Recent Submissions

  • Analysis of Fuel Properties on Combustion Characteristics in a Narrow-throat Pre-chamber Engine

    Hlaing, Ponnya; Marquez, Manuel Echeverri; Burgos, Paula; Cenker, Emre; Ben Houidi, Moez; Johansson, Bengt (The Society of Automotive Engineers, 2021-04-14) [Conference Paper]
    In this study, the authors investigated the effect of fuel properties on the combustion characteristics by employing methane, methanol, ethanol, and primary reference fuels (PRFs) as the main chamber fuel while using methane for the pre-chamber. Global excess air ratios (λ) from 1.6 to lean limit were tested, while 13% of total fuel energy supplied to the engine was delivered via the pre-chamber. The gaseous methane was injected into the pre-chamber at the gas exchange top-dead-center (TDC). Port fuel injection was tested with both open and closed inlet valves. The pre-chamber assembly was designed to fit into the diesel injector pocket of the base engine, which resulted in a narrow throat diameter of 3.3 mm. The combustion stability limit was set at 5% of the coefficient of variation of gross IMEP, and the knock intensity limit was set at 10 bar. GT-Power software was used to estimate the composition of pre-chamber species and was used in heat release analysis of the two chambers. It was found that the rich limit was controlled by engine knock. Hence a higher reactivity fuel (lower octane) had to be operated leaner. However, with the increasing reactivity, the lean limit was also extended, while the peak efficiency was also obtained with a leaner mixture. With PRF 90, the lean limit was at global-λ = 3.0, while the limit was 2.3 with methane. The alcohol fuels exhibited a different behavior from the methane and the PRFs. Ethanol has the same lean limit as PRF100, but methanol could be operated up to global-λ = 3.2. The pre-chamber combustion did not change much with the different fuels in the main chamber, so the combustion stability trends must be related to the transition from burning jets to ignition of the main chamber charge and its subsequent combustion.
  • Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field.

    Nasser, Badoor Ali Hassan; Saito, Yoshimoto; Alarawi, Mohammed; Humam, Abdulmohsen A; Mineta, Katsuhiko; Gojobori, Takashi (Gene, Elsevier BV, 2021-01-15) [Article]
    Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion (MIC) or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.
  • Development of a simplified n-heptane/methane model for high-pressure direct-injection natural gas marine engines

    Li, Jingrui; Liu, Haifeng; Liu, Xinlei; Ye, Ying; Wang, Hu; Wang, Xinyan; Zhao, Hua; Yao, Mingfa (Frontiers in Energy, Springer Science and Business Media LLC, 2021-01-15) [Article]
    High-pressure direct-injection (HPDI) of natural gas is one of the most promising solutions for future ship engines, in which the combustion process is mainly controlled by the chemical kinetics. However, the employment of detailed chemical models for the multi-dimensional combustion simulation is significantly expensive due to the large scale of the marine engine. In the present paper, a reduced n-heptane/methane model consisting of 35-step reactions was constructed using multiple reduction approaches. Then this model was further reduced to include only 27 reactions by utilizing the HyChem (Hybrid Chemistry) method. An overall good agreement with the experimentally measured ignition delay data of both n-heptane and methane for these two reduced models was achieved and reasonable predictions for the measured laminar flame speeds were obtained for the 35-step model. But the 27-step model cannot predict the laminar flame speed very well. In addition, these two reduced models were both able to reproduce the experimentally measured in-cylinder pressure and heat release rate profiles for a HPDI natural gas marine engine, the highest error of predicted combustion phase being 6.5%. However, the engine-out CO emission was over-predicted and the highest error of predicted NOx emission was less than 12.9%. The predicted distributions of temperature and equivalence ratio by the 35-step and 27-step models are similar to those of the 334-step model. However, the predicted distributions of OH and CH2O are significantly different from those of the 334-step model. In short, the reduced chemical kinetic models developed provide a high-efficient and dependable method to simulate the characteristics of combustion and emissions in HPDI natural gas marine engines.
  • Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field.

    Nasser, Badoor Ali Hassan; Saito, Yoshimoto; Alarawi, Mohammed; Humam, Abdulmohsen A; Mineta, Katsuhiko; Gojobori, Takashi (Gene, Elsevier BV, 2021-01-15) [Article]
    Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion (MIC) or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.
  • A first-principles approach for treating wastewaters

    Santana, Adriano; Farinha, Andreia S. F.; Zarzar Torano, Aniela; Ibrahim, Mahmoud; Mishra, Himanshu (International Journal of Quantum Chemistry, Wiley, 2021-01-15) [Article]
    Numerous materials are employed for the removal of contaminants from wastewaters. However, the regeneration/reuse of these materials is still seldom practiced. Quantitative insights into intermolecular forces between the contaminants and the functional surfaces might aid the rational design of reusable materials. Here, we compare the efficacies of aliphatic (C8H18), aromatic (C6H6), and aromatic perfluorinated (C6F6) moieties at removing methylene blue (MB+) as a surrogate cationic dye from water. We employed density functional theory with an implicit polarizable continuum model for water to accurately determine the contributions of the solvent's electrostatics in the adsorption process. Our calculations pinpointed the relative contributions of ππ stacking, van der Waals complexation, hydrogen bonding, and cationπ interactions, predicting that MB+ would bind the strongest with C6F6 due to hydrogen bonding and the weakest with C8H18. Complementary laboratory experiments revealed that, despite the similar hydrophobicity of silica beads functionalized with SiC8H17, SiC6H5, and SiC6F5 groups, as characterized by their water contact angles, the relative uptake of aqueous MB+ varied as SiC6F5 (95%) > SiC6H5 (35%) > SiC8H17 (3%). This first principles-led experimental approach can be easily extended to other classes of dyes, thereby advancing the rational design of adsorbents.
  • A zero liquid discharge system integrating multi-effect distillation and evaporative crystallization for desalination brine treatment

    Chen, Qian; Burhan, Muhammad; Shahzad, Muhammad Wakil; Ybyraiymkul, Doskhan; Akhtar, Faheem; Li, Yong; Ng, Kim Choon (Desalination, Elsevier BV, 2021-01-13) [Article]
    With growing global desalination capacity, brine from desalination plants has become an environmental threat to the ecosystems. One sustainable method for brine treatment is to develop zero liquid discharge systems that completely convert seawater into freshwater and salts. This paper presents a zero liquid discharge system, which consists of multi-effect distillation and evaporative crystallization, to treat desalination brine with a salinity of 70 g/kg. A thermodynamic analysis is firstly conducted for the proposed system. The specific heat consumption, specific heat transfer area, and Second-law efficiency are found to be 600–1100 kJ/kg, 110–340 m2/(kg/s), and 10–17%, respectively. The heat consumption can be effectively reduced by increasing the number of MED stages, while the specific heat transfer area decreases significantly with higher heat source temperatures. Based on the thermodynamic performance, a techno-economic analysis is conducted for the proposed system, and the specific cost is calculated to be $4.17/m3. Cost reduction can be achieved via employing cost-effective heat sources, reducing heat consumption, and scaling up the system. By selling the freshwater and salt crystals, the system will be more competitive than other existing brine treatment methods.
  • Influence of Side Chains on the n-Type Organic Electrochemical Transistor Performance

    Ohayon, David; Savva, Achilleas; du, weiyuan; Paulsen, Bryan D.; Uguz, Ilke; Ashraf, Raja; Rivnay, Jonathan; McCulloch, Iain; Inal, Sahika (ACS Applied Materials & Interfaces, American Chemical Society (ACS), 2021-01-13) [Article]
    n-Type (electron transporting) polymers can make suitable interfaces to transduce biological events that involve the generation of electrons. However, n-type polymers that are stable when electrochemically doped in aqueous media are relatively scarce, and the performance of the existing ones lags behind their p-type (hole conducting) counterparts. Here, we report a new family of donor-acceptor-type polymers based on a naphthalene-1,4,5,8-tetracarboxylic-diimide-bi-thiophene (NDI-T2) backbone where the NDI unit always bears an ethylene glycol (EG) side chain. We study how small variations in the side chains tethered to the acceptor as well as the donor unit affect the performance of the polymer films in the state-of-the-art bioelectronic device, the organic electrochemical transistor (OECT). First, we find that substitution of the T2 core with an electron-withdrawing group (i.e., methoxy) or an EG side chain leads to ambipolar charge transport properties and causes significant changes in film microstructure, which overall impairs the n-type OECT performance. We thus show that the best n-type OECT performer is the polymer that has no substitution on the T2 unit. Next, we evaluate the distance of the oxygen from the NDI unit as a design parameter by varying the length of the carbon spacer placed between the EG unit and the backbone. We find that the distance of the EG from the backbone affects the film order and crystallinity, and thus, the electron mobility. Consequently, our work reports the best-performing NDI-T2-based n-type OECT material to date, i.e., the polymer without the T2 substitution and bearing a six-carbon spacer between the EG and the NDI units. Our work provides new guidelines for the side-chain engineering of n-type polymers for OECTs and insights on the structure-performance relationships for mixed ionic-electronic conductors, crucial for devices where the film operates at the aqueous electrolyte interface.
  • Scalable Pulsed Laser Deposition of Transparent Rear Electrode for Perovskite Solar Cells

    Smirnov, Yury; Schmengler, Laura; Kuik, Riemer; Repecaud, Pierre-Alexis; Najafi, Mehrdad; Zhang, Dong; Theelen, Mirjam; Aydin, Erkan; Veenstra, Sjoerd; De Wolf, Stefaan; Morales-Masis, Monica (Advanced Materials Technologies, Wiley, 2021-01-12) [Article]
    Sputtered transparent conducting oxides (TCOs) are widely accepted transparent electrodes for several types of high-efficiency solar cells. However, the different sputtering yield of atoms makes stoichiometric transfer of target material challenging for multi-compounds. Additionally, the high kinetic energies of the arriving species may damage sensitive functional layers beneath. Conversely, pulsed laser deposition (PLD) is operated at higher deposition pressures promoting thermalization of particles. This leads to stoichiometric transfer and additionally reduces the kinetic energy of ablated species. Despite these advantages, PLD is rarely used within the photovoltaic community due to concerns about low deposition rates and the scalability of the technique. In this study, wafer-scale (4-inch) PLD of high-mobility Zr-doped In2O3 (IZrO) TCO for solar cells is demonstrated. IZrO films are grown at room temperature with deposition rate on par with RF-sputtering (>4 nm min−1). As-deposited IZrO films are mostly amorphous and exhibit excellent optoelectronic properties after solid phase crystallization at <200 °C. 100-nm thick films feature a sheet resistance of 21 Ω◻−1 with electron mobilities ≈70 cm2 V−1s−1. PLD-grown IZrO is applied as rear electrode in efficient semi-transparent halide perovskite solar cells leading to the improved stabilized maximum power point efficiency (15.1%) as compared to the cells with sputtered ITO electrodes (11.9%).
  • Impacts of hypoxic events surpass those of future ocean warming and acidification

    Sampaio, Eduardo; Santos, Catarina; Rosa, Inês C.; Ferreira, Verónica; Pörtner, Hans-Otto; Duarte, Carlos M.; Levin, Lisa A.; Rosa, Rui (Nature Ecology & Evolution, Springer Science and Business Media LLC, 2021-01-11) [Article]
    Over the past decades, three major challenges to marine life have emerged as a consequence of anthropogenic emissions: ocean warming, acidification and oxygen loss. While most experimental research has targeted the first two stressors, the last remains comparatively neglected. Here, we implemented sequential hierarchical mixed-model meta-analyses (721 control–treatment comparisons) to compare the impacts of oxygen conditions associated with the current and continuously intensifying hypoxic events (1–3.5 O2 mg l−1) with those experimentally yielded by ocean warming (+4 °C) and acidification (−0.4 units) conditions on the basis of IPCC projections (RCP 8.5) for 2100. In contrast to warming and acidification, hypoxic events elicited consistent negative effects relative to control biological performance—survival (–33%), abundance (–65%), development (–51%), metabolism (–33%), growth (–24%) and reproduction (–39%)—across the taxonomic groups (mollusks, crustaceans and fish), ontogenetic stages and climate regions studied. Our findings call for a refocus of global change experimental studies, integrating oxygen concentration drivers as a key factor of ocean change. Given potential combined effects, multistressor designs including gradual and extreme changes are further warranted to fully disclose the future impacts of ocean oxygen loss, warming and acidification.
  • The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals

    Le Roy, Nathalie; Ganot, Philippe; Aranda, Manuel; Allemand, Denis; Tambutté, Sylvie (BMC Ecology and Evolution, Springer Science and Business Media LLC, 2021-01-11) [Article]
    Abstract Background The process of calcium carbonate biomineralization has arisen multiple times during metazoan evolution. In the phylum Cnidaria, biomineralization has mostly been studied in the subclass Hexacorallia (i.e. stony corals) in comparison to the subclass Octocorallia (i.e. red corals); the two diverged approximately 600 million years ago. The precious Mediterranean red coral, Corallium rubrum, is an octocorallian species, which produces two distinct high-magnesium calcite biominerals, the axial skeleton and the sclerites. In order to gain insight into the red coral biomineralization process and cnidarian biomineralization evolution, we studied the protein repertoire forming the organic matrix (OM) of its two biominerals. Results We combined High-Resolution Mass Spectrometry and transcriptome analysis to study the OM composition of the axial skeleton and the sclerites. We identified a total of 102 OM proteins, 52 are found in the two red coral biominerals with scleritin being the most abundant protein in each fraction. Contrary to reef building corals, the red coral organic matrix possesses a large number of collagen-like proteins. Agrin-like glycoproteins and proteins with sugar-binding domains are also predominant. Twenty-seven and 23 proteins were uniquely assigned to the axial skeleton and the sclerites, respectively. The inferred regulatory function of these OM proteins suggests that the difference between the two biominerals is due to the modeling of the matrix network, rather than the presence of specific structural components. At least one OM component could have been horizontally transferred from prokaryotes early during Octocorallia evolution. Conclusion Our results suggest that calcification of the red coral axial skeleton likely represents a secondary calcification of an ancestral gorgonian horny axis. In addition, the comparison with stony coral skeletomes highlighted the low proportion of similar proteins between the biomineral OMs of hexacorallian and octocorallian corals, suggesting an independent acquisition of calcification in anthozoans.
  • Boron-catalyzed Polymerization of Dienyltriphenylarsonium Ylides: on the Way to Pure C5 Polymerization

    Hadjichristidis, Nikos; Wang, Xin (Angewandte Chemie, Wiley, 2021-01-11) [Article]
    The first C5 polymerization is reported, where the main-chain is growing by five carbon atoms of the monomer at a time. Three dienyltriphenylarsonium ylide monomers were synthesized and polymerized with triethylborane as initiator leading to random terpolymers (C1, C3, C5) with mainly C5 repeating units (up to 84.1%). It has been found that the methyl group (electron-donating substituent) on the conjugated double bond of ylides facilitates the formation of C5 segments. A mechanism was proposed based on NMR characterization and DFT calculations. The high C5 content ensures that we are on the right track for pure C5 homopolymerization.
  • MAAS: Multi-modal Assignation for Active Speaker Detection

    León-Alcázar, Juan; Heilbron, Fabian Caba; Thabet, Ali Kassem; Ghanem, Bernard (arXiv, 2021-01-11) [Preprint]
    Active speaker detection requires a solid integration of multi-modal cues. While individual modalities can approximate a solution, accurate predictions can only be achieved by explicitly fusing the audio and visual features and modeling their temporal progression. Despite its inherent muti-modal nature, current methods still focus on modeling and fusing short-term audiovisual features for individual speakers, often at frame level. In this paper we present a novel approach to active speaker detection that directly addresses the multi-modal nature of the problem, and provides a straightforward strategy where independent visual features from potential speakers in the scene are assigned to a previously detected speech event. Our experiments show that, an small graph data structure built from a single frame, allows to approximate an instantaneous audio-visual assignment problem. Moreover, the temporal extension of this initial graph achieves a new state-of-the-art on the AVA-ActiveSpeaker dataset with a mAP of 88.8\%.
  • Efficient bifacial monolithic perovskite/silicon tandem solar cells via bandgap engineering

    de Bastiani, Michele; Mirabelli, Alessandro J.; Hou, Yi; Gota, Fabrizio; Aydin, Erkan; Allen, Thomas; Troughton, Joel; Subbiah, Anand Selvin; Isikgor, Furkan Halis; Liu, Jiang; Xu, Lujia; Chen, Bin; Van Kerschaver, Emmanuel; Baran, Derya; Fraboni, Beatrice; Salvador, Michael F.; Paetzold, Ulrich W.; Sargent, E.; De Wolf, Stefaan (Nature Energy, Springer Science and Business Media LLC, 2021-01-11) [Article]
    Bifacial monolithic perovskite/silicon tandem solar cells exploit albedo—the diffuse reflected light from the environment—to increase their performance above that of monofacial perovskite/silicon tandems. Here we report bifacial tandems with certified power conversion efficiencies >25% under monofacial AM1.5G 1 sun illumination that reach power-generation densities as high as ~26 mW cm–2 under outdoor testing. We investigated the perovskite bandgap required to attain optimized current matching under a variety of realistic illumination and albedo conditions. We then compared the properties of these bifacial tandems exposed to different albedos and provide energy yield calculations for two locations with different environmental conditions. Finally, we present a comparison of outdoor test fields of monofacial and bifacial perovskite/silicon tandems to demonstrate the added value of tandem bifaciality for locations with albedos of practical relevance.
  • Population structure of indigenous inhabitants of Arabia

    Mineta, Katsuhiko; Goto, Kosuke; Gojobori, Takashi; Alkuraya, Fowzan S. (PLOS Genetics, Public Library of Science (PLoS), 2021-01-11) [Article]
    Modern day Saudi Arabia occupies the majority of historical Arabia, which may have contributed to ancient waves of migration out of Africa. This ancient history has left a lasting imprint in the genetics of the region, including the diverse set of tribes that call Saudi Arabia their home. How these tribes relate to each other and to the world’s major populations remains an unanswered question. In an attempt to improve our understanding of the population structure of Saudi Arabia, we conducted genomic profiling of 957 unrelated individuals who self-identify with 28 large tribes in Saudi Arabia. Consistent with the tradition of intra-tribal unions, the subjects showed strong clustering along tribal lines with the distance between clusters correlating with their geographical proximities in Arabia. However, these individuals form a unique cluster when compared to the world’s major populations. The ancient origin of these tribal affiliations is supported by analyses that revealed little evidence of ancestral origin from within the 28 tribes. Our results disclose a granular map of population structure and have important implications for future genetic studies into Mendelian and common diseases in the region.
  • Coating of Conducting and Insulating Threads with Porous MOF Particles through Langmuir-Blodgett Technique

    Rauf, Sakandar; Andrés, Miguel A.; Roubeau, Olivier; Gascón, Ignacio; Serre, Christian; Eddaoudi, Mohamed; Salama, Khaled N. (Nanomaterials, MDPI AG, 2021-01-10) [Article]
    The Langmuir-Blodgett (LB) method is a well-known deposition technique for the fabrication of ordered monolayer and multilayer thin films of nanomaterials onto different substrates that plays a critical role in the development of functional devices for various applications. This paper describes detailed studies about the best coating configuration for nanoparticles of a porous metal-organic framework (MOF) onto both insulating or conductive threads and nylon fiber. We design and fabricate customized polymethylmethacrylate sheets (PMMA) holders to deposit MOF layers onto the threads or fiber using the LB technique. Two different orientations, namely, horizontal and vertical, are used to deposit MIL-96(Al) monolayer films onto five different types of threads and nylon fiber. These studies show that LB film formation strongly depends on deposition orientation and the type of threads or fiber. Among all the samples tested, cotton thread and nylon fiber with vertical deposition show more homogenous monolayer coverage. In the case of conductive threads, the MOF particles tend to aggregate between the conductive thread’s fibers instead of forming a continuous monolayer coating. Our results show a significant contribution in terms of MOF monolayer deposition onto single fiber and threads that will contribute to the fabrication of single fiber or thread-based devices in the future.
  • Root endophyte induced plant thermotolerance by constitutive chromatin modification at heat stress memory gene loci

    Shekhawat, Kirti; Saad, Maged; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Al-Mahmoudi, Henda; abdulhakim, fatimah; Eida, Abdul Aziz; Jalal, Rewaa S.; Masmoudi, Khaled; Hirt, Heribert (EMBO reports, EMBO, 2021-01-10) [Article]
    Global warming has become a critical challenge to food security, causing severe yield losses of major crops worldwide. Conventional and transgenic breeding strategies to enhance plant thermotolerance are laborious and expensive. Therefore, the use of beneficial microbes could be an alternative approach. Here, we report that the root endophyte Enterobacter sp. SA187 induces thermotolerance in wheat in the laboratory as well as in open-field agriculture. To unravel the molecular mechanisms, we used Arabidopsis thaliana as model plant. SA187 reprogramed the Arabidopsis transcriptome via HSFA2-dependent enhancement of H3K4me3 levels at heat stress memory gene loci. Unlike thermopriming, SA187-induced thermotolerance is mediated by ethylene signaling via the transcription factor EIN3. In contrast to the transient chromatin modification by thermopriming, SA187 induces constitutive H3K4me3 modification of heat stress memory genes, generating robust thermotolerance in plants. Importantly, microbial community composition of wheat plants in open-field agriculture is not influenced by SA187, indicating that beneficial microbes can be a powerful tool to enhance thermotolerance of crops in a sustainable manner.
  • Metabolomic and Biochemical Analysis of Two Potato (Solanum tuberosum L.) Cultivars Exposed to In Vitro Osmotic and Salt Stresses.

    Hamooh, Bahget Talat; Sattar, Farooq Abdul; Wellman, Gordon; Mousa, Magdi Ali Ahmed (Plants (Basel, Switzerland), MDPI AG, 2021-01-09) [Article]
    Globally, many crop production areas are threatened by drought and salinity. Potato ($\textit{Solanum tuberosum}$ L.) is susceptible to these challenging environmental conditions. In this study, an in vitro approach was employed to compare the tolerance of potato cultivars 'BARI-401' (red skin) and 'Spunta' (yellow skin). To simulate ionic and osmotic stress, MS media was supplemented with lithium chloride (LiCl 20 mM) and mannitol (150 mM). GC-MS and spectrophotometry techniques were used to determine metabolite accumulation. Other biochemical properties, such as total phenols concentration (TPC), total flavonoids concentration (TFC), antioxidant capacity (DPPH free radical scavenging capacity), polyphenol oxidase (PPO), and peroxidase (POD) activities, were also measured. The two cultivars respond differently to ionic and osmotic stress treatments, with Spunta accumulating more defensive metabolites in response, indicating a higher level of tolerance. While further investigation of the physiological and biochemical responses of these varieties to drought and salinity is required, the approach taken in this paper provides useful information prior to open field evaluation.
  • Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

    Rayapuram, Naganand; Jarad, Mai; Alhoraibi, Hanna; Bigeard, Jean; Abulfaraj, Aala A.; Volz, Ronny; Mariappan, Kiruthiga; Almeida-Trapp, Marilia; Schlöffel, Maria; Lastrucci, Emmanuelle; Bonhomme, Ludovic; Gust, Andrea A.; Mithöfer, Axel; Arold, Stefan T.; Pflieger, Delphine; Hirt, Heribert (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-01-08) [Article]
    In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.
  • Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites.

    Zhang, Lin; Fan, Ming; Napolitano, Francesco; Gao, Xin; Xu, Ying; Li, Lihua (Journal of translational medicine, Springer Science and Business Media LLC, 2021-01-08) [Article]
    BackgroundMetastasis is the most devastating stage of cancer progression and often shows a preference for specific organs.MethodsTo reveal the mechanisms underlying organ-specific metastasis, we systematically analyzed gene expression profiles for three common metastasis sites across all available primary origins. A rank-based method was used to detect differentially expressed genes between metastatic tumor tissues and corresponding control tissues. For each metastasis site, the common differentially expressed genes across all primary origins were identified as organ-specific metastasis genes.ResultsPathways enriched by these genes reveal an interplay between the molecular characteristics of the cancer cells and those of the target organ. Specifically, the neuroactive ligand-receptor interaction pathway and HIF-1 signaling pathway were found to have prominent roles in adapting to the target organ environment in brain and liver metastases, respectively. Finally, the identified organ-specific metastasis genes and pathways were validated using a primary breast tumor dataset. Survival and cluster analysis showed that organ-specific metastasis genes and pathways tended to be expressed uniquely by a subgroup of patients having metastasis to the target organ, and were associated with the clinical outcome.ConclusionsElucidating the genes and pathways underlying organ-specific metastasis may help to identify drug targets and develop treatment strategies to benefit patients.
  • Elucidating the Role of Virulence Traits in the Survival of Pathogenic E. coli PI-7 Following Disinfection

    Sivakumar, Krishnakumar; Lehmann, Robert; Rachmadi, Andri Taruna; Augsburger, Nicolas; Zaouri, Noor A.; Tegner, Jesper; Hong, Pei-Ying (Frontiers in bioengineering and biotechnology, Frontiers Media SA, 2021-01-08) [Article]
    Reuse and discharge of treated wastewater can result in dissemination of microorganisms into the environment. Deployment of disinfection strategies is typically proposed as a last stage remediation effort to further inactivate viable microorganisms. In this study, we hypothesize that virulence traits, including biofilm formation, motility, siderophore, and curli production along with the capability to internalize into mammalian cells play a role in survival against disinfectants. Pathogenic E. coli PI-7 strain was used as a model bacterium that was exposed to diverse disinfection strategies such as chlorination, UV and solar irradiation. To this end, we used a random transposon mutagenesis library screening approach to generate 14 mutants that exhibited varying levels of virulence traits. In these 14 isolated mutants, we observed that an increase in virulence traits such as biofilm formation, motility, curli production, and internalization capability, increased the inactivation half-lives of mutants compared to wild-type E. coli PI-7. In addition, oxidative stress response and EPS production contributed to lengthening the lag phase duration (defined as the time required for exposure to disinfectant prior to decay). However, traits related to siderophore production did not help with survival against the tested disinfection strategies. Taken together, the findings suggested that selected virulence traits facilitate survival of pathogenic E. coli PI-7, which in turn could account for the selective enrichment of pathogens over the nonpathogenic ones after wastewater treatment. Further, the study also reflected on the effectiveness of UV as a more viable disinfection strategy for inactivation of pathogens.

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