Foxtail Millet NF-Y Families: Genome-Wide Survey and Evolution Analyses Identified Two Functional Genes Important in Abiotic Stresses

It was reported that Nuclear Factor Y (NF-Y) genes were involved in abiotic stress in plants. Foxtail millet (Setaria italica), an elite stress tolerant crop, provided an impetus for the investigation of the NF-Y families in abiotic responses. In the present study, a total of 39 NF-Y genes were identified in foxtail millet. Synteny analyses suggested that foxtail millet NF-Y genes had experienced rapid expansion and strong purifying selection during the process of plant evolution. De novo transcriptome assembly of foxtail millet revealed 11 drought up-regulated NF-Y genes. SiNF-YA1 and SiNF-YB8 were highly activated in leaves and/or roots by drought and salt stresses. Abscisic acid (ABA) and H2O2 played positive roles in the induction of SiNF-YA1 and SiNF-YB8 under stress treatments. Transient luciferase (LUC) expression assays revealed that SiNF-YA1 and SiNF-YB8 could activate the LUC gene driven by the tobacco (Nicotiana tobacam) NtERD10, NtLEA5, NtCAT, NtSOD or NtPOD promoter under normal or stress conditions. Overexpression of SiNF-YA1 enhanced drought and salt tolerance by activating stress-related genes NtERD10 and NtCAT1 and by maintaining relatively stable relative water content (RWC) and contents of chlorophyll, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and malondialdehyde (MDA) in transgenic lines under stresses. SiNF-YB8 regulated expression of NtSOD, NtPOD, NtLEA5 and NtERD10 and conferred relatively high RWC and chlorophyll contents and low MDA content, resulting in drought and osmotic tolerance in transgenic lines under stresses. Therefore, SiNF-YA1 and SiNF-YB8 could activate stress-related genes and improve physiological traits, resulting in tolerance to abiotic stresses in plants. All these results will facilitate functional characterization of foxtail millet NF-Ys in future studies

Toxicokinetic modeling challenges for aquatic nanotoxicology

Nanotoxicity has become of increasing concern since the rapid development of metal nanoparticles (NPs). Aquatic nanotoxicity depends on crucial qualitative and quantitative properties of nanomaterials that induce adverse effects on subcellular, tissue, and organ level. The dose-response effects of size-dependent metal NPs, however, are not well investigated in aquatic organisms. In order to determine the uptake and elimination rate constants for metal NPs in the metabolically active/ detoxified pool of tissues, a one-compartmental toxicokinetic model can be applied when subcellular partitioning of metal NPs data would be available. The present review is an attempt to describe the nano-characteristics of toxicokinetics and subcellular partitioning on aquatic organisms with the help of the mechanistic modeling for NP size-dependent physiochemical properties and parameters. Physiologically-based pharmacokinetic (PBPK) models can provide an effective tool to estimate the time course of NP accumulation in target organs and is useful in quantitative risk assessments. NP accumulation in fish should take into account different effects of different NP sizes to better understand tissue accumulative capacities and dynamics. The size-dependent NP partition coefficient is a crucial parameter that influences tissue accumulation levels in PBPK modeling. Further research is needed to construct the effective systems-level oriented toxicokinetic model that can provide a useful tool to develop quantitatively the robustly approximate relations that convey a better insight into the impacts of environmental metal NPs on subcellular and tissue/organ responses in aquatic organisms

Central plasticity and dysfunction elicited by aural deprivation in the critical period

The acoustic signal is crucial for animals to obtain information from the surrounding environment. Like other sensory modalities, the central auditory system undergoes adaptive changes (i.e., plasticity) during the developmental stage as well as other stages of life. Owing to its plasticity, auditory centers may be susceptible to various factors, such as medical intervention, variation in ambient acoustic signals and lesion of the peripheral hearing organ. There are critical periods during which auditory centers are easier to suffer from abnormal experiences. Particularly in the early postnatal development period, aural inputs are essential for functional maturity of auditory centers. An aural deprivation model, which can be achieved by attenuating or blocking the peripheral acoustic afferent input to the auditory center, is ideal for investigating plastic changes of auditory centers. Generally, auditory plasticity includes structural and functional changes, and some of which can be irreversible. Aural deprivation can distort tonotopic maps, disrupt the binaural integration, reorganize the neural network and change the synaptic transmission in the primary auditory cortex or at lower levels of the auditory system. The regulation of specific gene expression and the modified signal pathway may be the deep molecular mechanism of these plastic changes. By studying this model, researchers may explore the pathogenesis of hearing loss and reveal plastic changes of the auditory cortex, which will facilitate the therapeutic advancement in patients with severe hearing loss. After summarizing developmental features of auditory centers in auditory deprived animals and discussing changes of central auditory remodeling in hearing loss patients, we are aimed at stressing the significant of an early and well-designed auditory training program for the hearing rehabilitation

Measuring Information Flow in Cellular Networks by the Systems Biology Method through Microarray Data

In general, it is very difficult to measure the information flow in a cellular network directly. In this study, based on an information flow model and microarray data, we measured the information flow in cellular networks indirectly by using a systems biology method. First, we used a recursive least square parameter estimation algorithm to identify the system parameters of coupling signal transduction pathways and the cellular gene regulatory network (GRN). Then, based on the identified parameters and systems theory, we estimated the signal transductivities of the coupling signal transduction pathways from the extracellular signals to each downstream protein and the information transductivities of the GRN between transcription factors in response to environmental events. According to the proposed method, the information flow, which is characterized by signal transductivity in coupling signaling pathways and information transductivity in the GRN, can be estimated by microarray temporal data or microarray sample data. It can also be estimated by other high-throughput data such as next-generation sequencing or proteomic data. Finally, the information flows of the signal transduction pathways and the GRN in leukemia cancer cells and non-leukemia normal cells were also measured to analyze the systematic dysfunction in this cancer from microarray sample data. The results show that the signal transductivities of signal transduction pathways change substantially from normal cells to leukemia cancer cells

ADHD Classification by a Texture Analysis of Anatomical Brain MRI Data

The ADHD-200 Global Competition provides an excellent opportunity for building diagnostic classifiers of Attention-Deficit/Hyperactivity Disorder (ADHD) based on resting-state functional MRI (rs-fMRI) and structural MRI data. Here, we introduce a simple method to classify ADHD based on morphological information without using functional data. Our test results show that the accuracy of this approach is competitive with methods based on rs-fMRI data. We used isotropic local binary patterns on three orthogonal planes (LBP-TOP) to extract features from MR brain images. Subsequently, support vector machines (SVM) were used to develop classification models based on the extracted features. In this study, a total of 436 male subjects (210 with ADHD and 226 controls) were analyzed to show the discriminative power of the method. To analyze the properties of this approach, we tested disparate LBP-TOP features from various parcellations and different image resolutions. Additionally, morphological information using a single brain tissue type (i.e., gray matter, white matter, and CSF) was tested. The highest accuracy we achieved was 0.6995. The LBP-TOP was found to provide better discriminative power using whole-brain data as the input. Datasets with higher resolution can train models with increased accuracy. The information from gray matter plays a more important role than that of other tissue types. These results and the properties of LBP-TOP suggest that most of the disparate feature distribution comes from different patterns of cortical folding. Using LBP-TOP, we provide an ADHD classification model based only on anatomical information, which is easier to obtain in the clinical environment and which is simpler to preprocess compared with rs-fMRI data

Spatial ability explains the male advantage in approximate arithmetic

Previous research has shown that females consistently outperform males in exact arithmetic, perhaps due to the former’s advantage in language processing. Much less is known about gender difference in approximate arithmetic. Given that approximate arithmetic is highly associated with visuospatial processing and there is a male advantage in visuospatial processing, we hypothesized that males would perform better than females in approximate arithmetic. In two experiments (496 children in Experiment 1 and 554 college students in Experiment 2), we found that males showed better performance in approximate arithmetic. Furthermore, gender differences in approximate were accounted for by gender differences in spatial ability

In vitro and in vivo analysis of antimicrobial agents alone and in combination against multi-drug resistant Acinetobacter baumannii

Objective To investigate the in vitro and in vivo antibacterial activities of tigecycline and other 13 common antimicrobial agents, alone or in combination, against multi-drug resistant Acinetobacter baumannii.MethodsAn in vitro susceptibility test of 101 Acinetobacter baumannii was used to detect minimal inhibitory concentrations (MICs). A mouse lung infection model of multi-drug resistant Acinetobacter baumannii,established by the ultrasonic atomization method, was used to define in vivo antimicrobial activities.Results Multi-drug resistant Acinetobacter baumannii showed high sensitivity to tigecycline (98% inhibition), polymyxin B (78.2% inhibition), and minocycline (74.2% inhibition). However, the use of these antimicrobial agents in combination with other antimicrobial agents produced synergistic or additive effects. In vivo data showed that white blood cell (WBC) counts in drug combination groups C (minocycline + amikacin) and D (minocycline + rifampicin) were significantly higher than in groups A (tigecycline) and B (polymyxin B) (P < 0.05), after administration of the drugs 24h post-infection. Lung tissue inflammation gradually increased in the model group during the first 24h after ultrasonic atomization infection; vasodilation, congestion with hemorrhage were observed 48h post infection. After three days of anti-infective therapy in groups A, B, C and D, lung tissue inflammation in each group gradually recovered with clear structures. The mortality rates in drug combination groups (groups C and D) were much lower than in groups A and B.ConclusionThe combination of minocycline with either rifampicin or amikacin is more effective against multidrug-resistant Acinetobacter baumannii than single-agent tigecycline or polymyxin B. In addition, the mouse lung infection by ultrasonic atomization is a suitable model for drug screening and analysis of infection mechanism

The intestinal microbiome and the leaky gut as therapeutic targets in alcoholic liver disease

Alcoholic liver disease (ALD) encompasses hepatic steatosis, which may progress to alcoholic hepatitis, fibrosis, and cirrhosis. It remains a leading cause of morbidity and mortality in the US and worldwide. The severity of liver disease correlates with plasma levels of bacterial products in patients, and experimental ALD depends on the level of gut derived bacterial products in rodents. Since intestinal decontamination and deficiency of bacterial product receptors or their downstream signaling molecules protect from alcohol-induced liver disease, bacterial translocation, qualitative and quantitative changes of the enteric microbiome are considered as being of fundamental importance in the pathogenesis of ALD. Recent enhancements in diagnostic technologies provide a better insight into these shifts. This review highlights vital events in ALD such as bacterial translocation, the importance of Toll-like receptor (TLR) signaling, intestinal bacterial overgrowth and changes in the intestinal microbiome. Furthermore, a treatment trial section of patients reviews possible future options of therapy for ALD modifying the enteric microbiome

The sequence analysis of origin of replication in Saccharomyces cerevisiae genomes

DNA replication is a highly precise process that is initiated from origins of replication (ORI) and is regulated by a set of regulatory proteins. The mining of DNA sequence information will be not only beneficial for understanding the regulatory mechanism of replication initiation, but also for accurately identifying ORI. In this study, the GC profile and GC skew were calculated for the analysis of compositional bias in the Saccharomyces cerevisiae (S. cerevisiae) genome. We found that the GC content in the region of replication origins is significantly lower than that in the flanking regions. By calculating the information redundancy, an estimation of the correlation of nucleotides, we found that the intensity of adjoining correlation in replication origins is dramatically higher than that in flanking regions. Furthermore, the relation between ORIs and nucleosome as well as transcription start sites were investigated. Results show that ORIs are usually not occupied by nucleosomes. Finally, we calculated the distribution of ORIs in yeast chromosomes and found that most ORIs prefer to transcription terminal regions. We hope that these results will contribute to the identification of ORIs and to the mechanisms of DNA replication

β-Amyloid: The Key Peptide in the Pathogenesis of Alzheimer’s Disease

The amyloid β peptide (Aβ) is a critical initiator that triggers the progression of Alzheimer’s Disease (AD) via accumulation and aggregation, of which the process may be caused by Aβ overproduction or perturbation clearance. Aβ is generated from amyloid precursor protein (APP) through sequential cleavage of β- and γ-secretases while Aβ removal is dependent on the proteolysis and lysosome degradation system. Here, we overviewed the biogenesis and toxicity of Aβ as well as the regulation of Aβ production and clearance. Moreover, we also summarized the animal models correlated with Aβ that are essential in AD research. In addition, we discussed current immunotherapeutic approaches targeting Aβ to give some clues for exploring the more potentially efficient drugs for treatment of AD