bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA Repair Gene Polymorphisms and Chromosomal Aberrations in Exposed Populations
Authors: Niazi Yasmeen , Thomsen Hauke , Smolkova Bozena , Vodickova Ludmila , Vodenkova Sona , Kroupa Michal , Vymetalkova Veronika , Kazimirova Alena , Barancokova Magdalena , Volkovova Katarina , Staruchova Marta , Hoffmann Per , Nöthen Markus M. , Dusinska Maria , Musak Ludovit , Vodicka Pavel , Hemminki Kari , Försti Asta
Published: June 2021

DNA damage and unrepaired or insufficiently repaired DNA double-strand breaks as well as telomere shortening contribute to the formation of structural chromosomal aberrations (CAs). Non-specific CAs have been used in the monitoring of individuals exposed to potential carcinogenic chemicals and radiation. The frequency of CAs in peripheral blood lymphocytes (PBLs) has been associated with cancer risk and the association has also been found in incident cancer patients. CAs include chromosome-type aberrations (CSAs) and chromatid-type aberrations (CTAs) and their sum CAtot. In the present study, we used data from our published genome-wide association studies (GWASs) and extracted the results for 153 DNA repair genes for 607 persons who had occupational exposure to diverse harmful substances/radiation and/or personal exposure to tobacco smoking. The analyses were conducted using linear and logistic regression models to study the association of DNA repair gene polymorphisms with CAs. Considering an arbitrary cutoff level of 5 × 10–3, 14 loci passed the threshold, and included 7 repair pathways for CTA, 4 for CSA, and 3 for CAtot; 10 SNPs were eQTLs influencing the expression of the target repair gene. For the base excision repair pathway, the implicated genes PARP1 and PARP2 encode poly(ADP-ribosyl) transferases with multiple regulatory functions. PARP1 and PARP2 have an important role in maintaining genome stability through diverse mechanisms. Other candidate genes with known roles for CSAs included GTF2H (general transcription factor IIH subunits 4 and 5), Fanconi anemia pathway genes, and PMS2, a mismatch repair gene. The present results suggest pathways with mechanistic rationale for the formation of CAs and emphasize the need to further develop techniques for measuring individual sensitivity to genotoxic exposure.
Immune Tolerance-Adjusted Personalized Immunogenicity Prediction for Pompe Disease
Authors: De Groot Anne S. , Desai Ankit K. , Lelias Sandra , Miah S. M. Shahjahan , Terry Frances E. , Khan Sundos , Li Cindy , Yi John S. , Ardito Matt , Martin William D. , Kishnani Priya S.
Published: June 2021

Infantile-onset Pompe disease (IOPD) is a glycogen storage disease caused by a deficiency of acid alpha-glucosidase (GAA). Treatment with recombinant human GAA (rhGAA, alglucosidase alfa) enzyme replacement therapy (ERT) significantly improves clinical outcomes; however, many IOPD children treated with rhGAA develop anti-drug antibodies (ADA) that render the therapy ineffective. Antibodies to rhGAA are driven by T cell responses to sequences in rhGAA that differ from the individuals’ nativeGAA(nGAA). The goal of this study was to develop a tool forpersonalizedimmunogenicity riskassessment (PIMA) that quantifies T cell epitopes that differ between nGAA and rhGAA using information about an individual’s native GAA gene and their HLA DR haplotype, and to use this information to predict the risk of developing ADA. Four versions of PIMA have been developed. They use EpiMatrix, a computational tool for T cell epitope identification, combined with an HLA-restricted epitope-specific scoring feature (iTEM), to assess ADA risk. One version of PIMA also integrates JanusMatrix, a Treg epitope prediction tool to identify putative immunomodulatory (regulatory) T cell epitopes in self-proteins. Using the JanusMatrix-adjusted version of PIMA in a logistic regression model with data from 48 cross-reactive immunological material (CRIM)-positive IOPD subjects, those with scores greater than 10 were 4-fold more likely to develop ADA (p<0.03) than those that had scores less than 10. We also confirmed the hypothesis that some GAA epitopes are immunomodulatory. Twenty-one epitopes were tested, of which four were determined to have an immunomodulatory effect on T effector responsein vitro. The implementation of PIMA V3J on a secure-access website would allow clinicians to input the individual HLA DR haplotype of their IOPD patient and the GAA pathogenic variants associated with each GAA allele to calculate the patient’s relative risk of developing ADA, enhancing clinical decision-making prior to initiating treatment with ERT. A better understanding of immunogenicity risk will allow the implementation of targeted immunomodulatory approaches in ERT-naïve settings, especially in CRIM-positive patients, which may in turn improve the overall clinical outcomes by minimizing the development of ADA. The PIMA approach may also be useful for other types of enzyme or factor replacement therapies.
High Antibodies to VAR2CSA in Response to Malaria Infection Are Associated With Improved Birthweight in a Longitudinal Study of Pregnant Women
Authors: McLean Alistair R. D. , Opi D. Herbert , Stanisic Danielle I. , Cutts Julia C. , Feng Gaoqian , Ura Alice , Mueller Ivo , Rogerson Stephen J. , Beeson James G. , Fowkes Freya J. I.
Published: June 2021

Introduction

Pregnant women have an increased risk of P. falciparum infection, which is associated with low birth weight and preterm delivery. VAR2CSA, a variant surface antigen expressed on the parasitized erythrocyte surface, enables sequestration in the placenta. Few studies have prospectively examined relationships between antibody responses during pregnancy and subsequent adverse birth outcomes, and there are limited data outside Africa.

Methods

Levels of IgG against VAR2CSA domains (DBL3; DBL5) and a VAR2CSA-expressing placental-binding P. falciparum isolate (PfCS2-IE) were measured in 301 women enrolled at their first visit to antenatal care which occurred mid-pregnancy (median = 26 weeks, lower and upper quartiles = 22, 28). Associations between antibody levels at enrolment and placental infection, birthweight and estimated gestational age at delivery were assessed by linear and logistic regression with adjustment for confounders. For all outcomes, effect modification by gravidity and peripheral blood P. falciparum infection at enrolment was assessed.

Results

Among women who had acquired P. falciparum infection at enrolment, those with higher levels of VAR2CSA antibodies (75th percentile) had infants with higher mean birthweight (estimates varied from +35g to +149g depending on antibody response) and reduced adjusted odds of placental infection (aOR estimates varied from 0.17 to 0.80), relative to women with lower levels (25th percentile) of VAR2CSA antibodies. However, among women who had not acquired an infection at enrolment, higher VAR2CSA antibodies were associated with increased odds of placental infection (aOR estimates varied from 1.10 to 2.24).

Conclusions

When infected by mid-pregnancy, a better immune response to VAR2CSA-expressing parasites may contribute to protecting against adverse pregnancy outcomes.
Significance of PD1 Alternative Splicing in Celiac Disease as a Novel Source for Diagnostic and Therapeutic Target
Authors: Ponce de León Candelaria , Lorite Pedro , López-Casado Miguel Ángel , Barro Francisco , Palomeque Teresa , Torres María Isabel
Published: June 2021

Background

We have focused on the alteration of the PD-1/PD-L1 pathway in celiac disease and discussed the roles of the PD1 pathway in regulating the immune response. We explored the idea that the altered mRNA splicing process in key regulatory proteins could represent a novel source to identify diagnostic, prognostic, and therapeutic targets in celiac disease.

Methods

We characterized the PD1 mRNA variants’ profile in CD patients and in response to gluten peptides’ incubation after in vitro experiments. Total RNA from whole blood was isolated, and the coding region of the human PD-1 mRNA was amplified by cDNA PCR.

Results

PCR amplification of the human PD-1 coding sequence revealed an association between the over-expression of the sPD-1 protein and the PD-1Δex3 transcript in celiac disease. Thus, we have found three novel alternative spliced isoforms, two of which result in a truncated protein and the other isoform with a loss of 14 aa of exon 2 and complete exon 3 (Δ3) which could encode a new soluble form of PD1 (sPD-1).

Conclusions

Our study provides evidence that dietary gluten can modulate processes required for cell homeostasis through the splicing of pre-mRNAs encoding key regulatory proteins, which represents an adaptive mechanism in response to different nutritional conditions.
Regulatory T Cells Increase After rh-MOG Stimulation in Non-Relapsing but Decrease in Relapsing MOG Antibody-Associated Disease at Onset in Children
Authors: Horellou Philippe , de Chalus Aliénor , Giorgi Laetitia , Leroy Carole , Chrétien Pascale , Hacein-Bey-Abina Salima , Bourgeois Christine , Mariette Xavier , Serguera Ché , Le Grand Roger , Deiva Kumaran
Published: June 2021

Background

Myelin oligodendrocytes glycoprotein (MOG) antibody-associated disease (MOGAD) represent 25% of pediatric acquired demyelinating syndrome (ADS); 40% of them may relapse, mimicking multiple sclerosis (MS), a recurrent and neurodegenerative ADS, which is MOG-Abs negative.

Aims

To identify MOG antigenic immunological response differences between MOGAD, MS and control patients, and between relapsing versus non-relapsing subgroups of MOGAD.

Methods

Three groups of patients were selected: MOGAD (n=12 among which 5 relapsing (MOGR) and 7 non-relapsing (MOGNR)), MS (n=10) and control patients (n=7). Peripheral blood mononuclear cells (PBMC) collected at the time of the first demyelinating event were cultured for 48 h with recombinant human (rh)-MOG protein (10 μg/ml) for a specific stimulation or without stimulation as a negative control. The T cells immunophenotypes were analyzed by flow cytometry. CD4+ T cells, T helper (Th) cells including Th1, Th2, and Th17 were analyzed by intracellular staining of cytokines. Regulatory T cells (Tregs, Foxp3+), CD45RA-Foxp3+ Tregs and subpopulation naive Tregs (CD45RA+Foxp3int), effector Tregs (CD45RA-Foxp3high) and non-suppressive Tregs (CD45RA-Foxp3int) proportions were determined.

Results

The mean onset age of each group, ranging from 9.9 to 13.8, and sex ratio, were similar between MOGR, MOGNR, MS and control patients as analyzed by one-way ANOVA and Chi-square test. When comparing unstimulated to rh-MOG stimulated T cells, a significant increase in the proportion of Th2 and Th17 cells was observed in MOGAD. Increase of Th17 cells was significant in MOGNR (means: 0.63 ± 0.15 vs. 1.36 ± 0.43; Wilcoxon-test p = 0.03) but not in MOGR. CD4+ Tregs were significantly increased in MOGNR (means: 3.51 ± 0.7 vs. 4.59 ± 1.33; Wilcoxon-test p = 0.046) while they decreased in MOGR. CD45RA-Foxp3+ Tregs were significantly decreased in MOGR (means: 2.37 ± 0.23 vs. 1.99 ± 0.17; paired t-test p = 0.021), but not in MOGNR. MOGR showed the highest ratio of effector Tregs/non suppressive-Tregs, which was significantly higher than in MOGNR.

Conclusions

Our findings suggest that CD4+ Th2 and Th17 cells are involved in the pathophysiology of MOGAD in children. The opposite response of Tregs to rh-MOG in MOGNR, where CD4+ Tregs increased, and in MOGR, where CD45RA-Foxp3+ Tregs decreased, suggests a probable loss of tolerance toward MOG autoantigen in MOGR which may explain relapses in this recurrent pediatric autoimmune disease.
Endogenous Fructose Metabolism Could Explain the Warburg Effect and the Protection of SGLT2 Inhibitors in Chronic Kidney Disease
Authors: Nakagawa Takahiko , Sanchez-Lozada Laura G. , Andres-Hernando Ana , Kojima Hideto , Kasahara Masato , Rodriguez-Iturbe Bernardo , Bjornstad Petter , Lanaspa Miguel A. , Johnson Richard J.
Published: June 2021

Chronic low-grade inflammation underlies the pathogenesis of non-communicable diseases, including chronic kidney diseases (CKD). Inflammation is a biologically active process accompanied with biochemical changes involving energy, amino acid, lipid and nucleotides. Recently, glycolysis has been observed to be increased in several inflammatory disorders, including several types of kidney disease. However, the factors initiating glycolysis remains unclear. Added sugars containing fructose are present in nearly 70 percent of processed foods and have been implicated in the etiology of many non-communicable diseases. In the kidney, fructose is transported into the proximal tubules via several transporters to mediate pathophysiological processes. Fructose can be generated in the kidney during glucose reabsorption (such as in diabetes) as well as from intra-renal hypoxia that occurs in CKD. Fructose metabolism also provides biosynthetic precursors for inflammation by switching the intracellular metabolic profile from mitochondrial oxidative phosphorylation to glycolysis despite the availability of oxygen, which is similar to the Warburg effect in cancer. Importantly, uric acid, a byproduct of fructose metabolism, likely plays a key role in favoring glycolysis by stimulating inflammation and suppressing aconitase in the tricarboxylic acid cycle. A consequent accumulation of glycolytic intermediates connects to the production of biosynthetic precursors, proteins, lipids, and nucleic acids, to meet the increased energy demand for the local inflammation. Here, we discuss the possibility of fructose and uric acid may mediate a metabolic switch toward glycolysis in CKD. We also suggest that sodium-glucose cotransporter 2 (SGLT2) inhibitors may slow the progression of CKD by reducing intrarenal glucose, and subsequently fructose levels.
Dynamical Downscaling of Coastal Dynamics for Two Extreme Storm Surge Events in Japan
Authors: Trošelj Joško , Ninomiya Junichi , Takewaka Satoshi , Mori Nobuhito
Published: June 2021

Graphical Abstract

Study domains and model setup (up-left), Sea Surface Height results validation (up-right), Sea Surface Salinity results validation (down-left) and impact of the two storm surge events to the associated coastal dynamics variables (down-right).
The Sargasso Sea Commission: An Evolving New Paradigm for High Seas Ecosystem Governance?
Authors: Freestone David
Published: June 2021

The Sargasso Sea is to be found within the North Atlantic Subtropical Gyre. Its borders are the major ocean currents. These boundaries shift with these currents, but there is a core area that covers approximately 2 million square nautical miles situated around the Bermuda archipelago, the majority of which is beyond the national jurisdiction of any State. Ten governments have now signed the 2014 Hamilton Declaration on Collaboration for the Conservation of the Sargasso Sea, which mandated the Government of Bermuda to appoint the members of the Sargasso Sea Commission—the first such body to take on a stewardship role for a high seas ecosystem. The Commission has committed to working with the existing international organizations with jurisdictional competences over a myriad of high seas activities. This paper will examine the work of the Commission and lessons learned over the past decade; it will discuss its possible role as a “boundary spanning” organization and look forward to its future in the light of recent grants from the Global Environment Facility (GEF) and the Fonds Francais pour l’Environnement Mondial (FFEM).
Indirect Impacts of COVID-19 on a Tropical Lobster Fishery’s Harvest Strategy and Supply Chain
Authors: Plagányi Éva , Deng Roy Aijun , Tonks Mark , Murphy Nicole , Pascoe Sean , Edgar Steven , Salee Kinam , Hutton Trevor , Blamey Laura , Dutra Leo
Published: June 2021

The Torres Strait tropical rock lobster Panulirus ornatus (TRL) fishery is of immense social, cultural and economic importance to the region’s Indigenous fishers from both Australia and Papua New Guinea (PNG). During 2020, the COVID-19 pandemic indirectly impacted this fishery as well as a number of other fisheries reliant on international export markets. The TRL fishery is managed using an empirical (data-based) Harvest Control Rule (eHCR) to rapidly provide a recommended biological catch (RBC), based on catch, fishery-independent survey indices and catch-per-unit-effort (CPUE). Here, we summarize the impacts of COVID-19 on each of these critical data inputs and discuss whether the eHCR was considered adequately resilient to this unprecedented disruption to the system. Next, we use a quantitative supply chain index to analyze the impact of disruptions to the supply chain, and inform on potential adaptation strategies. The catch and CPUE data were impacted to varying degrees by external constraints influencing fishing effort, but the fishery-independent survey wasn’t affected and hence there remains an unbroken survey time-series for the fishery extending back to 1989. The eHCR was shown to be reasonably robust because it incorporates longer-term trends over a 5-year period, and accords substantially more weighting (80%) to the fishery-independent survey rather than CPUE data which can be affected by trade and other disruptions. Despite the eHCR not having been tested for scenarios such as a global pandemic, this robustness is a positive given the types of disruptions we will likely face in future climate. The weak links identified in the supply chain were the same as those previously highlighted as sensitive to climate change disruptions. Our supply chain analysis quantifies the impact on system resilience of alternative paths connecting producers to consumers and reinforces that supply chains may be particularly vulnerable to external disruptions if they are not sufficiently diverse.
Prediction of Left Double-Lumen Tube Size by Measurement of Cricoid Cartilage Transverse Diameter by Ultrasound and CT Multi-Planar Reconstruction
Authors: Zhang Chengchao , Qin Xinlei , Zhou Wenyi , He Shuaijie , Liu Ao , Zhang Yu , Dai Zhigang , Yin Jiangwen
Published: June 2021

Background: Currently, there is no uniform standard for selecting the left double lumen tubes (LDLT). Advantages, such as safety and convenience of the ultrasonic technology, and measurement accuracy, make it more widely applied in the clinical anesthesia, and computed tomography (CT) multi-planar reconstruction (MPR) technology will certainly provide a more accurate measurement. For better application for thoracic surgery choice LDLT, relieving the injury to patients, and reducing the complications, this study will compare the two approaches.

Methods: The first part, 120 cases of patients were selected according to the height and gender; recording the patient's optimum LDLT and measurement the transverse diameter of the cricoid cartilage (TD-C) by ultrasound and CT MPR, and then obtained the TD-C range measurement by ultrasound and CT MPR corresponding to different types of LDLT. The second part, total of 102 patients were divided into the ultrasound group and the CT MPR group. In the ultrasound group, TD-C was measured by ultrasound, the corresponding size for intubation was selected based on the conclusions derived from the first part. In the CT MPR group, TD-C was measured by CT MPR, the corresponding size of LDLT based on the conclusions derived from the first part.

Results: In the first part, 120 patients were no significant difference in the basic characteristics (P > 0.05). The accuracy of selecting the LDLT by conventional experience, namely height and gender was 58.3%. Ultrasonic measurement TD-C range was as follows: 32 Fr <15.88, 35 Fr: 15.88–16.80, 37 Fr: 16.75–17.81, and 39 Fr > 17.80. CT MPR measurement TD-C range was as follows: 32 Fr <15.74, 35 Fr: 15.74–16.65, 37 Fr: 16.56–17.68, and 39 Fr > 17.65. In the second part, there was no significant difference in the basic characteristics between the two groups (P > 0.05). The accuracy of intubation in the ultrasound group was 90.2% and the corresponding in the CT MPR group was 94.1% (P > 0.05).

Conclusions: The accuracy of selecting the LDLT based on TD-C is significantly higher than conventional experience; it can significantly reduce the post-operative complications and there was no statistical significance in the accuracy of LDLT selected for TD-C measurement by ultrasound vs. CT, and both of them could be safely used for the evaluation before intubation under anesthesia in thoracic surgery.
Early Life Microbial Exposure and Immunity Training Effects on Asthma Development and Progression
Authors: Cereta Andressa Daronco , Oliveira Vinícius Rosa , Costa Ivan Peres , Guimarães Letícia Lopes , Afonso João Pedro Ribeiro , Fonseca Adriano Luís , Sousa Alan Robson Trigueiro de , Silva Guilherme Augusto Moreira , Mello Diego A. C. P. G. , Oliveira Luis Vicente Franco de , da Palma Renata Kelly
Published: June 2021

Asthma is the most common inflammatory disease affecting the lungs, which can be caused by intrauterine or postnatal insults depending on the exposure to environmental factors. During early life, the exposure to different risk factors can influence the microbiome leading to undesired changes to the immune system. The modulations of the immunity, caused by dysbiosis during development, can increase the susceptibility to allergic diseases. On the other hand, immune training approaches during pregnancy can prevent allergic inflammatory diseases of the airways. In this review, we focus on evidence of risk factors in early life that can alter the development of lung immunity associated with dysbiosis, that leads to asthma and affect childhood and adult life. Furthermore, we discuss new ideas for potential prevention strategies that can be applied during pregnancy and postnatal period.
Microbial Communities on Plastic Polymers in the Mediterranean Sea
Authors: Vaksmaa Annika , Knittel Katrin , Abdala Asbun Alejandro , Goudriaan Maaike , Ellrott Andreas , Witte Harry J. , Vollmer Ina , Meirer Florian , Lott Christian , Weber Miriam , Engelmann Julia C. , Niemann Helge
Published: June 2021

Plastic particles in the ocean are typically covered with microbial biofilms, but it remains unclear whether distinct microbial communities colonize different polymer types. In this study, we analyzed microbial communities forming biofilms on floating microplastics in a bay of the island of Elba in the Mediterranean Sea. Raman spectroscopy revealed that the plastic particles mainly comprised polyethylene (PE), polypropylene (PP), and polystyrene (PS) of which polyethylene and polypropylene particles were typically brittle and featured cracks. Fluorescence in situ hybridization and imaging by high-resolution microscopy revealed dense microbial biofilms on the polymer surfaces. Amplicon sequencing of the 16S rRNA gene showed that the bacterial communities on all plastic types consisted mainly of the orders Flavobacteriales, Rhodobacterales, Cytophagales, Rickettsiales, Alteromonadales, Chitinophagales, and Oceanospirillales. We found significant differences in the biofilm community composition on PE compared with PP and PS (on OTU and order level), which shows that different microbial communities colonize specific polymer types. Furthermore, the sequencing data also revealed a higher relative abundance of archaeal sequences on PS in comparison with PE or PP. We furthermore found a high occurrence, up to 17% of all sequences, of different hydrocarbon-degrading bacteria on all investigated plastic types. However, their functioning in the plastic-associated biofilm and potential role in plastic degradation needs further assessment.
Directional Selection of Microbial Community Reduces Propionate Accumulation in Glycerol and Glucose Anaerobic Bioconversion Under Elevated pCO2
Authors: Ceron-Chafla Pamela , Chang Yu-ting , Rabaey Korneel , van Lier Jules B. , Lindeboom Ralph E. F.
Published: June 2021

Volatile fatty acid accumulation is a sign of digester perturbation. Previous work showed the thermodynamic limitations of hydrogen and CO2 in syntrophic propionate oxidation under elevated partial pressure of CO2 (pCO2). Here we study the effect of directional selection under increasing substrate load as a strategy to restructure the microbial community and induce cross-protection mechanisms to improve glucose and glycerol conversion performance under elevated pCO2. After an adaptive laboratory evolution (ALE) process, viable cell density increased and predominant microbial groups were modified: an increase in Methanosaeta and syntrophic propionate oxidizing bacteria (SPOB) associated with the Smithella genus was found with glycerol as the substrate. A modest increase in SPOB along with a shift in the predominance of Methanobacterium toward Methanosaeta was observed with glucose as the substrate. The evolved inoculum showed affected diversity within archaeal spp. under 5 bar initial pCO2; however, higher CH4 yield resulted from enhanced propionate conversion linked to the community shifts and biomass adaptation during the ALE process. Moreover, the evolved inoculum attained increased cell viability with glucose and a marginal decrease with glycerol as the substrate. Results showed differences in terms of carbon flux distribution using the evolved inoculum under elevated pCO2: glucose conversion resulted in a higher cell density and viability, whereas glycerol conversion led to higher propionate production whose enabled conversion reflected in increased CH4 yield. Our results highlight that limited propionate conversion at elevated pCO2 resulted from decreased cell viability and low abundance of syntrophic partners. This limitation can be mitigated by promoting alternative and more resilient SPOB and building up biomass adaptation to environmental conditions via directional selection of microbial community.
Recent Advances in Molecular Biology of Human Bocavirus 1 and Its Applications
Authors: Shao Liting , Shen Weiran , Wang Shengqi , Qiu Jianming
Published: June 2021

Human bocavirus 1 (HBoV1) was discovered in human nasopharyngeal specimens in 2005. It is an autonomous human parvovirus and causes acute respiratory tract infections in young children. HBoV1 infects well differentiated or polarized human airway epithelial cells in vitro. Unique among all parvoviruses, HBoV1 expresses 6 non-structural proteins, NS1, NS1-70, NS2, NS3, NS4, and NP1, and a viral non-coding RNA (BocaSR), and three structural proteins VP1, VP2, and VP3. The BocaSR is the first identified RNA polymerase III (Pol III) transcribed viral non-coding RNA in small DNA viruses. It plays an important role in regulation of viral gene expression and a direct role in viral DNA replication in the nucleus. HBoV1 genome replication in the polarized/non-dividing airway epithelial cells depends on the DNA damage and DNA repair pathways and involves error-free Y-family DNA repair DNA polymerase (Pol) η and Pol κ. Importantly, HBoV1 is a helper virus for the replication of dependoparvovirus, adeno-associated virus (AAV), in polarized human airway epithelial cells, and HBoV1 gene products support wild-type AAV replication and recombinant AAV (rAAV) production in human embryonic kidney (HEK) 293 cells. More importantly, the HBoV1 capsid is able to pseudopackage an rAAV2 or rHBoV1 genome, producing the rAAV2/HBoV1 or rHBoV1 vector. The HBoV1 capsid based rAAV vector has a high tropism for human airway epithelia. A deeper understanding in HBoV1 replication and gene expression will help find a better way to produce the rAAV vector and to increase the efficacy of gene delivery using the rAAV2/HBoV1 or rHBoV1 vector, in particular, to human airways. This review summarizes the recent advances in gene expression and replication of HBoV1, as well as the use of HBoV1 as a parvoviral vector for gene delivery.
Mutations in NOTCH3 Gene may Promote the Clinical Presentation of Spinocerebellar Ataxia Type 37 Caused by Mutations in DAB1 Gene
Authors: Wang Zhao-Wei , Wang Li-Ping , Du Ye , Liu Qi
Published: June 2021

Background: Autosomal dominant spinocerebellar ataxia type 37 (SCA37) and Cerebral autosomal dominant arteriopathy with subcortical infarct and leukoencephalopathy (CADASIL) result from DAB1 and NOTCH3 gene mutations, respectively.

Methods: In addition to conventional diagnostic methods, next-generation sequencing (NGS) and Sanger sequencing were performed to define and confirm the DAB1 and NOTCH3 gene mutation for a Chinese pedigree. Bioinformatics analysis was also applied for the mutated DAB1 and NOTCH3 protein using available software tools.

Results: Brain magnetic resonance imaging shows diffuse leukoencephalopathy and cerebellar atrophy in the proband. NGS and Sanger sequencing identified two novel heterozygous mutations: NM_021080:c.318T > G (p.H106Q) in the DAB1 gene and NM_000435:c.3298C > T (p.R1100C) in the NOTCH3 gene. Bioinformatics analysis suggested that the DAB1 and NOTCH3 gene mutations are disease-causing and may be responsible for the phenotypes.

Conclusion: This is the first report of a pedigree with both SAC37 and CADASIL phenotypes carrying corresponding gene mutations. Mutations in the NOTCH3 gene may promote the clinical presentation of spinocerebellar ataxia type 37 caused by mutations in the DAB1 gene. In addition to general examinations, it is vital for physicians to apply molecular genetics to get an accurate diagnosis in the clinic, especially for rare diseases.
Blocking K-Ras Interaction With the Plasma Membrane Is a Tractable Therapeutic Approach to Inhibit Oncogenic K-Ras Activity
Authors: Henkels Karen M. , Rehl Kristen M. , Cho Kwang-jin
Published: June 2021

Ras proteins are membrane-bound small GTPases that promote cell proliferation, differentiation, and apoptosis. Consistent with this key regulatory role, activating mutations of Ras are present in ∼19% of new cancer cases in the United States per year. K-Ras is one of the three ubiquitously expressed isoforms in mammalian cells, and oncogenic mutations in this isoform account for ∼75% of Ras-driven cancers. Therefore, pharmacological agents that block oncogenic K-Ras activity would have great clinical utility. Most efforts to block oncogenic Ras activity have focused on Ras downstream effectors, but these inhibitors only show limited clinical benefits in Ras-driven cancers due to the highly divergent signals arising from Ras activation. Currently, four major approaches are being extensively studied to target K-Ras–driven cancers. One strategy is to block K-Ras binding to the plasma membrane (PM) since K-Ras requires the PM binding for its signal transduction. Here, we summarize recently identified molecular mechanisms that regulate K-Ras–PM interaction. Perturbing these mechanisms using pharmacological agents blocks K-Ras–PM binding and inhibits K-Ras signaling and growth of K-Ras–driven cancer cells. Together, these studies propose that blocking K-Ras–PM binding is a tractable strategy for developing anti–K-Ras therapies.
Investigating the Role of Root Exudates in Recruiting Streptomyces Bacteria to the Arabidopsis thaliana Microbiome
Authors: Worsley Sarah F. , Macey Michael C. , Prudence Samuel M. M. , Wilkinson Barrie , Murrell J. Colin , Hutchings Matthew I.
Published: June 2021

Streptomyces species are saprophytic soil bacteria that produce a diverse array of specialized metabolites, including half of all known antibiotics. They are also rhizobacteria and plant endophytes that can promote plant growth and protect against disease. Several studies have shown that streptomycetes are enriched in the rhizosphere and endosphere of the model plant Arabidopsis thaliana. Here, we set out to test the hypothesis that they are attracted to plant roots by root exudates, and specifically by the plant phytohormone salicylate, which they might use as a nutrient source. We confirmed a previously published report that salicylate over-producing cpr5 plants are colonized more readily by streptomycetes but found that salicylate-deficient sid2-2 and pad4 plants had the same levels of root colonization by Streptomyces bacteria as the wild-type plants. We then tested eight genome sequenced Streptomyces endophyte strains in vitro and found that none were attracted to or could grow on salicylate as a sole carbon source. We next used 13CO2 DNA stable isotope probing to test whether Streptomyces species can feed off a wider range of plant metabolites but found that Streptomyces bacteria were outcompeted by faster growing proteobacteria and did not incorporate photosynthetically fixed carbon into their DNA. We conclude that, given their saprotrophic nature and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of biocontrol strains.
Sensorineural Hearing Loss and Mitochondrial Apoptosis of Cochlear Spiral Ganglion Neurons in Fibroblast Growth Factor 13 Knockout Mice
Authors: Yu Yulou , Yang Jing , Luan Feng , Gu Guoqiang , Zhao Ran , Wang Qiong , Dong Zishan , Tang Junming , Wang Wei , Sun Jinpeng , Lv Ping , Zhang Hailin , Wang Chuan
Published: June 2021

Deafness is known to occur in more than 400 syndromes and accounts for almost 30% of hereditary hearing loss. The molecular mechanisms underlying such syndromic deafness remain unclear. Furthermore, deafness has been a common feature in patients with three main syndromes, the BÖrjeson-Forssman-Lehmann syndrome, Wildervanck syndrome, and Congenital Generalized Hirsutism, all of which are characterized by loss-of-function mutations in the Fgf13 gene. Whether the pathogenesis of deafness in these syndromes is associated with the Fgf13 mutation is not known. To elucidate its role in auditory function, we generated a mouse line with conditional knockout of the Fgf13 gene in the inner ear (Fgf13 cKO). FGF13 is expressed predominantly in the organ of Corti, spiral ganglion neurons (SGNs), stria vascularis, and the supporting cells. Conditional knockout of the gene in the inner ear led to sensorineural deafness with low amplitude and increased latency of wave I in the auditory brainstem response test but had a normal distortion product otoacoustic emission threshold. Fgf13 deficiency resulted in decreased SGN density from the apical to the basal region without significant morphological changes and those in the number of hair cells. TUNEL and caspase-3 immunocytochemistry assays showed that apoptotic cell death mediated the loss of SGNs. Further detection of apoptotic factors through qRT-PCR suggested the activation of the mitochondrial apoptotic pathway in SGNs. Together, this study reveals a novel role for Fgf13 in auditory function, and indicates that the gene could be a potential candidate for understanding deafness. These findings may provide new perspectives on the molecular mechanisms and novel therapeutic targets for treatment deafness.
Double Two-State Opsin Model With Autonomous Parameter Inference
Authors: Schoeters Ruben , Tarnaud Thomas , Martens Luc , Joseph Wout , Raedt Robrecht , Tanghe Emmeric
Published: June 2021

Optogenetics has a lot of potential to become an effective neuromodulative therapy for clinical applications. Selecting the correct opsin is crucial to have an optimal optogenetic tool. With computational modeling, the neuronal response to the current dynamics of an opsin can be extensively and systematically tested. Unlike electrical stimulation where the effect is directly defined by the applied field, the stimulation in optogenetics is indirect, depending on the selected opsin's non-linear kinetics. With the continuous expansion of opsin possibilities, computational studies are difficult due to the need for an accurate model of the selected opsin first. To this end, we propose a double two-state opsin model as alternative to the conventional three and four state Markov models used for opsin modeling. Furthermore, we provide a fitting procedure, which allows for autonomous model fitting starting from a vast parameter space. With this procedure, we successfully fitted two distinctive opsins (ChR2(H134R) and MerMAID). Both models are able to represent the experimental data with great accuracy and were obtained within an acceptable time frame. This is due to the absence of differential equations in the fitting procedure, with an enormous reduction in computational cost as result. The performance of the proposed model with a fit to ChR2(H134R) was tested, by comparing the neural response in a regular spiking neuron to the response obtained with the non-instantaneous, four state Markov model (4SB), derived by Williams et al. (2013). Finally, a computational speed gain was observed with the proposed model in a regular spiking and sparse Pyramidal-Interneuron-Network-Gamma (sPING) network simulation with respect to the 4SB-model, due to the former having two differential equations less. Consequently, the proposed model allows for computationally efficient optogenetic neurostimulation and with the proposed fitting procedure will be valuable for further research in the field of optogenetics.
Distinct MicroRNA Profiles in the Perilymph and Serum of Patients With Menière's Disease
Authors: Shew Matthew , Wichova Helena , St. Peter Madeleine , Warnecke Athanasia , Staecker Hinrich
Published: June 2021

Hypothesis: Menière's disease microRNA (miRNA) profiles are unique and are reflected in the perilymph and serum of patients.

Background: Development of effective biomarkers for Menière's disease are needed. miRNAs are small RNA sequences that downregulate mRNA translation and play a significant role in a variety of disease states, ultimately making them a promising biomarker. miRNAs can be readily isolated from human inner ear perilymph and serum, and may exhibit disease-specific profiles.

Methods: Perilymph sampling was performed in 10 patients undergoing surgery; 5 patients with Meniere's disease and 5 patients with otosclerosis serving as controls. miRNAs were isolated from the serum of 5 patients with bilateral Menière's disease and compared to 5 healthy age-matched controls. For evaluation of miRNAs an Agilent miRNA gene chip was used. Analysis of miRNA expression was carried out using Qlucore and Ingenuitey Pathway Analysis software. Promising miRNAs biomarkers were validated using qPCR.

Results: In the perilymph of patients with Menière's disease, we identified 16 differentially expressed miRNAs that are predicted to regulate over 220 different cochlear genes. Six miRNAs are postulated to regulate aquaporin expression and twelve miRNAs are postulated to regulate a variety of inflammatory and autoimmune pathways. When comparing perilymph with serum samples, miRNA-1299 and−1270 were differentially expressed in both the perilymph and serum of Ménière's patients compared to controls. Further analysis using qPCR confirmed miRNA-1299 is downregulated over 3-fold in Meniere's disease serum samples compared to controls.

Conclusions: Patients with Ménière's disease exhibit distinct miRNA expression profiles within both the perilymph and serum. The altered perilymph miRNAs identified can be linked to postulated Ménière's disease pathways and may serve as biomarkers. miRNA-1299 was validated to be downregulated in both the serum and perilymph of Menière's patients.
Staged Endovascular Treatment for Symptomatic Occlusion Originating From the Intracranial Vertebral Arteries in the Early Non-acute Stage
Authors: Duan Hongzhou , Chen Li , Shen Shengli , Zhang Yang , Li Chunwei , Yi Zhiqiang , Wang Yingjin , Zhang Jiayong , Li Liang
Published: June 2021

Background: The ideal treatment for patients who survive from acute vertebrobasilar artery occlusion but develop aggressive ischemic events despite maximal medical therapy in the early non-acute stage is unknown. This paper reports the technical feasibility and outcome of staged endovascular treatment in a series of such patients with symptomatic intracranial vertebral artery occlusion.

Methods: Ten consecutive patients who presented with aggressive ischemic events in the early non-acute stage of intracranial vertebral artery occlusion from Jan 2015 to Nov 2020 were retrospectively reviewed. Among them, eight male and two female patients with a mean age of 66.7 years developed aggressive ischemic events, and the NIHSS score was elevated by a median of 7 points despite medical therapy. All patients received staged endovascular treatment 4–21 days from onset, at an average of 11 days. The strategy of staged treatment was as follows: first, a microwire was passed through the portion of the occlusion, which was then dilated with balloon inflation to maintain the perfusion above TICI grade 2b. Then, with the use of antiplatelet drugs, the residual intravascular thrombus was gradually eliminated by the continuous perfusion and an activated fibrinolytic system, leaving the residual stenosis. A second stage of angioplasty with stent implantation was subsequently performed if residual stenosis was ≥50%. The NIHSS scores and mRS scores were compared between pre- and post-endovascular treatment groups and in the follow-up period.

Results: Technical success was achieved in 9 patients who received staged endovascular treatment (perforation occurred in one patient during the first stage). The NIHSS scores were significantly improved, with a median score 7 points lower on discharge compared with the scores for the most severe status. Favorable outcomes with mRS score ≤ 2 were achieved in 7 and 9 patients at the 3-month follow-up and the latest follow-up, respectively, which was better than the preoperative status.

Conclusion: Staged endovascular treatment might be a safe, efficient, and viable option in carefully selected patients with symptomatic intracranial vertebral artery occlusion in the early non-acute stage. However, this needs to be confirmed by further investigation, preferably in a large, controlled setting.
A Short-Term Intervention of High-Intensity Exercise and Anodal-tDCS on Motor Learning in Middle-Aged Adults: An RCT
Authors: Quinlan Clare , Rattray Ben , Pryor Disa , Northey Joseph M. , Coxon James , Cherbuin Nicolas , Andrews Sophie C.
Published: June 2021

High-intensity exercise has enhanced motor learning in healthy young adults. Anodal-transcranial direct current stimulation (a-tDCS) may optimize these effects. This study aimed to determine the effects of a short-term high-intensity interval exercise intervention either with or without a-tDCS on the learning and retention of a novel motor task in middle-aged adults. Forty-two healthy middle-aged adults (age = 44.6 ± 6.3, female = 76%) were randomized into three groups: exercise and active a-tDCS, exercise and sham a-tDCS, and a non-exercise and sham a-tDCS control. Participants completed a baseline testing session, followed by three intervention sessions 48-h apart. The exercise groups completed 20-min of high-intensity exercise followed by a novel sequential visual isometric pinch task (SVIPT) while receiving 20-min of 1.5 mA a-tDCS, or sham tDCS. The control group completed 20-min of reading before receiving sham a-tDCS during the SVIPT. Learning was assessed by skill change within and between intervention sessions. Participants returned 5–7 days after the final intervention session and performed the SVIPT task to assess retention. All three groups showed evidence of learning on the SVIPT task. Neither group displayed enhanced overall learning or retention when compared to the control group. High-intensity exercise with or without a-tDCS did not improve learning or retention of a novel motor task in middle-aged adults. The methodological framework provides direction for future research to investigate the potential of differing exercise intensity effects on learning and retention.
Reassessment of Pioglitazone for Alzheimer’s Disease
Authors: Saunders Ann M. , Burns Daniel K. , Gottschalk William Kirby
Published: June 2021

Alzheimer’s disease is a quintessential ‘unmet medical need’, accounting for ∼65% of progressive cognitive impairment among the elderly, and 700,000 deaths in the United States in 2020. In 2019, the cost of caring for Alzheimer’s sufferers was $244B, not including the emotional and physical toll on caregivers. In spite of this dismal reality, no treatments are available that reduce the risk of developing AD or that offer prolonged mitiagation of its most devestating symptoms. This review summarizes key aspects of the biology and genetics of Alzheimer’s disease, and we describe how pioglitazone improves many of the patholophysiological determinants of AD. We also summarize the results of pre-clinical experiments, longitudinal observational studies, and clinical trials. The results of animal testing suggest that pioglitazone can be corrective as well as protective, and that its efficacy is enhanced in a time- and dose-dependent manner, but the dose-effect relations are not monotonic or sigmoid. Longitudinal cohort studies suggests that it delays the onset of dementia in individuals with pre-existing type 2 diabetes mellitus, which small scale, unblinded pilot studies seem to confirm. However, the results of placebo-controlled, blinded clinical trials have not borne this out, and we discuss possible explanations for these discrepancies.
Hypofractionated Volumetric-Modulated Arc Radiotherapy for Patients With Non-Small-Cell Lung Cancer Not Suitable for Surgery or Conventional Chemoradiotherapy or SBRT
Authors: Shen Junyue , Yang Dan , Chen Mailin , Jiang Leilei , Dong Xin , Li Dongming , Yu Rong , Yu Huiming , Shi Anhui
Published: June 2021

Background

Hypofractionated radiotherapy (HypoRT) has been used to pursue an alternative treatment regimen for patients with non-small-cell lung cancer (NSCLC) who are not eligible for stereotactic ablative radiotherapy (SABR), surgery or concurrent chemoradiotherapy (CCRT) and has shown good local control and safety. We analyzed the feasibility of using volumetric-modulated arc radiotherapy (VMAT) with the simultaneous integrated boost (SIB) technique to achieve high local control with few treatment-related toxicities.

Patients and Methods

A total of 55 patients with stage I-IV NSCLC who were not candidates for SABR, surgery or CCRT were included in the present study. All patients received a prescribed dose of 60 to 66 Gy in 15 fractions. Local progression-free survival (LPFS), PFS, overall survival (OS), and toxicities were retrospectively analyzed.

Results

Thirty-three patients (60.0%) had stage IV or recurrent disease in this study. The median follow-up time was 8 months (interquartile range: 5.0-16.3 months). The 1-year and 2-year OS rates were 84.3% and 69.9%, and the 1-year and 2-year LPFS rates were 91.0% and 63.0%. The median OS (mOS) and median LPFS (mLPFS) were not reached, and median PFS (mPFS) was 15 months. Twenty-eight (51.9%) patients had disease progression at the time of analysis. Of these, 7 (13.0%), 7 (13.0%) and 21 (38.9%) had local recurrence, locoregional failure and distant metastasis, respectively. All cases of local recurrence were found within the SIB region. Four patients had grade 2-3 pneumonitis, and 8 patients had grade 2-3 esophagitis. Patients with grade 2-3 esophagitis had significantly higher maximum dose and dose to 5 cm3 volume to esophagus than those with grade 0-1 esophagitis. No grade 4 or higher toxicity was observed.

Conclusion

The 60 to 66 Gy in 15 fractions RT regimen provides favorable local control and survival with well-tolerated toxicities. Hypofractionated VMAT+SIB is an alternative treatment option for patients with NSCLC who cannot tolerate standard definitive therapy.