-altitude occupations more generally.

[Meta-analysis of voice outcomes after steroid injection on benign vocal fold lesions]

Objective:The aim of this study is to perform a meta-analysis of vocal changes after vocal cord steroid injection (VFSI) in the treatment of benign lesions. Method:Pubmed, Embase, CNKI and Wanfang database were searched using the keywords. A total of 7 articles were characterized based on our keyword search. The chi-square-based I² statistic test was employed to assess the between-study heterogeneity. Additionally, random effects models were used to calculate mean differences with 95% confidence intervals. Result:A total of 344 cases were included in 7 literatures. Meta-analysis demonstrated a significant increase in maximal phonation time(MPT) and decrease Jitter after VFSI.The index and amplitude perturbations were not statistically significant before and after hormone injection. Conclusion:Our results support that VFSI has advantages in terms of voice quality. However, we need more studies with longer follow-up periods to validate our findings.