Recent Submissions

  • Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs.

    Alam, Tanvir; Alazmi, Meshari; Naser, Rayan Mohammad Mahmoud; Huser, Franceline; Momin, Afaque Ahmad Imtiyaz; Astro, Veronica; Hong, Seungbeom; Walkiewicz, Katarzyna Wiktoria; Canlas, Christian G; Huser, Raphaël; Ali, Amal J.; Merzaban, Jasmeen; Adamo, Antonio; Jaremko, Mariusz; Jaremko, Lukasz; Bajic, Vladimir B.; Gao, Xin; Arold, Stefan T. (Bioinformatics (Oxford, England), Oxford University Press (OUP), 2019-10-05) [Article]
    MOTIVATION:Leucine-aspartic acid (LD) motifs are short linear interaction motifs (SLiMs) that link paxillin family proteins to factors controlling cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. RESULTS:To enable a proteome-wide assessment of LD motifs, we developed an active-learning based framework (LDmotif finder; LDMF) that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome revealed a dozen new proteins containing LD motifs. We found that LD motif signalling evolved in unicellular eukaryotes more than 800 Myr ago, with paxillin and vinculin as core constituents, and nuclear export signal (NES) as a likely source of de novo LD motifs. We show that LD motif proteins form a functionally homogenous group, all being involved in cell morphogenesis and adhesion. This functional focus is recapitulated in cells by GFP-fused LD motifs, suggesting that it is intrinsic to the LD motif sequence, possibly through their effect on binding partners. Our approach elucidated the origin and dynamic adaptations of an ancestral SLiM, and can serve as a guide for the identification of other SLiMs for which only few representatives are known. AVAILABILITY:LDMF is freely available online at www.cbrc.kaust.edu.sa/ldmf; Source code is available at https://github.com/tanviralambd/LD/. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
  • Disruption of the coordination between host circadian rhythms and malaria parasite development alters the duration of the intraerythrocytic cycle

    Subudhi, Amit; O'Donnell, Aidan John; Ramaprasad, Abhinay; Abkallo, Hussein M.; Kaushik, Abhinav; Ansari, Hifzur Rahman; Abdel-Haleem, Alyaa M.; Rached, Fathia Ben; Kaneko, Osamu; Culleton, Richard; Reece, Sarah E.; Pain, Arnab (Cold Spring Harbor Laboratory, 2019-10-03) [Preprint]
    Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 hours (depending on the species), suggesting a circadian basis to the asexual cell cycle, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches using rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit 24 h circadian periodicity in transcription; (ii) 58% of these genes lose transcriptional rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 9% of Plasmodium falciparum genes show circadian transcription under free-running conditions; (iv) Serpentine receptor 10 (SR10) has a circadian transcription profile and disrupting it in rodent malaria parasites shortens the IDC by 2-3 hours; (v) Multiple processes including DNA replication and the ubiquitin and proteasome pathways are affected by loss of coordination with host rhythms and by disruption of SR10. Our results show that malaria parasites are at least partly responsible for scheduling their IDCs explaining the fitness benefits of coordination with host rhythms.
  • Factors Regulating the Relationship Between Total and Size-Fractionated Chlorophyll-a in Coastal Waters of the Red Sea.

    Brewin, Robert J W; Moran, Xose Anxelu G.; Raitsos, Dionysios E; Gittings, John A; Calleja Cortes, Maria de Lluch; Viegas, Miguel; Ansari, Mohd Ikram; Al-otaibi, Najwa Aziz; Huete-Stauffer, Tamara M; Hoteit, Ibrahim (Frontiers in microbiology, Frontiers Media SA, 2019-09-26) [Article]
    Phytoplankton biomass and size structure are recognized as key ecological indicators. With the aim to quantify the relationship between these two ecological indicators in tropical waters and understand controlling factors, we analyzed the total chlorophyll-a concentration, a measure of phytoplankton biomass, and its partitioning into three size classes of phytoplankton, using a series of observations collected at coastal sites in the central Red Sea. Over a period of 4 years, measurements of flow cytometry, size-fractionated chlorophyll-a concentration, and physical-chemical variables were collected near Thuwal in Saudi Arabia. We fitted a three-component model to the size-fractionated chlorophyll-a data to quantify the relationship between total chlorophyll and that in three size classes of phytoplankton [pico- (<2 μm), nano- (2-20 μm) and micro-phytoplankton (>20 μm)]. The model has an advantage over other more empirical methods in that its parameters are interpretable, expressed as the maximum chlorophyll-a concentration of small phytoplankton (pico- and combined pico-nanophytoplankton, Cpm and Cp,nm , respectively) and the fractional contribution of these two size classes to total chlorophyll-a as it tends to zero (D p and D p,n ). Residuals between the model and the data (model minus data) were compared with a range of other environmental variables available in the dataset. Residuals in pico- and combined pico-nanophytoplankton fractions of total chlorophyll-a were significantly correlated with water temperature (positively) and picoeukaryote cell number (negatively). We conducted a running fit of the model with increasing temperature and found a negative relationship between temperature and parameters Cpm and Cp,nm and a positive relationship between temperature and parameters D p and D p,n . By harnessing the relative red fluorescence of the flow cytometric data, we show that picoeukaryotes, which are higher in cell number in winter (cold) than summer (warm), contain higher chlorophyll per cell than other picophytoplankton and are slightly larger in size, possibly explaining the temperature shift in model parameters, though further evidence is needed to substantiate this finding. Our results emphasize the importance of knowing the water temperature and taxonomic composition of phytoplankton within each size class when understanding their relative contribution to total chlorophyll. Furthermore, our results have implications for the development of algorithms for inferring size-fractionated chlorophyll from satellite data, and for how the partitioning of total chlorophyll into the three size classes may change in a future ocean.
  • 3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat.

    Cali, Corrado; Agus, Marco; Kare, Kalpana; Boges, Daniya J; Lehväslaiho, Heikki; Hadwiger, Markus; Magistretti, Pierre J. (Progress in neurobiology, Elsevier BV, 2019-09-25) [Article]
    With the rapid evolution in the automation of serial electron microscopy in life sciences, the acquisition of terabyte-sized datasets is becoming increasingly common. High resolution serial block-face imaging (SBEM) of biological tissues offers the opportunity to segment and reconstruct nanoscale structures to reveal spatial features previously inaccessible with simple, single section, two-dimensional images, with a particular focus on glial cells, whose reconstruction efforts in literature are still limited, compared to neurons. Here, we imaged a 750000 cubic micron volume of the somatosensory cortex from a juvenile P14 rat, with 20 nm accuracy. We recognized a total of 186 cells using their nuclei, and classified them as neuronal or glial based on features of the soma and the processes. We reconstructed for the first time 4 almost complete astrocytes and neurons, 4 complete microglia and 4 complete pericytes, including their intracellular mitochondria, 186 nuclei and 213 myelinated axons. We then performed quantitative analysis on the three-dimensional models. Out of the data that we generated, we observed that neurons have larger nuclei, which correlated with their lesser density, and that astrocytes and pericytes have a higher surface to volume ratio, compared to other cell types. All reconstructed morphologies represent an important resource for computational neuroscientists, as morphological quantitative information can be inferred, to tune simulations that take into account the spatial compartmentalization of the different cell types.
  • Lactate and pyruvate promote oxidative stress resistance through hormetic ROS signaling.

    Tauffenberger, Arnaud; Fiumelli, Hubert; Almustafa, Salam; Magistretti, Pierre J. (Cell death & disease, Springer Science and Business Media LLC, 2019-09-12) [Article]
    L-lactate was long considered a glycolytic by-product but is now being recognized as a signaling molecule involved in cell survival. In this manuscript, we report the role of L-lactate in stress resistance and cell survival mechanisms using neuroblastoma cells (SH-SY5Y) as well as the C. elegans model. We observed that L-lactate promotes cellular defense mechanisms, including Unfolded Protein Response (UPR) and activation of nuclear factor erythroid 2-related factor 2 (NRF2), by promoting a mild Reactive Oxygen Species (ROS) burst. This increase in ROS triggers antioxidant defenses and pro-survival pathways, such as PI3K/AKT and Endoplasmic Reticulum (ER) chaperones. These results contribute to the understanding of the molecular mechanisms involved in beneficial effects of L-lactate, involving mild ROS burst, leading to activation of unfolded protein responses and detoxification mechanisms. We present evidence that this hormetic mechanism induced by L-lactate protects against oxidative stress in vitro and in vivo. This work contributes to the identification of molecular mechanisms, which could serve as targets for future therapeutic approaches for cell protection and aging-related disorders.
  • Monitoring of the toxic dinoflagellate Alexandrium catenella in Osaka Bay, Japan using a massively parallel sequencing (MPS)-based technique

    Nagai, Satoshi; Chen, Hungyen; Kawakami, Yoko; Yamamoto, Keigo; Sildever, Sirje; Kanno, Nanako; Oikawa, Hiroshi; Yasuike, Motoshige; Nakamura, Yoji; Hongo, Yuki; Fujiwara, Atushi; Kobayashi, Takanori; Gojobori, Takashi (Harmful Algae, Elsevier BV, 2019-09-12) [Article]
    Since 2002, blooms of Alexandrium catenella sensu Fraga et al. (2015) and paralytic shellfish toxicity events have occurred almost yearly in Osaka Bay, Japan. To better understand the triggers for reoccurring A. catenella blooms in Osaka Bay, phytoplankton community was monitored during the spring seasons of 2012–2015. Monitoring was performed using massively parallel sequencing (MPS)-based technique on amplicon sequences of the 18S rRNA gene. Dense blooms of A. catenella occurred every year except in 2012, however, there was no significant correlation with the environmental parameters investigated. Plankton community diversity decreased before and middle of the A. catenella blooms, suggesting that the decline in diversity could be an indicator for the bloom occurrence. The yearly abundance pattern of A. catenella cells obtained by morphology-based counting coincided with the relative sequence abundances, which supports the effectiveness of MPS-based phytoplankton monitoring.
  • Developmental stages and gut microenvironments influence gut microbiota dynamics in the invasive beetle Popillia japonica Newman (Coleoptera: Scarabaeidae)

    Chouaia, Bessem; Goda, Nizar; Mazza, Giuseppe; Alali, Sumer; Florian, Fiorella; Gionechetti, Fabrizia; Callegari, Matteo; Gonella, Elena; Magoga, Giulia; Fusi, Marco; Crotti, Elena; Daffonchio, Daniele; Alma, Alberto; Paoli, Francesco; Roversi, Pio Federico; Marianelli, Leonardo; Montagna, Matteo (Environmental Microbiology, Wiley, 2019-09-10) [Article]
    Popillia japonica Newman (Coleoptera: Scarabaeidae) is a highly polyphagous invasive beetle originating from Japan. This insect is highly resilient and able to rapidly adapt to new vegetation. Insect-associated microorganisms can play important roles in insect physiology, helping their hosts to adapt to changing conditions and potentially contributing to an insect's invasive potential. Such symbiotic bacteria can be part of a core microbiota that is stably transmitted throughout the host's life cycle or selectively recruited from the environment at each developmental stage. The aim of this study was to investigate the origin, stability and turnover of the bacterial communities associated with an invasive population of P. japonica from Italy. Our results demonstrate that soil microbes represent an important source of gut bacteria for P. japonica larvae, but as the insect develops, its gut microbiota richness and diversity decreased substantially, paralleled by changes in community composition. Notably, only 16.75% of the soil bacteria present in larvae are maintained until the adult stage. We further identified the micro-environments of different gut sections as an important factor shaping microbiota composition in this species, likely due to differences in pH, oxygen availability and redox potential. In addition, P. japonica also harbored a stable bacterial community across all developmental stages, consisting of taxa well-known for the degradation of plant material, namely the families Ruminococcacae, Christensenellaceae and Lachnospiraceae. Interestingly, the family Christensenallaceae had so far been observed exclusively in humans. However, the Christensenellaceae OTUs found in P. japonica belong to different taxonomic clades within this family.
  • Label-Free Detection of Ovarian Cancer Antigen CA125 by Surface Enhanced Raman Scattering.

    TunÇ, İlknur; Susapto, Hepi Hari (Journal of nanoscience and nanotechnology, American Scientific Publishers, 2019-09-08) [Article]
    Surface-enhanced Raman spectroscopy (SERS) has drawn attention in recent years for imaging biologicalmolecules as an analytical tool due to its label-free approach. The SERS approach can be used in tracking organic molecules and monitoring unique Raman spectra of the organic molecules bound to metal nanoparticles (NPs). In this paper, the molecular specifity of Raman Spectroscopy was used together with self-assembled monolayer of metallic AuNPs as a sensor platform in order to detect CA125 antibody-antigen probe molecules. Highly enhanced electromagnetic fields localized around neighboring AuNPs provide hot-spot construction due to the spatial distribution of SERS enhancement on the CA125 proteins at nM concentration level. Time resolved SERS mapping of CA125 antibody and antigen couples was recorded. Even though blinking behavior was observed for some cases, vast variety SERS signals from CA125 proteins were highly reproducible. Blinking behavior is attributed to single molecular detection. Distinguished feature of SERS mapping images of CA125 antibody and antigen with such a low concentration level is very promising for this technique to be used for diagnostic purposes.
  • Mining biosynthetic gene clusters in Virgibacillus genomes.

    Othoum, Ghofran K.; Bougouffa, Salim; Bokhari, Ameerah; Lafi, Feras Fawzi; Gojobori, Takashi; Hirt, Heribert; Mijakovic, Ivan; Bajic, Vladimir B.; Essack, Magbubah (BMC genomics, Springer Science and Business Media LLC, 2019-09-05) [Article]
    BACKGROUND:Biosynthetic gene clusters produce a wide range of metabolites with activities that are of interest to the pharmaceutical industry. Specific interest is shown towards those metabolites that exhibit antimicrobial activities against multidrug-resistant bacteria that have become a global health threat. Genera of the phylum Firmicutes are frequently identified as sources of such metabolites, but the biosynthetic potential of its Virgibacillus genus is not known. Here, we used comparative genomic analysis to determine whether Virgibacillus strains isolated from the Red Sea mangrove mud in Rabigh Harbor Lagoon, Saudi Arabia, may be an attractive source of such novel antimicrobial agents. RESULTS:A comparative genomics analysis based on Virgibacillus dokdonensis Bac330, Virgibacillus sp. Bac332 and Virgibacillus halodenitrificans Bac324 (isolated from the Red Sea) and six other previously reported Virgibacillus strains was performed. Orthology analysis was used to determine the core genomes as well as the accessory genome of the nine Virgibacillus strains. The analysis shows that the Red Sea strain Virgibacillus sp. Bac332 has the highest number of unique genes and genomic islands compared to other genomes included in this study. Focusing on biosynthetic gene clusters, we show how marine isolates, including those from the Red Sea, are more enriched with nonribosomal peptides compared to the other Virgibacillus species. We also found that most nonribosomal peptide synthases identified in the Virgibacillus strains are part of genomic regions that are potentially horizontally transferred. CONCLUSIONS:The Red Sea Virgibacillus strains have a large number of biosynthetic genes in clusters that are not assigned to known products, indicating significant potential for the discovery of novel bioactive compounds. Also, having more modular synthetase units suggests that these strains are good candidates for experimental characterization of previously identified bioactive compounds as well. Future efforts will be directed towards establishing the properties of the potentially novel compounds encoded by the Red Sea specific trans-AT PKS/NRPS cluster and the type III PKS/NRPS cluster.
  • Oxygen supersaturation protects coastal marine fauna from ocean warming

    Giomi, Folco; Barausse, Alberto; Duarte, Carlos M.; Booth, Jenny; Agusti, Susana; Saderne, Vincent; Anton Gamazo, Andrea; Daffonchio, Daniele; Fusi, Marco (Science Advances, American Association for the Advancement of Science (AAAS), 2019-09-04) [Article]
    Ocean warming affects the life history and fitness of marine organisms by, among others, increasing animal metabolism and reducing oxygen availability. In coastal habitats, animals live in close association with photosynthetic organisms whose oxygen supply supports metabolic demands and may compensate for acute warming. Using a unique high-frequency monitoring dataset, we show that oxygen supersaturation resulting from photosynthesis closely parallels sea temperature rise during diel cycles in Red Sea coastal habitats. We experimentally demonstrate that oxygen supersaturation extends the survival to more extreme temperatures of six species from four phyla. We clarify the mechanistic basis of the extended thermal tolerance by showing that hyperoxia fulfills the increased metabolic demand at high temperatures. By modeling 1 year of water temperatures and oxygen concentrations, we predict that oxygen supersaturation from photosynthetic activity invariably fuels peak animal metabolic demand, representing an underestimated factor of resistance and resilience to ocean warming in ectotherms.
  • Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing

    Sanada, Takahiro; Tsukiyama-Kohara, Kyoko; Shin-I, Tadasu; Yamamoto, Naoki; Kayesh, Mohammad Enamul Hoque; Yamane, Daisuke; Takano, Jun ichiro; Shiogama, Yumiko; Yasutomi, Yasuhiro; Ikeo, Kazuho; Gojobori, Takashi; Mizokami, Masashi; Kohara, Michinori (Scientific Reports, Nature Publishing GroupHoundmillsBasingstoke, HampshireRG21 6XS, 2019-08-26) [Article]
    The northern tree shrew (Tupaia belangeri) possesses high potential as an animal model of human diseases and biology, given its genetic similarity to primates. Although genetic information on the tree shrew has already been published, some of the entire coding sequences (CDSs) of tree shrew genes remained incomplete, and the reliability of these CDSs remained difficult to determine. To improve the determination of tree shrew CDSs, we performed sequencing of the whole-genome, mRNA, and total RNA and integrated the resulting data. Additionally, we established criteria for the selection of reliable CDSs and annotated these sequences by comparison to the human transcriptome, resulting in the identification of complete CDSs for 12,612 tree shrew genes and yielding a more accurate tree shrew genome database (TupaiaBase: http://tupaiabase.org). Transcriptome profiles in hepatitis B virus infected tree shrew livers were analyzed for validation. Gene ontology analysis showed enriched transcriptional regulation at 1 day post-infection, namely in the “type I interferon signaling pathway”. Moreover, a negative regulator of type I interferon, SOCS3, was induced. This work, which provides a tree shrew CDS database based on genomic DNA and RNA sequencing, is expected to serve as a powerful tool for further development of the tree shrew model.
  • Membrane-Free Detection of Metal Cations with an Organic Electrochemical Transistor

    Wustoni, Shofarul; Combe, Craig; ohayon, David; Akhtar, Mahmood Hassan; McCulloch, Iain; Inal, Sahika (Advanced Functional Materials, Wiley, 2019-08-26) [Article]
    Alkali-metal ions, particularly sodium (Na+) and potassium (K+), are the messengers of living cells, governing a cascade of physiological processes through the action of ion channels. Devices that can monitor, in real time, the concentrations of these cations in aqueous media are in demand not only for the study of cellular machinery, but also to detect conditions in the human body that lead to electrolyte imbalance. In this work, conducting polymers are developed that respond rapidly and selectively to varying concentrations of Na+ and K+ in aqueous media. These polymer films, bearing crown-ether-functionalized thiophene units specific to either Na+ or K+, generate an electrical output proportional to the cation type and concentration. Using electropolymerization, the ion-selective polymers are integrated as the gate electrode of an organic electrochemical transistor (OECT). The OECT current changes with respect to the concentration of the ion to which the polymer electrode is selective. Designed as a single, miniaturized chip, the OECT enables the selective detection of the cations within a physiologically relevant range. These electrochemical ion sensors require neither ion-selective membranes nor a reference electrode to operate and have the potential to surpass existing technologies for the detection of alkali-metal ions in aqueous media.
  • An organic electrochemical transistor integrated with a molecularly selective isoporous membrane for amyloid-β detection.

    Wustoni, Shofarul; Wang, Shaofei; Alvarez, Juan R; Hidalgo, Tania C; Nunes, Suzana Pereira; Inal, Sahika (Biosensors & bioelectronics, Elsevier BV, 2019-08-26) [Article]
    Alzheimer's disease (AD) is a progressive neurodegenerative disease associated with severe memory loss and impaired cognitive skills. A common pathological change found in AD-affected brains is the accumulation of a peptide named amyloid-β (Aβ) that can form plaques. Aβ aggregates are visible to structural scanning tools; however, these bulky and expensive instruments are accessible to trained personnel in clinical settings only, thus hampering timely diagnosis of the disease, particularly in low-resource settings. In this work, we design an organic electrochemical transistor (OECT) for in vitro detection of Aβ aggregates in human serum. The OECT channel is integrated with a nanostructured isoporous membrane which has a strong affinity for Aβ aggregates. The detection mechanism relies on the membrane capturing Aβ aggregates larger than the size of its pores and thus blocking the penetration of electrolyte ions into the channel underneath. Combining the high transconductance of the OECT with the precise porosity and selectivity of the membrane, the device detects the presence of Aβ aggregates in human serum samples with excellent sensitivity. This is the first-time demonstration of a biofunctionalized, nanostructured, and isoporous membrane integrated with a high-performance transistor for biosensing. This robust, low-power, non-invasive, and miniaturized sensor aids in the development of point-of-care tools for early diagnosis of AD.
  • Precise in vivo genome editing via single homology arm donor mediated intron-targeting gene integration for genetic disease correction.

    Suzuki, Keiichiro; Yamamoto, Mako; Hernandez-Benitez, Reyna; Li, Zhe; Wei, Christopher; Soligalla, Rupa Devi; Aizawa, Emi; Hatanaka, Fumiyuki; Kurita, Masakazu; Reddy, Pradeep; Ocampo, Alejandro; Hishida, Tomoaki; Sakurai, Masahiro; Nemeth, Amy N; Nuñez Delicado, Estrella; Campistol, Josep M; Magistretti, Pierre J.; Guillen, Pedro; Rodriguez Esteban, Concepcion; Gong, Jianhui; Yuan, Yilin; Gu, Ying; Liu, Guang-Hui; López-Otín, Carlos; Wu, Jun; Zhang, Kun; Izpisua Belmonte, Juan Carlos (Cell research, Springer Science and Business Media LLC, 2019-08-25) [Article]
    In vivo genome editing represents a powerful strategy for both understanding basic biology and treating inherited diseases. However, it remains a challenge to develop universal and efficient in vivo genome-editing tools for tissues that comprise diverse cell types in either a dividing or non-dividing state. Here, we describe a versatile in vivo gene knock-in methodology that enables the targeting of a broad range of mutations and cell types through the insertion of a minigene at an intron of the target gene locus using an intracellularly linearized single homology arm donor. As a proof-of-concept, we focused on a mouse model of premature-aging caused by a dominant point mutation, which is difficult to repair using existing in vivo genome-editing tools. Systemic treatment using our new method ameliorated aging-associated phenotypes and extended animal lifespan, thus highlighting the potential of this methodology for a broad range of in vivo genome-editing applications.
  • Gangliosides: Treatment Avenues in Neurodegenerative Disease.

    Magistretti, Pierre J.; Geisler, Fred H.; Schneider, Jay S.; Li, P. Andy; Fiumelli, Hubert; Sipione, Simonetta (Frontiers in Neurology, Frontiers Media SA, 2019-08-25) [Article]
    Gangliosides are cell membrane components, most abundantly in the central nervous system (CNS) where they exert among others neuro-protective and -restorative functions. Clinical development of ganglioside replacement therapy for several neurodegenerative diseases was impeded by the BSE crisis in Europe during the 1990s. Nowadays, gangliosides are produced bovine-free and new pre-clinical and clinical data justify a reevaluation of their therapeutic potential in neurodegenerative diseases. Clinical experience is greatest with monosialo-tetrahexosyl-ganglioside (GM1) in the treatment of stroke. Fourteen randomized controlled trials (RCTs) in overall >2,000 patients revealed no difference in survival, but consistently superior neurological outcomes vs. placebo. GM1 was shown to attenuate ischemic neuronal injuries in diabetes patients by suppression of ERK1/2 phosphorylation and reduction of stress to the endoplasmic reticulum. There is level-I evidence from 5 RCTs of a significantly faster recovery with GM1 vs. placebo in patients with acute and chronic spinal cord injury (SCI), disturbance of consciousness after subarachnoid hemorrhage, or craniocerebral injuries due to closed head trauma. In Parkinson's disease (PD), two RCTs provided evidence of GM1 to be superior to placebo in improving motor symptoms and long-term to result in a slower than expected symptom progression, suggesting disease-modifying potential. In Alzheimer's disease (AD), the role of gangliosides has been controversial, with some studies suggesting a “seeding” role for GM1 in amyloid β polymerization into toxic forms, and others more recently suggesting a rather protective role in vivo. In Huntington's disease (HD), no clinical trials have been conducted yet. However, low GM1 levels observed in HD cells were shown to increase cell susceptibility to apoptosis. Accordingly, treatment with GM1 increased survival of HD cells in vitro and consistently ameliorated pathological phenotypes in several murine HD models, with effects seen at molecular, cellular, and behavioral level. Given that in none of the clinical trials using GM1 any clinically relevant safety issues have occurred to date, current data supports expanding GM1 clinical research, particularly to conditions with high, unmet medical need.
  • Exhaustion of CD4+ T-cells mediated by the Kynurenine Pathway in Melanoma.

    Rad Pour, Soudabeh; Morikawa, Hiromasa; Kiani, Narsis A; Yang, Muyi; Azimi, Alireza; Shafi, Gowhar; Shang, Mingmei; Baumgartner, Roland; Ketelhuth, Daniel F J; Kamleh, Muhammad Anas; Wheelock, Craig E; Lundqvist, Andreas; Hansson, Johan; Tegner, Jesper (Scientific reports, Springer Science and Business Media LLC, 2019-08-23) [Article]
    Kynurenine pathway (KP) activation by the enzymatic activity of indoleamine 2,3-dioxygenase1 (IDO1) and kynurenine (KYN) production represents an attractive target for reducing tumour progression and improving anti-tumour immunity in multiple cancers. However, immunomodulatory properties of other KP metabolites such as 3-hydroxy kynurenine (3-HK) and kynurenic acid (KYNA) are poorly understood. The association of the kynurenine metabolic pathway with T-cell status in the tumour microenvironment were characterized, using gene expression data of 368 cutaneous skin melanoma (SKCM) patients from the TCGA cohort. Based on the identified correlations, we characterized the production of KYN, 3-HK, and KYNA in vitro using melanoma-derived cell lines and primary CD4+ CD25- T-cells. Activation of the CD4+ T-cells produced IFNγ, which yielded increased levels of KYN and KYNA. Concurrently, kynurenine 3-monooxygenase (KMO) expression and proliferation of CD4+ T-cells were reduced, whereas exhaustion markers such as PD-L1, AHR, FOXP3, and CTLA4 were increased. Additionally, an analysis of the correlation network reconstructed using TCGA-SKCM emphasized KMO and KYNU with high variability among BRAF wild-type compared with V600E, which underscored their role in distinct CD4+ T-cell behavior in tumour immunity. Our results suggest that, in addition to IDO1, there is an alternative immune regulatory mechanism associated with the lower KMO expression and the higher KYNA production, which contributes to dysfunctional effector CD4+ T-cell response.
  • Near-Infrared OAM Communication Using 3D-Printed Microscale Spiral Phase Plates

    Stegenburgs, Edgars; Bertoncini, Andrea; Trichili, Abderrahmen; Alias, Mohd Sharizal; Ng, Tien Khee; Alouini, Mohamed-Slim; Liberale, Carlo; Ooi, Boon S. (IEEE Communications Magazine, Institute of Electrical and Electronics Engineers (IEEE), 2019-08-22) [Article]
    We report the use of 3D-printed microscale spiral phase plates to generate orbital angular momentum (OAM) carrying beams. We confirm that the generated beams have high purity, and we have successfully tested them to convey data signals with low bit error rates at the wavelength of 980 nm. This method will open new opportunities for generating OAM beams for many applications in optical communications, including free-space optics, as well as underwater, chip-to-chip, and quantum communications.
  • Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.

    Fernandes, Sunjay Jude; Morikawa, Hiromasa; Ewing, Ewoud; Ruhrmann, Sabrina; Joshi, Rubin Narayan; Lagani, Vincenzo; Karathanasis, Nestoras; Khademi, Mohsen; Planell, Nuria; Schmidt, Angelika; Tsamardinos, Ioannis; Olsson, Tomas; Piehl, Fredrik; Kockum, Ingrid; Jagodic, Maja; Tegner, Jesper; Gomez-Cabrero, David (Scientific reports, Springer Science and Business Media LLC, 2019-08-21) [Article]
    Multiple Sclerosis (MS) is an autoimmune disease of the central nervous system with prominent neurodegenerative components. The triggering and progression of MS is associated with transcriptional and epigenetic alterations in several tissues, including peripheral blood. The combined influence of transcriptional and epigenetic changes associated with MS has not been assessed in the same individuals. Here we generated paired transcriptomic (RNA-seq) and DNA methylation (Illumina 450 K array) profiles of CD4+ and CD8+ T cells (CD4, CD8), using clinically accessible blood from healthy donors and MS patients in the initial relapsing-remitting and subsequent secondary-progressive stage. By integrating the output of a differential expression test with a permutation-based non-parametric combination methodology, we identified 149 differentially expressed (DE) genes in both CD4 and CD8 cells collected from MS patients. Moreover, by leveraging the methylation-dependent regulation of gene expression, we identified the gene SH3YL1, which displayed significant correlated expression and methylation changes in MS patients. Importantly, silencing of SH3YL1 in primary human CD4 cells demonstrated its influence on T cell activation. Collectively, our strategy based on paired sampling of several cell-types provides a novel approach to increase sensitivity for identifying shared mechanisms altered in CD4 and CD8 cells of relevance in MS in small sized clinical materials.
  • Engineering a Polyspecific Pyrrolysyl-tRNA Synthetase by a High Throughput FACS Screen.

    Hohl, Adrian; Karan, Ram; Gespers (Akal), Anastassja; Renn, Dominik; Liu, Xuechao; Ghoprade, Seema Arun; Groll, Michael; Rueping, Magnus; Eppinger, Jörg (Scientific reports, Springer Science and Business Media LLC, 2019-08-21) [Article]
    The Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNAPyl are extensively used to add non-canonical amino acids (ncAAs) to the genetic code of bacterial and eukaryotic cells. However, new ncAAs often require a cumbersome de novo engineering process to generate an appropriate PylRS/tRNAPyl pair. We here report a strategy to predict a PylRS variant with novel properties. The designed polyspecific PylRS variant HpRS catalyzes the aminoacylation of 31 structurally diverse ncAAs bearing clickable, fluorinated, fluorescent, and for the first time biotinylated entities. Moreover, we demonstrated a site-specific and copper-free conjugation strategy of a nanobody by the incorporation of biotin. The design of polyspecific PylRS variants offers an attractive alternative to existing screening approaches and provides insights into the complex PylRS-substrate interactions.
  • A Cell Density-Dependent Reporter in the Drosophila S2 Cells

    Romine, Matthew L.; Li, Mo; Liu, Kevin Jiayang; Patel, Sapna K.; Nelson, Julie G.; Shen, Ping; Cai, Haini N. (Scientific Reports, Springer Science and Business Media LLC, 2019-08-14) [Article]
    Cell density regulates many aspects of cell properties and behaviors including metabolism, growth, cytoskeletal structure and locomotion. Importantly, the responses by cultured cells to density signals also uncover key mechanisms that govern animal development and diseases in vivo. Here we characterized a density-responsive reporter system in transgenic Drosophila S2 cells. We show that the reporter genes are strongly induced in a cell density-dependent and reporter-independent fashion. The rapid and reversible induction occurs at the level of mRNA accumulation. We show that multiple DNA elements within the transgene sequences, including a metal response element from the metallothionein gene, contribute to the reporter induction. The reporter induction correlates with changes in multiple cell density and growth regulatory pathways including hypoxia, apoptosis, cell cycle and cytoskeletal organization. Potential applications of such a density-responsive reporter will be discussed.

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