Blood-Based Transcriptomic Biomarkers Are Predictive of Neurodegeneration Rather Than Alzheimer's Disease

Alzheimer's disease (AD) is a growing global health crisis affecting millions and incurring substantial economic costs. However, clinical diagnosis remains challenging, with misdiagnoses and underdiagnoses being prevalent. There is an increased focus on putative, blood-based biomarkers that may be useful for the diagnosis as well as early detection of AD. In the present study, we used an unbiased combination of machine learning and functional network analyses to identify blood gene biomarker candidates in AD. Using supervised machine learning, we also determined whether these candidates were indeed unique to AD or whether they were indicative of other neurodegenerative diseases, such as Parkinson's disease (PD) and amyotrophic lateral sclerosis (ALS). Our analyses showed that genes involved in spliceosome assembly, RNA binding, transcription, protein synthesis, mitoribosomes, and NADH dehydrogenase were the best-performing genes for identifying AD patients relative to cognitively healthy controls. This transcriptomic signature, however, was not unique to AD, and subsequent machine learning showed that this signature could also predict PD and ALS relative to controls without neurodegenerative disease. Combined, our results suggest that mRNA from whole blood can indeed be used to screen for patients with neurodegeneration but may be less effective in diagnosing the specific neurodegenerative disease.

High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)

Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.

Protective effects of black cumin (Nigella sativa) oil on TNBS-induced experimental colitis in rats

BACKGROUND

The pathogenesis and treatment of ulcerative colitis remain poorly understood. The aim of the present study is to investigate the effects of black cumin (Nigella sativa) oil on rats with colitis.

METHODS

Experimental colitis was induced with 1 mL trinitrobenzene sulfonic acid (TNBS) in 40% ethanol by intracolonic administration with 8-cm-long cannula under ether anesthesia to rats in colitis group and colitis + black cumin oil group. Rats in the control group were given saline at the same volume by intracolonic administration. Black cumin oil (BCO, Origo "100% natural Black Cumin Seed Oil," Turkey) was given to colitis + black cumin oil group by oral administration during 3 days, 5 min after colitis induction. Saline was given to control and colitis groups at the same volume by oral administration. At the end of the experiment, macroscopic lesions were scored and the degree of oxidant damage was evaluated by colonic total protein, sialic acid, malondialdehyde, and glutathione levels, collagen content, and tissue factor, superoxide dismutase, and myeloperoxidase activities. Tissues were also examined by histological and cytological analysis. Proinflammatory cytokines [tumor necrosis factor-alpha (TNF-α), interleukin (IL)-1β, and IL-6], lactate dehydrogenase activity, and triglyceride and cholesterol levels were analyzed in blood samples.

RESULTS

We found that black cumin oil decreased the proinflammatory cytokines, lactate dehydrogenase, triglyceride, and cholesterol, which were increased in colitis.

CONCLUSIONS

BCO, by preventing inflammatory status in the blood, partly protected colonic tissue against experimental ulcerative colitis.

Bone marker levels in gingival crevicular fluid during orthodontic intrusive tooth movement: a preliminary study

The aim of the present study is to observe the changes in bone turnover markers, deoxypyridinoline (Dpd), osteocalcin, n-telopeptide (NTx), and bone alkaline phosphatase (balp) during the experimental orthodontic intrusion of maxillary premolar teeth. The study population required fixed appliance therapy involving the extraction of the maxillary first premolar teeth. Gingival crevicular fluid (GCF) samples were collected from each patient by using paper strips before the appliances were fitted and 1, 24, and 168 hours after the activation of appliances. After the second activation on the 21st, 22nd, and 28th days of the study, samples were collected. Enzyme-Linked Immunosorbent Assay (ELISA) tests were performed following manufacturer's recommendations. The results of the study indicate Dpd, osteocalcin, and balp values decrease with force application. Among the tested parameters only Dpd values showed statistically significant changes through time. One, 7, 22, and 28 day results show a significant amount of decrease when compared to 0 days. The extra decrease on the 22nd day (the day after the second activation) is also significantly lower. NTx crosslink values could not be detected in the experimental samples.

Early gene expression profile of human skin to injury using high-density cDNA microarrays

Disturbances in normal wound healing may be traced to perturbations in gene expression following injury. To decipher normal and abnormal genetic responses to cutaneous injury, baseline gene expression of uninjured skin and injured skin must be better defined. Our aim for this study was to determine the gene expression profile of human skin immediately following injury using cDNA microarrays. Samples of normal and injured skin were obtained from 5 healthy females undergoing breast reduction surgery. Specimens of the epidermis and dermis were obtained at 30 minutes and 1 hour after the initial injury. RNA was extracted, reverse transcribed into cDNA and hybridized onto high-density cDNA microarray membranes of 4,000 genes. At 30 minutes, injury resulted in a consistent increase (> 2x) in gene expression of 124 out of 4,000 genes (3%). These genes were primarily involved in transcription and signaling. None of the 4,000 genes were decreased (< 2x) at 30 minutes. At 1 hour only 46 out of the 4,000 genes were increased in expression (1.15%) but 264 out of 4,000 (6.6%) genes were decreased greater than 2 fold, indicating a silencing of many structural genes. We have identified several genes, namely, suppressor of cytokine signaling-1, rho HP1, and BB1, that are highly expressed after injury and may have an unappreciated role in regulating the initial inflammatory response. These data provide an initial high-throughput analysis of gene expression immediately following human skin injury and show the utility and future importance of high-throughput analysis in skin biology and wound repair.

COMPARISON OF NORMAL HUMAN SKIN GENE EXPRESSION USING CDNA MICROARRAYS

Perturbations in normal wound healing may be traced to perturbations in gene expression in uninjured skin. In order to decipher normal and abnormal genetic responses to cutaneous injury, baseline gene expression in uninjured skin must first be defined. There is little data on gene expression profiles of normal human skin, i.e., which genes tend to be variable in expression and which tend to remain comparable. Therefore this study was designed to determine the degree of variability in human skin mRNA expression. Samples of normal skin were obtained from 9 healthy females undergoing breast reduction surgery. RNA was extracted, reverse transcribed into radiolabeled cDNA and hybridized onto cDNA microarrays of approximately 4400 genes. Gene expression intensities from the 9 samples were normalized and compared as a ratio of highest/lowest expression intensity. Deviation greater than 2 standard deviations from the mean of each gene was used as a cut-off. Seventy-one genes (1.7%) were substantially variable in their expression. These included genes coding for transport proteins, gene transcription, cell signaling proteins, and cell surface proteins. We found minimal variability in the matrix genes, growth factor genes and other groups of genes that are the most often studied in wound healing research. A small but definite variability in gene expression across 9 samples of clinically comparable specimens of normal skin was detected. This is in keeping with clinical observations of the variability in normal skin across individuals. These data provide high-throughput comparison of normal skin gene expression and suggest new molecules that may be studied in skin biology and perhaps, wound repair.

Effects of folic acid upon filopodia of Dictyostelium discoideum vegetative amoebae

Living vegetative D, discoideum amoebae were studied to determine whether their filopodia respond to folic acid, a chemoattractant for these cells. Exponentially growing amoebae (ca. 10 micron diameter) exhibit 5-30 micron long filopodia; at stationary phase, aggregation competent amoebae have numerous multibranched filopodia up to 100 micron long. Folic acid was observed to stimulate production, elongation, and branching of filopodia with its effects progressively changing as the amoebae approach aggregation. Filopodial construction was also found to be dependent upon Mg2+ levels. The significance of these results is discussed with respect to progressive changes within the vegetative phase as well as to the mechanisms of amoeboid movement, pseudopodial activity, and chemotaxis.