Site specific properties of carious dentin matrices biomodified with collagen cross-linkers

A heterogeneous phantom study for investigating the stability of PET images radiomic features with varying reconstruction settings

The purpose of this work was to assess the capability of radiomic features in distinguishing PET image regions with different uptake patterns. Furthermore, we assessed the stability of PET radiomic features with varying image reconstruction settings. An in-house phantom was designed and constructed, consisting of homogenous and heterogenous artificial phantom inserts. Four artificially constructed inserts were placed into a water filled phantom and filled with varying levels of radioactivity to simulate homogeneous and heterogeneous uptake patterns. The phantom was imaged for 80 min. PET images were reconstructed whilst varying reconstruction parameters. The parameters adjusted included, number of ordered subsets, number of iterations, use of time-of-flight and filter cut off. Regions of interest (ROI) were established by segmentation of the phantom inserts from the reconstructed images. In total seventy eight 3D radiomic features for each ROI with unique reconstructed parameters were extracted. The Friedman test was used to determine the statistical power of each radiomic feature in differentiating phantom inserts with different hetero/homogeneous configurations. The Coefficient of Variation (COV) of each feature, with respect to the reconstruction setting was used to determine feature stability. Forty three out of seventy eight radiomic features were found to be stable (COV ≤ 5%) against all reconstruction settings. To provide any utility, stable features are required to differentiate between regions with different hetro/homogeneity. Of the forty three stable features, fifteen (35%) features showed a statistically significant difference between the artificially constructed inserts. Such features included GLCM (Difference average, Difference entropy, Dissimilarity and Inverse difference), GLRL (Long run emphasis, Grey level non uniformity and Run percentage) and NGTDM (Complexity and Strength). The finding of this work suggests that radiomic features are capable of distinguishing between radioactive distribution patterns that demonstrate different levels of heterogeneity. Therefore, radiomic features could serve as an adjuvant diagnostic tool along with traditional imaging. However, the choice of the radiomic features needs to account for variability introduced when different reconstruction settings are used. Standardization of PET image reconstruction settings across sites performing radiomic analysis in multi-centre trials should be considered.

CFTR Modulators Restore Acidification of Autophago-Lysosomes and Bacterial Clearance in Cystic Fibrosis Macrophages

Cystic fibrosis (CF) human and mouse macrophages are defective in their ability to clear bacteria such as Burkholderia cenocepacia. The autophagy process in CF (F508del) macrophages is halted, and the underlying mechanism remains unclear. Furthermore, the role of CFTR in maintaining the acidification of endosomal and lysosomal compartments in CF cells has been a subject of debate. Using 3D reconstruction of z-stack confocal images, we show that CFTR is recruited to LC3-labeled autophagosomes harboring B. cenocepacia. Using several complementary approaches, we report that CF macrophages display defective lysosomal acidification and degradative function for cargos destined to autophagosomes, whereas non-autophagosomal cargos are effectively degraded within acidic compartments. Notably, treatment of CF macrophages with CFTR modulators (tezacaftor/ivacaftor) improved the autophagy flux, lysosomal acidification and function, and bacterial clearance. In addition, CFTR modulators improved CFTR function as demonstrated by patch-clamp. In conclusion, CFTR regulates the acidification of a specific subset of lysosomes that specifically fuse with autophagosomes. Therefore, our study describes a new biological location and function for CFTR in autophago-lysosomes and clarifies the long-standing discrepancies in the field.

The Reliability and Validity of Response-Based Measures of Attention Bias

Background

Attention bias to threat is a fundamental transdiagnostic component and potential vulnerability factor for internalizing psychopathologies. However, the measurement of attentional bias, such as traditional scores from the dot-probe paradigm, evidence poor reliability and do not measure intra-individual variation in attentional bias.

Methods

The present study examined, in three independent samples, the psychometric properties of a novel attentional bias (AB) scoring method of the dot-probe task based on responses to individual trials. For six AB scores derived using the response-based approach, we assessed the internal consistency, test-retest reliability, familial associations, and external validity (using Social Anxiety Disorder, a disorder strongly associated with attentional bias to threatening faces).

Results

Compared to traditional AB scores, response-based scores had generally better internal consistency (range of Cronbach's alphas: 0.68-0.92 vs. 0.41-0.71), higher test-retest reliabilities (range of Pearson's correlations: 0.26-0.77 vs. -0.05-0.35), and were more strongly related in family members (range of ICCs: 0.11-0.27 vs. 0-0.05). Furthermore, three response-based scores added incremental validity beyond traditional scores and gender in the external validators of current and lifetime Social Anxiety Disorder.

Conclusions

Findings indicate that response-based AB scores from the dot-probe task have better psychometric properties than traditional scores.

The Relationship Between Workplace Spirituality and Work-to-Family Enrichment in Selected Public Sector Organizations in Malaysia

Workplace spirituality (WPS) has been associated with various benefits, including its potential to reduce work-family conflict. Previous studies have established that individual religiosity influences work-family enrichment. To date, there has been no reliable evidence on the relationship between WPS and work-to-family enrichment (WFE). Hence, the present research aimed to identify the relationship between the three components of WPS, namely inner life, meaningful work, and sense of community and WFE among employees of the public sector in Malaysia. In this study, data collection was conducted using questionnaires that were distributed to two public organizations, which managed to receive a total of 81% response rate. The results were in line with past studies, which indicated a significant and positive relationship between workplace spirituality dimensions (inner life, meaningful work, and sense of community) and WFE. The significant influence of the sense of community toward WFE is believed to be caused by the collectivist culture of Malaysians. Therefore, the aspect of community must be taken into consideration in order to increase work-family enrichment among employees, particularly in the context of religious and collectivist society.

Shifting attention between modalities: Revisiting the modality-shift effect in autism

Selective attention to a sensory modality has been observed experimentally in studies of the modality-shift effect – a relative performance benefit for targets preceded by a target in the same modality, compared to a different modality. Differences in selective attention are commonly observed in autism and we investigated whether exogenous (automatic) shift costs between modalities are increased. Autistic adults and neurotypical controls made speeded discrimination responses to simple visual, tactile and auditory targets. Shift costs were observed for each target modality in participant response times and were largest for auditory targets, reflective of fast responses on auditory repeat trials. Critically, shift costs were similar between the groups. However, integrating speed and accuracy data using drift-diffusion modelling revealed that shift costs in drift rates (reflecting the quality of information extracted from the stimulus) were reduced for autistic participants compared with neurotypicals. It may be that, unlike neurotypicals, there is little difference between attention within and between sensory modalities for autistic people. This finding also highlights the benefit of combining reaction time and accuracy data using decision models to better characterise selective attention in autism.

Neurotransmitters Modulate Intrathymic T-cell Development

The existence of a crosstalk between the nervous and immune systems is well established. Neurotransmitters can be produced by immune cells, whereas cytokines can be secreted by cells of nervous tissues. Additionally, cells of both systems express the corresponding receptors. Herein, we discuss the thymus as a paradigm for studies on the neuroimmune network. The thymus is a primary lymphoid organ responsible for the maturation of T lymphocytes. Intrathymic T-cell development is mostly controlled by the thymic microenvironment, formed by thymic epithelial cells (TEC), dendritic cells, macrophages, and fibroblasts. Developing thymocytes and microenvironmental cells can be influenced by exogenous and endogenous stimuli; neurotransmitters are among the endogenous molecules. Norepinephrine is secreted at nerve endings in the thymus, but are also produced by thymic cells, being involved in controlling thymocyte death. Thymocytes and TEC express acetylcholine receptors, but the cognate neurotransmitter seems to be produced and released by lymphoid and microenvironmental cells, not by nerve endings. Evidence indicates that, among others, TECs also produce serotonin and dopamine, as well as somatostatin, substance P, vasoactive intestinal peptide (VIP) and the typical pituitary neurohormones, oxytocin and arg-vasopressin. Although functional data of these molecules in the thymus are scarce, they are likely involved in intrathymic T cell development, as exemplified by somatostatin, which inhibits thymocyte proliferation, differentiation, migration and cytokine production. Overall, intrathymic neuroimmune interactions include various neurotransmitters, most of them of non-neuronal origin, and that should be placed as further physiological players in the general process of T-cell development.

Validation of the Brazilian Version of the Patient Activation Measure 13

BACKGROUND AND PURPOSE

To assess the psychometric properties of the PAM13 Brazilian-Portuguese (PAM13-B) among outpatients with chronic diseases.

METHODS

513 adults participated, diagnosed with a chronic disease for more than 6 months, under outpatient monitoring. Reliability was tested using internal consistency and test-retest reliability. Construct validity was verified through different techniques (correlation between activation and self-esteem measures, anxiety, depression and health status), known-groups validity and dimensionality by means of confirmatory factor analysis. Significance was set at 0.05.

RESULTS

The PAM13-B presented appropriate results for internal consistency (α = 0.83) and test-retest reliability (intraclass correlation coefficient [ICC] = 0.81). A moderate correlation was found between activation and self-esteem only (r = 0.43, p < 0.001). The one-dimensional structure was not confirmed in the sample analyzed.

CONCLUSIONS

In the study sample, the version PAM13-B demonstrated its reliability and validity, but with a two-factor structure.

Association Between Heart Rate Variability and Decompression-Induced Physiological Stress

The purpose of this study was to analyze the correlation between decompression-related physiological stress markers, given by inflammatory processes and immune system activation and changes in Heart Rate Variability, evaluating whether Heart Rate Variability can be used to estimate the physiological stress caused by the exposure to hyperbaric environments and subsequent decompression. A total of 28 volunteers participated in the experimental protocol. Electrocardiograms were performed; blood samples were obtained for the quantification of red cells, hemoglobin, hematocrit, neutrophils, lymphocytes, platelets, aspartate transaminase (AST), alanine aminotransferase (ALT), and for immunophenotyping and microparticles (MP) research through Flow Cytometry, before and after each experimental protocol from each volunteer. Also, myeloperoxidase (MPO) expression and microparticles (MPs) deriving from platelets, neutrophils and endothelial cells were quantified. Negative associations between the standard deviation of normal-to-normal intervals (SDNN) in the time domain, the High Frequency in the frequency domain and the total number of circulating microparticles was observed (p-value = 0.03 and p-value = 0.02, respectively). The pre and post exposure ratio of variation in the number of circulating microparticles was negatively correlated with SDNN (p-value = 0.01). Additionally, a model based on the utilization of Radial Basis Function Neural Networks (RBF-NN) was created and was able to predict the SDNN ratio of variation based on the variation of specific inflammatory markers (RMSE = 0.06).

Dyslipidemia in adolescents and young adults with type 1 and type 2 diabetes: a retrospective analysis

Background

Youth onset type 1 diabetes (T1D) and type 2 diabetes (T2D) is increasing and associated with earlier vascular complications and mortality. Dyslipidemia is an important modifiable cardiovascular (CVD) risk factor that is under-recognized and undertreated in youth with T1D and T2D. Given this, we evaluated the prevalence and associations between lipid concentrations and clinical CVD risk factors in youth with T1D compared to T2D at our large ethnically diverse diabetes center.

Methods

A retrospective chart review was performed, evaluating patients with T1D or T2D seen at least once in clinic from 2015 to 2017, age 10–22 years of age, duration of diabetes at least 6 months on the date of most recent LDL-cholesterol (LDL-C) concentration, and not on statin therapy. We performed independent and multivariable linear regressions of LDL-C and HDL-cholesterol (HDL-C) concentrations.

Results

There were 32.7% with T1D (n = 1701) and 47.7% with T2D (n = 298) with LDL-C above recommend goal (> 100 mg/dL/2.6 mmol/L). Furthermore, there were 9% with T1D and 16.4% with T2D with LDL > 130 mg/dL (> 3.4 mmol/L), who likely met criteria for starting statin therapy. Higher LDL-C and/or lower HDL-C were associated with increased age, diabetes duration, higher HbA1C, female sex, Hispanic ethnicity, obesity, and T2D. After adjusting for these risk factors in a multivariable linear regression model, the association of higher LDL-C and lower HDL-C was higher with T2D than T1D.

Conclusions

This highlights the need for more aggressive dyslipidemia screening and treatment in youth with diabetes, especially T2D. At our institution we have created and instituted quality improvement algorithms to try to address this need.

An inter-species computational analysis of vibrotactile sensitivity in Pacinian and Herbst corpuscles

Vibration sensing is ubiquitous among vertebrates, with the sensory end organ generally being a multilayered ellipsoidal structure. There is, however, a wide range of sizes and structural arrangements across species. In this work, we applied our earlier computational model of the Pacinian corpuscle to predict the sensory response of different species to various stimulus frequencies, and based on the results, we identified the optimal frequency for vibration sensing and the bandwidth over which frequencies should be most detectable. We found that although the size and layering of the corpuscles were very different, almost all of the 19 species studied showed very similar sensitivity ranges. The human and goose were the notable exceptions, with their corpuscle tuned to higher frequencies (130-170 versus 40-50 Hz). We observed no correlation between animal size and any measure of corpuscle geometry in our model. Based on the results generated by our computational model, we hypothesize that lamellar corpuscles across different species may use different sizes and structures to achieve similar frequency detection bands.

On Nonregularized Estimation of Psychological Networks

An important goal for psychological science is developing methods to characterize relationships between variables. Customary approaches use structural equation models to connect latent factors to a number of observed measurements, or test causal hypotheses between observed variables. More recently, regularized partial correlation networks have been proposed as an alternative approach for characterizing relationships among variables through off-diagonal elements in the precision matrix. While the graphical Lasso (glasso) has emerged as the default network estimation method, it was optimized in fields outside of psychology with very different needs, such as high dimensional data where the number of variables (p) exceeds the number of observations (n). In this article, we describe the glasso method in the context of the fields where it was developed, and then we demonstrate that the advantages of regularization diminish in settings where psychological networks are often fitted ( p≪n ). We first show that improved properties of the precision matrix, such as eigenvalue estimation, and predictive accuracy with cross-validation are not always appreciable. We then introduce nonregularized methods based on multiple regression and a nonparametric bootstrap strategy, after which we characterize performance with extensive simulations. Our results demonstrate that the nonregularized methods can be used to reduce the false-positive rate, compared to glasso, and they appear to provide consistent performance across sparsity levels, sample composition (p/n), and partial correlation size. We end by reviewing recent findings in the statistics literature that suggest alternative methods often have superior performance than glasso, as well as suggesting areas for future research in psychology. The nonregularized methods have been implemented in the R package GGMnonreg.

Biomechanical modeling of transcatheter aortic valve replacement in a stenotic bicuspid aortic valve: deployments and paravalvular leakage

Calcific aortic valve disease (CAVD) is characterized by stiffened aortic valve leaflets. Bicuspid aortic valve (BAV) is the most common congenital heart disease. Transcatheter aortic valve replacement (TAVR) is a treatment approach for CAVD where a stent with mounted bioprosthetic valve is deployed on the stenotic valve. Performing TAVR in calcified BAV patients may be associated with post-procedural complications due to the BAV asymmetrical structure. This study aims to develop refined computational models simulating the deployments of Evolut R and PRO TAVR devices in a representative calcified BAV. The paravalvular leakage (PVL) was also calculated by computational fluid dynamics simulations. Computed tomography scan of severely stenotic BAV patient was acquired. The 3D calcium deposits were generated and embedded inside a parametric model of the BAV. Deployments of the Evolut R and PRO inside the calcified BAV were simulated in five bioprosthesis leaflet orientations. The hypothesis of asymmetric and elliptic stent deployment was confirmed. Positioning the bioprosthesis commissures aligned with the native commissures yielded the lowest PVL (15.7 vs. 29.5 mL/beat). The Evolut PRO reduced the PVL in half compared with the Evolut R (15.7 vs. 28.7 mL/beat). The proposed biomechanical computational model could optimize future TAVR treatment in BAV patients. Graphical abstract.

Interaction between functionalized multiwalled carbon nanotubes and MS2 bacteriophages in water

Fate and transport of carbon nanomaterials can be strongly dependent on the interaction with secondary particulates in the aquatic systems. Bio-particulates in water, e.g., viruses with charged and hydrophobic surface moieties, may profoundly influence the interfacial behavior and hence the environmental fate of nanomaterials (and vice versa). This study systematically evaluates the interfacial interaction of acid-functionalized multiwalled carbon nanotubes (MWNTs) with MS2 bacteriophages, or heteroaggregation behavior of these particulates, under mono- and di-valent cations and with Suwannee River humic acid (SRHA). Results indicate that the highest concentration of MS2 (i.e., MWNT:MS2 of 100:1) renders exceptional stability of MWNTs, even in high salinity conditions. However, at lower MS2 concentrations (i.e., MWNT:MS2 of 1000:1 and 10,000:1), the suppression of MWNT heteroaggregation rate is not as significant. The observed enhanced stability is likely caused by the preferential attachment of the MS2 capsids onto MWNT surfaces, which is mediated by electrostatic attraction (between negatively charged oxygen-containing moieties on MWNTs and positively charged amino acid residues on MS2 surfaces) and/or by MS2 capsids with positive hydropathy index (indicating strong hydrophobicity). Presence of SRHA also shows stability enhancement; however, at lower MS2 concentrations, SRHA dominated the heteroaggregation behavior. These results implicate that preferential interaction between virus capsids (i.e., MS2 and may be other waterborne viruses) and carbonaceous nanomaterials may influence environmental transport of both in aquatic environments.

Food processing, gut microbiota and the globesity problem

In the context of diseases of affluence, western diets have in the past years mainly been studied on their fat and sugar content and lack of dietary fiber. Yet, the more general aspect of food processing has recently sparked scientific interest as well. In addition, the gut microbiota have been put forward as an important link between diet, obesity and non-communicable diseases (NCD). Western dietary patterns, containing large amounts of processed foods might create an imbalance in the gut system by affecting gut bacteria and their metabolism. Here we discuss what has been already published regarding the relationship between several recently researched features of processed foods and the etiology of obesity and NCD. The addressed features concern micronutrient and energy density, several types of food additives and the generation of advanced glycation end products by thermal treatment during food processing. Overall, literature indicates that all discussed aspects can be linked to western ailments and that they can have a potential negative impact on human microbiota. Therefore, we propose that the thesis that a distressed gut microbiota is a mechanism that might explain how food processing features could harm human health is gaining empirical evidence. Future research will need to address the question whether the alteration of the gut microbiota is a direct or an indirect (via the host) effect. These conclusions are important assets in the fight against the continuing worldwide upsurge of obesity and NCD.

Clusterin in Alzheimer's Disease: Mechanisms, Genetics, and Lessons From Other Pathologies

Clusterin (CLU) or APOJ is a multifunctional glycoprotein that has been implicated in several physiological and pathological states, including Alzheimer's disease (AD). With a prominent extracellular chaperone function, additional roles have been discussed for clusterin, including lipid transport and immune modulation, and it is involved in pathways common to several diseases such as cell death and survival, oxidative stress, and proteotoxic stress. Although clusterin is normally a secreted protein, it has also been found intracellularly under certain stress conditions. Multiple hypotheses have been proposed regarding the origin of intracellular clusterin, including specific biogenic processes leading to alternative transcripts and protein isoforms, but these lines of research are incomplete and contradictory. Current consensus is that intracellular clusterin is most likely to have exited the secretory pathway at some point or to have re-entered the cell after secretion. Clusterin's relationship with amyloid beta (Aβ) has been of great interest to the AD field, including clusterin's apparent role in altering Aβ aggregation and/or clearance. Additionally, clusterin has been more recently identified as a mediator of Aβ toxicity, as evidenced by the neuroprotective effect of CLU knockdown and knockout in rodent and human iPSC-derived neurons. CLU is also the third most significant genetic risk factor for late onset AD and several variants have been identified in CLU. Although the exact contribution of these variants to altered AD risk is unclear, some have been linked to altered CLU expression at both mRNA and protein levels, altered cognitive and memory function, and altered brain structure. The apparent complexity of clusterin's biogenesis, the lack of clarity over the origin of the intracellular clusterin species, and the number of pathophysiological functions attributed to clusterin have all contributed to the challenge of understanding the role of clusterin in AD pathophysiology. Here, we highlight clusterin's relevance to AD by discussing the evidence linking clusterin to AD, as well as drawing parallels on how the role of clusterin in other diseases and pathways may help us understand its biological function(s) in association with AD.

Hippocampal network oscillations at the interplay between innate anxiety and learned fear

The hippocampus plays a central role as a hub for episodic memory and as an integrator of multimodal sensory information in time and space. Thereby, it critically determines contextual setting and specificity of episodic memories. It is also a key site for the control of innate anxiety states and involved in psychiatric diseases with heightened anxiety and generalized fear memory such as post-traumatic stress disorder (PTSD). Expression of both innate "unlearned" anxiety and "learned" fear requires contextual processing and engagement of a brain-wide network including the hippocampus together with the amygdala and medial prefrontal cortex. Strikingly, the hippocampus is also the site of emergence of oscillatory rhythms that coordinate information processing and filtering in this network. Here, we review data on how the hippocampal network oscillations and their coordination with amygdalar and prefrontal oscillations are engaged in innate threat evaluation. We further explore how such innate oscillatory communication might have an impact on contextualization and specificity of "learned" fear. We illustrate the partial overlap of fear and anxiety networks that are built by the hippocampus in conjunction with amygdala and prefrontal cortex. We further propose that (mal)-adaptive interplay via (dis)-balanced oscillatory communication between the anxiety network and the fear network may determine the strength of fear memories and their resistance to extinction.

Young adult cancer survivors' experiences with a mindful self-compassion (MSC) video-chat intervention: A qualitative analysis

Young adult cancer survivors (YACS) are a vulnerable population that reports high anxiety, social isolation, and feelings of inadequacy after cancer treatment completion. Mindful self-compassion (MSC) provides strategies for coping with suffering. We explored how MSC practices addressed the psychosocial needs of a nationally recruited YACS sample (N=20, all female, age M=27.00, various cancer types) that participated in an 8-week MSC video-chat intervention. Descriptive qualitative analysis of the intervention recordings revealed three YACS' psychosocial needs: peer isolation, body concerns, and health-related anxiety. MSC practices addressed these in a number of ways including: self-reliance for emotional support, common humanity within the YACS community, gratitude, self-kindness, and acceptance. Meanwhile, the body scan practice initially triggered distress for some; implications are discussed.

Does near-infrared (NIR) fluorescence angiography modify operative strategy during emergency procedures?

INTRODUCTION

Bowel viability can be difficult to evaluate during emergency surgery. Near-infrared (NIR) fluorescence angiography allows an intraoperative assessment of organ perfusion during elective surgery and might help to evaluate intestinal perfusion during emergency procedures. The aim of this study was to assess if NIR modified operative strategy during emergency surgery.

MATERIALS AND METHODS

From July 2014 to December 2015, we prospectively evaluated all consecutive patients, who had NIR assessment during emergency surgery. Primary endpoint was the modification of operative strategy after the assessment with NIR. Secondary endpoints were general post-operative outcomes, including reoperation rate.

RESULTS

Fifty-six patients were included in the study. Mean age was 64 ± 17 years. An exploratory laparoscopy was performed in 39% (n = 22) and an open surgery in 61% of cases (n = 34). Conversion rate to open surgery was 41% (n = 9). 32 patients had a bowel resection. In 32% of the cases (n = 18), the result of the NIR test led to a modification of the operative strategy. Among them, 33% (n = 6) had a larger resection or a resection, which was initially not planned. The other 12 patients (67%) had finally no resection, which was initially thought to be performed. Importantly, none of those patients needed a reoperation for ischemia. Mean time for performing NIR test was 167 s (± 121). Overall reoperation rate was 16.1% (n = 9). Two patients had an anastomotic leak. Eight patients (14.3%) died within the first 30 post-operative days; however, none of them presented a bowel ischemia or an anastomotic leak.

CONCLUSION

NIR is an easy and short procedure, which can be performed during emergency surgery to assess bowel perfusion. It may help the surgeon to preserve intestinal length or to define the exact limits of resection. Overall, we report a modification of operative strategy in up to one-third of evaluated patients.

The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing

The cow rumen harbors a great variety of diverse microbes, which form a complex, organized community. Understanding the behavior of this multifarious network is crucial in improving ruminant nutrient use efficiency. The aim of this study was to expand our knowledge by examining 10 Holstein dairy cow rumen fluid fraction whole metagenome and transcriptome datasets. DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements. The taxonomic core microbiome consisted of 48 genera belonging to Bacteria (47) and Archaea (1). The genus Prevotella predominated the planktonic core community. Core functional groups were identified using co-occurrence analysis and resulted in 587 genes, from which 62 could be assigned to metabolic functions. Although this was a minimal functional core, it revealed key enzymes participating in various metabolic processes. A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified. Transcripts coding for enzymes active in methanogenesis made up 1% of the core functions. The genera associated with the core enzyme functions were also identified. Linking genera to functions showed that the main metabolic pathways are primarily provided by Bacteria and several genera may serve as a “back-up” team for the central functions. The key actors in most essential metabolic routes belong to the genus Prevotella. Confirming earlier studies, the genus Methanobrevibacter carries out the overwhelming majority of rumen methanogenesis and therefore methane emission mitigation seems conceivable via targeting the hydrogenotrophic methanogenesis.

Role of Cytokine Combinations on CD4+ T Cell Differentiation, Partial Polarization, and Plasticity: Continuous Network Modeling Approach

Purpose: We put forward a theoretical and dynamical approach for the semi-quantitative analysis of CD4+ T cell differentiation, the process by which cells with different functions are derived from activated CD4+ T naïve lymphocytes in the presence of particular cytokine microenvironments. We explore the system-level mechanisms that underlie CD4+ T plasticity-the conversion of polarized cells to phenotypes different from those originally induced. Methods: In this paper, we extend a previous study based on a Boolean network to a continuous framework. The network includes transcription factors, signaling pathways, as well as autocrine and exogenous cytokines, with interaction rules derived using fuzzy logic. Results: This approach allows us to assess the effect of relative differences in the concentrations and combinations of exogenous and endogenous cytokines, as well as of the expression levels of diverse transcription factors. We found either abrupt or gradual differentiation patterns between observed phenotypes depending on critical concentrations of single or multiple environmental cytokines. Plastic changes induced by environmental cytokines were observed in conditions of partial phenotype polarization in the T helper 1 to T helper 2 transition. On the other hand, the T helper 17 to induced regulatory T-cells transition was highly dependent on cytokine concentrations, with TGFβ playing a prime role. Conclusion: The present approach is useful to further understand the system-level mechanisms underlying observed patterns of CD4+ T differentiation and response to changing immunological challenges.

Effect of Chronic Administration of Nickel on Affective and Cognitive Behavior in Male and Female Rats: Possible Implication of Oxidative Stress Pathway

Nickel (Ni) toxicity has been reported to produce biochemical and behavioral dysfunction. The present study was undertaken to examine whether Ni chronic administration can induce alterations of affective and cognitive behavior and oxidative stress in male and female rats. Twenty-four rats, for each gender, divided into control and three test groups (n = 6), were injected intraperitoneally with saline (0.9% NaCl) or NiCl2 (0.25 mg/kg, 0.5 mg/kg and 1 mg/kg) for 8 weeks. After treatment period, animals were tested in the open-field, elevated plus maze tests for anxiety-like behavior, and forced swimming test for depression-like behavior. The Morris Water Maze was used to evaluate the spatial learning and memory. The hippocampus of each animal was taken for biochemical examination. The results showed that Ni administration dose dependently increased anxiety-like behavior in both tests. A significant increase in depression-like symptoms was also exhibited by Ni treated rats. In the Morris Water Maze test, the spatial learning and memory were significantly impaired just in males treated with 1 mg/kg of Ni. With regard to biochemical analysis, activity of catalase (CAT) and superoxide dismutase (SOD) were significantly decreased, while the levels of nitric oxide (NO) and lipid peroxidation (LPO) in the hippocampus were significantly increased in the Ni-treated groups. Consequently, chronic Ni administration induced behavioral and biochemical dysfunctions.

Correlation of Apiose Levels and Growth Rates in Duckweeds

The carbon assimilated by photosynthesis in plants can be partitioned into starch, soluble sugars, and cell wall polymers. Higher levels of starch accumulation in leaves are usually correlated with a lower growth capacity. Duckweeds are fast-growing aquatic monocot plants that can accumulate high levels of starch. They are an unusual group because their cell wall has very low levels of lignin while accumulating apiogalacturonan, a pectic polysaccharide that could be involved with boron assimilation. In this work, five duckweed species from different genera (Spirodela polyrhiza, Landoltia punctata, Lemna gibba, Wolffiella caudata, and Wolffia borealis) were cultivated under two light intensities (20 and 500 μmoles of photons m⁻² s⁻¹) to evaluate the effects of growth rate on carbohydrate metabolism. A comparative analysis was performed by measuring their relative growth rates (RGR), and their content for starch, as well as soluble and cell wall carbohydrates. We found that the faster-growing species (the Lemnoideae) accumulate lower starch and higher soluble sugars than the slower-growing species within the Wolffioideae. Interestingly, analysis of the cell wall monosaccharides revealed that the slower-growing species displayed lower content of apiose in their walls. Our results indicate that higher accumulation of apiose observed in cell walls of the Lemnoideae species, which likely correlates with a higher proportion of apiogalacturonan, may lead to higher efficiency in the assimilation of boron. This is consistent with the increased RGR observed under conditions with higher apiose in the cell wall, such as higher light intensity. Consistent with their lower growth capacity, the Wolffioideae species we studied shows higher starch accumulation in comparison with the Lemnoideae species. We suggest that apiose levels could be good biomarkers for growth capacity of duckweeds and suggest that boron uptake could be an important factor for growth control in this aquatic plant family.

Filamentous Bacteriophage Proteins and Assembly

Filamentous bacteriophages, also known as filamentous bacterial viruses or Inoviruses, have been studied extensively over the years. They are interesting paradigms in structural molecular biology and offer insight into molecular assembly, a process that remains to be fully understood. In this chapter, an overview on filamentous bacteriophages will be provided. In particular, we review the constituent proteins of filamentous bacteriophage and discuss assembly by examining the structure of the major coat protein at various stages of the process. The minor coat proteins will also be briefly reviewed. Structural information provides key snapshots into the dynamic process of assembly.