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Olive ( Olea europaea L.) is an evergreen xerophytic tree characterizing vegetative landscape and historical-cultural identity of the Mediterranean Basin. More than 2600 cultivars constitute the rich genetic patrimony of the species cultivated in approximately 60 countries. As a subtropical species, the olive tree is quite sensitive to low temperatures, and air temperature is the most critical environmental factor limiting olive tree growth and production. In this present review, we explored the detrimental effects caused of low temperatures on olive cultivars, and analyzed the most frequently experimental procedures used to evaluate cold stress. Then, current findings freezing stress physiology and gene are summarized in olive tree, with an emphasis on adaptive mechanisms for cold tolerance. This review might clear the way for new research on adaptive mechanisms for cold acclimation and for improvement of olive growing management.

Polymer materials have been widely used in the remediation of soil heavy metal contamination for their good performance in the absorption of metal ions. To reveal the effect of polymer amendment (PA) on the remediation of cadmium-contaminated cotton fields, the cadmium (Cd) fractions in soil, Cd concentration in cotton organs, bioconcentration factor (BCF) of Cd, translocation factor (TF) of Cd, and the antioxidant capacity and photosynthesis of functional leaves were evaluated combining with the transcriptomic and metabolomic analyses, in barrel experiments in the field at the flowering and boll-forming stage of cotton. The results showed that, cotton improved the tolerance to Cd through self-regulation in Cd-contaminated soil. The expression of oxoglutaric acid and jasmonic acid were down-regulated by the application of PA to improve the photosynthetic rate (7.71%-46.20%), chlorophyll content (17.59%-63.18%), chlorophyll fluorescence (7.66%-32.25%), and antioxidant enzyme activity (15.49%-45.50%) of functional leaves, and the down-regulation of the expression of jasmonic acid and up-regulation of the expression of stearic acid reduced the exchangeable Cd concentration in the soil, which reduced the transport of Cd from the root to the bolls (54.39%). Thereby, the balance of the genetic adaptation and phenotypic plasticity of cotton was achieved, and the cell structure of leaves was restored. This study deepens our understanding of the molecular mechanism of PA in the remediation of Cd contamination in cotton fields, and provides guidance for the remediation of heavy metal contamination in farmland soil and agricultural safety under drip irrigation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Published by Elsevier B.V.)

Infertility is one of the main social and health problems among young couples. Although a noticeable ratio of infertilities are asymptomatic, about half of the cases are observed among males. Various environmental factors such as life style, dietary patterns, and pathogens are associated with male infertility. Mutations and chromosomal abnormalities are also the most important genetic risk factors of male infertility. Similar to other populations, there is a dramatically rising trend of male infertility among Iranian. Regarding the high ratio of asymptomatic cases, it is required to clarify the molecular biology and cellular processes involved in male infertility in this population to suggest an efficient panel of diagnostic markers. In this review, we have summarized all of the cellular and molecular processes which have been reported among Iranian infertile males to clarify the molecular biology of male infertility in this population. It was observed that the stress response, cellular detoxification, and DNA repair processes were the most common aberrant cellular mechanisms among Iranian infertile males. This review paves the way of introducing a population-based diagnostic panel of genetic markers among Iranian infertile males., Competing Interests: None., (AJTR Copyright © 2021.)

We report the first detection in space of the two doubly deuterated isotopologues of methyl acetylene. The species CHD 2 CCH and CH 2 DCCD were identified in the dense core L483 through nine and eight, respectively, rotational lines in the 72-116 GHz range using the IRAM 30m telescope. The astronomical frequencies observed here were combined with laboratory frequencies from the literature measured in the 29-47 GHz range to derive more accurate spectroscopic parameters for the two isotopologues. We derive beam-averaged column densities of (2.7 ± 0.5) × 10 12 cm -2 for CHD 2 CCH and (2.2 ± 0.4) × 10 12 cm -2 for CH 2 DCCD, which translate to abundance ratios CH 3 CCH/CHD 2 CCH = 34 ± 10 and CH 3 CCH/CH 2 DCCD = 42 ± 13. The doubly deuterated isotopologues of methyl acetylene are only a few times less abundant than the singly deuterated ones, concretely around 2.4 times less abundant than CH 3 CCD. The abundances of the different deuterated isotopologues with respect to CH 3 CCH are reasonably accounted for by a gas-phase chemical model in which deuteration occurs from the precursor ions C 3 H 6 D + and C 3 H 5 D + , when the ortho-to-para ratio of molecular hydrogen is sufficiently low. This points to gas-phase chemical reactions, rather than grain-surface processes, as responsible for the formation and deuterium fractionation of CH 3 CCH in L483. The abundance ratios CH 2 DCCH/CH 3 CCD = 3.0 ± 0.9 and CHD 2 CCH/CH 2 DCCD = 1.25 ± 0.37 observed in L483 are consistent with the statistically expected values of three and one, respectively, with the slight overabundance of CHD 2 CCH compared to CH 2 DCCD being well explained by the chemical model.

Background: Hepatitis B virus infection co-occurs in 33% of individuals with hepatocellular carcinoma worldwide. However, the molecular link between hepatitis B virus and hepatocellular carcinoma is unknown. Thus, we aimed to elucidate molecular linkages underlying pathogenesis through in-depth data mining analysis., Materials and Methods: Differentially expressed genes were identified from patients with chronic hepatitis B virus infection, hepatocellular carcinoma, or both. Gene set enrichment analysis revealed signaling pathways involving differentially expressed genes. Protein-protein interaction networks, protein crosstalk, and enrichment were analyzed to determine whether differentially expressed gene products might serve as a bridge from hepatitis B virus infection to hepatocellular carcinoma pathogenesis. Prognostic potential and transcriptional and post-transcriptional regulators of bridge genes were also examined., Results: We identified vital bridge factors in hepatitis B virus infection-associated hepatocellular carcinoma. Differentially expressed genes were clustered into modules based on relative protein function. Signaling pathways associated with cancer, inflammation, immune system, and microenvironment showed significant crosstalk between modules. Thirty-two genes were dysregulated in hepatitis B virus infection-mediated hepatocellular carcinoma. CPEB3, RAB26, SLCO1B1, ST3GAL6 and XK had higher connectivity in the modular network, suggesting significant associations with survival. CDC20 and NUP107 were identified as driver genes as well as markers of poor prognosis., Conclusion: Our results suggest that the sustained inflammatory environment created by hepatitis B virus infection is a risk factor for hepatocellular carcinoma. The identification of hepatitis B virus infection-related hepatocellular carcinoma bridge genes provides testable hypotheses about the pathogenesis of hepatocellular carcinoma., Competing Interests: The authors report no conflicts of interest for this work., (© 2021 Nong et al.)

The reaction between atomic oxygen and molecular hydrogen is an important one in astrochemistry as it regulates the abundance of the hydroxyl radical and serves to open the chemistry of oxygen in diverse astronomical environments. However, the existence of a high activation barrier in the reaction with ground state oxygen atoms limits its efficiency in cold gas. In this study we calculate the dependence of the reaction rate coefficient on the rotational and vibrational state of H 2 and evaluate the impact on the abundance of OH in interstellar regions strongly irradiated by far-UV photons, where H 2 can be efficiently pumped to excited vibrational states. We use a recently calculated potential energy surface and carry out time-independent quantum mechanical scattering calculations to compute rate coefficients for the reaction O( 3 P ) + H 2 ( v , j ) → OH + H, with H 2 in vibrational states v = 0-7 and rotational states j = 0-10. We find that the reaction becomes significantly faster with increasing vibrational quantum number of H 2 , although even for high vibrational states of H 2 ( v = 4-5) for which the reaction is barrierless, the rate coefficient does not strictly attain the collision limit and still maintains a positive dependence with temperature. We implemented the calculated state-specific rate coefficients in the Meudon PDR code to model the Orion Bar PDR and evaluate the impact on the abundance of the OH radical. We find the fractional abundance of OH is enhanced by up to one order of magnitude in regions of the cloud corresponding to A V = 1.3-2.3, compared to the use of a thermal rate coefficient for O + H 2 , although the impact on the column density of OH is modest, of about 60%. The calculated rate coefficients will be useful to model and interpret JWST observations of OH in strongly UV-illuminated environments.

We present the first identification in interstellar space of the propargyl radical (CH 2 CCH). This species was observed in the cold dark cloud TMC-1 using the Yebes 40m telescope. The six strongest hyperfine components of the 2 0,2 -1 0,1 rotational transition, lying at 37.46 GHz, were detected with signal-to-noise ratios in the range 4.6-12.3 σ. We derive a column density of 8.7 × 10 13 cm -2 for CH 2 CCH, which translates to a fractional abundance relative to H 2 of 8.7 × 10 -9 . This radical has a similar abundance to methyl acetylene, with an abundance ratio CH 2 CCH/CH 3 CCH close to one. The propargyl radical is thus one of the most abundant radicals detected in TMC-1, and it is probably the most abundant organic radical with a certain chemical complexity ever found in a cold dark cloud. We constructed a gas-phase chemical model and find calculated abundances that agree with, or fall two orders of magnitude below, the observed value depending on the poorly constrained low-temperature reactivity of CH 2 CCH with neutral atoms. According to the chemical model, the propargyl radical is essentially formed by the C + C 2 H 4 reaction and by the dissociative recombination of C 3 H n + ions with n = 4-6. The propargyl radical is believed to control the synthesis of the first aromatic ring in combustion processes, and it probably plays a key role in the synthesis of large organic molecules and cyclization processes to benzene in cold dark clouds.

Context: Cyanoacetamide is a -CN bearing molecule that is also an amide derivative target molecule in the interstellar medium., Aims: The aim of our investigation is to analyze the feasibility of a plausible formation process of protonated cyanoacetamide under interstellar conditions and to provide direct experimental frequencies of the ground vibrational state of the neutral form in the microwave region in order to enable its eventual identification in the interstellar medium., Methods: We used high-level theoretical computations to study the formation process of protonated cyanoacetamide. Furthermore, we employed a high-resolution laser-ablation molecular beam Fourier transform spectroscopic technique to measure the frequencies of the neutral form., Results: We report the first rotational characterization of cyanoacetamide, and a precise set of the relevant rotational spectroscopic constants have been determined as a first step to identifying the molecule in the interstellar medium. We fully explored the potential energy surface to study a gas-phase reaction on the formation process of protonated cyanoacetamide. We found that an exothermic process with no net activation barrier is initiated by the high-energy isomer of protonated hydroxylamine, which leads to protonated cyanoacetamide.

Cadmium (Cd) is a detrimental element that can be toxic to plants. The physiological and biochemical responses of plants to Cd stress have been extensively studied, but the molecular mechanisms remain unclear. The present study showed that Cd severely inhibited the growth of roots and shoots and reduced plant biomass of mung bean seedlings. To further investigate the gene profiles and molecular processes in response Cd stress, transcriptome analyses of mung bean roots exposed to 100 μM Cd for 1, 5, and 9 days were performed. Cd treatment significantly decreased global gene expression levels at 5 and 9 d compared with the control. A total of 6737, 10279, and 9672 differentially expressed genes (DEGs) were identified in the 1-, 5-, and 9-day Cd-treated root tissues compared with the controls, respectively. Based on the analysis of DEG function annotation and enrichment, a pattern of mung bean roots response to Cd stress was proposed. The processes detoxification and antioxidative defense were involved in the early response of mung bean roots to Cd. Cd stress downregulated the expressions of a series of genes involved in cell wall biosynthesis, cell division, DNA replication and repair, and photosynthesis, while genes involved in signal transduction and regulation, transporters, secondary metabolisms, defense systems, and mitochondrial processes were upregulated in response to Cd, which might be contributed to the improvement of plant tolerance. Our results provide some novel insights into the molecular processes for growth and adaption of mung bean roots in response to Cd and many candidate genes for further biotechnological manipulations to improve plant tolerance to heavy metals., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Aims: We aim to determine the abundances of SiO, CS, SiS, SO, and SO 2 in a large sample of oxygen-rich asymptotic giant branch (AGB) envelopes covering a wide range of mass loss rates to investigate the potential role that these molecules could play in the formation of dust in these environments., Methods: We surveyed a sample of 30 oxygen-rich AGB stars in the λ 2 mm band using the IRAM 30m telescope. We performed excitation and radiative transfer calculations based on the large velocity gradient (LVG) method to model the observed lines of the molecules and to derive their fractional abundances in the observed envelopes., Results: We detected SiO in all 30 targeted envelopes, as well as CS, SiS, SO, and SO 2 in 18, 13, 26, and 19 sources, respectively. Remarkably, SiS is not detected in any envelope with a mass loss rate below 10 -6 M ⊙ yr -1 , whereas it is detected in all envelopes with mass loss rates above that threshold. From a comparison with a previous, similar study on C-rich sources, it becomes evident that the fractional abundances of CS and SiS show a marked differentiation between C-rich and O-rich sources, being two orders of magnitude and one order of magnitude more abundant in C-rich sources, respectively, while the fractional abundance of SiO turns out to be insensitive to the C/O ratio. The abundance of SiO in O-rich envelopes behaves similarly to C-rich sources, that is, the denser the envelope the lower its abundance. A similar trend, albeit less clear than for SiO, is observed for SO in O-rich sources., Conclusions: The marked dependence of CS and SiS abundances on the C/O ratio indicates that these two molecules form more efficiently in C- than O-rich envelopes. The decline in the abundance of SiO with increasing envelope density and the tentative one for SO indicate that SiO and possibly SO act as gas-phase precursors of dust in circumstellar envelopes around O-rich AGB stars.

The first computational model of solid-phase chemistry in cometary nuclear ices is presented. An astrochemical kinetics model, MAGICKAL , is adapted to trace the chemical evolution in multiple layers of cometary ice, over a representative period of 5 Gyr. Physical conditions are chosen appropriate for "cold storage" of the cometary nucleus in the outer Solar System, prior to any active phase. The chemistry is simulated at a selection of static temperatures in the range 5 - 60 K, while the ice is exposed to the interstellar radiation field, inducing a photo-chemistry in the outer ice layers that produces significant formation of complex organic molecules. A treatment for the chemistry resulting from cosmic-ray bombardment of the ices is also introduced into the model, along with a new formulation for low-temperature photo-chemistry. Production of simple and complex molecules to depth on the order of 10 m or more is achieved, with local fractional abundances comparable to observed values in many cases. The production of substantial amounts of O 2 (and H 2 O 2 ) is found, suggesting that long-term processing by high-energy cosmic rays of cometary ices in situ , over a period on the order of 1 Gyr, may be sufficient to explain the large observed abundances of O 2 , if the overall loss of material from the comet is limited to a depth on the order of 10 m. Entry into the inner solar system could produce a further enhancement in the molecular content of the nuclear ices that may be quantifiable using this modeling approach.

Context: Collisions between cometary neutrals in the inner coma of a comet and cometary ions that have been picked up into the solar wind flow and return to the coma lead to the formation of a broad inner boundary known as a collisionopause. This boundary is produced by a combination of charge transfer and chemical reactions, both of which are important at the location of the collisionopause boundary. Four spacecraft measured ion densities and velocities in the inner region of comets, exploring the part of the coma where an ion-neutral collisionopause boundary is expected to form., Aims: The aims are to determine the dominant physics behind the formation of the ion-neutral collisionopause and to evaluate where this boundary has been observed by spacecraft., Methods: We evaluated observations from three spacecraft at four different comets to determine if a collisionopause boundary was observed based on the reported ion velocities. We compared the measured location of the ion-neutral collisionopause with measurements of the collision cross sections to evaluate whether chemistry or charge exchange are more important at the location where the collisionopause is observed., Results: Based on measurements of the cross sections for charge transfer and for chemical reactions, the boundary observed by Rosetta appears to be the location where chemistry becomes the more probable result of a collision between H 2 O and H 2 O + than charge exchange. Comparisons with ion observations made by Deep Space 1 at 19P/Borrelly and Giotto at 1P/Halley and 26P/Grigg-Skjellerup show that similar boundaries were observed at 19P/Borrelly and 1P/Halley. The ion composition measurements made by Giotto at Halley confirm that chemistry becomes more important inside of this boundary and that electron-ion dissociative recombination is a driver for the reported ion pileup boundary.

Aims: We aim to determine the abundances of CS, SiO, and SiS in a large sample of carbon star envelopes covering a wide range of mass loss rates to investigate the potential role that these molecules could play in the formation of dust in the surroundings of the central AGB star., Methods: We surveyed a sample of 25 carbon-rich AGB stars in the λ 2 mm band, more concretely in the J = 3 - 2 line of CS and SiO, and in the J = 7 - 6 and J = 8 - 7 lines of SiS, using the IRAM 30 m telescope. We performed excitation and radiative transfer calculations based on the large velocity gradient (LVG) method to model the observed lines of the molecules and to derive their fractional abundances in the observed envelopes. We also assessed the effect of infrared pumping in the excitation of the molecules., Results: We detected CS in all 25 targeted envelopes, SiO in 24 of them, and SiS in 17 sources. Remarkably, SiS is not detected in any envelope with a mass loss rate below 10 -6 M ⊙ yr -1 while it is detected in all envelopes with mass loss rates above that threshold. We found that CS and SiS have similar abundances in carbon star envelopes, while SiO is present with a lower abundance. We also found a strong correlation in which the denser the envelope, the less abundant are CS and SiO. The trend is however only tentatively seen for SiS in the range of high mass loss rates. Furthermore, we found a relation in which the integrated flux of the MgS dust feature at 30 μm increases as the fractional abundance of CS decreases., Conclusions: The decline in the fractional abundance of CS with increasing density could be due to gas-phase chemistry in the inner envelope or to adsorption onto dust grains. The latter possibility is favored by a correlation between the CS fractional abundance and the 30 μm feature, which suggests that CS is efficiently incorporated onto MgS dust around C-rich AGB stars. In the case of SiO, the observed abundance depletion with increasing density is most likely caused by an efficient incorporation onto dust grains. We conclude that CS, SiO (very likely), and SiS (tentatively) are good candidates to act as gas-phase precursors of dust in C-rich AGB envelopes.

Water is one of the most abundant molecules in the form of solid ice phase in the different regions of the interstellar medium (ISM). This large abundance cannot be properly explained by using only traditional low temperature gas-phase reactions. Thus, surface chemical reactions are believed to be major synthetic channels for the formation of interstellar water ice. Among the different proposals, hydrogenation of atomic O ( i.e. , 2H + O → H 2 O) is a chemically "simple" and plausible reaction toward water formation occurring on the surfaces of interstellar grains. Here, novel theoretical results concerning the formation of water adopting this mechanism on the crystalline (010) Mg 2 SiO 4 surface (a unequivocally identified interstellar silicate) are presented. The investigated reaction aims to simulate the formation of the first water ice layer covering the silicate core of dust grains. Adsorption of the atomic O as a first step of the reaction has been computed, results indicating that a peroxo ( O 2 2 - ) group is formed. The following steps involve the adsorption, diffusion and reaction of two successive H atoms with the adsorbed O atom. Results indicate that H diffusion on the surface has barriers of 4-6 kcal mol -1 , while actual formation of OH and H 2 O present energy barriers of 22-23 kcal mol -1 . Kinetic study results show that tunneling is crucial for the occurrence of the reactions and that formation of OH and H 2 O are the bottlenecks of the overall process. Several astrophysical implications derived from the theoretical results are provided as concluding remarks.

We present a new experimental setup devoted to the study of gas phase molecules and processes using broad band high spectral resolution rotational spectroscopy. A reactor chamber has been equipped with radio receivers similar to those used by radio astronomers to search for molecular emission in space. The whole Q (31.5-50 GHz) and W bands (72-116.5 GHz) are available for rotational spectroscopy observations. The receivers are equipped with 16×2.5 GHz Fast Fourier Transform spectrometers with a spectral resolution of 38.14 kHz allowing the simultaneous observation of the complete Q band and one third of the W band. The whole W band can be observed in three settings in which the Q band is always observed. Species such as CH 3 CN, OCS, and SO 2 are detected, together with many of their isotopologues and vibrationally excited states, in very short observing times. The system permits automatic overnight observations and integration times as long as 2.4×10 5 seconds have been reached. The chamber is equipped with a radiofrequency source to produce cold plasmas and with four ultraviolet lamps to study photochemical processes. Plasmas of CH 4 , N 2 , CH 3 CN, NH 3 , O 2 , and H 2 , among other species, have been generated and the molecular products easily identified by their rotational spectrum, and mass spectrometry and optical spectroscopy. Finally, the rotational spectrum of the lowest energy conformer of CH 3 CH 2 NHCHO (N-Ethylformamide), a molecule previously characterized in microwave rotational spectroscopy, has been measured up to 116.5 GHz allowing the accurate determination of its rotational and distortion constants and its search in space.

Context: Infrared and (sub-)mm observations of disks around T Tauri and Herbig Ae/Be stars point to a chemical differentiation between both types of disks, with a lower detection rate of molecules in disks around hotter stars., Aims: To investigate the underlying causes of the chemical differentiation indicated by observations we perform a comparative study of the chemistry of T Tauri and Herbig Ae/Be disks. This is one of the first studies to compare chemistry in the outer regions of these two types of disks., Methods: We developed a model to compute the chemical composition of a generic protoplanetary disk, with particular attention to the photochemistry, and applied it to a T Tauri and a Herbig Ae/Be disk. We compiled cross sections and computed photodissociation and photoionization rates at each location in the disk by solving the FUV radiative transfer in a 1+1D approach using the Meudon PDR code and adopting observed stellar spectra., Results: The warmer disk temperatures and higher ultraviolet flux of Herbig stars compared to T Tauri stars induce some differences in the disk chemistry. In the hot inner regions, H 2 O, and simple organic molecules like C 2 H 2 , HCN, and CH 4 are predicted to be very abundant in T Tauri disks and even more in Herbig Ae/Be disks, in contrast with infrared observations that find a much lower detection rate of water and simple organics toward disks around hotter stars. In the outer regions, the model indicates that the molecules typically observed in disks, like HCN, CN, C 2 H, H 2 CO, CS, SO, and HCO + , do not have drastic abundance differences between T Tauri and Herbig Ae disks. Some species produced under the action of photochemistry, like C 2 H and CN, are predicted to have slightly lower abundances around Herbig Ae stars due to a narrowing of the photochemically active layer. Observations indeed suggest that these radicals are somewhat less abundant in Herbig Ae disks, although in any case the inferred abundance differences are small, of a factor of a few at most. A clear chemical differentiation between both types of disks concerns ices. Owing to the warmer temperatures of Herbig Ae disks, one expects snowlines lying farther away from the star and a lower mass of ices compared to T Tauri disks., Conclusions: The global chemical behavior of T Tauri and Herbig Ae/Be disks is quite similar. The main differences are driven by the warmer temperatures of the latter, which result in a larger reservoir or water and simple organics in the inner regions and a lower mass of ices in the outer disk.

Context: In bright photodissociation regions (PDRs) associated to massive star formation, the presence of dense "clumps" that are immersed in a less dense interclump medium is often proposed to explain the difficulty of models to account for the observed gas emission in high-excitation lines., Aims: We aim at presenting a comprehensive view of the modeling of the CO rotational ladder in PDRs, including the high-J lines that trace warm molecular gas at PDR interfaces., Methods: We observed the 12 CO and 13 CO ladders in two prototypical PDRs, the Orion Bar and NGC 7023 NW using the instruments onboard Herschel . We also considered line emission from key species in the gas cooling of PDRs (C + , O, H 2 ) and other tracers of PDR edges such as OH and CH + . All the intensities are collected from Herschel observations, the literature and the Spitzer archive and are analyzed using the Meudon PDR code., Results: A grid of models was run to explore the parameter space of only two parameters: thermal gas pressure and a global scaling factor that corrects for approximations in the assumed geometry. We conclude that the emission in the high-J CO lines, which were observed up to J up =23 in the Orion Bar (J up =19 in NGC 7023), can only originate from small structures of typical thickness of a few 10 -3 pc and at high thermal pressures ( P th ~ 10 8 K cm -3 )., Conclusions: Compiling data from the literature, we found that the gas thermal pressure increases with the intensity of the UV radiation field given by G 0 , following a trend in line with recent simulations of the photoevaporation of illuminated edges of molecular clouds. This relation can help rationalising the analysis of high-J CO emission in massive star formation and provides an observational constraint for models that study stellar feedback on molecular clouds.

Context: Silicon carbide dust is ubiquitous in circumstellar envelopes around C-rich AGB stars. However, the main gas-phase precursors leading to the formation of SiC dust have not yet been identified. The most obvious candidates among the molecules containing an Si-C bond detected in C-rich AGB stars are SiC 2 , SiC, and Si 2 C. To date, the ring molecule SiC 2 has been observed in a handful of evolved stars, while SiC and Si 2 C have only been detected in the C-star envelope IRC +10216., Aims: We aim to study how widespread and abundant SiC 2 , SiC, and Si 2 C are in envelopes around C-rich AGB stars and whether or not these species play an active role as gas-phase precursors of silicon carbide dust in the ejecta of carbon stars., Methods: We carried out sensitive observations with the IRAM 30m telescope of a sample of 25 C-rich AGB stars to search for emission lines of SiC 2 , SiC, and Si 2 C in the λ 2 mm band. We performed non-LTE excitation and radiative transfer calculations based on the LVG method to model the observed lines of SiC 2 and to derive SiC 2 fractional abundances in the observed envelopes., Results: We detect SiC 2 in most of the sources, SiC in about half of them, and do not detect Si 2 C in any source, at the exception of IRC +10216. Most of these detections are reported for the first time in this work. We find a positive correlation between the SiC and SiC 2 line emission, which suggests that both species are chemically linked, the SiC radical probably being the photodissociation product of SiC 2 in the external layer of the envelope. We find a clear trend in which the denser the envelope, the less abundant SiC 2 is. The observed trend is interpreted as an evidence of efficient incorporation of SiC 2 onto dust grains, a process which is favored at high densities owing to the higher rate at which collisions between particles take place., Conclusions: The observed behavior of a decline in the SiC 2 abundance with increasing density strongly suggests that SiC 2 is an important gas-phase precursor of SiC dust in envelopes around carbon stars.

Comet composition provides critical information on the chemical and physical processes that took place during the formation of the Solar System. We report here on millimeter spectroscopic observations of the long-period bright comet C/2014 Q2 (Lovejoy) using the Atacama Pathfinder Experiment (APEX) band 1 receiver between UT 16.948 to 18.120 January 2015, when the comet was at heliocentric distance of 1.30 au and geocentric distance of 0.53 au. Bright comets allow for sensitive observations of gaseous volatiles that sublimate in their coma. These observations allowed us to detect HCN, CH 3 OH (multiple transitions), H 2 CO and CO, and to measure precise molecular production rates. Additionally, sensitive upper limits were derived on the complex molecules acetaldehyde (CH 3 CHO) and formamide (NH 2 CHO) based on the average of the strongest lines in the targeted spectral range to improve the signal-to-noise ratio. Gas production rates are derived using a non-LTE molecular excitation calculation involving collisions with H 2 O and radiative pumping that becomes important in the outer coma due to solar radiation. We find a depletion of CO in C/2014 Q2 (Lovejoy) with a production rate relative to water of 2.0 %, and relatively low abundances of Q (HCN)/ Q (H 2 O),0.1%, and Q (H 2 CO)/ Q (H 2 O), 0.2 %. In contrast the CH 3 OH relative abundance Q (CH 3 OH)/ Q (H 2 O),2.2 %, is close to the mean value observed in other comets. The measured production rates are consistent with values derived for this object from other facilities at similar wavelengths taking into account the difference in the fields of view. Based on the observed mixing ratios of organic molecules in four bright comets including C/2014 Q2, we find some support for atom addition reactions on cold dust being the origin of some of the molecules.

The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a "covalent-bond stage" to a "hydrogen-bond stage" in prebiotic chemistry., Competing Interests: The authors declare no conflict of interest.

Previous modeling studies of Titan's dayside ionosphere predict electron number densities that are roughly a factor of 2 higher than those observed by the RPWS/Langmuir probe. The issue can equivalently be described as the ratio between the calculated electron production rates and the square of the observed electron number densities resulting in roughly a factor of 4 higher effective recombination coefficient than expected from the ion composition and the electron temperature. Here we make an extended reassessment of Titan's dayside ionization balance, focusing on 34 flybys between TA and T120. Using a recalibrated data set and by taking the presence of negative ions into account, we arrive at lower effective recombination coefficients compared with earlier studies. The values are still higher than expected from the ion composition and the electron temperature, but by a factor of ~2-3 instead of a factor of ~4. We have also investigated whether the derived effective recombination coefficients display dependencies on the solar zenith angle (SZA), the integrated solar EUV intensity (<80 nm), and the corotational plasma ram direction (RAM), and found statistically significant trends, which may be explained by a declining photoionization against the background ionization by magnetospheric particles (trends in SZA and RAM) and altered photochemistry (trend in EUV). We find that a series of flybys that occurred during solar minimum (2008) and with similar flyby geometries are associated with enhanced values of the effective recombination coefficient compared with the remaining data set, which also suggests a chemistry dependence on the sunlight conditions.

Chemical kinetics of neutral-neutral gas-phase reactions at ultralow temperatures is a fascinating research subject with important implications on the chemistry of complex organic molecules in the interstellar medium (T∼10-100K). Scarce kinetic information is currently available for this kind of reactions at T<200 K. In this work we use the CRESU ( Cinétique de Réaction en Ecoulement Supersonique Uniforme , which means Reaction Kinetics in a Uniform Supersonic Flow) technique to measure for the first time the rate coefficients ( k ) of the gas-phase OH+H 2 CO reaction between 22 and 107 K. k values greatly increase from 2.1×10 -11 cm 3 s -1 at 107 K to 1.2×10 -10 cm 3 s -1 at 22 K. This is also confirmed by quasi-classical trajectories (QCT) at collision energies down to 0.1 meV performed using a new full dimension and ab initio potential energy surface, recently developed which generates highly accurate potential and includes long range dipole-dipole interactions. QCT calculations indicate that at low temperatures HCO is the exclusive product for the OH+H 2 CO reaction. In order to revisit the chemistry of HCO in cold dense clouds, k is reasonably extrapolated from the experimental results at 10K (2.6×10 -10 cm 3 s -1 ). The modeled abundances of HCO are in agreement with the observations in cold dark clouds for an evolving time of 10 5 -10 6 yrs. The different sources of production of HCO are presented and the uncertainties in the chemical networks discussed. This reaction can be expected to be a competitive process in the chemistry of prestellar cores. The present reaction is shown to account for a few percent of the total HCO production rate. Extensions to photodissociation regions and diffuse clouds environments are also commented.

We present a detailed theoretical study of the rotational excitation of CH + due to reactive and nonreactive collisions involving C + ( 2 P ), H 2 , CH + , H and free electrons. Specifically, the formation of CH + proceeds through the reaction between C + ( 2 P ) and H 2 ( ν H 2 = 1, 2), while the collisional (de)excitation and destruction of CH + is due to collisions with hydrogen atoms and free electrons. State-to-state and initial-state-specific rate coefficients are computed in the kinetic temperature range 10-3000 K for the inelastic, exchange, abstraction and dissociative recombination processes using accurate potential energy surfaces and the best scattering methods. Good agreement, within a factor of 2, is found between the experimental and theoretical thermal rate coefficients, except for the reaction of CH + with H atoms at kinetic temperatures below 50 K. The full set of collisional and chemical data are then implemented in a radiative transfer model. Our Non-LTE calculations confirm that the formation pumping due to vibrationally excited H 2 has a substantial effect on the excitation of CH + in photon-dominated regions. In addition, we are able to reproduce, within error bars, the far-infrared observations of CH + toward the Orion Bar and the planetary nebula NGC 7027. Our results further suggest that the population of ν H 2 = 2 might be significant in the photon-dominated region of NGC 7027.

Linear carbon chains are common in various types of astronomical molecular sources. Possible formation mechanisms involve both bottom-up and top-down routes. We have carried out a combined observational and modeling study of the formation of carbon chains in the C-star envelope IRC +10216, where the polymerization of acetylene and hydrogen cyanide induced by ultraviolet photons can drive the formation of linear carbon chains of increasing length. We have used ALMA to map the emission of λ 3 mm rotational lines of the hydrocarbon radicals C 2 H, C 4 H, and C 6 H, and the CN-containing species CN, C 3 N, HC 3 N, and HC 5 N with an angular resolution of ~1″. The spatial distribution of all these species is a hollow, 5-10″ wide, spherical shell located at a radius of 10-20″ from the star, with no appreciable emission close to the star. Our observations resolve the broad shell of carbon chains into thinner sub-shells which are 1-2″ wide and not fully concentric, indicating that the mass loss process has been discontinuous and not fully isotropic. The radial distributions of the species mapped reveal subtle differences: while the hydrocarbon radicals have very similar radial distributions, the CN-containing species show more diverse distributions, with HC 3 N appearing earlier in the expansion and the radical CN extending later than the rest of the species. The observed morphology can be rationalized by a chemical model in which the growth of polyynes is mainly produced by rapid gas-phase chemical reactions of C 2 H and C 4 H radicals with unsaturated hydrocarbons, while cyanopolyynes are mainly formed from polyynes in gas-phase reactions with CN and C 3 N radicals.

Aims: Our knowledge of the chemical properties of the circumstellar ejecta of the most massive evolved stars is particularly poor. We aim to study the chemical characteristics of the prototypical yellow hypergiant star, IRC +10420. For this purpose, we obtained full line surveys at 1 and 3 mm atmospheric windows., Methods: We have identified 106 molecular emission lines from 22 molecular species. Approximately half of the molecules detected are N-bearing species, in particular HCN, HNC, CN, NO, NS, PN, and N 2 H + . We used rotational diagrams to derive the density and rotational temperature of the different molecular species detected. We introduced an iterative method that allows us to take moderate line opacities into account., Results: We have found that IRC +10420 presents high abundances of the N-bearing molecules compared with O-rich evolved stars. This result supports the presence of a N-rich chemistry, expected for massive stars. Our analysis also suggests a decrease of the 12 C/ 13 C ratio from ≳ 7 to ~ 3.7 in the last 3800 years, which can be directly related to the nitrogen enrichment observed. In addition, we found that SiO emission presents a significant intensity decrease for high- J lines when compared with older observations. Radiative transfer modeling shows that this variation can be explained by a decrease in the infrared (IR) flux of the dust. The origin of this decrease might be an expansion of the dust shell or a lower stellar temperature due to the pulsation of the star.

Cancer is a complex disease, characterized by alteration of different physiological molecular processes and cellular features. Keeping this in mind, the possibility of early identification and detection of specific tumor biomarkers by non-invasive approaches could improve early diagnosis and patient management.Different molecular imaging procedures provide powerful tools for detection and non-invasive characterization of oncological lesions. Clinical studies are mainly based on the use of computed tomography, nuclear-based imaging techniques and magnetic resonance imaging. Preclinical imaging in small animal models entails the use of dedicated instruments, and beyond the already cited imaging techniques, it includes also optical imaging studies. Optical imaging strategies are based on the use of luminescent or fluorescent reporter genes or injectable fluorescent or luminescent probes that provide the possibility to study tumor features even by means of fluorescence and luminescence imaging. Currently, most of these probes are used only in animal models, but the possibility of applying some of them also in the clinics is under evaluation.The importance of tumor imaging, the ease of use of optical imaging instruments, the commercial availability of a wide range of probes as well as the continuous description of newly developed probes, demonstrate the significance of these applications. The aim of this review is providing a complete description of the possible optical imaging procedures available for the non-invasive assessment of tumor features in oncological murine models. In particular, the characteristics of both commercially available and newly developed probes will be outlined and discussed., Competing Interests: The authors declare that they have no conflict of interest.

We report laboratory spectroscopy for the first time of the J = 1-0 and J = 2-1 lines of Na 35 Cl and Na 37 Cl in several vibrational states. The hyperfine structure has been resolved in both transitions for all vibrational levels, which permit us to predict with high accuracy the hyperfine splitting of the rotational transitions of the two isotopologues at higher frequencies. The new data have been merged with all previous works at microwave, millimeter, and infrared wavelengths and fitted to a series of mass-independent Dunham parameters and to a potential energy function. The obtained parameters have been used to compute a new dipole moment function, from which the dipole moment for infrared transitions up to Δ v = 8 has been derived. Frequency and intensity predictions are provided for all rovibrational transitions up to J = 150 and v = 8, from which the ALMA data of evolved stars can be modeled and interpreted.

Context: Despite the fact that many sulfur-bearing molecules, ranging from simple diatomic species up to astronomical complex molecules, have been detected in the interstellar medium, the sulfur chemistry in space is largely unknown and a depletion in the abundance of S-containing species has been observed in the cold, dense interstellar medium (ISM). The chemical form of the missing sulfur has yet to be identified., Aims: For these reasons, in view of the fact that there is a large abundance of triatomic species harbouring sulfur, oxygen, and hydrogen, we decided to investigate the HSO radical in the laboratory to try its astronomical detection., Methods: High-resolution measurements of the rotational spectrum of the HSO radical were carried out within a frequency range well up into the THz region. Subsequently, a rigorous search for HSO in the two most studied high-mass star-forming regions, Orion KL and Sagittarius (Sgr) B2, and in the cold dark cloud Barnard 1 (B1-b) was performed., Results: The frequency coverage and the spectral resolution of our measurements allowed us to improve and extend the existing dataset of spectroscopic parameters, thus enabling accurate frequency predictions up to the THz range. These were used to derive the synthetic spectrum of HSO, by means of the MADEX code, according to the physical parameters of the astronomical source under consideration. For all sources investigated, the lack of HSO lines above the confusion limit of the data is evident., Conclusions: The derived upper limit to the abundance of HSO clearly indicates that this molecule does not achieve significant abundances in either the gas phase or in the ice mantles of dust grains.

In the last years, ultra-low temperature chemical kinetic experiments have demonstrated that some gas-phase reactions are much faster than previously thought. One example is the reaction between OH and CH 3 OH, which has been recently found to be accelerated at low temperatures yielding CH 3 O as main product. This finding opened the question of whether the CH 3 O observed in the dense core Barnard 1b could be formed by the gas-phase reaction of CH 3 OH and OH. Several chemical models including this reaction and grain-surface processes have been developed to explain the observed abundance of CH 3 O with little success. Here we report for the first time rate coefficients for the gas-phase reaction of OH and CH 3 OH down to a temperature of 22 K, very close to those in cold interstellar clouds. Two independent experimental set-ups based on the supersonic gas expansion technique coupled to the pulsed laser photolysis-laser induced fluorescence technique were used to determine rate coefficients in the temperature range 22-64 K. The temperature dependence obtained in this work can be expressed as k (22-64 K) = (3.6 ± 0.1) × 10 -12 ( T/ 300 K) -(1.0±0.2) cm 3 molecule -1 s -1 . Implementing this expression in a chemical model of a cold dense cloud results in CH 3 O/CH 3 OH abundance ratios similar or slightly lower than the value of ∼ 3 × 10 -3 observed in Barnard 1b. This finding confirms that the gas-phase reaction between OH and CH 3 OH is an important contributor to the formation of interstellar CH 3 O. The role of grain-surface processes in the formation of CH 3 O, although it cannot be fully neglected, remains controversial.

IRC +10216 is a circumstellar envelope around a carbon-rich evolved star which contains a large variety of molecules. According to interferometric observations, molecules are distributed either concentrated around the central star or as a hollow shell with a radius of ~15″. We present ALMA Cycle 0 band 6 observations of the J = 14 - 13 rotational transition of CH 3 CN in IRC +10216, obtained with an angular resolution of [Formula: see text]. The bulk of the emission is distributed as a hollow shell located at just ~2″ from the star, with a void of emission in the central region up to a radius of ~1″. This spatial distribution is markedly different from those found to date in this source for other molecules. Our analysis indicate that methyl cyanide is not formed neither in the stellar photosphere nor far in the outer envelope, but at radial distances as short as 1-2″, reaching a maximum abundance of ~ 0.02 molecules cm -3 at 2″ from the star. Standard chemical models of IRC +10216 predict that the bulk of CH 3 CN molecules should be present at a radius of ~ 15″, where other species such as polyyne radicals and cyanopolyynes are observed, with an additional inner component within 1″ from the star. The non-uniform structure of the circumstellar envelope and grain surface processes are discussed as possible causes of the peculiar distribution of methyl cyanide in IRC +10216.

Alternanthera philoxeroides is an amphibious invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation. Little is known about the molecular basis underlying environment-induced phenotypic changes. Variation in transcript abundance in A. philoxeroides was characterized throughout the time-courses of pond and upland treatments using RNA-Sequencing. Seven thousand eight hundred and five genes demonstrated variable expression in response to different treatments, forming 11 transcriptionally coordinated gene groups. Functional enrichment analysis of plastically expressed genes revealed pathway changes in hormone-mediated signaling, osmotic adjustment, cell wall remodeling, and programmed cell death, providing a mechanistic understanding of the biological processes underlying the phenotypic changes in A. philoxeroides. Both transcriptional modulation of environmentally sensitive loci and environmentally dependent control of regulatory loci influenced the plastic responses to the environment. Phenotypic responses and gene expression patterns to contrasting hydrological conditions were compared between A. philoxeroides and its alien congener Alternanthera pungens. The terricolous A. pungens displayed limited phenotypic plasticity to different treatments. It was postulated based on gene expression comparison that the interspecific variation in plasticity between A. philoxeroides and A. pungens was not due to environmentally-mediated changes in hormone levels but to variations in the type and relative abundance of different signal transducers and receptors expressed in the target tissue.

Radiation processing of the surface ices of outer Solar System bodies may be an important process for the production of complex chemical species. The refractory materials resulting from radiation processing of known ices are thought to impart to them a red or brown color, as perceived in the visible spectral region. In this work, we analyzed the refractory materials produced from the 1.2-keV electron bombardment of low-temperature N 2 -, CH 4 -, and CO-containing ices (100:1:1), which simulates the radiation from the secondary electrons produced by cosmic ray bombardment of the surface ices of Pluto. Despite starting with extremely simple ices dominated by N 2 , electron irradiation processing results in the production of refractory material with complex oxygen- and nitrogen-bearing organic molecules. These refractory materials were studied at room temperature using multiple analytical techniques including Fourier-transform infrared spectroscopy, X-ray absorption near-edge structure (XANES) spectroscopy, and gas chromatography coupled with mass spectrometry (GC-MS). Infrared spectra of the refractory material suggest the presence of alcohols, carboxylic acids, ketones, aldehydes, amines, and nitriles. XANES spectra of the material indicate the presence of carboxyl groups, amides, urea, and nitriles, and are thus consistent with the IR data. Atomic abundance ratios for the bulk composition of these residues from XANES analysis show that the organic residues are extremely N-rich, having ratios of N/C ~ 0.9 and O/C ~ 0.2. Finally, GC-MS data reveal that the residues contain urea as well as numerous carboxylic acids, some of which are of interest for prebiotic and biological chemistries.

We report the detection of SiS rotational lines in high-vibrational states as well as SiO and SiC 2 lines in their ground vibrational state toward IRC+10216 during the Atacama Large Millimeter Array Cycle 0. The spatial distribution of these molecules shows compact emission for SiS and a more extended emission for SiO and SiC 2 , and also proves the existence of an increase in the SiC 2 emission at the outer shells of the circumstellar envelope. We analyze the excitation conditions of the vibrationally excited SiS using the population diagram technique, and we use a large velocity gradient model to compare with the observations. We found moderate discrepancies between the observations and the models that could be explained if SiS lines detected are optically thick. Additionally, the line profiles of the detected rotational lines in the high energy vibrational states show a decreasing linewidth with increasing energy levels. This may be evidence that these lines could be excited only in the inner shells, i.e., the densest and hottest, of the circumstellar envelope of IRC+10216.

Fullerenes have been recently detected in various circumstellar and interstellar environments, raising the question of their formation pathway. It has been proposed that they can form at the low densities found in the interstellar medium by the photo-chemical processing of large polycyclic aromatic hydrocarbons (PAHs). Following our previous work on the evolution of PAHs in the NGC 7023 reflection nebula, we evaluate, using photochemical modeling, the possibility that the PAH C 66 H 20 (i.e. circumovalene) can lead to the formation of C 60 upon irradiation by ultraviolet photons. The chemical pathway involves full dehydrogenation of C 66 H 20 , folding into a floppy closed cage and shrinking of the cage by loss of C 2 units until it reaches the symmetric C 60 molecule. At 10" from the illuminating star and with realistic molecular parameters, the model predicts that 100% of C 66 H 20 is converted into C 60 in ~ 10 5 years, a timescale comparable to the age of the nebula. Shrinking appears to be the kinetically limiting step of the whole process. Hence, PAHs larger than C 66 H 20 are unlikely to contribute significantly to the formation of C 60 , while PAHs containing between 60 and 66 C atoms should contribute to the formation of C 60 with shorter timescales, and PAHs containing less than 60 C atoms will be destroyed. Assuming a classical size distribution for the PAH precursors, our model predicts absolute abundances of C 60 are up to several 10 -4 of the elemental carbon, i.e. less than a percent of the typical interstellar PAH abundance, which is consistent with observational studies. According to our model, once formed, C 60 can survive much longer (> 10 7 years for radiation fields below G 0 = 10 4 ) than other fullerenes because of the remarkable stability of the C 60 molecule at high internal energies. Hence, a natural consequence is that C 60 is more abundant than other fullerenes in highly irradiated environments.

Interstellar Polycyclic Aromatic Hydrocarbons (PAH) are expected to be strongly processed by Vacuum Ultra-Violet (VUV) photons. Here, we report experimental studies on the ionization and fragmentation of coronene (C 24 H 12 ), ovalene (C 32 H 14 ) and hexa-peri-hexabenzocoronene (HBC; C 42 H 18 ) cations by exposure to synchrotron radiation in the range of 8-40 eV. The results show that for small PAH cations such as coronene, fragmentation (H-loss) is more important than ionization. However, as the size increases, ionization becomes more and more important and for the HBC cation, ionization dominates. These results are discussed and it is concluded that, for large PAHs, fragmentation only becomes important when the photon energy has reached the highest ionization potential accessible. This implies that PAHs are even more photo-stable than previously thought. The implications of this experimental study for the photo-chemical evolution of PAHs in the interstellar medium (ISM) are briefly discussed.