Making connections between novel transcription factors and their DNA motifs

The key components of a transcriptional regulatory network are the connections between trans-acting transcription factors and cis-acting DNA-binding sites. In spite of several decades of intense research, only a fraction of the estimated ∼300 transcription factors in Escherichia coli have been linked to some of their binding sites in the genome. In this paper, we present a computational method to connect novel transcription factors and DNA motifs in E. coli. Our method uses three types of mutually independent information, two of which are gleaned by comparative analysis of multiple genomes and the third one derived from similarities of transcription-factor-DNA-binding-site interactions. The different types of information are combined to calculate the probability of a given transcription-factor-DNA-motif pair being a true pair. Tested on a study set of transcription factors and their DNA motifs, our method has a prediction accuracy of 59% for the top predictions and 85% for the top three predictions. When applied to 99 novel transcription factors and 70 novel DNA motifs, our method predicted 64 transcription-factor-DNA-motif pairs. Supporting evidence for some of the predicted pairs is presented. Functional annotations are made for 23 novel transcription factors based on the predicted transcription-factor-DNA-motif connections

Development of titanium dioxide nanoparticles/nanosolution for photocatalytic activity

Biological and chemical contaminants by man-made activities have been serious global issue. Exposure of these contaminants beyond the limits may result in serious environmental and health problem. Therefore, it is important to develop an effective solution that can be easily utilized by mankind. One of the effective ways to overcome this problem is by using titanium dioxide (TiO2). TiO2 is a well-known photocatalyst that widely used for environmental clean-up due to its ability to decompose organic pollutant and kill bacteria. Although it is proven TiO2 has an advantage to solve this concern, its usefulness unfortunately is limited only under UV light irradiation. Therefore, the aim of this work was to investigate the potential of TiO2 that can be activated under visible light by the incorporation of metal ions (Fe, Ag, Zr and Ag-Zr). In this study, sol-gel method was employed for the synthesis of metal ions incorporated TiO2. XRD analysis revealed that all samples content biphasic anatase-brookite TiO2 of size 3 nm to 5 nm. It was found that the incorporation of these metal ions did not change the morphology of TiO2 but the crystallinity and optical properties were affected. The crystallinity of anatase in the biphasic TiO2 was found to be decreased and favored brookite formation. PL analysis showed metal ions incorporation suppressed the recombination of electron-hole pairs while the band gap energy of TiO2 (3.2 eV) was decreased by the incorporation of Fe (2.46 eV) and Ag (2.86 eV). Among this incorporation, Ag-Zr incorporated TiO2 showed highest performance for methyl orange degradation (93%) under fluorescent xxv light irradiation for 10 h. This follows by Zr-TiO2 (82%), Fe-TiO2 (75%) and Ag�TiO2 (43%). Meanwhile, the highest antibacterial performance was exhibited by Ag�TiO2. TEM images showed that E.coli bacterium was killed within 12 h after treated with Ag-TiO2. The results obtained from the fieldwork study established that Ag-Zr incorporation have excellent performances for VOC removal and antibacterial test. The VOC content after treated with Ag-Zr-TiO2 fulfilled the Industry Code of Practice on Indoor Air Quality 2010 which is lower than 3 ppm. In addition, the percentage of microbes also found to be decrease around 45 % within 5 days of monitoring

Spatiotemporally Constrained Action Space Attacks on Deep Reinforcement Learning Agents

Robustness of Deep Reinforcement Learning (DRL) algorithms towards adversarial attacks in real world applications such as those deployed in cyber-physical systems (CPS) are of increasing concern. Numerous studies have investigated the mechanisms of attacks on the RL agent's state space. Nonetheless, attacks on the RL agent's action space (AS) (corresponding to actuators in engineering systems) are equally perverse; such attacks are relatively less studied in the ML literature. In this work, we first frame the problem as an optimization problem of minimizing the cumulative reward of an RL agent with decoupled constraints as the budget of attack. We propose a white-box Myopic Action Space (MAS) attack algorithm that distributes the attacks across the action space dimensions. Next, we reformulate the optimization problem above with the same objective function, but with a temporally coupled constraint on the attack budget to take into account the approximated dynamics of the agent. This leads to the white-box Look-ahead Action Space (LAS) attack algorithm that distributes the attacks across the action and temporal dimensions. Our results shows that using the same amount of resources, the LAS attack deteriorates the agent's performance significantly more than the MAS attack. This reveals the possibility that with limited resource, an adversary can utilize the agent's dynamics to malevolently craft attacks that causes the agent to fail. Additionally, we leverage these attack strategies as a possible tool to gain insights on the potential vulnerabilities of DRL agents.Comment: Version 2 with supplementary material

Transgenic Plants: Gene Constructs, Vector and Transformation Method

The human population has reached 7 billion by 2015 and is estimated to exceed 10 billion by the end of 2050. As such, crops which are the main food source must be produced at a higher pace in order to cater in tandem with the food demand. In the past, traditional plant breeders practice classical breeding techniques to propagate plants with desirable traits. However, traditional breeding technique lies in that only individuals of the same or closely related species can be crossbred. Moreover, traditional breeders will not be able to obtain traits which are not inherent within the gene pool of their target plants through classical breeding. With recent advancements in the field of genetic engineering, it is now possible to insert beneficial genes from a completely different species or even kingdom into a target plant, yielding transgenic plants with multiple ideal traits. To develop a transgenic plant, parameters such as vector constructions, transformation methods, transgene integration, and inheritance of transgene need to be carefully considered to ensure the success of the transformation event. Hence, this chapter aimed to provide an overview of transgenic plants’ development, its advantages and disadvantages, as well as its application for the betterment of mankind

Co-infection of Haemonchus contortus and Trichostrongylus spp. among livestock in Malaysia as revealed by amplification and sequencing of the internal transcribed spacer II DNA region

Background: Haemonchus contortus and Trichostrongylus spp. are reported to be the most prevalent and highly pathogenic parasites in livestock, particularly in small ruminants. However, the routine conventional tool used in Malaysia could not differentiate the species accurately and therefore limiting the understanding of the co-infections between these two genera among livestock in Malaysia. This study is the first attempt to identify the strongylids of veterinary importance in Malaysia (i.e., H. contortus and Trichostrongylus spp.) by amplification and sequencing of the Internal Transcribed Spacer II DNA region. Results: Overall, 118 (cattle: 11 of 98 or 11.2%; deer: 4 of 70 or 5.7%; goats: 99 of 157 or 63.1%; swine: 4 of 91 or 4.4%) out of the 416 collected fecal samples were microscopy positive with strongylid infection. The PCR and sequencing results demonstrated that 93 samples (1 or 25.0% of deer; 92 or 92.9% of goats) contained H. contortus. In addition, Trichostrongylus colubriformis was observed in 75 (75.8% of 99) of strongylid infected goats and Trichostrongylus axei in 4 (4.0%) of 99 goats and 2 (50.0%) of 4 deer. Based on the molecular results, co-infection of H. contortus and Trichostrongylus spp. (H. contortus + T. colubriformis denoted as HTC; H. contortus + T. axei denoted as HTA) were only found in goats. Specifically, HTC co-infections have higher rate (71 or 45.2% of 157) compared to HTA co-infections (3 or 1.9% of 157). Conclusions: The present study is the first molecular identification of strongylid species among livestock in Malaysia which is essential towards a better knowledge of the epidemiology of gastro-intestinal parasitic infection among livestock in the country. Furthermore, a more comprehensive or nationwide molecular-based study on gastro-intestinal parasites in livestock should be carried out in the future, given that molecular tools could assist in improving diagnosis of veterinary parasitology in Malaysia due to its high sensitivity and accuracy

Optically Defined Modal Sensors Incorporating Spiropyran-Doped Liquid Crystals with Piezoelectric Sensors

We integrated a piezoelectric sensing layer lamina containing liquid crystals (LC) and spiropyran (SP) in a LC/SP mixture to create an optically reconfigurable modal sensor for a cantilever beam. The impedance of this LC/SP lamina was decreased by UV irradiation which constituted the underlying mechanism to modulate the voltage externally applied to the piezoelectric actuating layer. Illuminating a specific pattern onto the LC/SP lamina provided us with a way to spatially modulate the piezoelectric vibration signal. We showed that if an UV illuminated pattern matches the strain distribution of a specific mode, a piezoelectric modal sensor can be created. Since UV illumination can be changed in situ in real-time, our results confirm for the first time since the inception of smart sensors, that an optically tailored modal sensor can be created. Some potential applications of this type of sensor include energy harvesting devices, bio-chips, vibration sensing and actuating devices

Synergy study on charge transport dynamics in hybrid organic solar cell: photocurrent mapping and performance analysis under local spectrum

Charge transport dynamics in ZnO based inverted organic solar cell (IOSC) has been characterized with transient photocurrent spectroscopy and localised photocurrent mapping-atomic force microscopy. The value of maximum exciton generation rate was found to vary from 2.6 × 1027 m−3s−1 (Jsat = 79.7 A m−2) to 2.9 × 1027 m−3s−1 (Jsat = 90.8 A m−2) for devices with power conversion efficiency ranging from 2.03 to 2.51%. These results suggest that nanorods served as an excellent electron transporting layer that provides efficient charge transport and enhances IOSC device performance. The photovoltaic performance of OSCs with various growth times of ZnO nanorods have been analysed for a comparison between AM1.5G spectrum and local solar spectrum. The simulated PCE of all devices operating under local spectrum exhibited extensive improvement with the gain of 13.3–13.7% in which the ZnO nanorods grown at 15 min possess the highest PCE under local solar with the value of 2.82%