Molecular Species
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Mathematics ◽  
2021 ◽  
Vol 9 (15) ◽  
pp. 1809
Author(s):  
Bernat Bassols ◽  
Ernest Fontich ◽  
Daniel Oro ◽  
David Alonso ◽  
Josep Sardanyés

Research on hypercycles focuses on cooperative interactions among replicating species, including the emergence of catalytic parasites and catalytic shortcircuits. Further interactions may be expected to arise in cooperative systems. For instance, molecular replicators are subject to mutational processes and ecological species to behavioural shifts due to environmental and ecological changes. Such changes could involve switches from cooperative to antagonistic interactions, in what we call a functional shift. In this article, we investigate a model for a two-member hypercycle model, considering that one species performs a functional shift. First, we introduce the model dynamics without functional shifts to illustrate the dynamics only considering obligate and facultative cooperation. Then, two more cases maintaining cross-catalysis are considered: (i) a model describing the dynamics of ribozymes where a fraction of the population of one replicator degrades the other molecular species while the other fraction still receives catalytic aid; and (ii) a system in which a given fraction of the population predates on the cooperating species while the rest of the population still receives aid. We have characterised the key bifurcation parameters determining extinction, survival, and coexistence of species. We show that predation, regardless of the fraction that benefits from it, does not significantly change dynamics with respect to the degradative case (i), thus conserving dynamics and bifurcations. Their biological significance is interpreted, and their potential implications for the dynamics of early replicators and ecological species are outlined.


Chemistry ◽  
2021 ◽  
Vol 3 (3) ◽  
pp. 818-820
Author(s):  
Catherine E. Housecroft ◽  
Katharina M. Fromm

This Special Issue of Chemistry is dedicated to Dr. Howard D. Flack (1943–2017), a renowned crystallographer who transformed the way in which, by using single crystal X-ray diffraction, we are able to determine the absolute structure of a crystalline material, and thereby determine the absolute configuration of molecular species within the material [...]


2021 ◽  
Author(s):  
Kelsey H. Fisher-Wellman ◽  
James T Hagen ◽  
Miki Kassai ◽  
Li-Pin Kao ◽  
Margaret Nelson ◽  
...  

Abstract Modifications in sphingolipid (SL) metabolism and mitochondrial bioenergetics are key factors implicated in cancer cell response to chemotherapy, including chemotherapy resistance. Vinca alkaloids such as vincristine (VCR), widely used in cancer treatment, are no exception, as their beneficial actions are often supplanted by resistance. In the present work we utilized HL-60 human leukemia cells and a VCR-resistant counterpart, HL-60/VCR, as a model to determine potential interplay between SL metabolism and mitochondrial bioenergetics supportive of multidrug resistance (MDR). Relative to wild-type cells, HL-60/VCR presented with global alterations in SL composition, typified by upregulated expression of sphingosine kinase (SPHK1), which catalyzes formation of sphingosine 1-phosphate (S1P), glucosylceramide synthase (GCS), which catalyzes formation of glucosylceramides (GC), and acid ceramidase, responsible for ceramide hydrolysis. In support of these changes, VCR resistance was also characterized by increases in S1P, several molecular species of ceramide and GC, and changes in sphingomyelin (SM) molecular species. With respect to mitochondria, despite increased basal respiration in HL-60/VCR cells, direct interrogation of the mitochondrial network revealed intrinsic respiratory complex insufficiency, largely localized to complex I (CI). Importantly, forced ceramide accumulation in wild-type cells phenocopied the respiratory insufficiency observed in HL-60/VCR, and co-targeting SL metabolism and CI induced synergistic cytotoxicity in HL-60/VCR cells, as well as in other MDR leukemia models. Together, these data underscore the intimate connection between cellular sphingolipids and mitochondrial metabolism and suggest that pharmacological intervention across both pathways may represent a novel treatment strategy against MDR.


2021 ◽  
Author(s):  
Haruki Uchino ◽  
Hiroshi Tsugawa ◽  
Hidenori Takahashi ◽  
Makoto Arita

Abstract Mass spectrometry-based untargeted lipidomics has revealed the lipidome atlas of living organisms at the molecular species level. Despite the double bond (C=C) position being a crucial factor for enzyme preference, cellular membrane milieu, and biological activity, the C=C defined structures have not yet been characterized. Here, we present a novel approach for C=C position-resolved untargeted lipidomics using a combination of oxygen attachment dissociation and computational mass spectrometry to increase the rate of annotation. We validated the accuracy of our platform as per the authentic standards of 21 lipid subclasses and the biogenic standards of 51 molecules containing polyunsaturated fatty acids (PUFAs) from the cultured cells fed with various fatty acid-enriched media. By analyzing human and mice-derived biological samples, we characterized 675 unique lipid structures with the C=C position-resolved level encompassing 22 lipid subclasses defined by LIPID MAPS. Our platform also illuminated the unique profiles of tissue-specific lipids containing n-3 and/or n-6 very long-chain PUFAs (carbon M 28 and double bonds a 4) in the eye, testis, and brain of the mouse.


2021 ◽  
Author(s):  
Kateryna Frantseva ◽  
Michael Mueller ◽  
Floris F. S. van der Tak ◽  
Michiel Min ◽  
Petr Pokorny

<p>We are learning rapidly about the gas composition of exoplanet atmospheres, but know almost nothing about their solid composition. The upcoming James Webb Space Telescope will radically change this! The HR8799 exoplanetary system is a perfect candidate because it provides us with a unique opportunity of simultaneously measuring mineral clouds and refractory element composition of its four gas giant atmospheres. The HR8799 system is very young and additionally contains two particle belts. The giant planets are predicted to be bombarded with material from the belts, analogous to the Late Heavy Bombardment. Signatures of this bombardment, such as mineral clouds and refractory element composition, might be observable in their atmospheres. JWST MIRI will allow to characterise these exoplanets in the mid-infrared thermal regime (5-28 μm) which is not possible from the ground. We use the ARtful modeling Code for exoplanet Science (ARCiS) to calculate the mid-infrared spectra of planets HR 8799 b, c, d and e, and we simulate MIRI spectroscopic observations. Besides the dust features, we also expect to identify narrower gas features from molecular species such as CO<sub>2</sub>, H<sub>2</sub>O, HCN, C<sub>2</sub>H<sub>2</sub> etc.</p>


2021 ◽  
Author(s):  
Henrik Melin ◽  
Leigh Fletcher ◽  
Patrick Irwin ◽  
Davide Grassi

<p>The polar orbit of the Juno spacecraft provides an unprecedented view of Jupiter's atmosphere as it passes above the cloud tops every 53 days. The spectrum in the near infrared is dominated by reflected sunlight from aerosols (both condensate clouds and hazes) in the troposphere, as well as absorptions by the molecular species present. In addition, thermal emission longward of 4.5 µm provides access to the gaseous composition and aerosols below the top-most clouds.  Of particular importance in shaping the spectra are ammonia, phosphine and water, in addition to minor contributions from species such as arsine, germane and carbon monoxide. These regions also include emissions by ionospheric H<sub>3</sub><sup>+</sup>. Here, we produce meridionally averaged zonal profiles from the Juno-JIRAM observations obtained during PJ3, which provide almost complete latitude coverage. To analyse the observations, we use the radiative transfer and retrieval code NEMESIS (Irwin et al., 2008), which has been updated to cover this wavelength with the latest line-data from HITRAN. Our aim is to analyse both the reflected-sunlight region (2-4 µm) and the thermal emission region (4-5 µm) simultaneously for the first time, building on the work of Grassi et al. (2019) and Grassi et al. (2020).  We investigate the appropriate set of aerosol and haze layers, starting with NH4SH at 1.3 bars, NH3 and 0.7 bars and two grey hazes: one in the troposphere and one in the stratosphere.  The optical properties of these aerosols are tested to find the optimal cloud structure to reproduce the full JIRAM spectrum. From the retrievals of the zonally-averaged spectra we investigate whether spatial variations of tropospheric composition are truly required to fit the data, comparing gaseous contrasts to the expected circulation patterns associated with Jupiter’s belts and zones.</p>


2021 ◽  
Author(s):  
Maria Chiara Maimone ◽  
Andrea Chiavassa ◽  
Jeremy Leconte ◽  
Matteo Brogi

<p>The study of exoplanets atmospheres is one of the most intriguing challenges in the exoplanet field nowadays and the High Resolution Spectroscopy (HRS) has recently emerged as one of the leading methods for detecting atomic and molecular species in their atmospheres (e.g., Birkby, 2018). While this technique is particularly robust against contaminant absorption in the Earth’s atmosphere, the non-stationary stellar spectrum, in the form of either Doppler shift or distortion of the line profile during planetary transits, creates a non-negligible source of noise that can alter or even prevent detection. In the last years, it has become computationally possible to simulate the stellar surface convection that, in the end, allows to correctly reproduce asymmetric and blue-shifted spectral lines due to the granulation pattern of the stellar disk, which is a very important source of uncertainties (Chiavassa & Brogi, 2019). In the context of HRS and on the planet hand side, only recently multidimensional models have been used to detect the weak planet signal in the spectrum (e.g., Flowers et al. 2019).</p> <p>However, these numerical simulations have been computed independently for star and planet so far, while acquired spectra are the result of the natural coupling at each phase along the planet orbit. A next step forward is needed: coupling stellar and planetary 3D models dynamics during the transit.</p> <p>I will present the unprecedented precise synthetic spectra obtained with the upgraded 3D radiative transfer code Optim3D (Chiavassa et al. 2009). Optim3D takes as inputs the state-of-art 3D RHD stellar simulations (Stagger code, Nordlund et al. 2009, Magic et al. 2013) and the 3D Global Climate Models (SPARC/MITgcms, Showman et al. 2009, Parmentier et al. 2021) for stars and planets respectively, coupling them at any phase along the planet orbit. I will show the impact of this new approach on the detection of molecules by cross-correlating our spectra with HRS observations (e.g., Snellen et al 2010 and Brogi et al. 2016). This approach is particularly advantageous for those molecular species that are present in both the atmospheres and form in the same region of the spectrum, resulting in mixed and overlapped spectral lines (e.g. CO and H2O, crucial to constrain the C/O ratio). Moreover, the use of 3D models provides us with information about the dynamics processes at play, such as stellar convection and planetary winds.</p> <p> </p>


2021 ◽  
Author(s):  
Raymond Thomas ◽  
Charles Manful ◽  
Thu Pham

Abstract IntroductionMonoacetyldiglycerides (MAcDG), are acetylated triglycerides (TG) and an emerging class of bioactive or functional lipid with promising nutritional, medical, and industrial applications. A major challenge exists when analyzing MAcDG from other subclasses of TG in biological matrices, limiting knowledge on their applications and metabolism. Objective and MethodsHere in we demonstrate a multimodal analytical method for resolution, identification and quantitation of MAcDG in biological samples based on thin layer chromatography-flame ionization detection complimentary with C30-reversed phase liquid chromatography-high resolution accurate mass tandem mass spectrometry. We further apply this method to determine the MAcDG molecular species composition and quantity in E. solidaginis larvae. Results and ConclusionThese findings suggest that the proposed analytical method could simultaneously provide a fast, accurate, sensitive, high throughput analysis of MAcDG from other TG subclasses, including the fatty acids, isomers and molecular species composition. We believe this method will allow for MAcDG to be included during routine lipidomics analysis of biological samples and will have broad interests and applications in the scientific community in areas such as nutrition, climate change, medicine and biofuel innovations.


Author(s):  
Raffaella Mulas ◽  
Rubén J. Sánchez-García ◽  
Ben D. MacArthur

AbstractComplex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph representations only describe pairwise interactions between molecular species and so are not well suited to modelling complex sets of reactions that may involve numerous reactants and/or products. Here, we make use of a recently developed hypergraph theory of chemical reactions that naturally allows for higher-order interactions to explore the geometry and quantify functional redundancy in biochemical reactions systems. Our results constitute a general theory of automorphisms for oriented hypergraphs and describe the effect of automorphism group structure on hypergraph Laplacian spectra.


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