Neurological diseases are responsible for approximately 6.8 million deaths every year. They affect up to 1 billion people worldwide and cause significant disability and reduced quality of life. In most neurological disorders, the diagnosis can be challenging; it frequently requires long-term investigation. Thus, the discovery of better diagnostic methods to help in the accurate and fast diagnosis of neurological disorders is crucial. Circulating nucleic acids (CNAs) are defined as any type of DNA or RNA that is present in body biofluids. They can be found within extracellular vesicles or as cell-free DNA and RNA. Currently, CNAs are being explored as potential biomarkers for diseases because they can be obtained using non-invasive methods and may reflect unique characteristics of the biological processes involved in several diseases. CNAs can be especially useful as biomarkers for conditions that involve organs or structures that are difficult to assess, such as the central nervous system. This review presents a critical assessment of the most current literature about the use of plasma and serum CNAs as biomarkers for several aspects of neurological disorders: defining a diagnosis, establishing a prognosis, and monitoring the disease progression and response to therapy. We explored the biological origin, types, and general mechanisms involved in the generation of CNAs in physiological and pathological processes, with specific attention to neurological disorders. In addition, we present some of the future applications of CNAs as non-invasive biomarkers for these diseases.

The commensal yeast Candida albicans is an opportunistic pathogen. In order to successfully colonize or infect the human body, the fungus must adapt to the host’s environmental conditions, such as low oxygen tension (hypoxia), temperature (37°C), and the different carbon sources available. Previous studies demonstrated the adaptive importance of C. albicans genetic variability for its pathogenicity, although the contributions of epigenetic and the influence of environmental factors are not fully understood. Mitochondria play important roles in fungal energetic metabolism, regulation of nuclear epigenetic mechanisms and pathogenicity. However, the specific impact of inter-strain mitochondrial genome variability and mitochondrial epigenetics in pathogenicity is unclear. Here, we draw attention to this relevant organelle and its potential role in C. albicans pathogenicity and provide preliminary evidence, for the first time, for methylation of the yeast mitochondrial genome. Our results indicate that environmental conditions, such as continuous exposure for 12 weeks to hypoxia and 37°C, decrease the mitochondrial genome methylation in strains SC5314 and L757. However, the methylation decrease is quantitatively different in specific genome positions when strains SC5314 and L757 are compared. We hypothesize that this phenomenon can be promising for future research to understand how physical factors of the host affect the C. albicans mitochondrial genome and its possible impact on adaptation and pathogenicity.

The genetic variability of the opportunistic pathogen Candida albicans is an important adaptive mechanism. Here, we present the whole-genome sequences of the C. albicans SC5314 strain under two different growth conditions, providing useful information for comparative genomic studies and further intraspecific analysis.T he fungus Candida albicans is ubiquitously found in the human body and successfully colonizes diverse niches, such as skin and urogenital and gastrointestinal tracts, including internal organs, after tissue invasion and bloodstream dissemination (reviewed in references 1, 2, and 3). Although part of the human microbiota, C. albicans causes severe mucosal and bloodstream opportunistic infections in immunosuppressed hosts, with nearly 400,000 nosocomial cases worldwide with 46 to 75% mortality rates (4).We used the C. albicans strain SC5314, kindly provided to our laboratory by A. Mitchell in the mid-1990s. This strain is considered a reference strain and was isolated in 1984 from a candidemia patient (5). Since then, samples of this strain have been distributed to many laboratories and used in studies worldwide. The genome of one of these samples was previously sequenced by Muzzey and collaborators (6) using nextgeneration sequencing technologies.Our SC5314 (named SC5314-P0) yeast cells were grown on yeast extract-peptonedextrose (YPD) plates (1% wt/vol yeast extract; 2% wt/vol peptone, 2% wt/vol dextrose, and 2% wt/vol agar), and a single colony was used for overnight growth on YPD broth at 28°C and 150 rpm. Total yeast DNA was extracted from samples as described previously (7), and the complete sequencing of mitochondrial and nuclear genomes was carried out by using the Illumina MiSeq 2 ϫ 300-bp method in paired-end mode. The libraries were prepared with a TruSeq DNA v2 Illumina kit according to the manufacturer's technical specifications. FastQC v.0.11.4 software (8) was used to evaluate sequencing quality. Trimming was performed with the CLC Genomics Workbench v.7.5.1 (Qiagen) software with a quality score limit of 0.005 and removal of 45 bp and 20 bp from the 5= and 3= ends, respectively, and reads smaller than 25 bp were discarded. Once the quality filters were approved, reads were mapped to the assembly 22 of the reference strain SC5314 (A22-s07-m01-r18) (available at http://www .candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/archive/). Duplicated reads were removed after mapping and local realignment were carried out with the Guided Realignment tool (with "force realignment to guidance variants" selected) implemented in CLC Genomics Workbench v.7.5.1 (Qiagen). Genome annotation was performed with Annotate with the GFF file tool available on the same software using the corresponding GFF file (version A22-S05-M04-r02_features_with_ chromosome_sequences.gff). The fraction of the SC5314 genome sequenced was 0.99

Infection by Candida albicans requires its adaption to physical constraints in the human body, such as low oxygen tension (hypoxia), increased temperature (37°C) and different carbon sources. Previous studies demonstrated that the genetic variability of C. albicans isolates is an important adaptive mechanism, although little is known about the dynamics of this genetic diversity, and the influence of these environmental conditions on its mitochondrial genome (mtDNA). To test the synergistic effect of these stress conditions on C. albicans genome, reference strain SC5314 was subjected to an in vitro evolution scheme under hypoxia and 37°C, with two different carbon sources (glycerol and dextrose) for up to 48 weeks (approximately 4,000 generations). Experimental evolution results showed no sequence or copy number changes in the mtDNA, although sequence variants were detected on its nuclear genome by Multilocus sequence typing (MLST) and whole genome sequencing (WGS). After 12 weeks of experimental evolution, sample GTH12, grown under hypoxia at 37°C in glycerol, showed inferior growth and respiratory rates as compared to other conditions tested. Although WGS of GTH12 revealed no variants in its mtDNA, WGS with sodium bisulfite showed a significant reduction in mtDNA methylation in GTH12 in both non-coding and coding regions.Our results provide the first whole mitochondrial genome methylation map of C. albicans and show that environmental conditions promote the selective growth of specific variants and affect the methylation patterns of the mtDNA in a strain-specific manner.

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At least 25% of patients with positive Candida albicans bloodstream infection also have one or more bacterial species associated with the infection. These polymicrobial infections are usually caused by coagulase-negative staphylococci, most commonly Staphylococcus epidermidis and are associated with significantly worse clinical outcomes as compared to monomicrobial infections. Here we show bacteria are present in C. albicans cultures started from isolated single colony platting. These co-evolving bacteria can only be detected by the use of specific selective medium and/or long periods of incubation from 8 days up to 48 weeks (approximately 4,000 generations), used in experimental evolution methods. The detection of these co-evolving bacteria is highly dependent on the type of enzyme used for 16S rRNA gene amplification and is often missed in clinical laboratory analysis because of short incubation periods, media and temperatures, used in mycology clinical routine, that are unfavorable for bacterial growth. In this study, we identified bacteria in cultures of different C. albicans isolates from long term, continuous growth by molecular analysis and microscopy. Also, we confirmed the presence of these co-evolving bacteria by identification of S. epidermidis genome segments in sequencing reads of the C. albicans reference strain SC5314 genome sequencing project raw data deposited in GenBank. This result rules out the possibility of laboratory specific contamination. Also, we show that the presence of associated bacteria correlates with antifungal resistance alterations observed in growth under hypoxia. Our findings show the intense interaction between C. albicans yeasts and bacteria and have direct implications in yeast clinical procedures, especially concerning patient treatment.

Polymicrobial infections with mixed-species biofilms are important health problems because of increased antimicrobial resistance and worse patient outcomes than with monomicrobial infections. Here, we present the whole-genome sequence of Staphylococcus epidermidis strain GTH12, which was cocultured with the yeast Candida albicans SC5314 (generating C. albicans strain SC5314 GTH12), thus providing genomic information on polymicrobial infections.

A major challenge in the clinical management of patients with mesial temporal lobe epilepsy (MTLE) is identifying those who do not respond to antiseizure medication (ASM), allowing for the timely pursuit of alternative treatments such as epilepsy surgery. Here, we investigated changes in plasma metabolites as biomarkers of disease in patients with MTLE. Furthermore, we used the metabolomics data to gain insights into the mechanisms underlying MTLE and response to ASM. We performed an untargeted metabolomic method using magnetic resonance spectroscopy and multi- and univariate statistical analyses to compare data obtained from plasma samples of 28 patients with MTLE compared to 28 controls. The patients were further divided according to response to ASM for a supplementary and preliminary comparison: 20 patients were refractory to treatment, and eight were responsive to ASM. We only included patients using carbamazepine in combination with clobazam. We analyzed the group of patients and controls and found that the profiles of glucose (p = 0.01), saturated lipids (p = 0.0002), isoleucine (p = 0.0001), β-hydroxybutyrate (p = 0.0003), and proline (p = 0.02) were different in patients compared to controls (p < 0.05). In addition, we found some suggestive metabolites (without enough predictability) by multivariate analysis (VIP scores > 2), such as lipoproteins, lactate, glucose, unsaturated lipids, isoleucine, and proline, that might be relevant to the process of pharmacoresistance in the comparison between patients with refractory and responsive MTLE. The identified metabolites for the comparison between MTLE patients and controls were linked to different biological pathways related to cell-energy metabolism and pathways related to inflammatory processes and the modulation of neurotransmitter release and activity in MTLE. In conclusion, in addition to insights into the mechanisms underlying MTLE, our results suggest that plasma metabolites may be used as disease biomarkers. These findings warrant further studies exploring the clinical use of metabolites to assist in decision-making when treating patients with MTLE.