Phages are viruses that infect bacteria. The phages can be classified into two different categories based on their lifestyles: temperate and lytic. Now, the metavirome can generate a large number of ...fragments from the viral genomic sequences of entire environmental community, which makes it impossible to determine their lifestyles through experiments. Thus, there is a need to development computational methods for annotating phage contigs and making prediction of their lifestyles. Alignment-based methods for classifying phage lifestyle are limited by incomplete assembled genomes and nucleotide databases. Alignment-free methods based on the frequencies of
k
-mers were widely used for genome and metagenome comparison which did not rely on the completeness of genome or nucleotide databases. To mimic fragmented metagenomic sequences, the temperate and lytic phages genomic sequences were split into non-overlapping fragments with different lengths, then, I comprehensively compared nine alignment-free dissimilarity measures with a wide range of choices of
k
-mer length and Markov orders for predicting the lifestyles of these phage contigs. The dissimilarity measure,
d
2
S
, performed better than other dissimilarity measures for classifying the lifestyles of phages. Thus, I propose that the alignment-free method,
d
2
S
, can be used for predicting the lifestyles of phages which derived from the metagenomic data.
Ultraviolet (UV) disinfection is an effective technology for the inactivation of pathogens in water and is of growing interest for industrial application. A new UV source — ultraviolet light-emitting ...diode (UV-LED) — has emerged in the past decade with a number of advantages compared to traditional UV mercury lamps. This promising alternative raises great interest in the research on application of UV-LEDs for water treatment. Studies on UV-LED water disinfection have increased during the past few years. This article presents a comprehensive review of recent studies on UV-LEDs with various wavelengths for the inactivation of different microorganisms. Many inconsistent and incomparable data were found from published studies, which underscores the importance of establishing a standard protocol for studying UV-LED inactivation of microorganisms. Different UV sensitivities to UV-LEDs and traditional UV lamps were observed in the literature for some microorganisms, which requires further investigation for a better understanding of microorganism response to UV-LEDs. The unique aspects of UV-LEDs improve inactivation effectiveness by applying LED special features, such as multiple wavelengths and pulsed illumination; however, more studies are needed to investigate the influencing factors and mechanisms. The special features of UV-LEDs offer the flexibility of novel reactor designs for a broad application of UV-LED reactors.
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•The recent studies on newly emerging UV-LEDs for water disinfection are reviewed.•The inactivation effectiveness of different UV-LED wavelengths is illustrated.•The effects of UV-LED multiple wavelengths and pulsed illuminations are presented.•Mechanisms of microorganism inactivation by UV-LEDs are discussed.•Future research directions for UV-LED water disinfection are proposed.
Transcription is the first step in gene expression, and it is the step at which most of the regulation of expression occurs. Although sequenced prokaryotic genomes provide a wealth of information, ...transcriptional regulatory networks are still poorly understood using the available genomic information, largely because accurate prediction of promoters is difficult. To improve promoter recognition performance, a novel variable-window Z-curve method is developed to extract general features of prokaryotic promoters. The features are used for further classification by the partial least squares technique. To verify the prediction performance, the proposed method is applied to predict promoter fragments of two representative prokaryotic model organisms (Escherichia coli and Bacillus subtilis). Depending on the feature extraction and selection power of the proposed method, the promoter prediction accuracies are improved markedly over most existing approaches: for E. coli, the accuracies are 96.05% (σ70 promoters, coding negative samples), 90.44% (σ70 promoters, non-coding negative samples), 92.13% (known sigma-factor promoters, coding negative samples), 92.50% (known sigma-factor promoters, non-coding negative samples), respectively; for B. subtilis, the accuracies are 95.83% (known sigma-factor promoters, coding negative samples) and 99.09% (known sigma-factor promoters, non-coding negative samples). Additionally, being a linear technique, the computational simplicity of the proposed method makes it easy to run in a matter of minutes on ordinary personal computers or even laptops. More importantly, there is no need to optimize parameters, so it is very practical for predicting other species promoters without any prior knowledge or prior information of the statistical properties of the samples.
Metagenomes can be considered as mixtures of viral, bacterial, and other eukaryotic DNA sequences. Mining viral sequences from metagenomes could shed insight into virus-host relationships and expand ...viral databases. Current alignment-based methods are unsuitable for identifying viral sequences from metagenome sequences because most assembled metagenomic contigs are short and possess few or no predicted genes, and most metagenomic viral genes are dissimilar to known viral genes. In this study, I developed a Markov model-based method, VirMC, to identify viral sequences from metagenomic data. VirMC uses Markov chains to model sequence signatures and construct a scoring model using a likelihood test to distinguish viral and bacterial sequences. Compared with the other two state-of-the-art viral sequence-prediction methods, VirFinder and PPR-Meta, my proposed method outperformed VirFinder and had similar performance with PPR-Meta for short contigs with length less than 400 bp. VirMC outperformed VirFinder and PPR-Meta for identifying viral sequences in contaminated metagenomic samples with eukaryotic sequences. VirMC showed better performance in assembling viral-genome sequences from metagenomic data (based on filtering potential bacterial reads). Applying VirMC to human gut metagenomes from healthy subjects and patients with type-2 diabetes (T2D) revealed that viral contigs could help classify healthy and diseased statuses. This alignment-free method complements gene-based alignment approaches and will significantly improve the precision of viral sequence identification.
Synonymous codons have different frequencies of usage in many species. Based on the frequency of usage, the codons can be divided into two groups, rare codons and abundant codons. Rare codons are ...found to be enriched at the start regions of genes, and it is assumed that these codons can reduce elongation speed of genes. However, the rare codon usage in different genomic regions of mollusks and their relationship with selective pressure has not been systematically investigated. In this study, the patterns of rare codon usage are characterized at whole genome level, and their relationship with selective pressures is investigated in
Crassostrea gigas
. The rare codons are enriched at the start regions of genes with high and medium expression levels, and their proportion is higher than those in the genes with low expression level. The genes with longer coding sequences and more exon numbers have lower fraction of rare codons at start regions. Rare codons have lower level of nucleotide diversity and higher frequency of rare mutations at start regions. This work is the first comprehensive investigation of the relationships between rare codon usage and some intrinsic genetic factors in mollusca species. The results suggest that the selective pressures play an important role in shaping the rare codon usage in the
C. gigas
genome.
Breast cancer is the second common cancer and the leading cause of malignancy among females overall. Breast cancer stem cells (BCSCs) are a small population of breast cancer cells that play a ...critical role in the metastasis of breast cancer to other organs in the body. BCSCs have both self-renewal and differentiation capacities, which are thought to contribute to the aggressiveness of metastatic lesions. Therefore, targeting BCSCs can be a suitable approach for the treatment and metastasis of breast cancer. Growing evidence has indicated that the Wnt, NFκB, Notch, BMP2, STAT3, and hedgehog (Hh) signaling pathways govern epithelial-to-mesenchymal transition (EMT) activation, growth, and tumorigenesis of BCSCs in the primary regions. miRNAs as the central regulatory molecules also play critical roles in BCSC self-renewal, metastasis, and drug resistance. Hence, targeting these pathways might be a novel therapeutic approach for breast cancer diagnosis and therapy. This review discusses known signaling mechanisms involved in the stimulation or prevention of BCSC self-renewal, metastasis, and tumorigenesis.
Recently, ultraviolet light-emitting diodes (UV-LEDs) have emerged as a new UV source, bringing flexibility for various UV wavelength combinations due to their unique feature of wavelength diversity. ...In this study, we investigated inactivation mechanisms of representative microorganisms at different wavelength combinations using UV-LEDs. Two types of indicator microorganisms were examined, namely Escherichia coli (E. coli) as a representative bacteria and bacteriophage MS2 as a representative virus. Different inactivation effects were observed, and the results for UVA pretreatment followed by UVC inactivation were particularly interesting. While a substantial shoulder in the E. coli UVC inactivation curve was observed, this was reduced by UVA pretreatment (365 nm) at 17 J/cm2. Further, 52 J/cm2 UVA eliminated the shoulder in the fluence-response curves, resulting in improved UVC (265 nm) inactivation of E. coli by over two orders of magnitude. No inactivation improvement was observed for MS2. Moreover, UVA pretreatment eliminated photoreactivation of E. coli but did not affect dark repair. Detailed investigation of inactivation mechanisms revealed that hydroxyl radicals (•OH) played a significant role in the effects of UVA pretreatment. This study demonstrated that •OH radicals were generated inside E. coli cells during UVA pretreatment, which accounted for the subsequent effects on E. coli. The impact of UVA pretreatment on E. coli inactivation and reactivation was mainly due to increased levels of •OH radicals in E. coli cells, impairing cell functions such as DNA self-repair.
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•Inactivation mechanisms of UVA and UVC wavelength combinations were investigated.•UVA pretreatment largely improved E. coli inactivation and reduced reactivation.•Hydroxyl radicals were generated inside E. coli cells during UVA pretreatment.•Hydroxyl radicals played a significant role in the effects of UVA pretreatment.•E. coli cell function like DNA repair was impaired, causing improved inactivation.
Speech recognition is common in electronic appliances and personal services, but its use for industrial and medical purposes is rare because of the presence of motion ambiguity. For minimally ...invasive surgical robotic assistants, this ambiguity arises because the robotic motion is not calibrated to the camera images. This paper presents a design for a speech recognition interface for an HIWIN robotic endoscope holder. A new intentional speech control is proposed to control movement over long distances. To decrease ambiguity, a method is proposed for voice-to-motion calibration that compares the degree of change in the endoscope image for a voice command. A speech recognition algorithm is implemented on Ubuntu OS, using CMU Sphinx. The control signal is sent to the robot controller using serial-port communication through a RS232 cable. The experimental results show that the proposed intentional speech control strategy has a navigation precision of up to 3.1° of angular displacement for the endoscope. The overall system processing time, including robotic motion, is 3.22 s for ~1.8-s speech duration. The reference image navigation range is from 2.5 mm for ~0.5-s speech duration up to 6 mm for ~1.8-s speech duration, using a setup with camera tip that is located at a distance of 5 cm from the remote center of motion point.
Ultraviolet light-emitting diode (UV-LED) is an emerging UV source with many special features due to the nature of semiconductor devices. One such feature is wavelength diversity that does not exist ...in conventional mercury based UV lamps, which provides opportunities to selectively combine multiple wavelengths for potentially additional effects by UV-LEDs. In this work, the inactivation of different microorganisms in water was investigated by UV-LEDs wavelength combinations. Various wavelength combinations, including simultaneous and sequential exposures, in different UV ranges such as UVC, UVB and UVA, were examined. These combinations were applied to the inactivation of indicator bacterium E. coli and coliphage MS2 in water. The results showed the effect of UV-LEDs multiple wavelengths depends on which wavelengths (UVC, UVB and UVA) are combined and the manner that different wavelengths (simultaneous, sequential) are used. Also, different microorganisms (bacteria, virus) respond differently to wavelength combinations. Combinations of UVC/UVB always achieved additive effect on microorganisms inactivation due to the same photochemical reaction induced by UVC/UVB on DNA. Combining UVA with UVC/UVB simultaneously or applying UVA after UVC/UVB reduced the inactivation of bacterium E. coli due to DNA repair and photoreactivation effect of UVA. However, applying extended UVA exposure before UVC significantly improved E. coli inactivation. For virus MS2 inactivation, only additive effect was observed under various wavelength combinations. This study presented a comprehensive work on UV-LEDs wavelength combinations, which is of significance on the application of UV-LEDs for water disinfection.
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•UV-LEDs wavelength combinations were thoroughly investigated for water disinfection.•Inactivation of different types of microorganisms, E. coli and MS2, was examined.•The effect of multiple wavelengths depends on UV ranges and combining manners.•UVC- and UVB-LEDs combinations always achieved additive inactivation effect.•UVA may improve or reduce E. coli inactivation depending on the manner to apply UVA.
Chondrocyte apoptosis is closely related to the development and progression of osteoarthritis (OA); however, the underlying mechanisms remain enigmatic. Previous studies have confirmed that cell ...apoptosis is one of the main pathological alterations during oxidative stress, and chondrocyte apoptosis induced by oxidative stress plays an important role in the development of OA. Rat chondrocytes exposed to hydrogen peroxide (H₂O₂) were used as the experimental oxidative stress model. We assessed cell viability, cell apoptosis, levels of intracellular reactive oxygen species (ROS), nitric oxide (NO) production, gene relative expression level of inducible nitric oxide synthase (iNOS), and expressions of iNOS, PI3K, phospho-Akt, caspase-9, and caspase-3. With the rising of intracellular ROS and increasing iNOS synthesis, producing a large amount of NO in chondrocytes, H₂O₂ decreased the cell viability and induced cell apoptosis of chondrocytes. Furthermore, the levels of caspase-9 and caspase-3 protein expression were significantly elevated as well as the level of p-Akt protein expression when induced by oxidative stress. These findings suggest that oxidative stress-induced chondrocyte apoptosis occurred via activating both PI3K/Akt and caspase pathways in the early stage in these processes.
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