Fold Change Difference Research Articles

Proteomics Analysis of Human Chorionic Villi Reveals Dysregulated Pathways That Contribute to Recurrent Pregnancy Loss.

Recurrent pregnancy loss (RPL) represents a common disorder with consequences on family and society. As more than half of the RPL cases do not have a clearly identified cause, uncovering the mechanisms behind the idiopathic RPL is urgently needed. Using label-free data-independent LC-MS/MS acquisition coupled with ion mobility, we compared the proteome of chorionic villi from 13 RPL cases with 10 age and gestational week-matched elective pregnancies. Transcriptional levels of selected candidate biomarkers were determined in chorionic villi of 35 RPL cases and 25 controls using quantitative polymerase chain reaction (qPCR). Statistically significant difference in abundance (Benjamini-Hochberg [B-H] p≤0.05) and fold change ≥1.5 showed 128 proteins. Bioinformatics analysis identified complement and coagulation cascades, platelet activation, tricarboxylic acid cycle (TCA) cycle, and ferroptosis as pathways with the highest significance. Correlation with transcriptome datasets revealed a weak statistically significant positive correlation with 45% of the co-differentially expressed proteins/genes displaying the same regulation trend. The transcription levels of neurofilament light polypeptide (NEFL), dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex_mitochondrial (DLST), nitric oxide synthase3 (NOS3), and ceruloplasmin (CP) were significantly increased in the RPL, consistent with the proteomics findings. Our data suggests alteration of several pathways as potential causes of idiopathic RPL from the fetal side and opens the way for investigations concerning clinical management.

Alitretinoin versus phototherapy as the first-line treatment in adults with severe chronic hand eczema: the ALPHA RCT.

Hand eczema is common and a cause of morbidity and occupational disability. When education, irritant/contact allergen avoidance, moisturisation and topical corticosteroids are insufficient to control chronic hand eczema, ultraviolet therapy or systemic immune-modifying drugs are used. There is no treatment pathway generally accepted by UK dermatologists. Compare alitretinoin and ultraviolet therapy as first-line therapy in terms of disease activity at 12 weeks post planned start of treatment. Prospective, multicentre, open-label, two-arm parallel group, adaptive randomised controlled trial with one planned interim analysis, and an economic evaluation. UK secondary care dermatology outpatient clinics. Patients with severe chronic hand eczema unresponsive to at least 4 weeks of treatment with potent topical corticosteroids. Natural logarithm of the Hand Eczema Severity Index + 1, 12 weeks post planned start of treatment. Participants randomised 1:1 by minimisation to alitretinoin or ultraviolet therapy for 12 to 24 weeks. Blinded primary end-point assessor. Intention-to-treat population: 441 (100.0%) participants; 220 (49.9%) alitretinoin and 221 (50.1%) ultraviolet therapy. At least one dose was received by 212 (96.4%) alitretinoin and 196 (88.7%) ultraviolet therapy participants. The unadjusted median (interquartile range) relative change in hand eczema severity index at 12 weeks was 30% (10-70%) of that at baseline for alitretinoin compared with 50% (20-100%) for ultraviolet therapy. There was a statistically significant benefit of alitretinoin compared with ultraviolet therapy at 12 weeks, with an estimated fold change or relative difference (95% confidence interval) = 0.66 (0.52 to 0.82), p = 0.0003 at 12 weeks. There was no evidence of a difference at 24 or 52 weeks, with the estimated fold change (95% confidence interval) equal to 0.92 (0.798 to 1.08) and 1.27 (0.97 to 1.67), respectively. Fifty-nine per cent allocated to alitretinoin and 61% allocated to ultraviolet therapy achieved a clear/almost clear assessment during the trial period. Differential treatment compliance observed: 145 (65.9%) alitretinoin and 53 (24.0%) ultraviolet therapy participants confirmed compliance (≥80% received, no treatment breaks > 7 days during first 12 weeks). High levels of missing data were observed. One hundred and thirty-five reportable adverse events across 79 participants, 55 (25.0%) alitretinoin and 24 (10.9%) ultraviolet therapy. Four serious adverse events (two alitretinoin, two ultraviolet therapy). Four pregnancies reported (three alitretinoin, one ultraviolet therapy). No new safety signals were detected. As a first-line therapy, alitretinoin showed more rapid improvement and superiority to ultraviolet therapy at week 12. This difference was not observed at later time points. Alitretinoin is cost-effective at weeks 12 and 52. Ultraviolet therapy is cost-effective after 10 years, with a high degree of uncertainty. Hand eczema severity index may be a useful primary outcome measure for hand eczema trials; ALPHA results will inform future trials. Treatment compliance was poor for ultraviolet therapy. Regular twice weekly treatment was not received by most patients. Assessment of long-term effects of randomised treatments was complicated by use of second-line treatments post treatment phase. Further analysis of substudies and pilot data will provide valuable information for future studies. A clear need for better therapeutic approaches for severe chronic hand eczema remains. Future studies will need to further address long-term benefits of treatments given. This trial is registered as ISRCTN80206075. This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: 12/186/01) and is published in full in Health Technology Assessment; Vol. 28, No. 59. See the NIHR Funding and Awards website for further award information.

Suppression of the DNA repair enzyme NEIL2 promotes persistent inflammation and genomic damage in subjects with stable COPD and during severe exacerbations.

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory airway disease that is an independent risk factor for lung cancer. NEIL2, a DNA glycolase involved in DNA repair during transcription, has also been associated with an increased incidence of malignancies in humans. NEIL2 knockout mouse models have demonstrated increased inflammation and oxidative DNA damage in the lungs after exposure to an inflammatory insult, but data are lacking regarding NEIL2 function in individuals with stable COPD and during severe acute exacerbations of COPD (AECOPD). We investigated whether NEIL2 levels and oxidative DNA damage to the transcribed genome are altered in individuals with stable COPD and AECOPD. The study was conducted at a single center in the US. Eligible subjects underwent a one-time 30 cc venous blood draw. The population consisted of 50 adults: 16 with stable COPD, 11 hospitalized for AECOPD, and 23 volunteers. We analyzed blood leukocytes for NEIL2 mRNA and DNA damage by RT-qPCR and LA-qPCR, respectively, in all groups. Plasma levels of seven biomarkers, CXCL1, CXCL8, CXCL9, CXCL10, CCL2, CCL11 and IL-6, were analyzed in the COPD groups using a magnetic bead panel (Millipore®). The NEIL2 mRNA levels were lower in individuals with stable COPD and AECOPD than in controls (0.72 for COPD, p = 0.0289; 0.407 for AECOPD, p = 0.0002). The difference in NEIL2 mRNA expression between the stable COPD group and AECOPD group was also statistically significant (p < 0.001). The fold change in DNA lesions per 10 kb of DNA was greater in the stable COPD (9.38, p < 0.0008) and AECOPD (15.81, p < 0.0004) groups than in the control group. The difference in fold change was also greater in the AECOPD group versus stable COPD p < 0.0236). Biomarker levels were not significantly different between the COPD groups. NEIL2 levels were correlated with plasma eosinophil levels in the stable COPD group (r = 0.737, p < 0.0027). NEIL2 mRNA levels are significantly reduced in COPD subjects and are associated with increased DNA damage and inflammation. These results reveal a mechanism that promotes persistent airway inflammation and oxidative genomic damage and increases the risk of malignancy in this population.

Comparative proteomics analysis of decidua reveals altered RNA processing and impaired ribosome function in recurrent pregnancy loss

IntroductionFactors contributing to recurrent pregnancy loss (RPL) in more than half of the cases are still unknown. The incidence and societal impact of this condition requires urgent elucidation of the mechanisms behind it, which could aid in significant improvement of clinical management. Materials and methodsUsing a highly efficient in-solution digestion method and label-free data-independent LC-MS/MS acquisition with ion mobility, we performed comparative proteomics analysis of the decidua tissues from 19 RPL patients and 10 controls. Differentially abundant proteins (DAPs) were compared and correlated with 3 publicly available transcriptomic datasets and the expression of selected biomarkers was tested by qPCR in decidua and chorionic villi from an extended cohort. ResultsFrom 1952 proteins identified based on ≥2 peptides, the statistically significant difference in abundance (Anova p ≤ 0.05) and fold change ≥1.2 showed 85 proteins. Pathway analysis using Reactome, KEGG and Wiki pathways identified enrichment of “Signaling by ROBO receptors”, “RNA degradation” and “Cytoplasmic Ribosomal Proteins”. The correlation between protein and gene expression in decidua revealed that the down-regulated ribosomal proteins in our dataset (RPS15, RPS17, RPL27A, RPL35A and RPL18) showed the same regulation trend at the mRNA level, which was later confirmed for transcripts of RPS15 and RPL18 in our cohort. DiscussionOur data suggests that the potential causes of RPL from the maternal side could be associated with impaired RNA processing machinery. Furthermore, the list of DAPs in RPL opens future investigations in terms of screening novel gene variants predisposing to pregnancy failure and developing biomarkers for RPL risk.

Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays.

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires ongoing monitoring to judge the ability of newly arising variants to escape the immune response. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal serum samples. We compared 18 datasets generated using human, hamster, and mouse serum and six different neutralization assays. Datasets using animal model serum samples showed higher titer magnitudes than datasets using human serum samples in this comparison. Fold change in neutralization of variants compared to ancestral SARS-CoV-2, immunodominance patterns, and antigenic maps were similar among serum samples and assays. Most assays yielded consistent results, except for differences in fold change in cytopathic effect assays. Hamster serum samples were a consistent surrogate for human first-infection serum samples. These results inform the transition of surveillance of SARS-CoV-2 antigenic variation from dependence on human first-infection serum samples to the utilization of serum samples from animal models.

Distinct proteomes and allergen profiles appear across the life-cycle stages of Alternaria alternata

Alternaria alternata is associated with allergic respiratory diseases, which can be managed with allergen extract-based diagnostics and immunotherapy. It is not known how spores and hyphae contribute to allergen content. Commercial allergen extracts are manufactured by extracting proteins without separating the different forms of the fungus. We sought to determine differences between spore and hyphae proteomes and how allergens are distributed in Aalternata. Data-independent acquisition mass spectrometry was used to quantitatively compare the proteomes of asexual spores (nongerminating and germinating) with vegetative hyphae. We identified 4515 proteins in nongerminating spores, germinating spores, and hyphae; most known allergens are more abundant in nongerminating spores. On comparing significant protein fold-change differences between nongerminating spores and hyphae, we found that 174 proteins were upregulated in nongerminating spores and 80 proteins in hyphae. Among the spore proteins are ones functionally involved in cell wall synthesis, responding to cellular stress, and maintaining redox balance and homeostasis. On comparing nongerminating and germinating spores, 25 proteins were found to be upregulated in nongerminating spores and 54 in germinating spores. Among the proteins specific to germinating spores were proteases known to be virulence factors. One of the most abundant proteins in the spore proteome is sialidase, which has not been identified as an allergen but may be important in the pathogenicity of this fungus. Major allergen Alt a 1 is present at low levels in spores and hyphae and appears to be largely secreted into growth media. Spores and hyphae express overlapping but distinct proteomes. Most known allergens are found more abundantly in nongerminating spores.

Effector Repertoire of the Sweetpotato Black Rot Fungal Pathogen Ceratocystis fimbriata.

In 2015, sweetpotato producers in the United States experienced one of the worst outbreaks of black rot recorded in history, with up to 60% losses reported in the field and packing houses and at shipping ports. Host resistance remains the ideal management tool to decrease crop losses. Lack of knowledge of Ceratocystis fimbriata biology represents a critical barrier for the deployment of resistance to black rot in sweetpotato. In this study, we scanned the recent near chromosomal-level assembly for putative secreted effectors in the sweetpotato C. fimbriata isolate AS236 using a custom fungal effector annotation pipeline. We identified a set of 188 putative effectors on the basis of secretion signal and in silico prediction in EffectorP. We conducted a deep RNA time-course sequencing experiment to determine whether C. fimbriata modulates effectors in planta and to define a candidate list of effectors expressed during infection. We examined the expression profile of two C. fimbriata isolates, a pre-epidemic (1990s) isolate and a post-epidemic (2015) isolate. Our in planta expression profiling revealed clusters of co-expressed secreted effector candidates. Based on fold-change differences of putative effectors in both isolates and over the course of infection, we suggested prioritization of 31 effectors for functional characterization. Among this set, we identified several effectors that provide evidence for a marked biotrophic phase in C. fimbriata during infection of sweetpotato storage roots. Our study revealed a catalog of effector proteins that provide insight into C. fimbriata infection mechanisms and represent a core catalog to implement effector-assisted breeding in sweetpotato. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Comparative Evaluation of Bacterial Reduction by Laser-Activated Irrigation Technique (LAI) With Conventional Needle Irrigation (CNI) in Single-Rooted Teeth With Pulpal Necrosis: A Single-Blinded Randomized Controlled Trial.

Aim To compare the bacterial reduction in single-rooted teeth with pulpal necrosis after laser-activated irrigation technique(LAI) and conventional needle irrigation (CNI). Methodology In this clinical trial (CTRI/2021/09/047767), 32 patients with pulpal necrosis were enrolled. Under complete aseptic conditions, access cavity preparation was done and the baseline sample S1 was collectedfrom the root canal using paper points. After chemo-mechanical preparation they were allocated into two groups, following block randomization; Group A - CNI with 27 gauge side-vented needle, Group B - LAI with pulsed Er,Cr:YSGG (erbium, chromium:yttrium-scandium-gallium-garnet) (2780 nm) laser. After irrigant activation, canals were dried and a second sample S2 was taken using paper points. Microbial analysis using quantitative polymerase chain reaction (qPCR) was done to quantify the bacterial reduction among the two groups. Inter-group and intra-group analysis was done using the independent student t-test and Bonferroni test, respectively. The data was represented in terms of quantification cycle (Cq) values, which are inversely proportional to the microbial count. Results There was no significant difference in S1 between the two groups (mean difference=0.0205; p=0.912). There was a significant difference in S2 between the two groups for the organisms (mean difference=0.8042; p=0.000). The mean percentage of bacterial reduction in CNI was 10.82% and in LAI it was 25.92%. There was a significant difference in S1 through S2 within the two groups for the organisms (p=0.000). The mean difference of Cq value is high for LAI compared to CNI (1.3494). The fold change was calculated by taking the ΔCq value and ΔΔCq value after the logarithmic transformation of the Cq value. LAI showed lower levels of DNA at S2 similar to CNI. There is no significant difference in mean fold change between CNI and LAI (p=0.564). Conclusion This clinical trial concluded that both LAI and CNI were effective in bacterial reduction. There was greater bacterial reduction with LAI (25.92%) than with the CNI (10.82%) in single-rooted teeth with pulpal necrosis using qPCR analysis.

Evaluation of Mirna-155 and Mirna-223 in Blood in Patients with Ulcerative Colitis

Ulcerative colitis is common and complex conditions that are difficult to cure. MiRNAs are a class of small, non-coding, single-stranded RNA molecules which play a key role in autoimmune and inflammatory diseases especially in IBD. Despite the efficacy of biological treatment, a significant proportion of patients with IBD do not show an adequate response. For this reason it is crucial to identify biomarkers useful to predict clinical response. In present study, we aimed to evaluate the microRNA-155 (miR-155) and microRNA-223 (miR-223) as prognostic marker in disease response to therapy in patients with UC. This study included 80 patients with UC (40 patients who response to conventional treatment and 40 who resist and they are on biological treatment) and 40 healthy controls. Real-time polymerase chain reaction (RT-PCR) assay was performed for evaluation miRNA-155 and miRNA-223. According to the results of this study, There was significant variation in mean fold change of miR-155 among groups (p &lt;0.001), the level was highest in patients on conventional treatment followed by patients on biological therapy and then by control group. With respect to miR-223, the difference in mean fold change was significant among study groups (p &lt;0.001), the level was highest in patients on biological treatment followed control group and then by patients on conventional therapy. Receiver operator characteristic (ROC) curve analysis was carried, the cutoff value of miRNA-155 was ≤1.43 with 20 % sensitivity level, 95 % specificity level and 53.3% accuracy level. The cutoff vale of miRNA-223 was &gt;4.51with 25 % sensitivity level, 92.5% specificity level and 59.1 % accuracy level. In conclusion, this study have evaluated the therapeutic response to corticosteroid, or IFX therapy and blood expression of miRNA by screening the responses to anti-TNF-α and conventional therapy, this study demonstrated that the level of miRNA-223 associated with the response to IFX which is highly increased in biological therapy (negative response) comparing to the conventional therapy (positive response) group after IFX therapy while the present study demonstrated that miRNA-155 fold change upregulated in patients with ulcerative colitis and on conventional therapy (positive response) in comparison with healthy control group.

BIOL-05. IDENTIFICATION AND VALIDATION OF PA2G4 AS A POTENTIAL THERAPEUTIC TARGET IN PEDIATRIC DIFFUSE GLIOMAS

Abstract Brain tumors are the second most common pediatric malignancy after leukemia. High grade gliomas have a significantly high morbidity and mortality in children, with a 5-year survival rate under 20%. This study aims to identify important biological mechanisms and proteins as prognostic biomarkers and novel therapeutic targets. We hypothesize that higher grade pediatric diffuse gliomas can be effectively targeted by knocking down expression of the proliferation associated protein 2G4 (PA2G4) that binds to MYCN and prevents its ubiquitination. LC-MS/MS proteomic profiling was performed on 28 formalin-fixed paraffin embedded primary diffuse glioma samples from Nationwide Children’s Hospital (Columbus, OH). Cox proportional hazard models were used to correlate individual proteins with progression-free survival (PFS) and overall survival (OS). Differences in fold change were calculated for each protein between low grade (LGG, grade 2) and high-grade glioma (HGG, grades 3-4) patients. Ingenuity Pathway Analysis was performed considering only proteins with p-values &amp;lt;0.05. In vitro studies were performed to evaluate the roles of PA2G4 in the SF188 glioma cell line. In comparing high- and low-grade tumors, 471 proteins were found to be significantly differentially expressed. Eighty-six and 121 proteins were significantly associated with OS and PFS, respectively. PA2G4 was expressed 2.0-fold higher in HGG vs LGG (p=0.015). Additionally, high expression of PA2G4 protein was associated with significantly worse PFS (p=0.041) and OS (p=0.035) and selected for further studies. Preliminary in vitro results showed that knocking-down PA2G4 decreased AKT phosphorylation/activation and levels of MYCN protein. Given that activated MYCN plays critical oncogenic roles in patients with poor survival PA2G4 may serve as a novel therapeutic target in higher grade pediatric diffuse gliomas. Studies are underway to unfold how PA2G4 affects treatment resistance and tumor recurrence in pediatric patients.

Seminal extracellular vesicle sncRNA sequencing reveals altered miRNA/isomiR profiles as sperm retrieval biomarkers for azoospermia.

Non-invasive molecular biomarkers for classifying azoospermia by origin into either obstructive or non-obstructive/secretory azoospermia, as well as for inferring the spermatogenic reserve of the testis of non-obstructive/secretory azoospermia patients, are of great interest for testicular sperm retrieval outcome prediction for assisted reproduction. Prior analyses of semen small non-coding RNA expression in azoospermia have focused on microRNAs, but there has been a lack of attention on other regulatory small RNA species. In this regard, studying more in-depth expression changes of small non-coding RNA subtypes in small extracellular vesicles from semen of azoospermic individuals could be useful to select additional non-invasive biomarkers with diagnostic/prognostic purposes. A high-throughput small RNA profiling analysis to determine the expression pattern of seminal small extracellular vesicle microRNAs (analyzed at the isomiR level), PIWI-interacting RNAs, and transfer RNA-derived small RNAs in normozoospermic (n = 4) and azoospermic (obstructive azoospermia because of pathological occurring obstruction in the genital tract, n = 4; secretory azoospermic individuals with positive testicular sperm extraction value, n = 5; secretory azoospermic individuals with negative testicular sperm extraction value, n = 4) individuals was carried out. Reverse transcriptase-quantitative real-time polymerase chain reaction validation analysis of selected microRNAs was additionally performed in a larger number of individuals. Clinically relevant quantitative changes in the small non-coding RNA levels contained in semen small extracellular vesicles can be used as biomarkers for the origin of azoospermia and for predicting the presence of residual spermatogenesis. In this regard, canonical isoform microRNAs (n = 185) but also other isomiR variants (n = 238) stand out in terms of numbers and fold-change differences in expression, underlining the need to consider isomiRs when investigating microRNA-based regulation. Conversely, although transfer RNA-derived small RNAs are shown in our study to represent a high proportion of small non-coding RNA sequences in seminal small extracellular vesicle samples, they are not able to discriminate the origin of azoospermia. PIWI-interacting RNA cluster profiles and individual PIWI-interacting RNAs with significant differential expression were also not able to discriminate. Our study demonstrated that expression values of individual and/or combined canonical isoform microRNAs (miR-10a-5p, miR-146a-5p, miR-31-5p, miR-181b-5p; area under the receiver operating characteristic curve >0.8) in small extracellular vesicles provide considerable clinical value in identifying samples with a high likelihood of sperm retrieval while discriminating azoospermia by origin. Although no individual microRNA showed sufficient discriminating power on its own to identify severe spermatogenic disorders with focal spermatogenesis, multivariate microRNA models in semen small extracellular vesicles have the potential to identify those individuals with residual spermatogenesis. Availability and adoption of such non-invasive molecular biomarkers would represent a great improvement in reproductive treatment decision protocols for azoospermia in clinical practice.

Glucose and cell confluency regulation of HDGF and beta-catenin nuclear localization

Introduction: Diabetes mellitus (DM) is the seventh leading cause of death in the US and diabetic kidney disease (DKD)is the cause of nearly 50% of individuals receiving dialysis. Kidney proximal tubule (PT) cells are sensitive to injury under diabetic conditions of high glucose. Maladaptive repair can cause fibrosis and loss of PT function contributing to end-stage renal disease. PT cell proliferation re-establishes the monolayer responsible for PT functionality. Preliminary lab findings showed increased abundance and nuclear localization of Hepatoma-derived growth factor (HDGF), known to regulate proliferation, in cells grown at low (&lt;40%) confluency in high glucose supplemented growth media. This change associated with altered nuclear co-localization with β-catenin (ß-Cat), involved in renal fibrosis, suggesting crosstalk between both factors may be involved in PT cell responses in DKD. Hypothesis: Cell confluency and glucose concentrations regulate the spatial and absolute abundance/degradation of HDGF altering cell signaling pathways in PT cells. Methods: Cultured human kidney PT cells (HK-11 cell line) were grown to low and high confluency under normal (5mM) and high (25mM) glucose conditions. RNA was collected via column purification for analysis of cell signaling. RNASeq and bioinformatic analysis. revealed transcript abundances and respective statistical significances between normal and high glucose conditions grown to low confluency. MetaCore and STRING were utilized to examine fold change differences of the transcriptome and affected pathways. To determine regulation of protein abundance, HK-11 cells were cultured in normal glucose media to 80-90% confluency and treated with no agent (control), DMSO, MG132 (proteasome inhibitor), and chloroquine (lysosome inhibitor), and abundance of HDGF and β-Cat activation analyzed by immunoblot. Results: HDGF transcripts from conditions of normal and high glucose grown to low confluency were found in relatively equal abundance (q ≤ 1). Pathway analyses revealed genes associated with multiple pathways including nuclear signaling, ER stress, proliferation and ubiquitination exhibited differential transcript abundance at statistically significant values. Immunoblot analysis suggested that HDGF is degraded via the lysosome. Conclusions: HDGF regulation by diabetes-like high glucose does not occur at the level of transcription and but through lysosomal degradation. ß-Cat nuclear localization is increased under conditions of high glucose and low cellular confluency. To confirm HDGF degradation and ß-Cat activation, more replicates are needed for statistical analysis. Future studies will determine the role of β-cat activation on HDGF abundance and nuclear localization. NIH T35-DK072923, P20-GM103436, NIH P20 GM113226, P50 AA024337, P30 ES030283 This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Abstract NG06: Investigating biological mediators of social and environmental risk factors on cancer health disparities

Abstract NG06: Investigating biological mediators of social and environmental risk factors on cancer health disparities

Comparison of growth in neutered Domestic Shorthair kittens with growth in sexually-intact cats.

The first aim of these studies was to compare growth patterns of healthy kittens neutered during growth with growth standards created for sexually-intact kittens. A second aim was to clarify the impact of neutering in kittens on body composition and body shape. Study 1 was a retrospective observational study comparing median growth trajectories of healthy, client-owned domestic shorthair (DSH) kittens in optimal body condition and neutered at different ages, with previously-created growth standards from a similar, sexually-intact, population. The neuter groups contained between 3.0k and 9.3k cats. For all neuter groups in both sexes, the median growth trajectory inclined upwards after the procedure, with this being more marked in female than in male kittens. This upwards inclination was less marked for kittens neutered later during growth in both sexes, with the effect being least in kittens neutered after 28-29 weeks. Study 2 was an analysis of new body composition and zoometric data from a previously-published randomised study, comparing growth-related measures between 11 pairs of sexually-intact and neutered (at 19 weeks age) female DSH cats in a research population. Before neutering, the growth pattern in neutered kittens and sexually-intact kittens was similar, but neutered kittens were heavier by 52 weeks (mean difference in fold change vs. 10 weeks 1.34, 95-CI: 1.07-1.72), had a greater fat mass (mean difference in fold change vs. 10 weeks 1.91, 95-CI 1.09-3.21) and greater lean mass (mean difference in fold change vs. 10 weeks 1.23, 95-CI: 1.03-1.48). Abdominal girth (mean difference in fold change vs. 10 weeks 1.20, 95-CI: 1.04-1.39) and rib cage length (mean difference in fold change vs. 10 weeks 1.18, 95-CI: 1.02-1.36) were also greater, but there were no differences in other zoometric measurements. Veterinarians should consider the potential impact that neutering has on gain of adipose tissue, especially early neutering in female kittens. Bodyweight should be monitored closely during growth and especially after neutering to prevent inappropriate weight gain.

MiRNA-21 as High Potential Prostate Cancer Biomarker in Prostate Cancer Patients in Indonesia.

This study aimed to explore the diagnostic performance of miRNA-21 to differentiate between Prostate Cancer (PCa) and Benign Prostatic Hyperplasia (BPH) patients in Indonesia. Urine samples were collected from each PCa and BPH patient. miRNA-21 relative expression against the reference gene was analyzed and compared between the two. miRNA expression was then analyzed using the comparative quantification method to find the fold change. miR-21 validity in identifying PCa patients was performed by quantifying the sensitivity and specificity using samples in this study. The results of this study indicated that miRNA-21 relative expression against miRNA-16 in PCa and BPH showed 12.95 differences in fold change. Moreover, using prostate biopsy as the gold standard to differentiate PCa and BPH, miRNA-21 Cq expression has 100% sensitivity and 75% specificity in differentiating the two. miRNA-21 relative expression can be used to discriminate PCa from BPH by using a urine sample. Furthermore, the expression of miR-21 has higher sensitivity than PSA; therefore, miR-21 has a high potential to be analyzed and developed further for clinical diagnosis of prostate cancer.

Effects of increasing levels of whole Black Soldier Fly (Hermetia illucens) larvae in broiler rations on acceptance, nutrient and energy intakes and utilization, and growth performance of broilers

Meal of black soldier fly larvae (BSFL), which requires extraction of protein and fat, is a novel protein source for poultry, while unprocessed whole BSFL could even directly be fed to chickens. Newly hatched Ross-308 chicks (n = 252) received whole BSFL at 10% (L10), 20% (L20), or 30% (L30) of voluntary feed intake (FI) of control chickens (CON) that received no BSFL but only age-specific diets (n = 63 birds / group) for 42 days (d). Acceptance and nutrient and energy intake of birds by BSFL and FI were calculated. Plasma metabolites were measured using an automatic enzymatic analyzer and immunoglobulins with ELISA. Depending on the variable, data were analyzed using ANOVA or repeated measures ANOVA to address treatment, time and interaction effects. Birds consumed all offered larvae. With the exception of d1, time spent by birds eating their daily portion of larvae (TSL, min/pen) did not differ among the larvae supply groups (P = 0.982). The L10 had a higher larvae eating rate (LER) that is, speed of larvae intake than did L20 and L30 (P < 0.05), implying increased competition for less available BSFL. The ratio of LER to feed eating rate (FER) was greater than 50 fold change difference (FCD), indicating a strong interest of chickens in BSFL over regular feed. Whole BSFL intake up to 30% of voluntary FI did not adversely affect broiler growth (P > 0.05). The L30 had lower total dry matter and metabolizable energy intakes (P < 0.05), although total fat intake was higher in L30 than in CON (P < 0.05). Compared with CON, 30% whole BSFL increased dietary protein-to-energy ratios, plasma uric acid and serum alkaline phosphatase concentrations (P < 0.05). We conclude that whole BSFL can be included in broiler rations up to 20% without negatively affecting growth performance and nutrient conversion efficiency, whereas a higher proportion is associated with lower protein utilization efficiency, possibly due to lower total energy intake.

Fasting-mimicking diet cycles reduce neuroinflammation to attenuate cognitive decline in Alzheimer's models.

The effects of fasting-mimicking diet (FMD) cycles in reducing many aging and disease risk factors indicate it could affect Alzheimer's disease (AD). Here, we show that FMD cycles reduce cognitive decline and AD pathology in E4FAD and 3xTg AD mouse models, with effects superior to those caused by protein restriction cycles. In 3xTg mice, long-term FMD cycles reduce hippocampal Aβ load and hyperphosphorylated tau, enhance genesis of neural stem cells, decrease microglia number, and reduce expression of neuroinflammatory genes, including superoxide-generating NADPH oxidase (Nox2). 3xTg mice lacking Nox2 or mice treated with the NADPH oxidase inhibitor apocynin also display improved cognition and reduced microglia activation compared with controls. Clinical data indicate that FMD cycles are feasible and generally safe in a small group of AD patients. These results indicate that FMD cycles delay cognitive decline in AD models in part by reducing neuroinflammation and/or superoxide production in the brain.

Characterisation of the testicular transcriptome in stallions with age-related testicular degeneration.

Age-related testicular degeneration can be defined as the progressive deterioration of the testis that typically occurs in middle-aged or older males and that leads to diminished testicular function and subfertility. In the equine breeding industry, genetically valuable males maintain their value as breeding animals well into old age. Because testicular degeneration is common in middle-aged and older stallions, the disease often has a significant negative impact on a stallion's breeding career and leads to economic losses in the horse breeding industry. Because testicular degeneration is a tissue autologous disease in the horse, the objective of this study was to use whole-transcriptome sequencing to compare the testicular transcriptomes of normal, fertile stallions to those of stallions affected by age-related testicular degeneration in order to better understand the pathophysiology of the disease. Cross sectional. Testicular tissue samples from clinical castrations or euthanasia were collected from normal healthy (n=3) or older subfertile (n=4) stallions. Samples were processed and sequenced on an Illumina HiSeq™ 2000 Sequencing System. Bioinformatic analysis of the data was performed in R/RStudio, and the transcriptomes were compared between the two groups. Genes were considered to be differentially expressed between healthy and diseased tissue if they demonstrated at least a ±1.5× fold change difference and had a false discovery rate-adjusted P value <0.05. Gene ontology analysis was performed using Ingenuity® IPA. Analyses of differential expression of individual genes, as well as computer-based gene ontology analysis, identified upregulation of cytokine-mediated inflammatory pathways in testes from stallions affected with testicular degeneration. This upregulation of inflammation was associated with upregulation of cell survival pathways, inhibition of apoptotic pathways and increases in collagen formation. There are unavoidable confounding factors (e.g. differences in breed, management, environment, age) that could create non disease-related genetic variation between our normal and affected samples. In addition, there are practical limitations to applying computer-based gene ontology analysis to equine samples. Gene ontology software relies on published information (mostly non-equine), and some biological processes (e.g. apoptosis and inflammation) are more commonly studied than others and so are over-represented in the literature and therefore more likely to be identified by computer algorithms. Caution should be taken when interpreting the data, as alterations in gene expression can be the cause of disease processes or can be the result of disease processes. These results suggest that chronic, low-grade inflammation may be involved in the pathophysiology of age-related testicular degeneration in stallions.

Daphnia magna egg piRNA cluster expression profiles change as mothers age

BackgroundPiRNAs prevent transposable elements wreaking havoc on the germline genome. Changes in piRNA expression over the lifetime of an individual may impact on ageing through continued suppression, or release, of transposable element expression. We identified piRNA producing clusters in the genome of Daphnia magna by a combination of bioinformatic methods, and then contrasted their expression between parthenogenetically produced eggs representing maternally-deposited germline piRNAs of young (having their 1st clutch) and old (having their 5th clutch) mothers. Results from eggs were compared to cluster expression in three generations of adults.ResultsAs for other arthropods, D. magna encodes long uni-directionally transcribed non-coding RNAs consisting of fragmented transposable elements which account for most piRNAs expressed. Egg tissues showed extensive differences between clutches from young mothers and those from old mothers, with 578 and 686 piRNA clusters upregulated, respectively. Most log fold-change differences for significant clusters were modest, however. When considering only highly expressed clusters, there was a bias towards 1st clutch eggs at 41 upregulated versus eight clusters in the eggs from older mothers. F0 generation differences between young and old mothers were fewer than eggs, as 179 clusters were up-regulated in young versus 170 old mothers. This dropped to 31 versus 22 piRNA clusters when comparing adults in the F1 generation, and no differences were detected in the F3 generation. Inter-generational losses of differential piRNA cluster were similar to that observed for D. magna micro-RNA expression.ConclusionsLittle overlap in differentially expressed clusters was found between adults containing mixed somatic and germline (ovary) tissues and germ-line representing eggs. A cluster encompassing a Tudor domain containing gene important in the piRNA pathway was upregulated in the eggs from old mothers. We hypothesise that regulation of this gene could form part of a feedback loop that reduces piRNA pathway activity explaining the reduced number of highly-expressed clusters in eggs from old mothers.

Investigation of the Toll-like receptors expression profile in peripheral blood mononuclear cells in COVID-19 patients in Iran

Introduction: Coronavirus disease 2019 (COVID-19) spreads all around the world and leads to several new infection cases and mortality. A better understanding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis could lead to more efficient therapeutic approaches. Objectives: The current study aimed to investigate the Toll-like receptors expression profile in peripheral blood mononuclear cells in COVID-19 patients in Iran. Patients and Methods: In this cross-sectional study, we evaluated 32 COVID-19 patients. At the admission time based on the disease severity patients were divided into two groups of severe and mild COVID-19. A group of 16 normal people was evaluated as the healthy control. Blood samples were collected before any treatment from patients at the admission time. Peripheral blood mononuclear cell isolation preformed on blood samples. RNA is extracted from human peripheral blood mononuclear cells and use for the cDNA synthesis. The expression level of TLR-3, 4, and 7 were evaluated by using semi-quantitative real-time polymerase chain reaction (PCR). Results: The patient’s mean age was 57.12±3.08 years and 15 (47%) were male. The background disorders represent two patients in the severe group with respiratory disorders, four patients with cardiovascular disease, and seven patients with diabetes. The TLRs expression levels represent a higher expression of TLR-4 in COVID-19 in comparison with controls for TLR-4 (P=0.007), TLR-3 and 7 also represent up-regulation however there were no statistically significant differences in the relative fold changes (RFCs) between groups for all other evaluated TLRs (P&gt;0.05). Conclusion: The study highlights the importance of the TLR-4 in COVID-19 patients in expression level. Further studies for a clear conclusion about TLRs expression levels are recommended.