Deletional bias and the evolution of bacterial genomes

Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards higher numbers of deletions than insertions. When selection is not strong enough to maintain them, genes are lost in large deletions or inactivated and subsequently eroded. Gene inactivation and loss are particularly apparent in obligate parasites and symbionts, in which dramatic reductions in genome size can result not from selection to lose DNA, but from decreased selection to maintain gene functionality. Here we discuss the evidence showing that deletional bias is a major force that shapes bacterial genomes.

Efficacy of Self-guided Internet-Based Cognitive Behavioral Therapy in the Treatment of Depressive Symptoms: A Meta-analysis of Individual Participant Data

IMPORTANCE

Self-guided internet-based cognitive behavioral therapy (iCBT) has the potential to increase access and availability of evidence-based therapy and reduce the cost of depression treatment.

OBJECTIVES

To estimate the effect of self-guided iCBT in treating adults with depressive symptoms compared with controls and evaluate the moderating effects of treatment outcome and response.

DATA SOURCES

A total of 13 384 abstracts were retrieved through a systematic literature search in PubMed, Embase, PsycINFO, and Cochrane Library from database inception to January 1, 2016.

STUDY SELECTION

Randomized clinical trials in which self-guided iCBT was compared with a control (usual care, waiting list, or attention control) in individuals with symptoms of depression.

DATA EXTRACTION AND SYNTHESIS

Primary authors provided individual participant data from 3876 participants from 13 of 16 eligible studies. Missing data were handled using multiple imputations. Mixed-effects models with participants nested within studies were used to examine treatment outcomes and moderators.

MAIN OUTCOMES AND MEASURES

Outcomes included the Beck Depression Inventory, Center for Epidemiological Studies-Depression Scale, and 9-item Patient Health Questionnaire scores. Scales were standardized across the pool of the included studies.

RESULTS

Of the 3876 study participants, the mean (SD) age was 42.0 (11.7) years, 2531 (66.0%) of 3832 were female, 1368 (53.1%) of 2574 completed secondary education, and 2262 (71.9%) of 3146 were employed. Self-guided iCBT was significantly more effective than controls on depressive symptoms severity (β = -0.21; Hedges g  = 0.27) and treatment response (β = 0.53; odds ratio, 1.95; 95% CI, 1.52-2.50; number needed to treat, 8). Adherence to treatment was associated with lower depressive symptoms (β = -0.19; P = .001) and greater response to treatment (β = 0.90; P < .001). None of the examined participant and study-level variables moderated treatment outcomes.

CONCLUSIONS AND RELEVANCE

Self-guided iCBT is effective in treating depressive symptoms. The use of meta-analyses of individual participant data provides substantial evidence for clinical and policy decision making because self-guided iCBT can be considered as an evidence-based first-step approach in treating symptoms of depression. Several limitations of the iCBT should be addressed before it can be disseminated into routine care.

Resilience of the Oral Microbiota in Health: Mechanisms That Prevent Dysbiosis

Dental diseases are now viewed as a consequence of a deleterious shift in the balance of the normally stable resident oral microbiome. It is known that frequent carbohydrate consumption or reduced saliva flow can lead to caries, and excessive plaque accumulation increases the risk of periodontal diseases. However, when these "disease drivers" are present, while some individuals appear to be susceptible, others are more tolerant or resilient to suffering from undesirable changes in their oral microbiome. Health-maintaining mechanisms that limit the effect of disease drivers include the complex set of metabolic and functional interrelationships that develop within dental biofilms and between biofilms and the host. In contrast, "positive feedback loops" can develop within these microbial communities that disrupt resilience and provoke a large and abrupt change in function and structure of the ecosystem (a microbial "regime shift"), which promotes dysbiosis and oral disease. For instance, acidification due to carbohydrate fermentation or inflammation in response to accumulated plaque select for a cariogenic or periopathogenic microbiota, respectively, in a chain of self-reinforcing events. Conversely, in tolerant individuals, health-maintaining mechanisms, including negative feedback to the drivers, can maintain resilience and promote resistance to and recovery from disease drivers. Recently studied health-maintaining mechanisms include ammonia production, limiting a drop in pH that can lead to caries, and denitrification, which could inhibit several stages of disease-associated positive feedback loops. Omics studies comparing the microbiome of, and its interaction with, susceptible and tolerant hosts can detect markers of resilience. The neutralization or inhibition of disease drivers, together with the identification and promotion of health-promoting species and functions, for example, by pre- and probiotics, could enhance microbiome resilience and lead to new strategies to prevent disease.

Microbial geography of the oral cavity

We aimed to determine the bacterial diversity of different oral micro-niches and to assess whether saliva and plaque samples are representative of oral microbial composition. We took minute samples from each surface of the individual teeth and gingival crevices of two healthy volunteers (112 samples per donor), as well as samples from the tongue dorsum and non-stimulated and stimulated saliva. DNA was extracted from 67 selected samples of each donor, and the 16S rRNA gene was amplified by PCR and pyrosequenced to obtain, on average, over 2,700 reads per sample, which were taxonomically assigned to obtain a geographic map of bacterial diversity at each tooth and sulcus location. Analysis of the data shows considerable differences in bacterial composition between teeth at different intra-oral locations and between surfaces of the same tooth. The most pronounced differences were observed in incisors and canines, where genera like Streptococcus were found at 40% to 70% on the vestibular surfaces but were almost absent on the lingual sides. Saliva samples, especially non-stimulated saliva, were not representative of supra-and subgingival plaque in the two individuals tested. We suggest that more precise sampling is required for the proper determination of oral microbial composition and to relate that diversity to epidemiological, clinical, and etiological parameters.

Microbial mucosal colonic shifts associated with the development of colorectal cancer reveal the presence of different bacterial and archaeal biomarkers

BACKGROUND

Epidemiological studies demonstrate a link between gastrointestinal cancers and environmental factors such as diet. It has been suggested that environmental cancer risk is determined by the interaction between diet and microbes. Thus, the purpose of this study was to examine the hypothesis that microbiota composition during colorectal cancer (CRC) progression might differ depending on the stage of the disease.

METHODS

A total of 28 age-matched and sex-matched subjects, seven with CRC adenocarcinoma, 11 with tubular adenomas and ten healthy subjects with intact colon, were included into the study. Microbiomes from mucosal and fecal samples were analyzed with 16S ribosomal RNA gene pyrosequencing, together with quantitative PCR of specific bacteria and archaea.

RESULTS

The principal coordinates analysis clearly separated healthy tissue samples from polyps and tumors, supporting the presence of specific bacterial consortia that are associated with affected sites and that can serve as potential biomarkers of CRC progression. A higher presence of Fusobacterium nucleatum and Enterobacteriaceae was found by qPCR in samples from CRC compared to healthy controls. We observed a correlation between CRC process development and levels of Methanobacteriales (R = 0.537, P = 0.007) and Methanobrevibacterium (R = 0.574, P = 0.03) in fecal samples.

CONCLUSION

Differences in microbial and archaeal composition between mucosal samples from healthy and disease tissues were observed in tubular adenoma and adenocarcinoma. In addition, microbiota from mucosal samples represented the underlying dysbiosis, whereas fecal samples seem not to be appropriate to detect shifts in microbial composition. CRC risk is influenced by microbial composition, showing differences according to disease progression step and tumor severity.

The process of genome shrinkage in the obligate symbiont Buchnera aphidicola

BACKGROUND

Very small genomes have evolved repeatedly in eubacterial lineages that have adopted obligate associations with eukaryotic hosts. Complete genome sequences have revealed that small genomes retain very different gene sets, raising the question of how final genome content is determined. To examine the process of genome reduction, the tiny genome of the endosymbiont Buchnera aphidicola was compared to the larger ancestral genome, reconstructed on the basis of the phylogenetic distribution of gene orthologs among fully sequenced relatives of Escherichia coli and Buchnera.

RESULTS

The reconstructed ancestral genome contained 2,425 open reading frames (ORFs). The Buchnera genome, containing 564 ORFs, consists of 153 fragments of 1-34 genes that are syntenic with reconstructed ancestral regions. On the basis of this reconstruction, 503 genes were eliminated within syntenic fragments, and 1,403 genes were lost from the gaps between syntenic fragments, probably in connection with genome rearrangements. Lost regions are sometimes large, and often span functionally unrelated genes. In addition, individual genes and regulatory regions have been lost or eroded. For the categories of DNA repair genes and rRNA genes, most lost loci fall in regions between syntenic fragments. This history of gene loss is reflected in the sequences of intergenic spacers at positions where genes were once present.

CONCLUSIONS

The most plausible interpretation of this reconstruction is that Buchnera lost many genes through the fixation of large deletions soon after the acquisition of an obligate endosymbiotic lifestyle. An implication is that final genome composition may be partly the chance outcome of initial deletions and that neighboring genes influence the likelihood of loss of particular genes and pathways.

Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria

Many species of bacterial endosymbionts are acquired by animal hosts before birth, through direct transmission from mothers to eggs or embryos. This vertical transmission imposes a reduction in numbers or "bottleneck," and the size of this bottleneck affects the population structure and evolution of symbiotic lineages. We have estimated the size of the transmission bottleneck in Buchnera, the bacterial symbiont of aphids, using basic light and electron microscopy techniques. By serial-sectioning whole aphid abdomens, their eggs, and embryos, we determined the following parameters: (i) The average size of a Buchnera cell is 2.9 mm in diameter. (ii) The total number of Buchnera in an Acyrthosiphon pisum embryo was around 36700 whereas a first instar nymph contained more than 119000. (iii) The number of symbionts per bacteriocyte was around 800 in an embryo and 3200 in a first instar nymph. (iv) The total number of Buchnera transmitted to each sexual egg ranged from 850 in Nasonovia to 1800 in A. pisum to more than 8000 in Uroleucon ambrosiae. (v) The total number of secondary endosymbionts in A. pisum was 12170 for an embryo and 18360 for a first instar nymph. Secondary symbionts were arranged both extracellularly and in clusters of 2000-8000 bacteria inside bacteriocytes. These numbers are consistent with the few previous estimates of symbiont population sizes based on counts of gene copies.

Some adaptive monte carlo methods for Bayesian inference

Monte Carlo methods, in particular Markov chain Monte Carlo methods, have become increasingly important as a tool for practical Bayesian inference in recent years. A wide range of algorithms is available, and choosing an algorithm that will work well on a specific problem is challenging. It is therefore important to explore the possibility of developing adaptive strategies that choose and adjust the algorithm to a particular context based on information obtained during sampling as well as information provided with the problem. This paper outlines some of the issues in developing adaptive methods and presents some preliminary results.

Multidrug-resistant Acinetobacter baumannii: an emerging pathogen among older adults in community hospitals and nursing homes

BACKGROUND

Drug-resistant Acinetobacter species are problematic in tertiary-care hospitals. We describe the epidemiology, resistance patterns, and outcomes of older adults with Acinetobacter infection in community hospitals.

METHODS

We queried the microbiology databases of the Oakwood Healthcare System (4 hospitals with 632, 259, 199, and 168 beds) for clinical Acinetobacter cultures obtained in 2003-2008. Patients aged 60 years who were admitted from home or nursing homes were included. We recorded the initial Acinetobacter isolate and susceptibility to 8 antibiotics. Cultures obtained 48 h after hospitalization were categorized as "nosocomial." Administrative databases provided patients' origins (home or nursing home) and discharge destinations (home, nursing home, long-term acute-care facility, another hospital, or hospice care or death).

RESULTS

During the 6-year period, 560 community-dwelling (mean age +/- standard deviation, 74 +/- 8.6 years) and 280 nursing home-dwelling (78 +/- 9.1 years) patients had Acinetobacter isolated. During this period, Acinetobacter prevalence increased 25% (P<.001, by trend test). In comparison of 2003 with 2008, Acinetobacter resistance to imipenem and ampicillin/sulbactam increased (from 1.8% to 33.1%; P<.001), as did "panresistance" (ie, resistance to all 8 antibiotics; increase from 0.0% to 13.6%; P<.001). Although resistance was stable in community-acquired isolates (resistance to approximately 4.2 antibiotics), resistance increased among nursing home-acquired and nosocomial-acquired isolates (from 4.5 to 5.7 and from 5.0 to 6.0 antibiotics, respectively; P<.01). At discharge, only 25% of community-dwelling and 50% of nursing home-dwelling patients returned to their place of origin; the remainder required higher levels of care or died. After adjustment for age, length of stay, and origin, resistance to each additional antibiotic predicted a >20% increased risk for discharge to higher levels of care or death (odds ratio, 1.23; 95% confidence interval, 1.11-1.36).

CONCLUSIONS

The prevalence and resistance of Acinetobacter species are increasing in the community. Patients with resistant isolates are selectively discharged to nursing homes and long-term acute-care facilities, introducing resistance to new facilities.

A tissue-dependent hypothesis of dental caries

Current understanding of dental caries considers this disease a demineralization of the tooth tissues due to the acid produced by sugar-fermenting microorganisms. Thus, caries is considered a diet- and pH-dependent process. We present here the first metagenomic analysis of the bacterial communities present at different stages of caries development, with the aim of determining whether the bacterial composition and biochemical profile are specific to the tissue affected. The data show that microbial composition at the initial, enamel-affecting stage of caries is significantly different from that found at subsequent stages, as well as from dental plaque of sound tooth surfaces. Although the relative proportion of Streptococcus mutans increased from 0.12% in dental plaque to 0.72% in enamel caries, Streptococcus mitis and Streptococcus sanguinis were the dominant streptococci in these lesions. The functional profile of caries-associated bacterial communities indicates that genes involved in acid stress tolerance and dietary sugar fermentation are overrepresented only at the initial stage (enamel caries), whereas other genes coding for osmotic stress tolerance as well as collagenases and other proteases enabling dentin degradation are significantly overrepresented in dentin cavities. The results support a scenario in which pH and diet are determinants of the disease during the degradation of enamel, but in dentin caries lesions not only acidogenic but also proteolytic bacteria are involved. We propose that caries disease is a process of varying etiology, in which acid-producing bacteria are the vehicle to penetrate enamel and allow dentin degrading microorganisms to expand the cavity.

Smartphone Apps for the Treatment of Mental Disorders: Systematic Review

BACKGROUND

Smartphone apps are an increasingly popular means for delivering psychological interventions to patients suffering from a mental disorder. In line with this popularity, there is a need to analyze and summarize the state of the art, both from a psychological and technical perspective.

OBJECTIVE

This study aimed to systematically review the literature on the use of smartphones for psychological interventions. Our systematic review has the following objectives: (1) analyze the coverage of mental disorders in research articles per year; (2) study the types of assessment in research articles per mental disorder per year; (3) map the use of advanced technical features, such as sensors, and novel software features, such as personalization and social media, per mental disorder; (4) provide an overview of smartphone apps per mental disorder; and (5) provide an overview of the key characteristics of empirical assessments with rigorous designs (ie, randomized controlled trials [RCTs]).

METHODS

The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines for systematic reviews were followed. We performed searches in Scopus, Web of Science, American Psychological Association PsycNET, and Medical Literature Analysis and Retrieval System Online, covering a period of 6 years (2013-2018). We included papers that described the use of smartphone apps to deliver psychological interventions for known mental disorders. We formed multidisciplinary teams, comprising experts in psychology and computer science, to select and classify articles based on psychological and technical features.

RESULTS

We found 158 articles that met the inclusion criteria. We observed an increasing interest in smartphone-based interventions over time. Most research targeted disorders with high prevalence, that is, depressive (31/158,19.6%) and anxiety disorders (18/158, 11.4%). Of the total, 72.7% (115/158) of the papers focused on six mental disorders: depression, anxiety, trauma and stressor-related, substance-related and addiction, schizophrenia spectrum, and other psychotic disorders, or a combination of disorders. More than half of known mental disorders were not or very scarcely (<3%) represented. An increasing number of studies were dedicated to assessing clinical effects, but RCTs were still a minority (25/158, 15.8%). From a technical viewpoint, interventions were leveraging the improved modalities (screen and sound) and interactivity of smartphones but only sparingly leveraged their truly novel capabilities, such as sensors, alternative delivery paradigms, and analytical methods.

CONCLUSIONS

There is a need for designing interventions for the full breadth of mental disorders, rather than primarily focusing on most prevalent disorders. We further contend that an increasingly systematic focus, that is, involving RCTs, is needed to improve the robustness and trustworthiness of assessments. Regarding technical aspects, we argue that further exploration and innovative use of the novel capabilities of smartphones are needed to fully realize their potential for the treatment of mental health disorders.

Is self-guided internet-based cognitive behavioural therapy (iCBT) harmful? An individual participant data meta-analysis

BACKGROUND

Little is known about potential harmful effects as a consequence of self-guided internet-based cognitive behaviour therapy (iCBT), such as symptom deterioration rates. Thus, safety concerns remain and hamper the implementation of self-guided iCBT into clinical practice. We aimed to conduct an individual participant data (IPD) meta-analysis to determine the prevalence of clinically significant deterioration (symptom worsening) in adults with depressive symptoms who received self-guided iCBT compared with control conditions. Several socio-demographic, clinical and study-level variables were tested as potential moderators of deterioration.

METHODS

Randomised controlled trials that reported results of self-guided iCBT compared with control conditions in adults with symptoms of depression were selected. Mixed effects models with participants nested within studies were used to examine possible clinically significant deterioration rates.

RESULTS

Thirteen out of 16 eligible trials were included in the present IPD meta-analysis. Of the 3805 participants analysed, 7.2% showed clinically significant deterioration (5.8% and 9.1% of participants in the intervention and control groups, respectively). Participants in self-guided iCBT were less likely to deteriorate (OR 0.62, p < 0.001) compared with control conditions. None of the examined participant- and study-level moderators were significantly associated with deterioration rates.

CONCLUSIONS

Self-guided iCBT has a lower rate of negative outcomes on symptoms than control conditions and could be a first step treatment approach for adult depression as well as an alternative to watchful waiting in general practice.

Oral microbiota maturation during the first 7 years of life in relation to allergy development

BACKGROUND

Allergic diseases have become a major public health problem in affluent societies. Microbial colonization early in life seems to be critical for instructing regulation on immune system maturation and allergy development in children. Even though the oral cavity is the first site of encounter between a majority of foreign antigens and the immune system, the influence of oral bacteria on allergy development has not yet been reported.

OBJECTIVE

We sought to determine the bacterial composition in longitudinally collected saliva samples during childhood in relation to allergy development.

METHODS

Illumina sequencing of the 16S rDNA gene was used to characterize the oral bacterial composition in saliva samples collected at 3, 6, 12, 24 months, and 7 years of age from children developing allergic symptoms and sensitization (n = 47) and children staying healthy (n = 33) up to 7 years of age.

RESULTS

Children developing allergic disease, particularly asthma, had lower diversity of salivary bacteria together with highly divergent bacterial composition at 7 years of age, showing a clearly altered oral microbiota in these individuals, likely as a consequence of an impaired immune system during infancy. Moreover, the relative amounts of several bacterial species, including increased abundance of Gemella haemolysans in children developing allergies and Lactobacillus gasseri and L. crispatus in healthy children, were distinctive during early infancy, likely influencing early immune maturation.

CONCLUSION

Early changes in oral microbial composition seem to influence immune maturation and allergy development. Future experiments should test the probiotic potential of L. gasseri and L. crispatus isolates.

Positive and Negative Affect Schedule (PANAS): psychometric properties of the online Spanish version in a clinical sample with emotional disorders

BACKGROUND

The Positive and Negative Affect Schedule (PANAS) is the most widely and frequently used scale to assess positive and negative affect. The PANAS has been validated in several languages, and it has shown excellent psychometric properties in the general population and some clinical samples, such as forensic samples, substance users, and adult women with fibromyalgia. Nevertheless, the psychometric properties of the scale have not yet been examined in clinical samples with anxiety, depressive, and adjustment disorders. In addition, the proliferation of Internet-based treatments has led to the development of a wide range of assessments conducted online with digital versions of pen and paper self-report questionnaires. However, no validations have been carried out to analyze the psychometric properties of the online version of the PANAS. The present study investigates the psychometric properties of the online Spanish version of the PANAS in a clinical sample of individuals with emotional disorders.

METHODS

The sample was composed of 595 Spanish adult volunteers with a diagnosis of depressive disorder (n = 237), anxiety disorder (n = 284), or adjustment disorder (n = 74). Factor structure, construct validity, internal consistency, and sensitivity to change were analyzed.

RESULTS

Confirmatory factor analysis yielded a latent structure of two independent factors, consistent with previous validations of the instrument. The analyses showed adequate convergent and discriminant validity, good internal consistency as well as sensitivity to change.

CONCLUSIONS

Overall, the results obtained in this study show that the online version of the PANAS has adequate psychometric properties for the assessment of positive and negative affect in a Spanish clinical population.

Relationship between periodontitis-associated subgingival microbiota and clinical inflammation by 16S pyrosequencing

AIM

To analyse the relationship between the chronic periodontitis-associated subgingival microbiota and clinical inflammation.

MATERIAL AND METHODS

Sixty subjects with generalized chronic periodontitis participated in this study. Patients were divided into two groups according to their bleeding on probing (BOP) scores: BOP-1 group (mean scores ≤50% in sampled sites) and BOP-2 group (mean scores >50%). Subgingival bacterial samples from periodontal patients were studied by pyrosequencing PCR products of the 16S rRNA gene and by real-time PCR.

RESULTS

In all the analysed subgingival samples, 102 bacterial genera and 203 species (from 41 genera of interest) were identified. Rarefaction curves showed a greater number of bacterial species in samples from BOP-2 group compared to BOP-1 group. The BOP-1 group had significantly higher abundance percentages of Anaeroglobus (especifically, A. geminatus), Capnocytophaga (especifically C. gingivalis), TM7 and Veillonella. The BOP-2 had significantly higher abundance percentages of Desulfobulbus (especially D. propionicus), Eubacterium (especially E. saphenum), Filifactor alocis, Streptococcus constellatus, Tannerella (especially, T. forsythia) and Treponema.

CONCLUSION

16S pyrosequencing revealed that increased inflammation, at sites with periodontitis, is associated with a more diverse subgingival microbiota and specific changes in the bacterial composition, involving "established" periopathogens, symbionts and novel low-abundance pathobionts.

An Internet-based program for depressive symptoms using human and automated support: a randomized controlled trial

PURPOSE

The purpose of this study was to analyze the efficacy of an Internet-based program for depressive symptoms using automated support by information and communication technologies (ICTs) and human support.

PATIENTS AND METHODS

An Internet-based program was used to teach adaptive ways to cope with depressive symptoms and daily problems. A total of 124 participants who were experiencing at least one stressful event that caused interference in their lives, many of whom had clinically significant depressive symptoms, were randomly assigned into either an intervention group with ICT support (automated mobile phone messages, automated emails, and continued feedback through the program); an intervention group with ICT support plus human support (brief weekly support phone call without clinical content); or a waiting-list control. At pre-, post-, and 12-month follow-up, they completed depression, anxiety, positive and negative effect, and perceived stress measures. Results were analyzed using both intention-to-treat and completers data. The majority were women (67.7%), with a mean age of 35.6 years (standard deviation =9.7).

RESULTS

The analysis showed that the two intervention groups improved significantly pre- to posttreatment, compared with the control group. Furthermore, improvements were maintained at the 12-month follow-up. Adherence and satisfaction with the program was high in both conditions.

CONCLUSION

The Internet-based program was effective and well accepted, with and without human support, showing that ICT-based automated support may be useful. It is essential to continue to study other ICT strategies for providing support.

Antioxidant status in hyperphenylalaninemia

Abnormal oxidative stress was observed in some inborn errors of metabolism owing to the accumulation of toxic metabolites leading to excessive free radical production and to the influence of restricted diets on the antioxidant status. Erythrocyte antioxidant enzymes activities and tocopherol concentrations were measured in a group of phenylketonuric (n = 42) and mild-hyperphenylalaninemic (n = 28) patients compared with 45 age-matched controls. We also determined plasma selenium levels in these groups. We also evaluated the possible relationship between antioxidant status and neuropsychological disorders. Erythrocyte glutathione peroxidase (GSH-Px) activity was significantly lower (P < 0.001) in both phenylketonuric and mild-hyperphenylalaninemic patients compared with the control group, but no differences were observed between the two groups of patients. Neuropsychological disturbances were more frequent in the group of PKU patients with low GSH-Px activity than in PKU patients with normal GSH-Px. Low GSH-Px activity might be explained in phenylketonuria as a result of a selenium deficiency caused by a poor selenium intake or absorption, but not in mild hyperphenylalaninemic patients with free diet. Selenium levels were normal in both groups of patients, so low glutathione peroxidase activity in both phenylketonuric and hyperphenylalaninemic groups might be influenced by other factors, such as the consequences of an unbalanced amino acid profile, common to both conditions.

Oxidative stress in Rett syndrome

The investigation of parameters that might influence the neurological evolution of Rett syndrome might also yield new information about its pathogenic mechanisms. Oxidative stress caused by oxygen free radicals is involved in the neuropathology of several neurodegenerative disorders, as well as in stroke and seizures. To evaluate the free radical metabolism in Rett syndrome, we measured red blood cell antioxidant enzyme activities (superoxide dismutase, glutathione peroxidase, glutathione reductase and catalase) and plasma malondialdehyde, as lipid peroxidation marker in a group of patients with Rett syndrome. No significant differences were observed in erythrocyte glutathione peroxidase, glutathione reductase and catalase activities, between the Rett syndrome patients and the control group. Erythrocyte superoxide dismutase activities were significantly decreased in Rett syndrome patients (P<0.001) compared with the control group. Plasma malondialdehyde concentrations were significantly increased in Rett syndrome patients (P<0.001). An unbalanced nutritional status in Rett syndrome might explain the reduced enzyme activity found in these patients. Our results suggest that free radicals generated from oxidation reactions might contribute to the pathogenesis of Rett syndrome. The high levels of malondialdehyde reflect peroxidative damage of biomembranes that may contribute to progressive dementia, impaired motor function, behavioural changes, and seizures, in Rett syndrome. We found a probable relationship between the degree of oxidative stress and the severity of symptoms, which should be further investigated with a larger number of patients in different disease stages.

Comparative sensitivity of urinary CYFRA 21-1, urinary bladder cancer antigen, tissue polypeptide antigen, tissue polypeptide antigen and NMP22 to detect bladder cancer

PURPOSE

We compare the individual and combined sensitivity of urinary CYFRA 21-1, urinary bladder cancer antigen, tissue polypeptide antigen and NMP22 to detect bladder cancer, evaluate the false-positive rates for different pathological conditions, and assess differential sensitivity regarding histological and clinical characteristics of disease.

MATERIALS AND METHODS

A total of 267 subjects entered the study. Sensitivities of the tests were evaluated in 111 patients with active bladder cancer and 76 with no evidence of disease. False-positive rates were evaluated in 80 symptomatic and asymptomatic controls, including patients with benign urological conditions and nonbladder malignancies, and healthy subjects. CYFRA 21-1 was determined by electrochemoluminescent immunoassay in the Elecsys 2010, urinary bladder cancer antigen was quantified by enzyme linked immunosorbent assay (IDL Biotech), tissue polypeptide antigen was measured by the Prolifigen TPA-IRMA and NMP22 was assayed by enzyme linked immunosorbent assay (Matritech). Cutoffs were obtained by the 95% percentile in patients with no evidence of disease, which gave a 95% specificity for all biomarkers. Differences in sensitivity of urinary biomarkers regarding stage, grade, tumor size, pattern of growth, focality and recurrence were evaluated.

RESULTS

At a specificity of 95% cutoffs were 5.4 ng./ml. for CYFRA 21-1, 15.5 microg./l. for urinary bladder cancer antigen, 760.8 U./l. for tissue polypeptide antigen and 14.6 U./ml. for NMP22. Using these cutoffs sensitivities were 75.7% for NMP22, 83.8% for CYFRA 21-1, 73.9% for urinary bladder cancer antigen quantitative and 80.2% for tissue polypeptide antigen. The additional determination of cytokeratins increased the sensitivity of NMP22. Cytokeratins did not appear to be specific for bladder cancer, and false-positives rates were between 20% for urinary bladder cancer antigen and 36% for tissue polypeptide antigen for benign urological conditions, and between 40% and 52%, respectively, for nonbladder malignancies. NMP22 showed lower false-positives rates, mainly for benign diseases. Urinary tumor markers appeared to be associated with some of the most relevant histological and clinical parameters of bladder cancer.

CONCLUSIONS

Our preliminary evaluation showed the tests to be potential noninvasive adjuncts to help determine the need for cystoscopy. The combination of 2 tumor markers, NMP22 and 1 cytokeratin (CYFRA 21-1 or urinary bladder cancer antigen), seemed to be the most effective. Further comparative studies are needed to assess the promising diagnostic role of these markers.

Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications

Understanding the microbiology of dental caries is not a mere academic exercise; it provides the basis for preventive, diagnostic, and treatment strategies and gives the dentist a theoretical framework to become a better professional. The last years have seen the development of new research methodologies, ranging from high-throughput sequencing or "omics" techniques to new fluorescence microscopy applications and microfluidics, which have allowed the study of the oral microbiome to an unprecedented level of detail. Those studies have provided new insights about oral biofilm formation, biomarkers of caries risk, microbial etiology, appropriate sampling, identification of health-associated bacteria, and new anticaries strategies, among others. Several pitfalls are associated with the new technologies, including a small number of samples per study group, elevated cost, and genus- or species-based analyses that do not take into consideration intraspecies variability. However, the new data strongly suggest that saliva may not be an appropriate sample for etiological studies or for bacterial caries-risk tests, that microbial composition alone may be insufficient to predict caries risk, and that antimicrobial or immunization strategies targeting single species are unlikely to be effective. Strategies directed toward modulation of the oral biofilm, such as pre- and probiotics, emerge as promising new approaches to prevent tooth decay.