### Recent Submissions

• #### A zero liquid discharge system integrating multi-effect distillation and evaporative crystallization for desalination brine treatment

(Desalination, Elsevier BV, 2021-01-13) [Article]
• #### Generation of iPSC lines (KAUSTi011-A, KAUSTi011-B) from a Saudi patient with epileptic encephalopathy carrying homozygous mutation in the GLP1R gene.

(Stem cell research, Elsevier BV, 2021-01-09) [Article]
Glucagon-like peptide-1 receptor (GLP1R) is a seven-transmembrane-spanning helices membrane protein expressed in multiple human tissues including pancreatic islets, lung, brain, heart and central nervous system (CNS). GLP1R agonists are commonly used as antidiabetic drugs, but a neuroprotective function in neurodegenerative disorders is emerging. Here, we established two iPSC lines from a patient harboring a rare homozygous splice site variant in GLP1R (NM_002062.3; c.402 + 3delG). This patient displays severe developmental delay and epileptic encephalopathy. Therefore, the derivation of these iPSC lines constitutes a primary model to study the molecular pathology of GLP1R dysfunction and develop novel therapeutic targets.
• #### Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

(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.

(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

(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.
• #### Strong enhancement of Penning ionisation in cold Rydberg gases II: Tom and Jerry pairs for alkali-metal atoms

(Journal of Physics B: Atomic, Molecular and Optical Physics, IOP Publishing, 2021-01-08) [Article]
Penning ionisation (PI) processes involving pairs of Rydberg alkali-metal atoms, excited to different quantum states and experiencing dipole-dipole interactions, have a wide range of important properties in atomic physics. Within the framework of the semi-classical approximation, we have used both numerical and analytical approaches to examine the Penning autoionisation width dependence on the state quantum numbers in a quasi-molecule formed by the interacting partner atoms. We described the characteristics of optimal quantum numbers that lead to enhanced PI widths for the interacting Rydberg atom pairs of all alkali-metal atoms. The excited states of atoms in these pairs are asymmetric, resulting in a large atomic shell size difference: inspired by [1], we call such pair "Tom" and "Jerry" (for "big" and "small"). Compared to symmetric pairs, the optimal asymmetric pairs display a significant (by several orders of magnitude) increase in the PI rate. This property makes PI a relevant source for producing charged particles in cold Rydberg systems that spontaneously evolve into cold plasma. Contrary to hydrogen atoms examined in [1], the difference of quantum defects in alkali-metal atoms results in a strong Penning width dependence on the orbital quantum numbers l of the quasi-molecule. In particular, alkali-metal atoms exhibit two PI channels associated with bound-bound optical transitions showing ∆l = ±1 - individual and closely spaced (doublet-like) configurations of optimal pairs. Furthermore, we demonstrate that the presence of Förster resonances can lead to a notable (up to 5 times) increase of the PI efficiency.
• #### Adaptive weighted Gerchberg-Saxton algorithm for generation of phase-only hologram with artifacts suppression

(Optics Express, The Optical Society, 2021-01-08) [Article]
In the conventional weighted Gerchberg-Saxton (GS) algorithm, the feedback is used to accelerate the convergence. However, it will lead to the iteration divergence. To solve this issue, an adaptive weighted GS algorithm is proposed in this paper. By replacing the conventional feedback with our designed feedback, the convergence can be ensured in the proposed method. Compared with the traditional GS iteration method, the proposed method improves the peak signal-noise ratio of the reconstructed image with 4.8 dB on average. Moreover, an approximate quadratic phase is proposed to suppress the artifacts in optical reconstruction. Therefore, a high-quality image can be reconstructed without the artifacts in our designed Argument Reality device. Both numerical simulations and optical experiments have validated the effectiveness of the proposed method.
• #### Long-term stimulation of the anteromedial thalamus increases hippocampal neurogenesis and spatial reference memory in adult rats.

(Behavioural brain research, Elsevier BV, 2021-01-08) [Article]
Deep brain stimulation (DBS) has shown positive clinical results in neurodegenerative diseases. Previous work from our group showed that a single session of DBS to the anteromedial thalamic nucleus (AMN) in awake rats, increased proliferation of stem/progenitor cells in the dentate gyrus (DG) of the hippocampus. We thought to examine the effect of single versus multiple sessions of DBS to the AMN in modulating adult hippocampal neurogenesis. Rats received unilateral single session, multiple sessions or no electrical stimulation (sham) in the right AMN. Rats received 5'-bromo-2'-deoxyuridine (BrdU) injections and were followed over a period of 1 week or 4 weeks. Single session of electrical stimulation induced a 1.9-fold increase in the number of proliferating BrdU positive cells after one week from stimulation and a 1.8-fold increase at four weeks post stimulation, both in the ipsilateral DG. As for multiple sessions of stimulation, they induced a 3- fold increase that extended to the contralateral DG after 4 weeks from stimulation. Spatial reference memory was tested in the Y-maze test by examining novel arm exploration. Both single and multiple sessions of stimulation prompted an increase in novel arm exploration at week 4, while only the multiple sessions of stimulation had this effect starting from week 1. This study demonstrates that sustained activation of the AMN boosts neurogenesis and improves spatial reference memory.
• #### Molecular basis for the adaptive evolution of environment sensing by H-NS proteins

(eLife, eLife Sciences Publications, Ltd, 2021-01-07) [Article]
The DNA-binding protein H-NS is a pleiotropic gene regulator in gram-negative bacteria. Through its capacity to sense temperature and other environmental factors, H-NS allows pathogens like Salmonella to adapt their gene expression to their presence inside or outside warm-blooded hosts. To investigate how this sensing mechanism may have evolved to fit different bacterial lifestyles, we compared H-NS orthologs from bacteria that infect humans, plants, and insects, and from bacteria that live on a deep-sea hypothermal vent. The combination of biophysical characterization, high-resolution proton-less NMR spectroscopy and molecular simulations revealed, at an atomistic level, how the same general mechanism was adapted to specific habitats and lifestyles. In particular, we demonstrate how environment-sensing characteristics arise from specifically positioned intra- or intermolecular electrostatic interactions. Our integrative approach clarified the exact modus operandi for H-NS–mediated environmental sensing and suggests that this sensing mechanism resulted from the exaptation of an ancestral protein feature.
• #### Chain Conformation Control of Fluorene-Benzothiadiazole Copolymer Light-Emitting Diode Efficiency and Lifetime

(ACS Applied Materials & Interfaces, American Chemical Society (ACS), 2021-01-07) [Article]
The β-phase, in which the intermonomer torsion angle of a fraction of chain segments approaches ∼180°, is an intriguing conformational microstructure of the widely studied light-emitting polymer poly(9,9-dioctylfluorene) (PFO). Its generation can in turn be used to significantly improve the performance of PFO emission-layer-based light-emitting diodes (LEDs). Here, we report the generation of β-phase chain segments in a copolymer, 90F8:10BT, containing 90% 9,9-dioctylfluorene (F8) and 10% 2,1,3-benzothiadiazole (BT) units and show that significant improvements in performance also ensue for LEDs with β-phase 90F8:10BT emission layers, generalizing the earlier PFO results. The β-phase was induced by both solvent vapor annealing and dipping copolymer thin films into a solvent/nonsolvent mixture. Subsequent absorption spectra show the characteristic fluorene β-phase peak at ∼435 nm, but luminescence spectra (∼530 nm peak) and quantum yields barely change, with the emission arising following efficient energy transfer to the lowest-lying excited states localized in the vicinity of the BT units. For ∼5% β-phase chain segment fraction relative to 0% β-phase, the LED luminance at 10 V increased by ∼25% to 5940 cd m<sup>-2</sup>, the maximum external quantum efficiency by ∼61 to 1.91%, and the operational stability from 64% luminance retention after 20 h of operation to 90%. Detailed studies addressing the underlying device physics identify a reduced hole injection barrier, higher hole mobility, correspondingly more balanced electron and hole charge transport, and decreased carrier trapping as the dominant factors. These results confirm the effectiveness of chain conformation control for fluorene-based homo- and copolymer device optimization.
• #### Senescence-Associated Secretory Phenotype Suppression Mediated by Small-Sized Mesenchymal Stem Cells Delays Cellular Senescence through TLR2 and TLR5 Signaling.

(Cells, MDPI AG, 2021-01-06) [Article]
In order to provide a sufficient number of cells for clinical use, mesenchymal stem cells (MSCs) must be cultured for long-term expansion, which inevitably triggers cellular senescence. Although the small size of MSCs is known as a critical determinant of their fate, the main regulators of stem cell senescence and the underlying signaling have not been addressed. Umbilical cord blood-derived MSCs (UCB-MSCs) were obtained using size-isolation methods and then cultured with control or small cells to investigate the major factors that modulate MSC senescence. Cytokine array data suggested that the secretion of interukin-8 (IL-8) or growth-regulated oncogene-alpha (GROa) by senescent cells was markedly inhibited during incubation of small cells along with suppression of cognate receptor (C-X-C motif chemokine receptor2, CXCR2) via blockade of the autocrine/paracrine positive loop. Moreover, signaling via toll-like receptor 2 (TLR2) and TLR5, both pattern recognition receptors, drove cellular senescence of MSCs, but was inhibited in small cells. The activation of TLRs (2 and 5) through ligand treatment induced a senescent phenotype in small cells. Collectively, our data suggest that small cell from UCB-MSCs exhibit delayed cellular senescence by inhibiting the process of TLR signaling-mediated senescence-associated secretory phenotype (SASP) activation.
• #### Robust Mesoporous Zr-MOF with Pd Nanoparticles for Formic-Acid-Based Chemical Hydrogen Storage

(Matter, Elsevier BV, 2021-01-06) [Article]
Formic acid is a compelling chemical storage platform for hydrogen gas, but the lack of an efficient dehydrogenation catalyst is preventing its commercial use. In this issue of Matter, Wang et al. report a fine-tuned zirconium metal-organic framework with palladium nanoparticles that effectively dehydrogenates formic acid without degradation.
• #### Laminar Burning Velocities of Formic Acid and Formic Acid/Hydrogen Flames: An Experimental and Modeling Study

(Energy & Fuels, American Chemical Society (ACS), 2021-01-05) [Article]
Laminar flame speed of formic acid and formic acid/hydrogen (4/1) flames was studied both experimentally and numerically. Experiments with flames of pure formic acid were performed at temperatures of 373 and 423 K, while for formic acid/hydrogen flames the temperature value was 368 K. All of the experiments were performed under atmospheric pressure and at an equivalence ratio ranging from 0.5 to 1.5. To measure the laminar flame speed, the heat flux balance technique was applied. Three detailed chemical-kinetic mechanisms were tested on experimental data. Experiments showed that addition of 20% of hydrogen increases the laminar burning velocity of formic acid, for example, at around 1.5 for stoichiometric flames. The comparison of experimental and numerical data showed that all models tend to overestimate laminar burning velocities of studied flames, especially in the case of rich flames. The obtained results indicate that further improvement of existing chemical-kinetic models of formic acid oxidation is highly required.
• #### Generation and evolution of different terahertz singular beams from long gas-plasma filaments

(Optics Express, The Optical Society, 2021-01-05) [Article]
We theoretically and numerically investigate the generation and evolution of different pulsed terahertz (THz) singular beams with an ultrabroad bandwidth (0.1–40 THz) in long gas-plasma filaments induced by a shaped two-color laser field, i.e., a vortex fundamental pulse (ω0) and a Gaussian second harmonic pulse (2ω0). Based on the unidirectional propagation model under group-velocity moving reference frame, the simulating results demonstrate that three different THz singular beams, including the THz necklace beams with a π-stepwise phase profile, the THz angular accelerating vortex beams (AAVBs) with nonlinear phase profile, and the THz vortex beams with linear phase profile, are generated. The THz necklace beams are generated first at millimeter-scale length. Then, with the increase of the filament length, THz AAVBs and THz vortex beams appear in turn almost periodically. Our calculations confirm that all these different THz singular beams result from the coherent superposition of the two collinear THz vortex beams with variable relative amplitudes and conjugated topological charges (TCs), i.e., +2 and −2. These two THz vortex beams could come from the two four-wave mixing (FWM) processes, respectively, i.e., ω0+ω0−2ω0→ωTHz and –(ω0+ω0) + 2ω0→ωTHz. The evolution of the different THz singular beams depends on the combined effect of the pump ω0−2ω0 time delay and the separate, periodical, and helical plasma channels. And the TC sign of the generated THz singular beams can be easily controlled by changing the sign of the ω0−2ω0 time delay. We believe that these results will deepen the understanding of the THz singular beam generation mechanism and orbital angular momentum (OAM) conversion in laser induced gas-filamentation.