bluuebunny/crossref_metadata_2025 huggingface dataset:
The attenuation of insulin-like growth factor signaling may be responsible for relative reduction in matrix synthesis in degenerated areas of osteoarthritic cartilage
Authors: Tanaka Nobuho , Tsuno Hirotaka , Ohashi Satoru , Iwasawa Mitsuyasu , Furukawa Hiroshi , Kato Tomohiro , Fukui Naoshi
Published: February 2021

Background

In osteoarthritis (OA), cartilage matrix is lost gradually despite enhanced matrix synthesis by chondrocytes. This paradox may be explained, at least partly, by reduced chondrocyte anabolism in degenerated area of OA cartilage. However, to date, it is not known why chondrocyte anabolism is suppressed in those areas.

Methods

Cartilage was obtained from control knees and end-stage OA knees in macroscopically preserved areas and degenerated areas, and gene expression was analyzed in respective regions of cartilage using laser capture microdissection and qPCR. For the cartilage protein analysis, cartilage was obtained from preserved areas and degenerated areas of OA knees in pairs, and proteins were extracted using urea buffer. Protein concentrations were determined by Luminex and compared between the areas. Cartilage explants prepared from preserved areas and degenerated areas of OA knees were cultured in the presence or absence of an AKT inhibitor, and the gene expression was evaluated by qPCR. Finally, the expression of SP1 was evaluated in OA and control cartilage, and the significance of Sp1 on the expression of IGF1R and IRS1 was investigated in experiments using primary cultured chondrocytes.

Results

Within OA cartilage, the expression of IGF-1, IGF-2, IGF1R and IRS1 was reduced in degenerated areas compared to preserved areas, while the expression of all six IGF-binding protein genes examined was enhanced in the former areas. Consistent results were obtained by a protein analysis. In explant culture, the inhibition of AKT signaling abrogated the abundant matrix gene expression in the preserved areas over the degenerated areas, indicating that suppressed matrix synthesis in degenerated areas may be ascribed, at least partly, to attenuated IGF signaling. Within OA cartilage, the expression of Sp1 was considerably reduced in severely degenerated areas compared to preserved areas, which correlated well with the expression of IGF1R and IRS1. In experiments using primary cultured chondrocytes, the expression of IGF1R and IRS1 was enhanced by the induction of Sp1 expression and reduced by the suppression of Sp1 expression.

Conclusions

The results of this study suggest that attenuated IGF signaling may be responsible, at least partly, for the reduced matrix synthesis in degenerated areas of OA cartilage.
Persisting inter‐limb differences in patients following total hip arthroplasty four to five years after surgery? A preliminary cross‐sectional study
Authors: John Stefanie , Weizel David , Heumann Anna S. , Fischer Anja , Orlowski Katja , Mrkor Kai-Uwe , Edelmann-Nusser Jürgen , Witte Kerstin
Published: February 2021

Background

Total hip arthroplasty (THA) is an effective procedure for patients with end-stage hip osteoarthritis. However, whether or not pre-operatively existing functional deficits are persisting several years post-surgery in the affected limb has not been thoroughly researched. Therefore, the primary aim of this preliminary study was to include patients four to five years after undergoing THA and to investigate potential differences between the operated and non-operated leg in hip strength, range of motion (ROM), balance, and gait. The secondary aim was to compare these values from the operated leg of the patients to those of the legs of healthy subjects.

Methods

Sixteen patients (age: 65.20 ± 5.32 years) following unilateral THA (post-operation time: 4.7 ± 0.7 years) and ten, healthy, age-matched control subjects (age: 60.85 ± 7.57 years) were examined for maximum isometric hip muscle strength, active ROM of the hip joint, balance and gait on both limbs. Paired t-tests were used to assess the inter-limb differences in the THA group. Analyses of covariance (ANCOVA) were performed to compare groups, using age as a covariate.

Results

The analysis of inter-limb differences in patients following THA revealed significant deficits on the operated side for hip abduction strength (p = 0.02), for hip flexion ROM (p < 0.01) and for balance in terms of the length of center of pressure (COP) (p = 0.04). Compared to values of the control subjects, the patients demonstrated significantly reduced hip strength in flexion, extension and abduction (p < 0.05) on the operated leg as well as reduced ROM measures in hip flexion, extension and abduction (p < 0.05).

Conclusions

The first results of this explorative study indicated that inter-limb differences as well as reduced hip strength and hip ROM compared with control subjects were still present four to five years after THA. These persisting asymmetries and deficits in patients following THA may be one explanation for the decrease in health-related quality of life (HRQoL) seen in patients over the years after surgery. Further studies are required to replicate these findings with a larger sample size.

Trial registration

DRKS, DRKS00016945. Registered 12 March 2019 – Retrospectively registered,
Mutation-based clustering and classification analysis reveals distinctive age groups and age-related biomarkers for glioma
Authors: Jean-Quartier Claire , Jeanquartier Fleur , Ridvan Aydin , Kargl Matthias , Mirza Tica , Stangl Tobias , Markaĉ Robi , Jurada Mauro , Holzinger Andreas
Published: February 2021

Background

Malignant brain tumor diseases exhibit differences within molecular features depending on the patient’s age.

Methods

In this work, we use gene mutation data from public resources to explore age specifics about glioma. We use both an explainable clustering as well as classification approach to find and interpret age-based differences in brain tumor diseases. We estimate age clusters and correlate age specific biomarkers.

Results

Age group classification shows known age specifics but also points out several genes which, so far, have not been associated with glioma classification.

Conclusions

We highlight mutated genes to be characteristic for certain age groups and suggest novel age-based biomarkers and targets.
Implications for the design of a Diagnostic Decision Support System (DDSS) to reduce time and cost to diagnosis in paediatric shoulder instability
Authors: Philp Fraser , Faux-Nightingale Alice , Woolley Sandra , de Quincey Ed , Pandyan Anand
Published: February 2021

Background

Currently the diagnosis of shoulder instability, particularly in children, is difficult and can take time. These diagnostic delays can lead to poorer outcome and long-term complications. A Diagnostic Decision Support System (DDSS) has the potential to reduce time to diagnosis and improve outcomes for patients. The aim of this study was to develop a concept map for a future DDSS in shoulder instability.

Methods

A modified nominal focus group technique, involving three clinical vignettes, was used to elicit physiotherapists decision-making processes.

Results

Twenty-five physiotherapists, (18F:7 M) from four separate clinical sites participated. The themes identified related to ‘Variability in diagnostic processes and lack of standardised practice’ and ‘Knowledge and attitudes towards novel technologies for facilitating assessment and clinical decision making’.

Conclusion

No common structured approach towards assessment and diagnosis was identified. Lack of knowledge, perceived usefulness, access and cost were identified as barriers to adoption of new technology. Based on the information elicited a conceptual design of a future DDSS has been proposed. Work to develop a systematic approach to assessment, classification and diagnosis is now proposed.

Trial Registraty This was not a clinical trial and so no clinical trial registry is needed.
Spatial clustering of fourteen tick species across districts of Zimbabwe
Authors: Shekede Munyaradzi Davis , Chikerema Silvester Maravanyika , Spargo Moregood , Gwitira Isaiah , Kusangaya Samuel , Mazhindu Aldridge Nyasha , Ndhlovu Daud Nyosi
Published: February 2021

Background

Ticks transmit several diseases that result in high morbidity and mortality in livestock. Tick-borne diseases are an economic burden that negatively affect livestock production, cost countries billions of dollars through vaccine procurement and other disease management efforts. Thus, understanding the spatial distribution of tick hotspots is critical for identifying potential areas of high tick-borne disease transmission and setting up priority areas for targeted tick disease management. In this study, optimised hotspot analysis was applied to detect hotspots and coldspots of 14 common tick species in Zimbabwe. Data on the spatial distribution of tick species were obtained from the Epidemiology Unit of the Division of Veterinary Field Services of Zimbabwe.

Results

A total of 55,133 ticks were collected withRhipicephalus decoloratusbeing the most common species (28.7%), followed byAmblyomma hebraeum(20.6%), andRhipicephalus sanguineussensulato(0.06%) being the least common species. Results also showed that tick hotspots are species-specific with particular tick species occupying defined localities in the country. For instance,Amblyomma variegatum,Rhipicephalus appendiculatus,Rhipicephalus decoloratus, Rhipicephalus compostus, Rhipicephalus microplus,Rhipicephalus pravus, andRhipicephalus simuswere concentrated in the north and north eastern districts of the country. In contrast,Amblyomma hebraeum,Hyalomma rufipes, Hyalomma trancatumandRhipicephalus evertsi evertsiwere prevalent in the southern districts of Zimbabwe.

Conclusion

The occurrence of broadly similar hotspots of several tick species in different districts suggests presence of spatial overlaps in the niche of the tick species. As ticks are vectors of several tick-borne diseases, there is high likelihood of multiple disease transmission in the same geographic region. This study is the first in Zimbabwe to demonstrate unique spatial patterns in the distribution of several tick species across the country. The results of this study provide an important opportunity for the development of spatially-targeted tick-borne disease management strategies.
Yersinia pseudotuberculosis serotype O:1 infection in a captive Seba’s short tailed-fruit bat (Carollia perspicillata) colony in Switzerland
Authors: Hahn K. , Veiga I. B. , Schediwy M. , Wiederkehr D. , Meniri M. , Schneeberger M. , den Broek P. Rüegg-van , Gurtner C. , Fasel N. J. , Kittl S. , Fredriksson-Ahomaa M. , Schmitt S. , Stokar-Regenscheit N.
Published: February 2021

Background

Between February and April 2016, a slight increase in mortality was observed in a colony consisting of 400 captive Seba’s short-tailed bats (Carollia perspicillata). These animals cohabited with other nocturnal animal species in a dome of a private zoo in Switzerland.

Results

Gross and histological analysis of two (14.3%) out of the 13 animals submitted for necropsy within this period revealed a necrosuppurative pneumonia, hepatitis, splenitis, enterocolitis, and endometritis, with abundant intralesional colonies of Gram-negative rods.Yersinia(Y.)pseudotuberculosisserotype O:1 and biotype 1 belonging to the sequence type ST90 was isolated from the affected organs in both animals. Following this diagnosis, ¼ of the colony (99 animals) was culled and submitted for gross and histopathological analysis, and a bacterial culture selective forYersiniaspp. of lung, liver, and spleen was performed. From these 99 animals, one gravid female was tested and found to be positive forY. pseudotuberculosisin the absence of clinical symptoms and histopathological lesions.PCR analysis of altogether three bacterial isolates for virulence factors revealed the presence of theailgene, and one isolate was also positive for thevirFandyadAplasmid genes.

Conclusions

These findings suggest thatCarollia perspicillataare susceptible to lethal yersiniosis but do not represent a regular reservoir forY. pseudotuberculosis. Culling of ¼ of the population was sufficient to limit the spread of this infection among the colony. Moreover, no infections were detected in cohabitant nocturnal animals and caretakers, indicating that the zoonotic risk in this case was low.
Bioinformatic analysis reveals an exosomal miRNA-mRNA network in colorectal cancer
Authors: Ma Jun , Wang Peilong , Huang Lei , Qiao Jianxia , Li Jianhong
Published: February 2021

Background

Exosomes play important roles in angiogenesis, drug resistance, and metastasis of colorectal cancer (CRC), but the underlying mechanism has seldom been reported. Herein, our study aimed to reveal an exosomal miRNA-mRNA network involved in CRC by performing bioinformatical analysis.

Methods

The mRNA and miRNA data of colon adenocarcinoma and rectal adenocarcinoma were downloaded from The Cancer Genome Atlas (TCGA) database, and exosomal miRNAs data were downloaded from the GEO dataset GSE39833. The differential expression analysis was performed using “limma” and “edgeR”. Target mRNAs of miRNAs were predicted using FunRich 3.1.3, miRNAtap and multiMiR. The candidate mRNAs and exosomal miRNAs were obtained by intersecting two groups of differentially expressed miRNAs and intersection of the differential expressed mRNAs and the target mRNAs, respectively. Key mRNAs and exosomal miRNAs were identified by the least absolute shrinkage and selection operator regression analysis, and used to construct the exosomal miRNA-mRNA network. The network verified was by receiver operating characteristic curve, GEPIA and LinkedOmics. Functional enrichment analysis was also performed for studied miRNAs and mRNAs.

Results

A total of 6568 differentially expressed mRNAs and 531 differentially expressed miRNAs from TCGA data, and 166 differentially expressed exosomal miRNAs in GSE39833 dataset were identified. Next, 16 key mRNAs and five key exosomal miRNAs were identified from the 5284 candidate mRNAs and 61 candidate exosomal miRNAs, respectively. The exosomal miRNA-mRNA network with high connectivity contained 13 hub mRNAs (CBFB, CDH3, ETV4, FOXQ1, FUT1, GCNT2, GRIN2D, KIAA1549, KRT80, LZTS1, SLC39A10, SPTBN2, and ZSWIM4) and five hub exosomal miRNAs (hsa-miR-126, hsa-miR-139, hsa-miR-141, hsa-miR-29c, and hsa-miR-423). The functional annotation revealed that these hub mRNAs were mainly involved in the regulation of B cell receptor signaling pathway and glycosphingolipid biosynthesis related pathways. All hub mRNAs and hub exosomal miRNAs exhibited high diagnosis value for CRC. Furthermore, the association of the hub mRNAs with overall survival, stages, and MSI phenotype of CRC revealed their important roles in CRC progression.

Conclusion

This study constructed an exosomal miRNA-mRNA network which may play crucial roles in the carcinogenesis and progression of CRC, thus providing potential diagnostic biomarkers and therapeutic targets for CRC.
A multiplex PCR amplicon sequencing assay to screen genetic hearing loss variants in newborns
Authors: Yang Haiyan , Luo Hongyu , Zhang Guiwei , Zhang Junqing , Peng Zhiyu , Xiang Jiale
Published: February 2021

Background

Congenital hearing loss is one of the most common birth defects. Early identification and management play a crucial role in improving patients’ communication and language acquisition. Previous studies demonstrated that genetic screening complements newborn hearing screening in clinical settings.

Methods

We developed a multiplex PCR amplicon sequencing assay to sequence the full coding region of the GJB2 gene, the most pathogenic variants of the SLC26A4 gene, and hotspot variants in the MT-RNR1 gene. The sensitivity, specificity, and reliability were validated via samples with known genotypes. Finally, a pilot study was performed on 300 anonymous dried blood samples.

Results

Of 103 samples with known genotypes, the multiplex PCR amplicon sequencing assay accurately identified all the variants, demonstrating a 100% sensitivity and specificity. The consistency is high in the analysis of the test–retest reliability and internal consistency reliability. In the pilot study, 12.3% (37/300) of the newborns were found to carry at least one pathogenic variant, including 24, 10, and 3 from the GJB2, SLC26A4, and MT-RNR1 gene, respectively. With an allele frequency of 2.2%, the NM_004004.6(GJB2):c.109G>A was the most prevalent variant in the study population.

Conclusion

The multiplex PCR amplicon sequencing assay is an accurate and reliable test to detect hearing loss variants in the GJB2, SLC26A4, and MT-RNR1 genes. It can be used to screen genetic hearing loss in newborns.
A dynamic systems view of clinical genomics: a rich picture of the landscape in Australia using a complexity science lens
Authors: Long Janet C. , Gul Hossai , McPherson Elise , Best Stephanie , Augustsson Hanna , Churruca Kate , Ellis Louise A. , Braithwaite Jeffrey
Published: February 2021

Background

Clinical genomics represents a paradigm shifting change to health service delivery and practice across many conditions and life-stages. Introducing this complex technology into an already complex health system is a significant challenge that cannot be managed in a reductionist way. To build robust and sustainable, high quality delivery systems we need to step back and view the interconnected landscape of policymakers, funders, managers, multidisciplinary teams of clinicians, patients and their families, and health care, research, education, and philanthropic institutions as a dynamic whole. This study holistically mapped the landscape of clinical genomics within Australia by developing a complex graphic: a rich picture. Using complex systems theory, we then identified key features, challenges and leverage points of implementing clinical genomics.

Methods

We used a multi-stage, exploratory, qualitative approach. We extracted data from grey literature, empirical literature, and data collected by the Australian Genomic Health Alliance. Nine key informants working in clinical genomics critiqued early drafts of the picture, and validated the final version.

Results

The final graphic depicts 24 stakeholder groups relevant to implementation of genomics into Australia. Clinical genomics lies at the intersection of four nested systems, with interplay between government, professional bodies and patient advocacy groups. Barriers and uncertainties are also shown. Analysis using complexity theory showed far-reaching interdependencies around funding, and identified unintended consequences.

Conclusion

The rich picture of the clinical genomic landscape in Australia is the first to show key stakeholders, agencies and processes and their interdependencies. Participants who critiqued our results were instantly intrigued and engaged by the graphics, searching for their place in the whole and often commenting on insights they gained from seeing the influences and impacts of other stakeholder groups on their own work. Funding patterns showed unintended consequences of increased burdens for clinicians and inequity of access for patients. Showing the system as a dynamic whole is the only way to understand key drivers and barriers to largescale interventions.Trial Registration:Not applicable
MicroRNAs and long non-coding RNAs in the pathophysiological processes of diabetic cardiomyopathy: emerging biomarkers and potential therapeutics
Authors: Jakubik Daniel , Fitas Alex , Eyileten Ceren , Jarosz-Popek Joanna , Nowak Anna , Czajka Pamela , Wicik Zofia , Sourij Harald , Siller-Matula Jolanta M. , De Rosa Salvatore , Postula Marek
Published: February 2021

The epidemic of diabetes mellitus (DM) necessitates the development of novel therapeutic and preventative strategies to attenuate complications of this debilitating disease. Diabetic cardiomyopathy (DCM) is a frequent disorder affecting individuals diagnosed with DM characterized by left ventricular hypertrophy, diastolic and systolic dysfunction and myocardial fibrosis in the absence of other heart diseases. Progression of DCM is associated with impaired cardiac insulin metabolic signaling, increased oxidative stress, impaired mitochondrial and cardiomyocyte calcium metabolism, and inflammation. Various non-coding RNAs, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), as well as their target genes are implicated in the complex pathophysiology of DCM. It has been demonstrated that miRNAs and lncRNAs play an important role in maintaining homeostasis through regulation of multiple genes, thus they attract substantial scientific interest as biomarkers for diagnosis, prognosis and as a potential therapeutic strategy in DM complications. This article will review the different miRNAs and lncRNA studied in the context of DM, including type 1 and type 2 diabetes and the contribution of pathophysiological mechanisms including inflammatory response, oxidative stress, apoptosis, hypertrophy and fibrosis to the development of DCM .
Role of Snf-β in lipid accumulation in the high lipid‐producing fungus Mucor circinelloides WJ11
Authors: Nosheen Shaista , Naz Tahira , Yang Junhuan , Hussain Syed Ammar , Fazili Abu Bakr Ahmad , Nazir Yusuf , Li Shaoqi , Mohamed Hassan , Yang Wu , Mustafa Kiren , Song Yuanda
Published: February 2021

Background

Mucor circinelloides WJ11 is a high-lipid producing strain and an excellent producer of γ-linolenic acid (GLA) which is crucial for human health. We have previously identified genes that encode for AMP-activated protein kinase (AMPK) complex in M. circinelloides which is an important regulator for lipid accumulation. Comparative transcriptional analysis between the high and low lipid-producing strains of M. circinelloides showed a direct correlation in the transcriptional level of AMPK genes with lipid metabolism. Thus, the role of Snf-β, which encodes for β subunit of AMPK complex, in lipid accumulation of the WJ11 strain was evaluated in the present study.

Results

The results showed that lipid content of cell dry weight in Snf-β knockout strain was increased by 32 % (from 19 to 25 %). However, in Snf-β overexpressing strain, lipid content of cell dry weight was decreased about 25 % (from 19 to 14.2 %) compared to the control strain. Total fatty acid analysis revealed that the expression of the Snf-β gene did not significantly affect the fatty acid composition of the strains. However, GLA content in biomass was increased from 2.5 % in control strain to 3.3 % in Snf-β knockout strain due to increased lipid accumulation and decreased to 1.83 % in Snf-β overexpressing strain. AMPK is known to inactivate acetyl-CoA carboxylase (ACC) which catalyzes the rate-limiting step in lipid synthesis. Snf-β manipulation also altered the expression level of the ACC1 gene which may indicate that Snf-β control lipid metabolism by regulating ACC1 gene.

Conclusions

Our results suggested that Snf-β gene plays an important role in regulating lipid accumulation in M. circinelloides WJ11. Moreover, it will be interesting to evaluate the potential of other key subunits of AMPK related to lipid metabolism. Better insight can show us the way to manipulate these subunits effectively for upscaling the lipid production. Up to our knowledge, it is the first study to investigate the role of Snf-β in lipid accumulation in M. circinelloides.
Clinical and prognostic significances of cancer stem cell markers in gastric cancer patients: a systematic review and meta-analysis
Authors: Razmi Mahdieh , Ghods Roya , Vafaei Somayeh , Sahlolbei Maryam , Saeednejad Zanjani Leili , Madjd Zahra
Published: February 2021

Background

Gastric cancer (GC) is considered one of the most lethal malignancies worldwide, which is accompanied by a poor prognosis. Although reports regarding the importance of cancer stem cell (CSC) markers in gastric cancer progression have rapidly developed over the last few decades, their clinicopathological and prognostic values in gastric cancer still remain inconclusive. Therefore, the current meta-analysis aimed to quantitatively re-evaluate the association of CSC markers expression, overall and individually, with GC patients’ clinical and survival outcomes.

Methods

Literature databases including PubMed, Scopus, ISI Web of Science, and Embase were searched to identify the eligible articles. Hazard ratios (HRs) or odds ratios (ORs) with 95% confidence intervals (CIs) were recorded or calculated to determine the relationships between CSC markers expression positivity and overall survival (OS), disease-free survival (DFS)/relapse-free survival (RFS), disease-specific survival (DSS)/ cancer-specific survival (CSS), and clinicopathological features.

Results

We initially retrieved 4,425 articles, of which a total of 66 articles with 89 studies were considered as eligible for this meta-analysis, comprising of 11,274 GC patients. Overall data analyses indicated that the overexpression of CSC markers is associated with TNM stage (OR = 2.19, 95% CI 1.84–2.61, P = 0.013), lymph node metastasis (OR = 1.76, 95% CI 1.54–2.02, P < 0.001), worse OS (HR = 1.65, 95% CI 1.54–1.77, P < 0.001), poor CSS/DSS (HR = 1.69, 95% CI 1.33–2.15, P < 0.001), and unfavorable DFS/RFS (HR = 2.35, 95% CI 1.90–2.89, P < 0.001) in GC patients. However, CSC markers expression was found to be slightly linked to tumor differentiation (OR = 1.25, 95% CI 1.01–1.55, P = 0.035). Sub-analysis demonstrated a significant positive relationship between most of the individual markers, specially Gli-1, Oct-4, CD44, CD44V6, and CD133, and clinical outcomes as well as the reduced survival, whereas overexpression of Lgr-5, Nanog, and sonic hedgehog (Shh) was not found to be related to the majority of clinical outcomes in GC patients.

Conclusion

The expression of CSC markers is mostly associated with worse outcomes in patients with GC, both overall and individual. The detection of a combined panel of CSC markers might be appropriate as a prognostic stratification marker to predict tumor aggressiveness and poor prognosis in patients with GC, which probably results in identifying novel potential targets for therapeutic approaches.
Silencing of MEG3 attenuated the role of lipopolysaccharides by modulating the miR-93-5p/PTEN pathway in Leydig cells
Authors: Zhou Xu , He Jingliang , Chen Jinbo , Cui Yu , Ou Zhenyu , Zu Xiongbing , Liu Nenghui
Published: February 2021

Background

Leydig cells reflect the activation of inflammation, decrease of androgen production, inhibition of cell growth and promotion of cell apoptosis under orchitis. Maternally expressed gene 3 (MEG3) exerts a crucial role in various human diseases, but under orchitis, the role and underlying molecular mechanism of MEG3 in Leydig cells remain unclear.

Methods

Lipofectamine 2000 was used for the cell transfections. qPCR and western blots assay were applied to assess the gene expression. ELISA assay was used to measure the TNFα, IL6 and testosterone secretion. CCK8 and EdU assay was employ to test the cell viability and proliferation respectively. Luciferase reporter and RIP assay were introduced to detect the binding of miR-93-5p with MEG3 and PTEN.

Results

Lipopolysaccharides (LPS) induced TNFα and IL6 secretion, lowered testosterone production, inhibited cell viability and proliferation, and induced cell apoptosis in Leydig cells. MEG3 was upregulated in Leydig cells treated with LPS and that knockdown of MEG3 inhibited the role of LPS in Leydig cells. MEG3 absorbed miR-93-5p and that suppression of miR-93-5p restored the role of silenced MEG3 in Leydig cells under LPS treatment. miR-93-5p inhibited PTEN expression and that over-expressed PTEN alleviated the effect of miR-93-5p in Leydig cells treated with LPS. LPS activated the MEG3/miR-93-5p/PTEN signalling pathway in Leydig cells.

Conclusions

This study revealed that MEG3 serves as a molecular sponge to absorb miR-93-5p, thus leading to elevation of PTEN expression in Leydig cells under LPS treatment, offering a theoretical basis on which to establish potential new treatment strategies for orchitis.
Hyper‐metabolic B cells in the spleens of old mice make antibodies with autoimmune specificities
Authors: Frasca Daniela , Romero Maria , Garcia Denisse , Diaz Alain , Blomberg Bonnie B.
Published: February 2021

Background

Aging is associated with increased intrinsic B cell inflammation, decreased protective antibody responses and increased autoimmune antibody responses. The effects of aging on the metabolic phenotype of B cells and on the metabolic programs that lead to the secretion of protective versus autoimmune antibodies are not known.

Methods

Splenic B cells and the major splenic B cell subsets, Follicular (FO) and Age-associated B cells (ABCs), were isolated from the spleens of young and old mice and left unstimulated. The RNA was collected to measure the expression of markers associated with intrinsic inflammation and autoimmune antibody production by qPCR. B cells and B cell subsets were also stimulated with CpG and supernatants collected after 7 days to measure autoimmune IgG secretion by ELISA. Metabolic measures (oxygen consumption rate, extracellular acidification rate and glucose uptake) were performed using a Seahorse XFp extracellular flux analyzer.

Results

Results have identified the subset of ABCs, whose frequencies and numbers increase with age and represent the most pro-inflammatory B cell subset, as the cell type mainly if not exclusively responsible for the expression of inflammatory markers and for the secretion of autoimmune antibodies in the spleen of old mice. Hyper-inflammatory ABCs from old mice are also hyper-metabolic, as compared to those from young mice and to the subset of FO B cells, a feature needed not only to support their higher expression of RNA for inflammatory markers but also their higher autoimmune antibody secretion.

Conclusions

These results identify a relationship between intrinsic inflammation, metabolism and autoimmune B cells and suggest possible ways to understand cellular mechanisms that lead to the generation of pathogenic B cells, that are hyper-inflammatory and hyper-metabolic, and secrete IgG antibodies with autoimmune specificities.
Quantifying steric hindrance and topological obstruction to protein structure superposition
Authors: Røgen Peter
Published: February 2021

Background

In computational structural biology, structure comparison is fundamental for our understanding of proteins. Structure comparison is, e.g., algorithmically the starting point for computational studies of structural evolution and it guides our efforts to predict protein structures from their amino acid sequences. Most methods for structural alignment of protein structures optimize the distances between aligned and superimposed residue pairs, i.e., the distances traveled by the aligned and superimposed residues during linear interpolation. Considering such a linear interpolation, these methods do not differentiate if there is room for the interpolation, if it causes steric clashes, or more severely, if it changes the topology of the compared protein backbone curves.

Results

To distinguish such cases, we analyze the linear interpolation between two aligned and superimposed backbones. We quantify the amount of steric clashes and find all self-intersections in a linear backbone interpolation. To determine if the self-intersections alter the protein’s backbone curve significantly or not, we present a path-finding algorithm that checks if there exists a self-avoiding path in a neighborhood of the linear interpolation. A new path is constructed by altering the linear interpolation using a novel interpretation of Reidemeister moves from knot theory working on three-dimensional curves rather than on knot diagrams. Either the algorithm finds a self-avoiding path or it returns a smallest set of essential self-intersections. Each of these indicates a significant difference between the folds of the aligned protein structures. As expected, we find at least one essential self-intersection separating most unknotted structures from a knotted structure, and we find even larger motions in proteins connected by obstruction free linear interpolations. We also find examples of homologous proteins that are differently threaded, and we find many distinct folds connected by longer but simple deformations. TM-align is one of the most restrictive alignment programs. With standard parameters, it only aligns residues superimposed within 5 Ångström distance. We find 42165 topological obstructions between aligned parts in 142068 TM-alignments. Thus, this restrictive alignment procedure still allows topological dissimilarity of the aligned parts.

Conclusions

Based on the data we conclude that our program provides significant additional information to alignment scores based solely on distances between aligned and superimposed residue pairs.
Potential clinical utility of MUC5B und TOLLIP single nucleotide polymorphisms (SNPs) in the management of patients with IPF
Authors: Bonella Francesco , Campo Ilaria , Zorzetto Michele , Boerner Eda , Ohshimo Shinichiro , Theegarten Dirk , Taube Christian , Costabel Ulrich
Published: February 2021

Background

Genetic variants of TOLLIP and MUC5B, both on chromosome 11, have been reported to be associated with the development and/or prognosis of idiopathic pulmonary fibrosis (IPF). This retrospective study was conducted to investigate the association of MUC5B and TOLLIP SNPs with disease outcome in IPF. 62 IPF patients and 50 healthy controls (HC) from our Institution were genotyped for SNPs within MUC5B (rs35705950) and TOLLIP (rs3750920 and rs5743890). Correlation of SNPs genotypes with survival, acute exacerbation (AE) or disease progression (defined as a decline of ≥ 5% in FVC and or ≥ 10% in DLco in one year) was investigated.

Results

The MUC5B rs35705950 minor allele (T) was more frequent in IPF subjects than in HC (35% vs 9% p < 0.001). TOLLIP SNPs alleles and genotype distribution did not differ between IPF and HC and did not vary according to gender, age, BMI and lung functional impairment at baseline. The minor allele (C) in TOLLIP rs5743890 was associated with worse survival and with disease progression in all performed analyses. The MUC5B rs35705950 or the TOLLIP rs3750920 minor allele, were not associated with disease progression or AE.

Conclusion

We confirm that the minor allele of MUC5B rs35705950 is associated with IPF. The minor allele of TOLLIP rs5743890 appears to be a predictor of worse survival and more rapid disease progression, therefore being of potential utility to stratify IPF patients at baseline.
Diagnostic accuracy of a dynamically increased red blood cell distribution width in very low birth weight infants with serious bacterial infection
Authors: Guo Bin-Fang , Sun Su-Zhen
Published: February 2021

Objective

Serious bacterial infection (SBI) remains an important cause of morbidity and mortality in preterm infants. The objective of this study was to evaluate the dynamically increased value of the red cell distribution width (RDW) in the diagnosis of SBI.

Methods

This retrospective study enrolled 334 preterm infants with birth weight less than 1500 g. The initial RDW and the maximum value of RDW during hospitalization were extracted from the MIMIC-III database (version 1.4). Infants were categorized into four groups according to baseline RDW value and ΔRDW (ΔRDW = RDW at maximum- RDW at baseline). Logistic regression analysis was used to assess the risk of developing SBI in each group. A receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic value of RDW at baseline alone, ΔRDW alone, and in combination.

Results

Infants with increased RDW at baseline (> 17%) and ΔRDW > 2% exhibited the highest risk of developing SBI, whereas the patients with normal RDW level at baseline (≤ 17%) and ΔRDW≤2% (the reference group) had the lowest risk. This association remained unaltered even after adjustment in multivariable models. Basing on ROC curve analysis, the area under the curve predicted by the combination of RDW at baseline and ΔRDW for SBI was 0.81 (95% CI, 0.76–0.87). Sensitivity and specificity were 78.16 and 72.47% respectively.

Conclusions

We observed that combination of elevated RDW at baseline and dynamic increases during hospitalization is significantly associated with SBI. Therefore, that combination could be a promising independent diagnostic indicator of SBI in newborns.
iKanEat: protocol for a randomized controlled trial of megestrol as a component of a pediatric tube weaning protocol
Authors: Edwards Sarah , Hyman Paul E. , Mousa Hayat , Bruce Amanda , Cocjin Jose , Dean Kelsey , Fleming Kandace , Romine Rebecca Swinburne , Davis Ann M.
Published: February 2021

Background

Although tube feeding routinely saves the lives of children who do not eat by mouth, chronic tube feeding can be a burden to patients, caregivers, and families. Very few randomized trials exist regarding the best methods for weaning children from their feeding tubes.

Methods

The current paper describes a randomized controlled trial of an empirically supported outpatient treatment protocol for moving children from tube to oral eating called iKanEat. Specifically, we describe the methods of randomized double-blind, placebo-controlled trial which includes a 4-week course of megestrol, the only medication used in the iKanEat protocol, to determine whether the addition of megestrol results in improved child outcomes. The primary and secondary aims are to assess the safety and efficacy of megestrol as part of the iKanEat protocol. The third aim is to provide critical information about the impact of the transition from tube to oral feeding on parent stress and parent and child quality of life.

Discussion

This trial will provide data regarding whether megestrol is a safe and effective component of the iKanEat tube weaning protocol, as well as important data on how the tube weaning process impacts parent stress and parent and child quality of life.

Trial registration

ClinicalTrials.gov NCT#03815019. Registered on January 17, 2019
Colorimetric LPMO assay with direct implication for cellulolytic activity
Authors: Brander Søren , Lausten Stine , Ipsen Johan Ø. , Falkenberg Kristoffer B. , Bertelsen Andreas B. , Nørholm Morten H. H. , Østergaard Lars H. , Johansen Katja S.
Published: February 2021

Background

Lytic polysaccharide monooxygenases (LPMOs) are important industrial enzymes known for their catalytic degradation of recalcitrant polymers such as cellulose or chitin. Their activity can be measured by lengthy HPLC methods, while high-throughput methods are less specific. A fast and specific LPMO assay would simplify screening for new or engineered LPMOs and accelerate biochemical characterization.

Results

A novel LPMO activity assay was developed based on the production of the dye phenolphthalein (PHP) from its reduced counterpart (rPHP). The colour response of rPHP oxidisation catalysed by the cellulose-specific LPMO from Thermoascus aurantiacus (TaAA9A), was found to increase tenfold by adding dehydroascorbate (DHA) as a co-substrate. The assay using a combination of rPHP and DHA was tested on 12 different metallo-enzymes, but only the LPMOs catalysed this reaction. The assay was optimized for characterization of TaAA9A and showed a sensitivity of 15 nM after 30 min incubation. It followed apparent Michaelis–Menten kinetics with kcat = 0.09 s−1 and KM = 244 µM, and the assay was used to confirm stoichiometric copper–enzyme binding and enzyme unfolding at a temperature of approximately 60 °C. DHA, glutathione and fructose were found to enhance LPMO oxidation of rPHP and in the optimized assay conditions these co-substrates also enabled cellulose degradation.

Conclusions

This novel and specific LPMO assay can be carried out in a convenient microtiter plate format ready for high-throughput screening and enzyme characterization. DHA was the best co-substrate tested for oxidation of rPHP and this preference appears to be LPMO-specific. The identified co-substrates DHA and fructose are not normally considered as LPMO co-substrates but here they are shown to facilitate both oxidation of rPHP and degradation of cellulose. This is a rare example of a finding from a high-throughput assay that directly translate into enzyme activity on an insoluble substrate. The rPHP-based assay thus expands our understanding of LPMO catalysed reactions and has the potential to characterize LPMO activity in industrial settings, where usual co-substrates such as ascorbate and oxygen are depleted.
Extended-spectrum β-lactamase blaCTX-M-1 group in gram-negative bacteria colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital in Morogoro, Tanzania
Authors: Moremi Nyambura , Silago Vitus , Mselewa Erick G. , Chifwaguzi Ashery P. , Mirambo Mariam M. , Mushi Martha F. , Matemba Lucas , Seni Jeremiah , Mshana Stephen E.
Published: February 2021

Objective

The objective of this study was to determine the proportion of extended spectrum β-lactamase producing gram-negative bacteria (ESBL-GNB) colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital, in Morogoro, Tanzania. Rectal colonization with ESBL-GNB increases the risks of developing bacterial infections by extra-intestinal pathogenic ESBL-GNB.

Results

Of the 285 patients investigated, 123 (43.2%) carried ESBL-GNB in their intestines. Five of the 123 ESBL positive patients were colonized with two different bacteria, making a total of 128 ESBL producing isolates. Escherichia coli (n = 95, 74.2%) formed the majority of ESBL isolates. The proportion of CTX-M-1 group genes among ESBL isolates tested was 94.9% (93/98). History of antibiotic use (OR: 1.83, 95% CI: 1.1–3.2, P = 0.03), being on antibiotic treatment (OR: 2.61, 95% CI: 1.5–4.53, P = 0.001), duration of hospital stay (OR: 1.2, 95% CI: 1.1–1.3, P < 0.001) and history of previous admission (OR: 2.24, 95% CI: 1.2–4.1, P = 0.009) independently predicted ESBL-GNB carriage.
Osthole enhances the bone mass of senile osteoporosis and stimulates the expression of osteoprotegerin by activating β-catenin signaling
Authors: Jin Zhen-Xiong , Liao Xin-Yuan , Da Wei-Wei , Zhao Yong-Jian , Li Xiao-Feng , Tang De-Zhi
Published: February 2021

Introduction

Osthole has a potential therapeutic application for anti-osteoporosis. The present study verified whether osthole downregulates osteoclastogenesis via targeting OPG.

Methods

In vivo, 12-month-old male mice were utilized to evaluate the effect of osthole on bone mass. In vitro, bone marrow stem cells (BMSCs) were isolated and extracted from 3-month-old OPG−/− mice and the littermates of OPG+/+ mice. Calvaria osteoblasts were extracted from 3-day-old C57BL/6J mice or 3-day-old OPG−/− mice and the littermates of OPG+/+ mice.

Results

Osthole significantly increased the gene and protein levels of OPG in primary BMSCs in a dose-dependent manner. The deletion of the OPG gene did not affect β-catenin expression. The deletion of the β-catenin gene inhibited OPG expression in BMSCs, indicating that osthole stimulates the expression of OPG via activation of β-catenin signaling.

Conclusion

Osthole attenuates osteoclast formation by stimulating the activation of β-catenin-OPG signaling and could be a potential drug for the senile osteoporosis.
Taxonomy, virulence determinants and antimicrobial susceptibility of Aeromonas spp. isolated from bacteremia in southeastern China
Authors: Sun Yao , Zhao Yajie , Xu Wenya , Fang Renchi , Wu Qing , He Haokuang , Xu Chunquan , Zhou Cui , Cao Jianming , Chen Lijiang , Zhou Tieli
Published: February 2021

Background

The study aimed to elucidate the species taxonomy, clinical manifestations, virulence gene profiles and antimicrobial susceptibilities of Aeromonas strains isolated from life-threatening bacteremia in southeastern China.

Methods

Clinical samples of Aeromonas causing bacteremia were isolated from a teaching hospital in Wenzhou from 2013 to 2018 and a retrospective cohort study was performed. Aeromonas strains were identified at species level by housekeeping gene gyrB. Virulence and drug resistance-associated genes were screened by polymerase chain reaction (PCR) and antimicrobial susceptibility testing (AST) was performed by the VITEK 2 Compact system.

Results

A total of 58 Aeromonas isolated from patients with bacteremia were collected during 6 years (2013–2018). 58 isolates were identified to five different species, where Aeromonas dhakensis appeared to be the predominant species (26/58), followed by Aeromonas veronii (13/58), Aeromonas caviae (10/58), Aeromonas hydrophila (7/58) and Aeromonas jandaei (2/58). 16 of 58 patients had poor prognosis. Poor prognosis was significantly associated with liver cirrhosis and inappropriate empirical antimicrobials therapy. The progression of bacteremia caused by Aeromonas was extremely fast, especially in A. dhakensis infections. Virulence genes aer, lip, hlyA, alt, ast, and act, were detected at ratios of 24.1% (14/58), 62.1% (36/58), 65.5% (38/58), 58.6% (34/58), 15.5% (9/58) and 65.5% (38/58), respectively. Antimicrobial susceptibility testing exhibited that 9 out of 58 isolates were identified as multi-drug resistant (MDR) organism. The blaTEM gene was identified in all 9 MDR isolates. blaSHV, blaAQU-1, blaMOX, blaCepH, blaCphA and aac(6′)-Ib-cr were detected in 4 isolates, 2 isolates, 1 isolate, 3 isolates, 8 isolates, and 3 isolates, respectively. The majority of Aeromonas strains maintained susceptible to 3rd generation cephalosporins, aminoglycosides, fluoroquinolones and furantoin.

Conclusions

The prevalence and dangerousness of Aeromonas infections, especially A. dhakensis, are underestimated in clinic. Continuous monitoring is essential to keep track of MDR Aeromonas due to the increasing prevalence recently and a more effective measure is required to control the spread of resistance determinants.
Effect of wood biomass components on self-heating
Authors: Miyawaki Nozomi , Fukushima Takashi , Mizuno Takafumi , Inoue Miyao , Takisawa Kenji
Published: February 2021

Biomass may ignite due to biological oxidation and chemical oxidation. If this phenomenon (spontaneous ignition) is controlled, it would be possible to produce biochar at a lower cost without the need for an external heat resource. We investigated if self-heating could be controlled by using sawdust and bark chips. When sawdust and bark chips were used under controlled conditions, the bark chips temperature increased to the torrefaction temperature. The ash content of bark chips was ~ 2%d.b. higher than that of sawdust; consequently, the inorganic substances contained in the bark chips might affect the self-heating. Self-heating was suppressed when inorganic substances were removed by washing with water. Therefore, the inorganic substances in the biomass might have affected self-heating. The inorganic element contents of the bark chips were measured by inductively coupled plasma optical emission spectrometry before and after washing. The potassium content of the bark chips was reduced remarkably by washing, and there was a possible influence of potassium on self-heating. Finally, the effect of moisture content on self-heating was investigated to obtain stable reactivity. Thus, at a moisture content of 40%w.b., a steady self-heating behavior may be realized.