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  • The time course of molecular acclimation to seawater in a euryhaline fish.

    Bonzi, Lucrezia C; Monroe, Alison; Lehmann, Robert; Berumen, Michael L.; Ravasi, Timothy; Schunter, Celia (Scientific reports, Springer Science and Business Media LLC, 2021-09-14) [Article]
    The Arabian pupfish, Aphanius dispar, is a euryhaline fish inhabiting both inland nearly-freshwater desert ponds and highly saline Red Sea coastal lagoons of the Arabian Peninsula. Desert ponds and coastal lagoons, located respectively upstream and at the mouths of dry riverbeds ("wadies"), have been found to potentially become connected during periods of intense rainfall, which could allow the fish to migrate between these different habitats. Flash floods would therefore flush Arabian pupfish out to sea, requiring a rapid acclimation to a greater than 40 ppt change in salinity. To investigate the molecular pathways of salinity acclimation during such events, a Red Sea coastal lagoon and a desert pond population were sampled, with the latter exposed to a rapid increase in water salinity. Changes in branchial gene expression were investigated via genome-wide transcriptome measurements over time from 6 h to 21 days. The two natural populations displayed basal differences in genes related to ion transport, osmoregulation and immune system functions. These mechanisms were also differentially regulated in seawater transferred fish, revealing their crucial role in long-term adaptation. Other processes were only transiently activated shortly after the salinity exposure, including cellular stress response mechanisms, such as molecular chaperone synthesis and apoptosis. Tissue remodelling processes were also identified as transient, but took place later in the timeline, suggesting their importance to long-term acclimation as they likely equip the fish with lasting adaptations to their new environment. The alterations in branchial functional pathways displayed by Arabian pupfish in response to salinity increases are diverse. These reveal a large toolkit of molecular processes important for adaptation to hyperosmolarity that allow for successful colonization to a wide variety of different habitats.
  • Comprehensive analytical approaches reveal species-specific search strategies in sympatric apex predatory sharks

    Calich, Hannah J.; Rodríguez, J. P.; Eguíluz, V. M.; Hammerschlag, Neil; Pattiaratchi, Charitha; Duarte, Carlos M.; Sequeira, Ana M.M. (Ecography, Wiley, 2021-09-14) [Article]
    Animals follow specific movement patterns and search strategies to maximize encounters with essential resources (e.g. prey, favourable habitat) while minimizing exposures to suboptimal conditions (e.g. competitors, predators). While describing spatiotemporal patterns in animal movement from tracking data is common, understanding the associated search strategies employed continues to be a key challenge in ecology. Moreover, studies in marine ecology commonly focus on singular aspects of species' movements, however using multiple analytical approaches can further enable researchers to identify ecological phenomena and resolve fundamental ecological questions relating to movement. Here, we used a set of statistical physics-based methods to analyze satellite tracking data from three co-occurring apex predators (tiger, great hammerhead and bull sharks) that predominantly inhabit productive coastal regions of the northwest Atlantic Ocean and Gulf of Mexico. We analyzed data from 96 sharks and calculated a range of metrics, including each species' displacements, turning angles, dispersion, space-use and community-wide movement patterns to characterize each species' movements and identify potential search strategies. Our comprehensive approach revealed high interspecific variability in shark movement patterns and search strategies. Tiger sharks displayed near-random movements consistent with a Brownian strategy commonly associated with movements through resource-rich habitats. Great hammerheads showed a mixed-movement strategy including Brownian and resident-type movements, suggesting adaptation to widespread and localized high resource availability. Bull sharks followed a resident movement strategy with restricted movements indicating localized high resource availability. We hypothesize that the species-specific search strategies identified here may help foster the co-existence of these sympatric apex predators. Following this comprehensive approach provided novel insights into spatial ecology and assisted with identifying unique movement and search strategies. Similar future studies of animal movement will help characterize movement patterns and also enable the identification of search strategies to help elucidate the ecological drivers of movement and to understand species' responses to environmental change.
  • Naturally Extracted Hydrophobic Solvent and Self-Assembly in Interfacial Polymerization

    Falca, Gheorghe; Musteata, Valentina-Elena; Chisca, Stefan; Hedhili, Mohamed N.; Ong, Chi Siang; Nunes, Suzana Pereira (ACS Applied Materials & Interfaces, American Chemical Society (ACS), 2021-09-12) [Article]
    Pharmaceutical, chemical, and food industries are actively implementing membrane nanofiltration modules in their processes to separate valuable products and recover solvents. Interfacial polymerization (IP) is the most widely used method to produce thin-film composite membranes for nanofiltration and reverse osmosis processes. Although membrane processes are considered green and environmentally friendly, membrane fabrication has still to be further developed in such direction. For instance, the emission of volatile solvents during membrane production in the industry has to be carefully controlled for health reasons. Greener solvents are being proposed for phase-separation membrane manufacture. For the IP organic phase, the proposition of greener alternatives is in an early stage. In this work, we demonstrate the preparation of a high-performing composite membrane employing zero vapor pressure and naturally extracted oleic acid as the IP organic phase. Its long hydrophobic chain ensures intrinsic low volatility and acid monomer dissolution, while the polar head induces a unique self-assembly structure during the film formation. Membranes prepared by this technique were selective for small molecules with a molecular weight cutoff of 650 g mol–1 and a high permeance of ∼57 L m–2 h–1 bar–1.
  • Cancer-associated mutations in the p85α N-terminal SH2 domain activate a spectrum of receptor tyrosine kinases.

    Li, Xinran; Lau, Amy Y T; Ng, Angel S N; Aldehaiman, Abdullah; Zhou, Yuan; Ng, Patrick K S; Arold, Stefan T.; Cheung, Lydia W T (Proceedings of the National Academy of Sciences of the United States of America, 2021-09-11) [Article]
    The phosphoinositide 3-kinase regulatory subunit p85α is a key regulator of kinase signaling and is frequently mutated in cancers. In the present study, we showed that in addition to weakening the inhibitory interaction between p85α and p110α, a group of driver mutations in the p85α N-terminal SH2 domain activated EGFR, HER2, HER3, c-Met, and IGF-1R in a p110α-independent manner. Cancer cells expressing these mutations exhibited the activation of p110α and the AKT pathway. Interestingly, the activation of EGFR, HER2, and c-Met was attributed to the ability of driver mutations to inhibit HER3 ubiquitination and degradation. The resulting increase in HER3 protein levels promoted its heterodimerization with EGFR, HER2, and c-Met, as well as the allosteric activation of these dimerized partners; however, HER3 silencing abolished this transactivation. Accordingly, inhibitors of either AKT or the HER family reduced the oncogenicity of driver mutations. The combination of these inhibitors resulted in marked synergy. Taken together, our findings provide mechanistic insights and suggest therapeutic strategies targeting a class of recurrent p85α mutations.
  • Pulsating CO2 nucleation radically improves the efficiency of membrane backwash

    Al Ghamdi, Mohanned; Alpatova, Alla; Alhadidi, Abdulsalam; Ghaffour, NorEddine (Desalination, Elsevier BV, 2021-09-11) [Article]
    Although membrane filtration became a dominant water treatment technology globally, it suffers from membrane fouling which aggravates with time and imposes severe adverse effects on process performance, permeate quality and, eventually, its related costs. In this work, we introduce pulsating CO2 solution backwash with intermittent pressure drops to maximize CO2 bubbles yield and radically enhance membrane cleaning. The novel backwash technique was probed during ultrafiltration (UF) of feed waters containing sodium alginate, a model polysaccharide foulants, sea salts enriched in Ca2+, and SiO2. Transmembrane pressures (TMP) observed during the experiments with pulsating CO2 backwash acquired an up/down profile indicating that a considerable portion of TMP was recovered after each backwash cycle, in contrast to insufficient fouling removal and subsequent TMP build-up observed with continuous CO2 and Milli-Q backwashes. Notably, pulsating CO2 backwash alleviated irreversible membrane fouling in highly saline conditions with 30 g/L of sea salts and when it is combined with 1 mg/L of SiO2 (i.e., when conventional membrane backwash was not effective). Furthermore, intense cleaning of the membrane surface and its pores was resembled by a lower fouling resistance in the subsequent UF cycles implying potentially longer operation time with less cleaning frequency and substantial energy savings.
  • Symbiodinium microadriaticum (coral microalgal endosymbiont)

    Voolstra, Christian R.; Aranda, Manuel; Zhan, Ye; Dekker, Job (Trends in Genetics, Elsevier BV, 2021-09-11) [Article]
    Photosynthetic microalgae, from the family Symbiodiniaceae, engage in endosymbioses with marine invertebrates, including stony corals. More generally, dinoflagellates are ubiquitous protists and the main primary producers in the oceans. Despite their ecological and economic importance, their biology remains enigmatic. Here we assembled 94 chromosome-scale scaffolds of the ancestral Symbiodiniaceae species Symbiodinium microadriaticum. Contrary to the random order of genes typically found in eukaryotic cells, genes are enriched toward the ends of chromosomes in alternating unidirectional blocks that are sometimes enriched for genes of specific biological processes. These gene blocks are coexpressed and separated by structural boundaries where transcription converges. These structural domains, in turn, comprise the transcription-dependent basic building blocks of the chromosomes that fold as linear rods. Such a highly ordered structure linking gene orientation, transcription, and spatial organization of chromosomes is exceptional.
  • Relative Importance of Stochastic Assembly Process of Membrane Biofilm Increased as Biofilm Aged

    Matar, Gerald; Ali, Muhammad; Bagchi, Samik; Nunes, Suzana Pereira; Liu, Wen-Tso; Saikaly, Pascal (Frontiers in Microbiology, Frontiers Media SA, 2021-09-10) [Article]
    The relative importance of different ecological processes controlling biofilm community assembly over time on membranes with different surface characteristics has never been investigated in membrane bioreactors (MBRs). In this study, five ultrafiltration hollow-fiber membranes – having identical nominal pore size (0.1μm) but different hydrophobic or hydrophilic surface characteristics – were operated simultaneously in the same MBR tank with a constant flux of 10 liters per square meter per hour (LMH). In parallel, membrane modules operated without permeate flux (0 LMH) were submerged in the same MBR tank, to investigate the passive microbial adsorption onto different hydrophobic or hydrophilic membranes. Samples from the membrane biofilm were collected after 1, 10, 20, and 30days of continuous filtration. The membrane biofilm microbiome were investigated using 16S rRNA gene amplicon sequencing from DNA and cDNA samples. Similar beta diversity trends were observed for both DNA- and cDNA-based analyses. Beta diversity analyses revealed that the nature of the membrane surface (i.e., hydrophobic vs. hydrophilic) did not seem to have an effect in shaping the bacterial community, and a similar biofilm microbiome evolved for all types of membranes. Similarly, membrane modules operated with and without permeate flux did not significantly influence alpha and beta diversity of the membrane biofilm. Nevertheless, different-aged membrane biofilm samples exhibited significant differences. Proteobacteria was the most dominant phylum in early-stage membrane biofilm after 1 and 10days of filtration. Subsequently, the relative reads abundance of the phyla Bacteroidetes and Firmicutes increased within the membrane biofilm communities after 20 and 30days of filtration, possibly due to successional steps that lead to the formation of a relatively aged biofilm. Our findings indicate distinct membrane biofilm assembly patterns with different-aged biofilm. Ecological null model analyses revealed that the assembly of early-stage biofilm community developed after 1 and 10days of filtration was mainly governed by homogenous selection. As the biofilm aged (days 20 and 30), stochastic processes (e.g., ecological drift) started to become important in shaping the assembly of biofilm community.
  • Thermo-Responsive Membranes from Blends of PVDF and PNIPAM-b-PVDF Block Copolymers with Linear and Star Architectures

    Algarni, Fatimah; Musteata, Valentina-Elena; Falca, Gheorghe; Chisca, Stefan; Hadjichristidis, Nikos; Nunes, Suzana Pereira (Macromolecules, American Chemical Society (ACS), 2021-09-10) [Article]
    We report the synthesis of poly(n-isopropylacrylamide)-b-poly(vinylidene fluoride), (PNIPAM-b-PVDF), copolymers with linear and star structures, as well as the self-assembly and fabrication of thermo-responsive membranes from blends of these block copolymers and a linear PVDF homopolymer. The synthesis was achieved by reversible addition–fragmentation chain-transfer sequential copolymerization using mono- or multifunctional transfer agents. The self-assembly in bulk and selective solvents was investigated. The PVDF blocks are crystallizable and hydrophobic and the PNIPAM thermo-responsive in water. The morphology is dominated by the breakout crystallization of the PVDF block. Nanoporous membranes were fabricated by non-solvent-induced phase-separation method. The membranes revealed a macroscale zig–zag morphology, which is dependent on the block copolymer architecture. Due to the presence of PNIPAM, these membranes exhibited thermo-responsive behavior with water permeability and rejection alternately varying with the operating temperature, which is reversible in multiple heating–cooling cycles.
  • Real-time membrane fouling analysis for the assessment of reclamation potential of textile wastewater processed by membrane distillation

    Elcik, Harun; Fortunato, Luca; Vrouwenvelder, Johannes S.; Ghaffour, NorEddine (Journal of Water Process Engineering, Elsevier BV, 2021-09-09) [Article]
    Understanding the factors that specify the fouling development in membrane distillation (MD) plays a key role to develop effective control strategies with the aim of providing its widespread use in industrial applications, such as textile industry. The present study investigated the fouling mechanisms in textile wastewater treatment by direct contact MD (DCMD), employing an advanced in-situ optical coherence tomography (OCT) technology allowing to monitor MD fouling in real-time. The OCT analysis enabled evaluating the effect of feed temperature, flow rate, dye concentration on the membrane fouling and the long-term performance of MD operation that includes a periodical water flushing. The permeate flux decrease during the initial stages of experiments was attributed to the existence of attractive hydrophobic-hydrophobic interaction between the membrane and dye molecules as no cake fouling was observed at the early stages. Then, a flat and homogeneous cake layer was developed with time in all the fouled membranes regardless of the cake layer thickness. The long-term experiment resulted in both reversible and irreversible fouling and showed that water flushing had limited efficacy against reversible fouling. Additionally, electrostatic repulsive forces occurring between the membrane and textile dye molecules influenced the permeate flux depending on the dye concentration. Finally, among all the operating parameters, feed temperature had the highest impact on the membrane fouling and process performance, changed the heat transfer activity at the membrane-liquid frontier zone, in turn, leading to variations in the flux.
  • Synthetic Directed Evolution in Plants: Unlocking Trait Engineering and Improvement

    Gundra, Sivakrishna Rao; Jiang, Wenjun; Mahfouz, Magdy M. (Synthetic Biology, Oxford University Press (OUP), 2021-09-08) [Article]
    ABSTRACT Genetic variation accelerates adaptation and resilience and enables the survival of species to their changing environment. Increasing the genetic diversity of crop species is essential to improve their yield and enhance food security. Synthetic directed evolution (SDE) employs localized sequence diversification (LSD) of gene sequence and selection pressure to evolve gene variants with better fitness, improved properties, and desired phenotypes. Recently, CRISPR-Cas dependent and independent technologies have been applied for LSD to mediate synthetic evolution in diverse species, including plants. SDE holds excellent promise to discover, accelerate, and expand the range of traits of value in crop species. Here, we highlight the efficient SDE approaches for the LSD of plant genes, selection strategies, and critical traits for targeted improvement. We discuss the potential of emerging technologies, including CRISPR-Cas base editing, retron editing, EvolvR, and prime editing, to establish efficient SDE in plants. Moreover, we cover CRISPR-Cas independent technologies, including T7 polymerase editor for continuous evolution. We highlight the key challenges and potential solutions of applying SDE technologies to improve plant traits of value.
  • UV and bacteriophages as a chemical-free approach for cleaning membranes from anaerobic bioreactors

    Scarascia, Giantommaso; Fortunato, Luca; Myshkevych, Yevhen; Cheng, Hong; Leiknes, TorOve; Hong, Pei-Ying (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-09-07) [Article]
    Anaerobic membrane bioreactor (AnMBR) for wastewater treatment has attracted much interest due to its efficacy in providing high-quality effluent with minimal energy costs. However, membrane biofouling represents the main bottleneck for AnMBR because it diminishes flux and necessitates frequent replacement of membranes. In this study, we assessed the feasibility of combining bacteriophages and UV-C irradiation to provide a chemical-free approach to remove biofoulants on the membrane. The combination of bacteriophage and UV-C resulted in better log cells removal and ca. 2× higher extracellular polymeric substance (EPS) concentration reduction in mature biofoulants compared to either UV-C or bacteriophage alone. The cleaning mechanism behind this combined approach is by 1) reducing the relative abundance of Acinetobacter spp. and selected bacteria (e.g., Paludibacter, Pseudomonas, Cloacibacterium, and gram-positive Firmicutes) associated with the membrane biofilm and 2) forming cavities in the biofilm to maintain water flux through the membrane. When the combined treatment was further compared with the common chemical cleaning procedure, a similar reduction on the cell numbers was observed (1.4 log). However, the combined treatment was less effective in removing EPS compared with chemical cleaning. These results suggest that the combination of UV-C and bacteriophage have an additive effect in biofouling reduction, representing a potential chemical-free method to remove reversible biofoulants on membrane fitted to an AnMBR.
  • Aridity modulates belowground bacterial community dynamics in olive tree

    Marasco, Ramona; Fusi, Marco; ROLLI, Eleonora; Ettoumi, Besma; Tambone, Fulvia; Borin, Sara; Ouzari, Hadda-Imene; Boudabous, Abdellatif; Sorlini, Claudia; Cherif, Ameur; Adani, Fabrizio; Daffonchio, Daniele (Environmental Microbiology, Wiley, 2021-09-07) [Article]
    Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant-associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co-occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity-winner and aridity-loser bacteria negatively and positively correlate with increasing annual rainfall, respectively. Aridity regulated also the co-occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity-winners or aridity-losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.
  • Generation of human blastocyst-like structures from pluripotent stem cells

    Fan, Yong; Min, Zheying; Alsolami, Samhan M.; Ma, Zhenglai; Zhang, E.; Chen, Wei; Zhong, Ke; Pei, Wendi; Kang, Xiangjin; Zhang, Puyao; Wang, Yongliang; Zhang, Yingying; Zhan, Linfeng; Zhu, Haiying; An, Chenrui; Li, Rong; Qiao, Jie; Tan, Tao; Li, Mo; Yu, Yang (Cell Discovery, Springer Science and Business Media LLC, 2021-09-07) [Article]
    Human blastocysts are comprised of the first three cell lineages of the embryo: trophectoderm, epiblast and primitive endoderm, all of which are essential for early development and organ formation. However, due to ethical concerns and restricted access to human blastocysts, a comprehensive understanding of early human embryogenesis is still lacking. To bridge this knowledge gap, a reliable model system that recapitulates early stages of human embryogenesis is needed. Here we developed a three-dimensional (3D), two-step induction protocol for generating blastocyst-like structures (EPS-blastoids) from human extended pluripotent stem (EPS) cells. Morphological and single-cell transcriptomic analyses revealed that EPS-blastoids contain key cell lineages and are transcriptionally similar to human blastocysts. Furthermore, EPS-blastoids are similar with human embryos that were cultured for 8 or 10 days in vitro, in terms of embryonic structures, cell lineages and transcriptomic profiles. In conclusion, we developed a scalable system to mimic human blastocyst development, which can potentially facilitate the study of early implantation failure that induced by developmental defects at early stage.
  • Testing angular velocity as a new metric for metabolic demands of slow-moving marine fauna: a case study with Giant spider conchs Lambis truncata

    Hopkins, Lloyd W.; Geraldi, Nathan; Pope, Edward C.; Holton, Mark D.; Lurgi, Miguel; Duarte, Carlos M.; Wilson, Rory P. (Animal Biotelemetry, Springer Science and Business Media LLC, 2021-09-07) [Article]
    Abstract Background Quantifying metabolic rate in free-living animals is invaluable in understanding the costs of behaviour and movement for individuals and communities. Dynamic body acceleration (DBA) metrics, such as vectoral DBA (VeDBA), are commonly used as proxies for the energy expenditure of movement but are of limited applicability for slow-moving species. It has recently been suggested that metrics based on angular velocity might be better suited to characterise their energetics. We investigated whether a novel metric—the ‘Rate of change of Rotational Movement (RocRM)’, calculated from the vectoral sum of change in the pitch, roll and yaw/heading axes over a given length of time, is a suitable proxy for energy expenditure. Results We found that RocRM can be used as an alternative energy expenditure proxy in a slow-moving benthic invertebrate. Eleven Giant spider conchs Lambis truncata (collected in the Red Sea) were instrumented with multiple channel (Daily Diary) tags and kept in sealed chambers for 5 h while their oxygen consumption, V̇O2, was measured. We found RocRM to be positively correlated with V̇O2, this relationship being affected by the time-step (i.e. the range of the calculated differential) of the RocRM. Time steps of 1, 5, 10 and 60 s yielded an explained variability of between 15 and 31%. The relationship between V̇O2 and VeDBA was not statistically significant, suggesting RocRM to provide more accurate estimations of metabolic rates in L. truncata. Conclusions RocRM proved to be a statistically significant predictor of V̇O2 where VeDBA did not, validating the approach of using angular-based metrics over dynamic movement-based ones for slower moving animals. Further work is required to validate the use of RocRM for other species, particularly in animals with minimally dynamic movement, to better understand energetic costs of whole ecosystems. Unexplained variability in the models might be a consequence of the methodology used, but also likely a result of conch activity that does not manifest in movement of the shell. Additionally, density plots of mean RocRM at each time-step suggest differences in movement scales, which may collectively be useful as a species fingerprint of movement going forward.
  • Tunable membranes incorporating artificial water channels for high-performance brackish/low-salinity water reverse osmosis desalination

    Di Vincenzo, Maria; Tiraferri, Alberto; Musteata, Valentina-Elena; Chisca, Stefan; Deleanu, Mihai; Ricceri, Francesco; Cot, Didier; Nunes, Suzana Pereira; Barboiu, Mihail (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-09-07) [Article]
    Membrane-based technologies have a tremendous role in water purification and desalination. Inspired by biological proteins, artificial water channels (AWCs) have been proposed to overcome the permeability/selectivity trade-off of desalination processes. Promising strategies exploiting the AWC with angstrom-scale selectivity have revealed their impressive performances when embedded in bilayer membranes. Herein, we demonstrate that self-assembled imidazole-quartet (I-quartet) AWCs are macroscopically incorporated within industrially relevant reverse osmosis membranes. In particular, we explore the best combination between I-quartet AWC and m-phenylenediamine (MPD) monomer to achieve a seamless incorporation of AWC in a defect-free polyamide membrane. The performance of the membranes is evaluated by crossflow filtration under real reverse osmosis conditions (15 to 20 bar of applied pressure) by filtration of brackish feed streams. The optimized bioinspired membranes achieve an unprecedented improvement, resulting in more than twice (up to 6.9 L·m−2·h−1·bar−1) water permeance of analogous commercial membranes, while maintaining excellent NaCl rejection (>99.5%). They show also excellent performance in the purification of low-salinity water under low-pressure conditions (6 bar of applied pressure) with fluxes up to 35 L·m−2·h−1and 97.5 to 99.3% observed rejection.
  • The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptions to host-switching

    Mourier, Tobias; de Alvarenga, Denise Anete Madureira; Kaushik, Abhinav; de Pina-Costa, Anielle; Douvropoulou, Olga; Guan, Qingtian; Guzmán-Vega, Francisco J.; Forrester, Sarah; de Abreu, Filipe Vieira Santos; Júnior, Cesare Bianco; Junior, Julio Cesar de Souza; Moreira, Silvia Bahadian; Hirano, Zelinda Maria Braga; Pissinatti, Alcides; Ferreira-da-Cruz, Maria de Fátima; de Oliveira, Ricardo Lourenço; Arold, Stefan T.; Jeffares, Daniel C.; Brasil, Patrícia; de Brito, Cristiana Ferreira Alves; Culleton, Richard; Daniel-Ribeiro, Cláudio Tadeu; Pain, Arnab (NCBI, 2021-09-05) [Bioproject, Dataset]
    Plasmodium simium, a parasite of various species of Platyrrhini monkeys whose range is restricted to the Atlantic Forest of Brazil, is genetically and morphologically similar to P. vivax. Based on this similarity, it appears likely that P. simium originated as a parasite of monkeys in Brazil following a host switch from humans carrying P. vivax. The 2015 outbreak of P. simium in the local human population raised questions about the degree of divergence that has occurred between P. vivax and P. simium, and whether adaptation to monkeys has led to the evolution of a parasite with clinical relevance to human health that differs from that of P. vivax. The degree and nature of adaptation to a non-human primate host and a sylvatic transmission cycle that has occurred in P. simium following its anthroponotic origin is of relevance to the understanding of how malaria parasites adapt to new hosts. It is also of interest to determine whether the current, human-infecting P. simium parasites have recently undergone changes at the genomic level that have allowed them to infect people in this region, as it has previously been suggested that P. simium has historically lacked the ability to infect man.
  • Homozygous missense WIPI2 variants cause a congenital disorder of autophagy with neurodevelopmental impairments of variable clinical severity and disease course

    Maroofian, Reza; Gubas, Andrea; Kaiyrzhanov, Rauan; Scala, Marcello; Hundallah, Khalid; Severino, Mariasavina; Abdel-Hamid, Mohamed S; Rosenfeld, Jill A; Ebrahimi-Fakhari, Darius; Ali, Zahir; Rahim, Fazal; Houlden, Henry; Tooze, Sharon A; Alsaleh, Norah S; Zaki, Maha S (Brain Communications, Oxford University Press (OUP), 2021-09-03) [Article]
    WIPI2 is a member of the human WIPI protein family (seven-bladed b-propeller proteins binding phosphatidylinositols, PROPPINs), which play a pivotal role in autophagy and has been implicated in the pathogenesis of several neurological conditions. The homozygous WIPI2 variant c.745G>A; p.(Val249Met) (NM_015610.4) has recently been associated with a neurodevelopmental disorder in a single family. Using exome sequencing and Sanger segregation analysis, here two novel homozygous WIPI2 variants (c.551T>G; p.(Val184Gly) and c.724C>T; p.(Arg242Trp) (NM_015610.4)) were identified in four individuals of two consanguineous families. Additionally, follow-up clinical data were sought from the previously reported family. Three non-ambulant affected siblings of the first family harboring the p.(Val184Gly) missense variant presented with microcephaly, profound global developmental delay/intellectual disability, refractory infantile/childhood-onset epilepsy, progressive tetraplegia with joint contractures, and dyskinesia. In contrast, the proband of the second family carrying the p.(Arg242Trp) missense variant, similar to the initially reported WIPI2 cases, presented with a milder phenotype, encompassing moderate intellectual disability, speech and visual impairment, autistic features, and an ataxic gait. Brain MR imaging in five patients showed prominent white matter involvement with a global reduction in volume, posterior corpus callosum hypoplasia, abnormal dentate nuclei, and hypoplasia of the inferior cerebellar vermis. To investigate the functional impact of these novel WIPI2 variants, we overexpressed both in WIPI2-knockout HEK293A cells. In comparison to wildtype, expression of the Val166Gly WIPI2b mutant resulted in a deficient rescue of LC3 lipidation whereas Arg224Trp mutant increased LC3 lipidation, in line with the previously reported Val231Met variant. These findings support a dysregulation of the early steps of the autophagy pathway. Collectively, our findings provide evidence that biallelic WIPI2 variants cause a neurodevelopmental disorder of variable severity and disease course. Our report expands the clinical spectrum and establishes WIPI2-related disorder as a congenital disorders of autophagy.
  • Sustainable and Eco-Friendly Coral Restoration through 3D Printing and Fabrication

    Albalawi, Hamed I.; Khan, Zainab N.; Valle-Pérez, Alexander U.; Kahin, Kowther M.; Hountondji, Maria; Alwazani, Hibatallah; Schmidt-Roach, Sebastian; Bilalis, Panagiotis; Aranda, Manuel; Duarte, Carlos M.; Hauser, Charlotte (ACS Sustainable Chemistry & Engineering, American Chemical Society (ACS), 2021-09-02) [Article]
    Coral reef degradation is a rising problem, driven by marine heatwaves, the spread of coral diseases, and human impact by overfishing and pollution. Our capacity to restore coral reefs lags behind in terms of scale, effectiveness, and cost-efficiency. While common restoration efforts rely on the formation of carbonate skeletons on structural frames for supported coral growth, this technique is a rate-limiting step in the growth of scleractinian corals. Reverse engineering and additive manufacturing technologies offer an innovative shift in approach from the use of concrete blocks and metal frames to sophisticated efforts that use scanned geometries of harvested corals to fabricate artificial coral skeletons for installation in coral gardens and reefs. Herein, we present an eco-friendly and sustainable approach for coral fabrication by merging three-dimensional (3D) scanning, 3D printing, and molding techniques. Our method, 3D CoraPrint, exploits the 3D printing technology to fabricate artificial natural-based coral skeletons, expediting the growth rate of live coral fragments and quickening the reef transplantation process while minimizing nursery costs. It allows for flexibility, customization, and fast return time with an enhanced level of accuracy, thus establishing an environmentally friendly, scalable model for coral fabrication to boost restorative efforts around the globe.
  • Different resiliencies in coral communities over ecological and geological time scales in American Samoa

    Birkeland, C; Green, Alison Lesley; Lawrence, A; Coward, G; Vaeoso, M; Fenner, D (Marine Ecology Progress Series, Inter-Research Science Center, 2021-09-02) [Article]
    In 1917, Alfred Mayor surveyed a 270 m transect on a reef flat on American Samoa. Eleven surveys were conducted on the transect from 1917 to 2019. The coral community on the reef crest was resilient over the century, occasionally being seriously damaged but always recovering rapidly. In contrast, the originally most dense coral community on the reef flat has been steadily deteriorating throughout the century. Resilience of coral communities in regions of high wave energy on the reef crests was associated with the important binding function of the crustose coralline alga (CCA) Porolithon onkodes. Successful coral recruits were found on CCA 94% of the time, yet living coral cover correlated negatively with CCA cover as they became alternative winners in competition. Mayor drilled a core from the transect on the surface to the basalt base of the reef 48 m below. Communities on Aua reef were dominated by scleractinians through the Holocene, while cores on another transect 2 km away showed the reef was occupied by alcyonaceans of the genus Sinularia, which built the massive reef with spiculite to the basalt base 37 m below. Despite periods of sea levels rising 9 to 15 times the rate of reef accretion, the reefs never drowned. The consistency of scleractinians on Aua reef and Sinularia on Utulei Reef 2 km away during the Holocene was because the shape of the bay allowed more water motion on Aua reef. After 10700 yr of reef building by octocorals, coastal construction terminated this spiculite-reef development.
  • Inkjet-Printed In-Vitro Organic Electronic Devices

    Asghar, Hussain (2021-09) [Thesis]
    Advisor: Inal, Sahika
    Committee members: Baran, Derya; Salama, Khaled N.
    In-vitro electronic devices are promising to dynamically monitor minute-changes in biological systems. Electronic devices based on conducting polymers such as poly(3,4- ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) provide suitable and attractive substrates for biointerfacing. The soft polymer surface acts as a cushion for the living systems to interface while electronically detecting their properties. However, to this date, most bioelectronics devices have been fabricated via multi-step lithography techniques, which do not allow for mass fabrication and hence high throughput biosensing. Inkjet printing presents an alternative to fabricate organic bioelectronic devices. Besides being low-cost, inkjet printing allows to fabricate several devices in a short time with flexible design patterns and minimal material waste. Here, using inkjet printing, we fabricated PEDOT:PSS based organic electrochemical transistors (OECTs) for biomembrane interfacing. We optimized the deposition of various inks (silver nanoparticles (AgNPs), PEDOT:PSS, and the dielectric SU-8) used during the fabrication of these devices. We characterized the electrical characteristics of all-printed OECTs with various geometries and identified the high-performing ones. Due to the flexibility of ink optimization and design patterns, these all inkjet-printed electronic devices provide an alternative for mass production of biointerfacing platforms.

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