bluuebunny/crossref_metadata_2025 huggingface dataset:
The Birth Prevalence of Spinal Muscular Atrophy: A Population Specific Approach in Estonia
Authors: Sarv Siiri , Kahre Tiina , Vaidla Eve , Pajusalu Sander , Muru Kai , Põder Haide , Gross-Paju Katrin , Ütt Sandra , Žordania Riina , Talvik Inga , Õiglane-Shlik Eve , Muhu Kristina , Õunap Katrin
Published: December 2021

Background: Rare diseases are an important population health issue and many promising therapies have been developed in recent years. In light of novel genetic treatments expected to significantly improve spinal muscular atrophy (SMA) patients’ quality of life and the urgent need for SMA newborn screening (NBS), new epidemiological data were needed to implement SMA NBS in Estonia.

Objective: We aimed to describe the birth prevalence of SMA in the years 1996–2020 and to compare the results with previously published data.

Methods: We retrospectively analyzed clinical and laboratory data of SMA patients referred to the Department of Clinical Genetics of Tartu University Hospital and its branch in Tallinn.

Results: Fifty-seven patients were molecularly diagnosed with SMA. SMA birth prevalence was 1 per 8,286 (95% CI 1 per 6,130–11,494) in Estonia. Patients were classified as SMA type 0 (1.8%), SMA I (43.9%), SMA II (22.8%), SMA III (29.8%), and SMA IV (1.8%). Two patients were compound heterozygotes with an SMN1 deletion in trans with a novel single nucleotide variant NM_000344.3:c.410dup, p.(Asn137Lysfs*11). SMN2 copy number was assessed in 51 patients.

Conclusion: In Estonia, the birth prevalence of SMA is similar to the median birth prevalence in Europe. This study gathered valuable information on the current epidemiology of SMA, which can guide the implementation of spinal muscular atrophy to the newborn screening program in Estonia.
Cadaveric Stem Cells: Their Research Potential and Limitations
Authors: Cieśla Julia , Tomsia Marcin
Published: December 2021

In the era of growing interest in stem cells, the availability of donors for transplantation has become a problem. The isolation of embryonic and fetal cells raises ethical controversies, and the number of adult donors is deficient. Stem cells isolated from deceased donors, known as cadaveric stem cells (CaSCs), may alleviate this problem. So far, it was possible to isolate from deceased donors mesenchymal stem cells (MSCs), adipose delivered stem cells (ADSCs), neural stem cells (NSCs), retinal progenitor cells (RPCs), induced pluripotent stem cells (iPSCs), and hematopoietic stem cells (HSCs). Recent studies have shown that it is possible to collect and use CaSCs from cadavers, even these with an extended postmortem interval (PMI) provided proper storage conditions (like cadaver heparinization or liquid nitrogen storage) are maintained. The presented review summarizes the latest research on CaSCs and their current therapeutic applications. It describes the developments in thanatotranscriptome and scaffolding for cadaver cells, summarizes their potential applications in regenerative medicine, and lists their limitations, such as donor’s unknown medical condition in criminal cases, limited differentiation potential, higher risk of carcinogenesis, or changing DNA quality. Finally, the review underlines the need to develop procedures determining the safe CaSCs harvesting and use.
A Method for Identifying Environmental Stimuli and Genes Responsible for Genotype-by-Environment Interactions From a Large-Scale Multi-Environment Data Set
Authors: Onogi Akio , Sekine Daisuke , Kaga Akito , Nakano Satoshi , Yamada Tetsuya , Yu Jianming , Ninomiya Seishi
Published: December 2021

It has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G × E) interactions, when they occur, and what genes react to them. Large-scale multi-environment data sets are attractive data sources for these purposes because they potentially experienced various environmental conditions. Here we developed a data-driven approach termed Environmental Covariate Search Affecting Genetic Correlations (ECGC) to identify environmental stimuli and genes responsible for the G × E interactions from large-scale multi-environment data sets. ECGC was applied to a soybean (Glycine max) data set that consisted of 25,158 records collected at 52 environments. ECGC illustrated what meteorological factors shaped the G × E interactions in six traits including yield, flowering time, and protein content and when these factors were involved in the interactions. For example, it illustrated the relevance of precipitation around sowing dates and hours of sunshine just before maturity to the interactions observed for yield. Moreover, genome-wide association mapping on the sensitivities to the identified stimuli discovered candidate and known genes responsible for the G × E interactions. Our results demonstrate the capability of data-driven approaches to bring novel insights on the G × E interactions observed in fields.
Proteasome α6 Subunit Negatively Regulates the JAK/STAT Pathway and Blood Cell Activation in Drosophila melanogaster
Authors: Järvelä-Stölting Mirva , Vesala Laura , Maasdorp Matthew K. , Ciantar Joanna , Rämet Mika , Valanne Susanna
Published: December 2021

JAK/STAT signaling regulates central biological functions such as development, cell differentiation and immune responses. In Drosophila, misregulated JAK/STAT signaling in blood cells (hemocytes) induces their aberrant activation. Using mass spectrometry to analyze proteins associated with a negative regulator of the JAK/STAT pathway, and by performing a genome-wide RNAi screen, we identified several components of the proteasome complex as negative regulators of JAK/STAT signaling in Drosophila. A selected proteasome component, Prosα6, was studied further. In S2 cells, Prosα6 silencing decreased the amount of the known negative regulator of the pathway, ET, leading to enhanced expression of a JAK/STAT pathway reporter gene. Silencing of Prosα6 in vivo resulted in activation of the JAK/STAT pathway, leading to the formation of lamellocytes, a specific hemocyte type indicative of hemocyte activation. This hemocyte phenotype could be partially rescued by simultaneous knockdown of either the Drosophila STAT transcription factor, or MAPKK in the JNK-pathway. Our results suggest a role for the proteasome complex components in the JAK/STAT pathway in Drosophila blood cells both in vitro and in vivo.
Protective Effect Against Toxoplasmosis in BALB/c Mice Vaccinated With Recombinant Toxoplasma gondii MIF, CDPK3, and 14-3-3 Protein Cocktail Vaccine
Authors: Liu Fang , Wu Minmin , Wang Jie , Wen Hongyang , An Ran , Cai Haijian , Yu Li , Shen Jilong , Chen Lijian , Du Jian
Published: December 2021

Toxoplasma gondii can infect almost all endotherm organisms including humans and cause life-threatening toxoplasmosis in immunocompromised individuals, which leads to serious public health problems. Developing an excellent vaccine against this disease is impending. In present study, we formulated a cocktail protein vaccine including the TgMIF, TgCDPK3, and Tg14-3-3 proteins, which play critical roles in T. gondii infection. The recombinant protein vaccines were constructed and assessed by vaccination in BALB/c mice. We organized the mice in various protein combination groups of vaccines, and all mice were immunized with corresponding proteins at 0, 2, and 4 weeks. The specific protective effects of the vaccines on mice against T. gondii were analyzed by the mensuration of cytokines, serum antibodies, splenocyte proliferation assay, survival time, and parasite cyst burden of mice after the challenge. The study indicated that mice immunized with all three multicomponent proteins vaccine triggered a strong immune response with highest levels of IFN-γ production and IgG antibody compared with the other two protein combinations and controls. Moreover, there was an increase in IL-4 production and antigen-specific lymphocyte proliferation. The parasite cysts were significantly reduced (resulting in an 82.7% reduction), and survival time was longer in immunized mice with three multicomponent proteins compared with the other groups of mice. The enhanced humoral and cell-mediated immunity indicated that the protein cocktail vaccine containing three antigens provided effective protection for mice. These results indicated that recombinant TgMIF, TgCDPK3, and Tg14-3-3 multicomponent proteins were potential candidates for vaccine against toxoplasmosis.
The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung
Authors: Coppola Mariateresa , Lai Rachel P-J. , Wilkinson Robert J. , Ottenhoff Tom H. M.
Published: December 2021

Mycobacterium tuberculosis (Mtb) genes encoding proteins targeted by vaccines and drugs should be expressed in the lung, the main organ affected by Mtb, for these to be effective. However, the pulmonary expression of most Mtb genes and their proteins remains poorly characterized. The aim of this study is to fill this knowledge gap. We analyzed large scale transcriptomic datasets from specimens of Mtb-infected humans, TB-hypersusceptible (C3H/FeJ) and TB-resistant (C57BL/6J) mice and compared data to in vitro cultured Mtb gene-expression profiles. Results revealed high concordance in the most abundantly in vivo expressed genes between pulmonary Mtb transcriptomes from different datasets and different species. As expected, this contrasted with a lower correlation found with the highest expressed Mtb genes from in vitro datasets. Among the most consistently and highly in vivo expressed genes, 35 have not yet been explored as targets for vaccination or treatment. More than half of these genes are involved in protein synthesis or metabolic pathways. This first lung-oriented multi-study analysis of the in vivo expressed Mtb-transcriptome provides essential data that considerably increase our understanding of pulmonary TB infection biology, and identifies novel molecules for target-based TB-vaccine and drug development.
Menthol Targeting AMPK Alleviates the Inflammatory Response of Bovine Mammary Epithelial Cells and Restores the Synthesis of Milk Fat and Milk Protein
Authors: Liu Songqi , Guo Wenjin , Jia Yuxi , Ye Bojian , Liu Shu , Fu Shoupeng , Liu Juxiong , Hu Guiqiu
Published: December 2021

Mastitis is one of the most serious diseases that causes losses in the dairy industry, seriously impairing milk production and milk quality, and even affecting human health. Menthol is a cyclic monoterpene compound obtained from the stem and leaves of peppermint, which has a variety of biological activities, including anti-inflammatory and antioxidant activity. The purpose of this study was to investigate the preventive effect of menthol on the lipopolysaccharide-induced inflammatory response in primary bovine mammary gland epithelial cells (BMECs) and its anti-inflammatory mechanism. First, BMECs were isolated and amplified from the udders of Holstein cows by enzymatic hydrolysis. BMECs were treated with menthol (10, 50, 100, 200 μM) for 1h, followed by lipopolysaccharide (5μg/ml) for 12 h. Lipopolysaccharide treatment upregulated the protein levels of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (INOS) and the mRNA abundance of tumor necrosis factor α (TNF-α), interleukin-6 (IL-6), and interleukin-1β (IL-1β), while menthol was able to inhibit this effect. The inhibitory effect of menthol on proinflammatory factors was significantly reduced when autophagy was blocked using 3-Methyladenine (5μg/ml), an inhibitor of autophagy. Furthermore, lipopolysaccharide treatment reduced the expression levels of milk lipids and milk proteins, which were inhibited by menthol. In addition, menthol (200 μM) treatment was able to significantly upregulate the expression level of autophagy-related protein LC3B, downregulate the expression level of P62, promote the expression abundance of autophagy-related gene mRNA, and enhance significantly enhance autophagic flux. Interestingly, treatment of BMECs with menthol (200 μM) promoted the phosphorylation of AMP-activated protein kinase (AMPK) and unc-51 like kinase 1 (ULK1) and increased the nuclear localization of nuclear factor-E2 associated factor 2 (Nrf-2). When the AMPK pathway was blocked using compound C (10μg/ml), an inhibitor of AMPK, autophagy was significantly inhibited. Autophagy levels were significantly decreased after blocking the Nrf-2 pathway using ML385 (5μg/ml), an inhibitor of Nrf-2. Overall, the data suggest that menthol activates the AMPK-ULK1 pathway to initiate the onset of autophagy and maintains the level of autophagy through the AMPK-Nrf-2 pathway. In conclusion, the findings suggest that menthol may alleviate the inflammatory response in BMECs via the AMPK/ULK1/Nrf-2/autophagy pathway.
Anti-Interferon Autoantibodies in Adult-Onset Immunodeficiency Syndrome and Severe COVID-19 Infection
Authors: Chen Long-Fang , Yang Cheng-De , Cheng Xiao-Bing
Published: December 2021

Adult-onset immunodeficiency syndrome due to anti-interferon (IFN)-γ autoantibodies has attracted much attention in recent years. It usually occurs in previously healthy people and usually presents as chronic, recurrent, and hard-to-control infections that can be effectively treated with aggressive antibiotic therapy. Adult-onset immunodeficiency syndrome is also referred to as AIDS-like syndrome. Anti-type I IFN (IFN-I) autoantibodies have been reported to play a significant role in the pathogenesis of coronavirus disease 2019 (COVID-19) and preexisting anti-IFN-I autoantibodies are associated with an increased risk of severe COVID-19. This review summarizes the effects of anti-IFN autoantibodies on the susceptibility and severity of various infectious diseases, including SARS-CoV-2 infection. In addition, we discuss the role of anti-IFN autoantibodies in the pathogenesis of autoimmune diseases that are characterized by recurrent infections.
Activin and BMP Signaling Activity Affects Different Aspects of Host Anti-Nematode Immunity in Drosophila melanogaster
Authors: Ozakman Yaprak , Raval Dhaivat , Eleftherianos Ioannis
Published: December 2021

The multifaceted functions ranging from cellular and developmental mechanisms to inflammation and immunity have rendered TGF-ß signaling pathways as critical regulators of conserved biological processes. Recent studies have indicated that this evolutionary conserved signaling pathway among metazoans contributes to the Drosophila melanogaster anti-nematode immune response. However, functional characterization of the interaction between TGF-ß signaling activity and the mechanisms activated by the D. melanogaster immune response against parasitic nematode infection remains unexplored. Also, it is essential to evaluate the precise effect of entomopathogenic nematode parasites on the host immune system by separating them from their mutualistic bacteria. Here, we investigated the participation of the TGF-ß signaling branches, activin and bone morphogenetic protein (BMP), to host immune function against axenic or symbiotic Heterorhabditis bacteriophora nematodes (parasites lacking or containing their mutualistic bacteria, respectively). Using D. melanogaster larvae carrying mutations in the genes coding for the TGF-ß extracellular ligands Daw and Dpp, we analyzed the changes in survival ability, cellular immune response, and phenoloxidase (PO) activity during nematode infection. We show that infection with axenic H. bacteriophora decreases the mortality rate of dpp mutants, but not daw mutants. Following axenic or symbiotic H. bacteriophora infection, both daw and dpp mutants contain only plasmatocytes. We further detect higher levels of Dual oxidase gene expression in dpp mutants upon infection with axenic nematodes and Diptericin and Cecropin gene expression in daw mutants upon infection with symbiotic nematodes compared to controls. Finally, following symbiotic H. bacteriophora infection, daw mutants have higher PO activity relative to controls. Together, our findings reveal that while D. melanogaster Dpp/BMP signaling activity modulates the DUOX/ROS response to axenic H. bacteriophora infection, Daw/activin signaling activity modulates the antimicrobial peptide and melanization responses to axenic H. bacteriophora infection. Results from this study expand our current understanding of the molecular and mechanistic interplay between nematode parasites and the host immune system, and the involvement of TGF-ß signaling branches in this process. Such findings will provide valuable insight on the evolution of the immune role of TGF-ß signaling, which could lead to the development of novel strategies for the effective management of human parasitic nematodes.
Dual Host and Pathogen RNA-Seq Analysis Unravels Chicken Genes Potentially Involved in Resistance to Highly Pathogenic Avian Influenza Virus Infection
Authors: Perlas Albert , Argilaguet Jordi , Bertran Kateri , Sánchez-González Raúl , Nofrarías Miquel , Valle Rosa , Ramis Antonio , Cortey Martí , Majó Natàlia
Published: December 2021

Highly pathogenic avian influenza viruses (HPAIVs) cause severe systemic disease and high mortality rates in chickens, leading to a huge economic impact in the poultry sector. However, some chickens are resistant to the disease. This study aimed at evaluating the mechanisms behind HPAIV disease resistance. Chickens of different breeds were challenged with H7N1 HPAIV or clade 2.3.4.4b H5N8 HPAIV, euthanized at 3 days post-inoculation (dpi), and classified as resistant or susceptible depending on the following criteria: chickens that presented i) clinical signs, ii) histopathological lesions, and iii) presence of HPAIV antigen in tissues were classified as susceptible, while chickens lacking all these criteria were classified as resistant. Once classified, we performed RNA-Seq from lung and spleen samples in order to compare the transcriptomic signatures between resistant and susceptible chickens. We identified minor transcriptomic changes in resistant chickens in contrast with huge alterations observed in susceptible chickens. Interestingly, six differentially expressed genes were downregulated in resistant birds and upregulated in susceptible birds. Some of these genes belong to the NF-kappa B and/or mitogen-activated protein kinase signaling pathways. Among these six genes, the serine protease-encoding gene PLAU was of particular interest, being the most significantly downregulated gene in resistant chickens. Expression levels of this protease were further validated by RT-qPCR in a larger number of experimentally infected chickens. Furthermore, HPAIV quasi-species populations were constructed using 3 dpi oral swabs. No substantial changes were found in the viral segments that interact with the innate immune response and with the host cell receptors, reinforcing the role of the immune system of the host in the clinical outcome. Altogether, our results suggest that an early inactivation of important host genes could prevent an exaggerated immune response and/or viral replication, conferring resistance to HPAIV in chickens.
From the Lab to the Last Mile: Deploying Transgenic Approaches Against Mosquitoes
Authors: St. Leger Raymond J.
Published: December 2021

Ingenious exploitation of transgenic approaches to produce malaria resistant or sterile mosquitoes, or hypervirulent mosquito pathogens, has produced many potential solutions to vector borne diseases. However, in spite of technological feasibility, it has not been determined how well these new methods will work, and how they should be tested and regulated. Some self-limiting transgenic fungal pathogens and mosquitoes are almost field ready, and may be easier to regulate than self-sustaining strategies. However, they require repeat sales and so must show business viability; low-cost mass production is just one of a number of technical constraints that are sometimes treated as an afterthought in technology deployment. No transgenic self-sustaining approach to anopheline control has ever been deployed because of unresolved ethical, social and regulatory issues. These overlapping issues include: 1) the transparency challenge, which requires public discourse, particularly in Africa where releases are proposed, to determine what society is willing to risk given the potential benefits; 2) the transboundary challenge, self-sustaining mosquitoes or pathogens are potentially capable of crossing national boundaries and irreversibly altering ecosystems, and 3) the risk assessment challenge. The polarized debate as to whether these technologies will ever be used to save lives is ongoing; they will founder without a political answer as to how do we interpret the precautionary principle, as exemplified in the Cartagena protocol, in the global context of technological changes.
210Pb-Derived Bioturbation Rates in Sediments Around Seamounts in the Tropical Northwest Pacific
Authors: Lin Feng , Lin Cai , Lin Hui , Sun Xiuwu , Lin Li
Published: December 2021

To evaluate bioturbation coefficients (DB) and mixing depths (L), 210Pb and 226Ra activity was measured in two sediments cores (from water depths of 5,398 m and 4,428 m), which were collected from seamount areas in the Northwest Pacific. Using a steady-state diffusion mode, we estimated DB values of 16.8 and 24.1 cm2/a, higher than those in abyssal sediments and those predicted by traditional empirical equations. Corresponding L values varied between 19.3 and 23.1 cm. These high values indicate that seamounts are the area of active bioturbation. A one-dimensional model for the transport of total organic carbon (TOC) from the surface layer of sediments to the deep layer was developed using the distribution pattern of the specific activity of excess 210Pb (210Pbex) and its relationship with TOC. The model showed that the TOC flux transmitted downward by bioturbation was 0.09 mmol/(cm2⋅a) and 0.12 mmol/(cm2⋅a).
Temporal and Spatial Patterns of Harmful Algae Affecting Scottish Shellfish Aquaculture
Authors: Gianella Fatima , Burrows Michael T. , Swan Sarah C. , Turner Andrew D. , Davidson Keith
Published: December 2021

Consistent patterns of Harmful Algal Bloom (HAB) events are not evident across the scientific literature, suggesting that local or regional variability is likely to be important in modulating any overall trend. This study summarizes Scotland-wide temporal and spatial patterns in a robust 15-year high temporal frequency time series (2006–2020) of the incidence of HABs and shellfish biotoxins in blue Mussels (Mytilus edulis), collected as part of the Food Standards Scotland (FSS) regulatory monitoring program. The relationship between the countrywide annual incidence of HAB events and biotoxins with environmental variables was also explored. Temporal patterns exhibited interannual variability, with no year-on-year increase, nor any correlation between annual occurrences. Within years, there was a summer increase in bloom frequency, peaking in July for Dinophysis spp. and Pseudo-nitzschia spp., and a plateau from May to July for Alexandrium spp. Temporal-spatial patterns were analyzed with multivariate statistics on data from monitoring sites aggregated monthly into 50-km grid cells, using Principal Component Analysis (PCA) and cluster K-means analysis. PCA analyses showed correlation between areas with similar temporal dynamics, identifying seasonality as one of the main elements of HAB variability with temporal-spatial patterns being explained by the first and second principal components. Similar patterns among regions in timing and magnitude of blooms were evaluated using K-means clusters. The analysis confirmed that the highest risk from HABs generally occurred during summer, but demonstrated that areas that respond in a similar manner (high or low risk) are not always geographically close. For example, the occurrence of the most prevalent HAB genus, Dinophysis spp., is similar countrywide, but there is a regional trend in risk level with “very-high” and “high” clusters located primarily on the southwest coast, the islands of the central and northern west coast and the Shetland Islands. “Early” and “late” blooms were also associated with certain areas and level of risk. Overall, high risk areas mainly face in a southwest direction, whilst low risk locations face a south or southeast direction. We found relatively few countrywide relationships between environmental variables and HABs, confirming the need for regional analysis to support HAB early warning.
COVID-19 Generated Personal Protective Equipment: Sources of Microplastics and Pathogen Vectors in Marine Environments?
Authors: Noman Md Abu , Sun Jun , Hossain Mohammad Belal
Published: December 2021

The world has already experienced the severe adverse effects of COVID-19 at every level. When it became understood that the COVID-19 infection is spread in the community via respiratory transmission from humans, then the widespread use of plastic-made personal protective equipments (PPEs) like face masks and hand gloves tremendously increased throughout the world. Although it has reduced the spreading of virus, however, careless disposal or mismanagement of these single use PPEs has created another major concern for the environment, as plastics are a known source of environmental contamination. On one hand, they are infected with SARS-CoV-2, while on the other, they act as a carrier or vector or pathway for other pathogens or diseases, and hence can increase the degree of continuing the pandemic. Besides, there might be a chance that plastics or microplastics may be responsible for introducing new pathogenic viruses or bacteria to humankind. As such, it is clear that more research needs to be conducted to clarify this fact, and its underlying mechanisms. In this review, we briefly explored how PPE used in the COVID-19 pandemic aggravated existing microplastic pollution, how they could act as disease routes or vectors, and how they could introduce new pathogens to the terrestrial and marine environment. Addressing these questions may create awareness of plastic use, waste management, and enact relevant policy which may protect our environment and health.
Priming With Red Blood Cells Allows Red Blood Cell Exchange for Sickle Cell Disease in Low-Weight Children
Authors: Hequet Olivier , Boisson Camille , Joly Philippe , Revesz Daniela , Kebaili Kamila , Gauthier Alexandra , Renoux Celine , Creppy Severine , Nader Elie , Nicolas Jean François , Berard Frédéric , Cognasse Fabrice , Vocanson Marc , Bertrand Yves , Connes Philippe
Published: December 2021

Red blood cell exchanges are frequently used to treat and prevent cerebrovascular complications in patients with sickle cell anemia (SCA). However, the low weight of young children represents serious concerns for this procedure. The Spectra Optia device can perform automatic priming using red blood cells (RBCs) (RCE/RBC-primed) which could allow RBC exchanges (RCE) to be performed in young children without hypovolemic complications, but this method requires evaluation. We prospectively analyzed the clinical safety of the RCE/RBC-primed procedure in 12 SCA low-weight children under either a chronic RCE program or emergency treatment over 65 sessions. We monitored grade 2 adverse events (AEs) such as a decrease in blood pressure, increase in heart rate, fainting sensation, or transfusion reactions and identified the critical times during the sessions in which AEs could occur. Post-apheresis hematocrit (Hct) and a fraction of cell remaining (FCR) values were compared to the expected values. We also compared the impact of automatic RCE (n = 7) vs. RCE/RBC-primed (n = 8) on blood viscosity and RBC rheology. A low incidence of complications was observed in the 65 RCE sessions with only seven episodes of transient grade 2 AEs. Post-apheresis Hct and FCR reached expected values with the RCE/RBC-primed method. Both the automatic and priming procedures improved RBC deformability and decreased the sickling tendency during deoxygenation. Blood rheological features improved in both RCE/RBC-primed and automatic RCE without priming conditions. The RCE/RBC-primed procedure provides blood rheological benefits, and is safe and efficient to treat, notably in young children with SCA in prophylactic programs or curatively when a SCA complication occurs.
Solid Fuel Exposure and Chronic Obstructive Pulmonary Disease in Never-Smokers
Authors: Long HuanYu , Xing ZhenZhen , Chai Di , Liu WeiMing , Tong YaQi , Wang YuXia , Ma YaLi , Pan MingMing , Cui Jia , Guo YanFei
Published: December 2021

Background: Chronic obstructive pulmonary disease (COPD) is a public health challenge globally. The burden of COPD is high in never-smokers but little is known about its causes. We aimed to find the prevalence and correlates of COPD in never-smokers, with a special focus on solid fuel exposure.

Methods: We conducted a cross-sectional study in Western China. COPD was defined by FEV1/FVC < lower limits of normal (LLN). Descriptive statistics and multivariable logistic regression were used for analyses.

Results: Six thousand two hundred and seventy one patients were enrolled between June 2015 and August 2016. The prevalence of COPD in never-smokers was 15.0% (95% confidence interval 14.1–15.9). The common independent predictors of COPD in never-smokers included age ≥60 years, exposure to solid fuel, living in a rural area and a history of tuberculosis. Participants with solid fuel exposure were 69% more likely to have COPD (adjusted odds ratio 1.69, 95% CI 1.41–2.04) than those without such exposure. In addition, we found a positive association between small airway dysfunction and solid fuel exposure (OR 1.35, 95% CI 1.18–1.53).

Conclusions: This study confirmed the substantial burden of COPD among never-smokers and also defined the risk factors for COPD in never-smokers. Furthermore, we found a positive association between solid fuel exposure and COPD or small airway dysfunction.
Development of a Droplet Digital Polymerase Chain Reaction for Sensitive Detection of Pneumocystis jirovecii in Respiratory Tract Specimens
Authors: Yi Jie , Wang Nan , Wu Jie , Tang Yueming , Zhang Jingjia , Zhu Lingxiang , Rui Xiao , Guo Yong , Xu Yingchun
Published: December 2021

Background:Pneumocystis jirovecii is a human-specific opportunistic fungus that causes Pneumocystis pneumonia (PCP), a life-threatening opportunistic lung infection that affects immunocompromised patients. P. jirovecii colonization may be linked to the transmission of the infection. The detection of P. jirovecii in immunocompromised patients is thus especially important. The low fungal load and the presence of PCR inhibitors limit the usefulness of quantitative PCR (qPCR) for accurate absolute quantification of P. jirovecii in specimens. Droplet digital PCR (ddPCR), however, presents a methodology that allows higher sensitivity and accuracy. Here, we developed a ddPCR method for detecting P. jirovecii DNA in respiratory specimens, and evaluated its sensitivity against qPCR.

Materials and Methods: One bronchoalveolar fluid (BALF) sample each was collected from 82 patients with potential PCP to test the presence of P. jirovecii DNA using both ddPCR and qPCR, and samples with inconsistent results between the two methods were further tested by metagenomic next generation sequencing (mNGS). In addition, 37 sputum samples from 16 patients diagnosed with PCP, as well as continuous respiratory tract specimens from nine patients with PCP and treated with sulfonamides, were also collected for P. jirovecii DNA testing using both ddPCR and qPCR.

Results: ddPCR and qPCR gave the same results for 95.12% (78/82) of the BALF samples. The remaining four specimens tested positive using ddPCR but negative using qPCR, and they were found to be positive by mNGS. Detection results of 78.37% (29/37) sputum samples were consistent between ddPCR and qPCR, while the other eight samples tested positive using ddPCR but negative using qPCR. The P. jirovecii load of patients with PCP decreased to undetectable levels after treatment according to qPCR, but P. jirovecii was still detectable using ddPCR.

Conclusions: ddPCR was more sensitive than qPCR, especially at detecting low-pathogen-load P. jirovecii. Thus, ddPCR represents a useful, viable, and reliable alternative to qPCR in P. jirovecii testing in patients with immunodeficiency.
Urine β2-Microglobulin and Retinol-Binding Protein and Renal Disease Progression in IgA Nephropathy
Authors: Shen Xiaoqi , Cheng Jun , Yu Guizhen , Li Xiayu , Li Heng , Chen Jianghua
Published: December 2021

Background: Tubulointerstitial involvement has been reported to have a decisive influence on the progression of IgA nephropathy (IgAN). High levels of urine β2-microglobulin (β2-MG) and retinol-binding protein (RBP) were observed in patients with IgAN with tubulointerstitial lesions. However, their roles in disease progression remain unclear. This study aimed to evaluate the associations of urine β2-MG and RBP with the progression of IgAN.

Methods: We retrospectively investigated a cohort of 2,153 patients with IgAN. Clinical and pathological features, outcomes, and urine β2-MG, and RBP at the time of biopsy were collected. The associations, of urine β2-MG and RBP with the composite renal outcome, defined as a decline in estimated glomerular filtration rate (eGFR) of ≥50% from baseline or end-stage renal disease (ESRD), were examined using restricted cubic splines and the Cox proportional hazards models.

Results: During a median follow-up of 20.40 months, 140 (6.50%) patients reached the composite renal outcomes. Restricted cubic splines showed that patients with higher urinary β2-MG and RBP levels had worse renal outcomes. The Cox regression analysis revealed that urine β2-MG and RBP were associated with a risk of the composite renal outcome in the multivariate adjusted model [+1 SD for log β2-MG, hazard ratio (HR) = 1.462, 95% CI: 1.136–1.882, p = 0.003; +1 SD for log RBP, HR = 1.972, 95% CI: 1.486–2.617, p = 0.001]. The associations were detectable within patients with baseline eGFR <90 ml/min/1.73 m2 (+1 SD for log β2-MG, HR = 1.657, 95% CI: 1.260–2.180, p < 0.001; +1 SD for log RBP, HR = 1.618, 95% CI: 1.199–2.183, p = 0.002), but not among patients with eGFR ≥90 ml/min/1.73 m2.

Conclusion: Higher levels of urine β2-MG and RBP were independent risk factors for renal disease progression in IgAN.
Vascular Remodeling in Pulmonary Arterial Hypertension: The Potential Involvement of Innate and Adaptive Immunity
Authors: Tobal Rachid , Potjewijd Judith , Empel Vanessa P. M. van , Ysermans Renee , Schurgers Leon J. , Reutelingsperger Chris P. , Damoiseaux Jan G. M. C. , Paassen Pieter van
Published: December 2021

Pulmonary arterial hypertension (PAH) is a severe disease with high morbidity and mortality. Current therapies are mainly focused on vasodilative agents to improve prognosis. However, recent literature has shown the important interaction between immune cells and stromal vascular cells in the pathogenic modifications of the pulmonary vasculature. The immunological pathogenesis of PAH is known as a complex interplay between immune cells and vascular stromal cells, via direct contacts and/or their production of extra-cellular/diffusible factors such as cytokines, chemokines, and growth factors. These include, the B-cell—mast-cell axis, endothelium mediated fibroblast activation and subsequent M2 macrophage polarization, anti-endothelial cell antibodies and the versatile role of IL-6 on vascular cells. This review aims to outline the major pathophysiological changes in vascular cells caused by immunological mechanisms, leading to vascular remodeling, increased pulmonary vascular resistance and eventually PAH. Considering the underlying immunological mechanisms, these mechanisms may be key to halt progression of disease.
Duclauxin Derivatives From Fungi and Their Biological Activities
Authors: Shahid Hamza , Cai Teng , Wang Yuyang , Zheng Caiqing , Yang Yuting , Mao Ziling , Ding Ping , Shan Tijiang
Published: December 2021

Duclauxin is a heptacyclic oligophenalenone dimer consisting of an isocoumarin and a dihydroisocoumarin unit. These two tricyclic moieties are joined by a cyclopentane ring to form a unique hinge or castanets-like structure. Duclauxin is effective against numerous tumor cell lines because it prevents adenosine triphosphate (ATP) synthesis by inhibiting mitochondrial respiration. There are about 36 reported natural duclauxin analogs mainly produced by 9 Penicillium and Talaromyces species (T. duclauxii, T. aculeatus, T. stipitatus, T. bacillisporus, T. verruculosus, T. macrosporus, P. herquei, P. manginii, and Talaromyces sp.). These metabolites exhibit remarkable biological activities, including antitumor, enzyme inhibition, and antimicrobial, showing tremendous potential in agricultural and medical applications. This review highlights the chemical structures and biological activities of fungal duclauxins, together with biosynthesis, absolute configuration, and mode of action for important duclauxins. Furthermore, phylogenetic analysis and correct names of Penicillium and Talaromyces species producing duclauxins are presented in this review.
Single-Molecule RNA Sequencing Reveals IFNγ-Induced Differential Expression of Immune Escape Genes in Merkel Cell Polyomavirus–Positive MCC Cell Lines
Authors: Sauerer Tatjana , Lischer Christopher , Weich Adrian , Berking Carola , Vera Julio , Dörrie Jan
Published: December 2021

Merkel cell carcinoma (MCC) is a rare and highly aggressive cancer, which is mainly caused by genomic integration of the Merkel cell polyomavirus and subsequent expression of a truncated form of its large T antigen. The resulting primary tumor is known to be immunogenic and under constant pressure to escape immune surveillance. Because interferon gamma (IFNγ), a key player of immune response, is secreted by many immune effector cells and has been shown to exert both anti-tumoral and pro-tumoral effects, we studied the transcriptomic response of MCC cells to IFNγ. In particular, immune modulatory effects that may help the tumor evade immune surveillance were of high interest to our investigation. The effect of IFNγ treatment on the transcriptomic program of three MCC cell lines (WaGa, MKL-1, and MKL-2) was analyzed using single-molecule sequencingviathe Oxford Nanopore platform. A significant differential expression of several genes was detected across all three cell lines. Subsequent pathway analysis and manual annotation showed a clear upregulation of genes involved in the immune escape of tumor due to IFNγ treatment. The analysis of selected genes on protein level underlined our sequencing results. These findings contribute to a better understanding of immune escape of MCC and may help in clinical treatment of MCC patients. Furthermore, we demonstrate that single-molecule sequencing can be used to assess characteristics of large eukaryotic transcriptomes and thus contribute to a broader access to sequencing data in the community due to its low cost of entry.
Methylation of SDC2/TFPI2 and Its Diagnostic Value in Colorectal Tumorous Lesions
Authors: Zhang Lianglu , Dong Lanlan , Lu Changming , Huang Wenxian , Yang Cuiping , Wang Qian , Wang Qian , Lei Ruixue , Sun Rui , Wan Kangkang , Li Tingting , Sun Fan , Gan Tian , Lin Jun , Yin Lei
Published: December 2021

Background:SDC2 methylation is a feasible biomarker for colorectal cancer detection. Its specificity for colorectal cancer is higher than 90%, but the sensitivity is normally lower than 90%. This study aims to improve the sensitivity of SDC2 detection through finding a high positive target from the false-negative samples of SDC2 detection based on analysis of the bowel subsite difference in methylation.

Methods: Hypermethylated TFPI2 was identified in SDC2 hypomethylated colorectal cancer samples retrieved from TCGA database with the methylation level lower than 0.2. The methylation-specific PCR assay was developed and then evaluated using tissue samples (184 cancer and 54 healthy control samples) and stool samples (289 cancer, 190 adenoma, and 217 healthy control samples).

Results:TFPI2 was hypermethylated in most SDC2 hypomethylated colorectal cancer samples. When the SDC2/TFPI2-combined PCR assay was performed in stool specimens, the AUC value of cancer vs. control was 0.98, with the specificity of 96.40% and sensitivity of 96.60%, and the AUC value of adenoma vs. control was 0.87, with the specificity of 95.70% and the sensitivity of 80.00%. The improvement in sensitivity was the most momentous in the left colon. As the detection index, the Ct value was better in improving the sensitivity of detection than the methylation level based on the 2−ΔΔCt value.

Conclusion:TFPI2 can improve the sensitivity of SDC2 methylation–specific detection of colorectal tumorous lesions while maintaining high specificity, in particular reducing the missed detection of left colon cancer and adenoma.
Degradation of Components of the Lpt Transenvelope Machinery Reveals LPS-Dependent Lpt Complex Stability in Escherichia coli
Authors: Martorana Alessandra M. , Moura Elisabete C. C. M. , Sperandeo Paola , Di Vincenzo Flavia , Liang Xiaofei , Toone Eric , Zhou Pei , Polissi Alessandra
Published: December 2021

Lipopolysaccharide (LPS) is a peculiar component of the outer membrane (OM) of many Gram-negative bacteria that renders these bacteria highly impermeable to many toxic molecules, including antibiotics. LPS is assembled at the OM by a dedicated intermembrane transport system, the Lpt (LPS transport) machinery, composed of seven essential proteins located in the inner membrane (IM) (LptB2CFG), periplasm (LptA), and OM (LptDE). Defects in LPS transport compromise LPS insertion and assembly at the OM and result in an overall modification of the cell envelope and its permeability barrier properties. LptA is a key component of the Lpt machine. It connects the IM and OM sub-complexes by interacting with the IM protein LptC and the OM protein LptD, thus enabling the LPS transport across the periplasm. Defects in Lpt system assembly result in LptA degradation whose stability can be considered a marker of an improperly assembled Lpt system. Indeed, LptA recruitment by its IM and OM docking sites requires correct maturation of the LptB2CFG and LptDE sub-complexes, respectively. These quality control checkpoints are crucial to avoid LPS mistargeting. To further dissect the requirements for the complete Lpt transenvelope bridge assembly, we explored the importance of LPS presence by blocking its synthesis using an inhibitor compound. Here, we found that the interruption of LPS synthesis results in the degradation of both LptA and LptD, suggesting that, in the absence of the LPS substrate, the stability of the Lpt complex is compromised. Under these conditions, DegP, a major chaperone–protease in Escherichia coli, is responsible for LptD but not LptA degradation. Importantly, LptD and LptA stability is not affected by stressors disturbing the integrity of LPS or peptidoglycan layers, further supporting the notion that the LPS substrate is fundamental to keeping the Lpt transenvelope complex assembled and that LptA and LptD play a major role in the stability of the Lpt system.
Gut-Brain Axis: Possible Role of Gut Microbiota in Perioperative Neurocognitive Disorders
Authors: Wang Xiao-qing , Li He , Li Xiang-nan , Yuan Cong-hu , Zhao Hang
Published: December 2021

Aging is becoming a severe social phenomenon globally, and the improvements in health care and increased health awareness among the elderly have led to a dramatic increase in the number of surgical procedures. Because of the degenerative changes in the brain structure and function in the elderly, the incidence of perioperative neurocognitive disorders (PND) is much higher in elderly patients than in young people following anesthesia/surgery. PND is attracting more and more attention, though the exact mechanisms remain unknown. A growing body of evidence has shown that the gut microbiota is likely involved. Recent studies have indicated that the gut microbiota may affect postoperative cognitive function via the gut-brain axis. Nonetheless, understanding of the mechanistic associations between the gut microbiota and the brain during PND progression remains very limited. In this review, we begin by providing an overview of the latest progress concerning the gut-brain axis and PND, and then we summarize the influence of perioperative factors on the gut microbiota. Next, we review the literature on the relationship between gut microbiota and PND and discuss how gut microbiota affects cognitive function during the perioperative period. Finally, we explore effective early interventions for PND to provide new ideas for related clinical research.
Inhibitory Control in the Absence of Awareness: Interactions Between Frontal and Motor Cortex Oscillations Mediate Implicitly Learned Responses
Authors: Isabella Silvia L. , Cheyne J. Allan , Cheyne Douglas
Published: December 2021

Cognitive control of action is associated with conscious effort and is hypothesised to be reflected by increased frontal theta activity. However, the functional role of these increases in theta power, and how they contribute to cognitive control remains unknown. We conducted an MEG study to test the hypothesis that frontal theta oscillations interact with sensorimotor signals in order to produce controlled behaviour, and that the strength of these interactions will vary with the amount of control required. We measured neuromagnetic activity in 16 healthy adults performing a response inhibition (Go/Switch) task, known from previous work to modulate cognitive control requirements using hidden patterns of Go and Switch cues. Learning was confirmed by reduced reaction times (RT) to patterned compared to random Switch cues. Concurrent measures of pupil diameter revealed changes in subjective cognitive effort with stimulus probability, even in the absence of measurable behavioural differences, revealing instances of covert variations in cognitive effort. Significant theta oscillations were found in five frontal brain regions, with theta power in the right middle frontal and right premotor cortices parametrically increasing with cognitive effort. Similar increases in oscillatory power were also observed in motor cortical gamma, suggesting an interaction. Right middle frontal and right precentral theta activity predicted changes in pupil diameter across all experimental conditions, demonstrating a close relationship between frontal theta increases and cognitive control. Although no theta-gamma cross-frequency coupling was found, long-range theta phase coherence among the five significant sources between bilateral middle frontal, right inferior frontal, and bilateral premotor areas was found, thus providing a mechanism for the relay of cognitive control between frontal and motor areas via theta signalling. Furthermore, this provides the first evidence for the sensitivity of frontal theta oscillations to implicit motor learning and its effects on cognitive load. More generally these results present a possible a mechanism for this frontal theta network to coordinate response preparation, inhibition and execution.