Laser-Synthesized Germanium Nanoparticles as Biodegradable Material for Near-Infrared Photoacoustic Imaging and Cancer Phototherapy.

Biodegradable nanomaterials can significantly improve the safety profile of nanomedicine. Germanium nanoparticles (Ge NPs) with a safe biodegradation pathway are developed as efficient photothermal converters for biomedical applications. Ge NPs synthesized by femtosecond-laser ablation in liquids rapidly dissolve in physiological-like environment through the oxidation mechanism. The biodegradation of Ge nanoparticles is preserved in tumor cells in vitro and in normal tissues in mice with a half-life as short as 3.5 days. Biocompatibility of Ge NPs is confirmed in vivo by hematological, biochemical, and histological analyses. Strong optical absorption of Ge in the near-infrared spectral range enables photothermal treatment of engrafted tumors in vivo, following intravenous injection of Ge NPs. The photothermal therapy results in a 3.9-fold reduction of the EMT6/P adenocarcinoma tumor growth with significant prolongation of the mice survival. Excellent mass-extinction of Ge NPs (7.9 L g-1 cm-1 at 808 nm) enables photoacoustic imaging of bones and tumors, following intravenous and intratumoral administrations of the nanomaterial. As such, strongly absorbing near-infrared-light biodegradable Ge nanomaterial holds promise for advanced theranostics.

Limited Cheese Intake Paradigm Replaces Patterns of Behavioral Disorders in Experimental PTSD: Focus on Resveratrol Supplementation.

Currently, the efficacy of drug therapy for post-traumatic stress disorder or PTSD leaves much to be desired, making nutraceutical support a promising avenue for treatment. Recent research has identified the protective effects of resveratrol in PTSD. Here, we tested the behavioral and neurobiological effects of combining cheese consumption with resveratrol supplements in an experimental PTSD model. Using the elevated plus maze test, we observed that cheese intake resulted in a shift from anxiety-like behavior to depressive behavior, evident in increased freezing acts. However, no significant changes in the anxiety index value were observed. Interestingly, supplementation with cheese and resveratrol only led to the elimination of freezing behavior in half of the PTSD rats. We further segregated the rats into two groups based on freezing behavior: Freezing+ and Freezing0 phenotypes. Resveratrol ameliorated the abnormalities in Monoamine Oxidize -A and Brain-Derived Neurotrophic Factor gene expression in the hippocampus, but only in the Freezing0 rats. Moreover, a negative correlation was found between the number of freezing acts and the levels of Monoamine Oxidize-A and Brain-Derived Neurotrophic Factor mRNAs in the hippocampus. The study results show promise for resveratrol supplementation in PTSD treatment. Further research is warranted to better understand the underlying mechanisms and optimize the potential benefits of resveratrol supplementation for PTSD.

Isolation and Characterization of 1-Hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexene-1-acetic Acid, a Metabolite in Bacterial Transformation of Abscisic Acid.

We report the discovery of a new abscisic acid (ABA) metabolite, found in the course of a mass spectrometric study of ABA metabolism by the rhizosphere bacterium Rhodococcus sp. P1Y. Analogue of (+)-ABA, enriched in tritium in the cyclohexene moiety, was fed in bacterial cells, and extracts containing radioactive metabolites were purified and analyzed to determine their structure. We obtained mass spectral fragmentation patterns and nuclear magnetic resonance spectra of a new metabolite of ABA identified as 1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexene-1-acetic acid, which we named rhodococcal acid (RA) and characterized using several other techniques. This metabolite is the second bacterial ABA degradation product in addition to dehydrovomifoliol that we described earlier. Taken together, these data reveal an unknown ABA catabolic pathway that begins with side chain disassembly, as opposed to the conversion of the cyclohexene moiety in plants. The role of ABA-utilizing bacteria in interactions with other microorganisms and plants is also discussed.

Laser-ablative aqueous synthesis and characterization of elemental boron nanoparticles for biomedical applications.

Boron-based nano-formulations look very promising for biomedical applications, including photo- and boron neutron capture therapies, but the fabrication of non-toxic water-dispersible boron nanoparticles (NPs), which contain the highest boron atom concentration, is difficult using currently available chemical and plasma synthesis methods. Here, we demonstrate purely aqueous synthesis of clean boron NPs by methods of femtosecond laser ablation from a solid boron target in water, thus free of any toxic organic solvents, and characterize their properties. We show that despite highly oxidizing water ambience, the laser-ablative synthesis process follows an unusual scenario leading to the formation of boron NPs together with boric acid (H3BO3) as an oxidation by-product coating the nanoparticles, which acts to stabilize the elemental boron NPs dispersion. We then demonstrate the purification of boron NPs from residual boric acid in deionized water, followed by their coating with polyethylene glycol to improve colloidal stability and biocompatibility. It was found that the formed NPs have a spherical shape with averaged size of about 37 nm, and are composed of elemental boron in mostly amorphous phase with the presence of certain crystalline fraction. The synthesized NPs demonstrate low toxicity and exhibit strong absorption in the NIR window of relative tissue transparency, promising their use in photoacoustic imaging and phototherapy, in addition to their promise for neutron capture therapy. This combined potential ability of generating imaging and therapy functionalities makes laser-synthesized B NPs a very promising multifunctional agent for biomedical applications.

A small molecule compound berberine as an orally active therapeutic candidate against COVID-19 and SARS: A computational and mechanistic study.

The novel coronavirus disease, COVID-19, has grown into a global pandemic and a major public health threat since its breakout in December 2019. To date, no specific therapeutic drug or vaccine for treating COVID-19 and SARS has been FDA approved. Previous studies suggest that berberine, an isoquinoline alkaloid, has shown various biological activities that may help against COVID-19 and SARS, including antiviral, anti-allergy and inflammation, hepatoprotection against drug- and infection-induced liver injury, as well as reducing oxidative stress. In particular, berberine has a wide range of antiviral activities such as anti-influenza, anti-hepatitis C, anti-cytomegalovirus, and anti-alphavirus. As an ingredient recommended in guidelines issued by the China National Health Commission for COVID-19 to be combined with other therapy, berberine is a promising orally administered therapeutic candidate against SARS-CoV and SARS-CoV-2. The current study comprehensively evaluates the potential therapeutic mechanisms of berberine in preventing and treating COVID-19 and SARS using computational modeling, including target mining, gene ontology enrichment, pathway analyses, protein-protein interaction analysis, and in silico molecular docking. An orally available immunotherapeutic-berberine nanomedicine, named NIT-X, has been developed by our group and has shown significantly increased oral bioavailability of berberine, increased IFN-γ production by CD8+ T cells, and inhibition of mast cell histamine release in vivo, suggesting a protective immune response. We further validated the inhibition of replication of SARS-CoV-2 in lung epithelial cells line in vitro (Calu3 cells) by berberine. Moreover, the expression of targets including ACE2, TMPRSS2, IL-1α, IL-8, IL-6, and CCL-2 in SARS-CoV-2 infected Calu3 cells were significantly suppressed by NIT-X. By supporting protective immunity while inhibiting pro-inflammatory cytokines; inhibiting viral infection and replication; inducing apoptosis; and protecting against tissue damage, berberine is a promising candidate in preventing and treating COVID-19 and SARS. Given the high oral bioavailability and safety of berberine nanomedicine, the current study may lead to the development of berberine as an orally, active therapeutic against COVID-19 and SARS.

Laser Ablation-Assisted Synthesis of Plasmonic Si@Au Core-Satellite Nanocomposites for Biomedical Applications.

Owing to strong plasmonic absorption and excellent biocompatibility, gold nanostructures are among best candidates for photoacoustic bioimaging and photothermal therapy, but such applications require ultrapure Au-based nanoformulations of complex geometry (core-shells, nanorods) in order to shift the absorption band toward the region of relative tissue transparency (650-1000 nm). Here, we present a methodology for the fabrication of Si@Au core-satellite nanostructures, comprising of a Si core covered with small Au nanoparticles (NP), based on laser ablative synthesis of Si and Au NPs in water/ethanol solutions, followed by a chemical modification of the Si NPs by 3-aminopropyltrimethoxysilane (APTMS) and their subsequent decoration by the Au NPs. We show that the formed core-satellites have a red-shifted plasmonic absorption feature compared to that of pure Au NPs (520 nm), with the position of the peak depending on APTMS amount, water-ethanol solvent percentage and Si-Au volume ratio. As an example, even relatively small 40-nm core-satellites (34 nm Si core + 4 nm Au shell) provided a much red shifted peak centered around 610 nm and having a large tail over 700 nm. The generation of the plasmonic peak is confirmed by modeling of Si@Au core-shells of relevant parameters via Mie theory. Being relatively small and exempt of any toxic impurity due to ultraclean laser synthesis, the Si@Au core-satellites promise a major advancement of imaging and phototherapy modalities based on plasmonic properties of nanomaterials.

Laser-synthesized TiN nanoparticles for biomedical applications: Evaluation of safety, biodistribution and pharmacokinetics.

Having plasmonic absorption within the biological transparency window, titanium nitride (TiN) nanoparticles (NPs) can potentially outperform gold counterparts in phototheranostic applications, but characteristics of available TiN NPs are still far from required parameters. Recently emerged laser-ablative synthesis opens up opportunities to match these parameters as it makes possible the production of ultrapure low size-dispersed spherical TiN NPs, capable of generating a strong phototherapy effect under 750-800 nm excitation. This study presents the first assessment of toxicity, biodistribution and pharmacokinetics of laser-synthesized TiN NPs. Tests in vitro using 8 cell lines from different tissues evidenced safety of both as-synthesized and PEG-coated NPs (TiN-PEG NPs). After systemic administration in mice, they mainly accumulated in liver and spleen, but did not cause any sign of toxicity or organ damage up to concentration of 6 mg kg-1, which was confirmed by the invariability of blood biochemical parameters, weight and hemotoxicity examination. The NPs demonstrated efficient passive accumulation in EMT6/P mammary tumor, while concentration of TiN-PEG NPs was 2.2-fold higher due to "stealth" effect yielding 7-times longer circulation in blood. The obtained results evidence high safety of laser-synthesized TiN NPs for biological systems, which promises a major advancement of phototheranostic modalities on their basis.

Laser-Ablative Synthesis of Stable Aqueous Solutions of Elemental Bismuth Nanoparticles for Multimodal Theranostic Applications.

Elemental bismuth (Bi) nanoparticles (NPs), with the high atomic density of the Bi nuclei, could serve as efficient targeted agents for cancer treatment, with applications such as contrast agents for computed tomography (CT) imaging, sensitizers for image-guided X-ray radiotherapy, and photothermal therapy. However, the synthesis of elemental Bi NPs suitable for biological applications is difficult using conventional chemical routes. Here, we explore the fabrication of ultrapure Bi-based nanomaterials by femtosecond laser ablation from a solid Bi target in ambient liquids and characterize them by a variety of techniques, including TEM, SEM, XRD, FTIR, Raman, and optical spectroscopy. We found that laser-ablative synthesis using an elemental Bi solid target leads to the formation of spherical Bi NPs having the mean size of 20-50 nm and a low size-dispersion. The NPs prepared in water experience a fast (within a few minutes) conversion into 400-500 nm flake-like nanosheets, composed of bismuth subcarbonates, (BiO)2CO3 and (BiO)4CO3(OH)2, while the NPs prepared in acetone demonstrate high elemental stability. We introduce a procedure to obtain a stable aqueous solution of elemental Bi NPs suitable for biological applications, based on the coating of Bi NPs prepared in acetone with Pluronic® F68 and their subsequent transfer to water. We also show that the laser-synthesized elemental Bi NPs, due to their vanishing band gap, exhibit remarkable absorption in the infrared range, which can be used for the activation of photothermal therapy in the near IR-to-IR window with maximum optical transparency in biological media. Exempt of any toxic synthetic by-products, laser-ablated elemental Bi NPs present a novel appealing nanoplatform for combination image-guided photoradiotherapies.

The Yin and Yang of codon usage.

The genetic code is degenerate. With the exception of two amino acids (Met and Trp), all other amino acid residues are each encoded by multiple, so-called synonymous codons. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in genes/genomes suggested that codon choice might have functional implications beyond amino acid coding. The pattern of non-uniform codon use (known as codon usage bias) varies between organisms and represents a unique feature of an organism. Organism-specific codon choice is related to organism-specific differences in populations of cognate tRNAs. This implies that, in a given organism, frequently used codons will be translated more rapidly than infrequently used ones and vice versa A theory of codon-tRNA co-evolution (necessary to balance accurate and efficient protein production) was put forward to explain the existence of codon usage bias. This model suggests that selection favours preferred (frequent) over un-preferred (rare) codons in order to sustain efficient protein production in cells and that a given un-preferred codon will have the same effect on an organism's fitness regardless of its position within an mRNA's open reading frame. However, many recent studies refute this prediction. Un-preferred codons have been found to have important functional roles and their effects appeared to be position-dependent. Synonymous codon usage affects the efficiency/stringency of mRNA decoding, mRNA biogenesis/stability, and protein secretion and folding. This review summarizes recent developments in the field that have identified novel functions of synonymous codons and their usage.

Analgesia basada en infusión continua de anestésico local a nivel interfascial tras cirugía de colon laparoscópico: ensayo clínico / Analgesia with interfascial continuous wound infiltration after laparoscopic colon surgery: a randomized clinical trial

Objetivos. Tanto para cirugía laparoscópica como para cirugía abierta la analgesia multimodal puede ayudar a controlar el dolor postoperatorio. La colocación de un catéter en la herida quirúrgica de manera intraoperatoria tras cirugía de colon podría optimizar el control del dolor con menor consumo de opiáceos y menos efectos secundarios. Método. Realizamos un estudio prospectivo, aleatorizado de pacientes reclutados para cirugía de colon laparoscópica en el Hospital de Galdakao-Usansolo de enero de 2012 a enero de 2013. Los pacientes fueron asignados aleatoriamente al grupo del catéter o al grupo de la analgesia postoperatoria estándar. Un miembro de la Unidad de dolor agudo monitorizó todos los pacientes a lo largo de 48 h tras la cirugía. Las variables principales analizadas fueron la escala numérica verbal y la cantidad de morfina intravenosa utilizada por cada paciente mediante PCA. Resultados. Se incluyeron 92 pacientes en el estudio, 43 en el grupo con catéter y 49 en el estándar. Se observaron diferencias estadísticamente significativas en el consumo de morfina entre ambos grupos a lo largo de todo el periodo. La cantidad total de morfina consumida en el grupo del catéter fue de 5,63 ± 5,02 mg y de 21,86 ± 17,88 mg en el grupo de analgesia estándar (p = 0,0001). Los pacientes con catéter presentaban menores valores en la escala numérica verbal. No se encontraron efectos adversos asociados a la colocación del catéter y la administración de anestésico local. El grupo de catéter presentó menor estancia hospitalaria respecto al otro grupo (p = 0,02). Conclusión. En los pacientes intervenidos de cirugía de colon laparoscópico una infusión continua de anestésico local a través de un catéter interfascial durante 48 h tras la cirugía reduce la percepción del dolor y el consumo de morfina intravenosa, disminuyendo la estancia hospitalaria (AU)

Objectives. For major laparoscopic surgery, as with open surgery, a multimodal analgesia plan can help to control postoperative pain. Placing a wound catheter intraoperatively following colon surgery could optimize the control of acute pain with less consumption of opioids and few adverse effects. Methods. We conducted a prospective, randomized, study of patients scheduled to undergo laparoscopic colon surgery for cancer in Galdakao-Usansolo Hospital from January 2012 to January 2013. Patients were recruited and randomly allocated to wound catheter placement plus standard postoperative analgesia or standard postoperative analgesia alone. A physician from the acute pain management unit monitored all patients for pain at multiple points over the first 48 hours after surgery. The primary outcome variables were verbal numeric pain scale scores and amount of intravenous morphine used via patient controlled infusion. Results. 92 patients were included in the study, 43 had a wound catheter implanted and 49 did not. Statistically significant differences in morphine consumption were observed between groups throughout the course of the treatment period. The mean total morphine consumption at the end of the study was 5.63 ± 5.02 mg among wound catheter patients and 21. 86 ± 17.88 mg among control patients (P = .0001). Wound catheter patients had lower pain scale scores than control patients throughout the observation period. No adverse effects associated with the wound catheter technique were observed. The wound catheter group showed lower hospital stays with statistically significant difference (P = .02). Conclusions. In patients undergoing laparoscopic colon surgery, continuous infusion of local anaesthetics through interfascial wound catheters during the first 48 h aftersurgery reduced the level of perceived pain and also reduced parenteral morphine consumption with no associated adverse effects and lower hospital stays (AU)

Regulation of Selenocysteine Content of Human Selenoprotein P by Dietary Selenium and Insertion of Cysteine in Place of Selenocysteine.

Selenoproteins are a unique group of proteins that contain selenium in the form of selenocysteine (Sec) co-translationally inserted in response to a UGA codon with the help of cis- and trans-acting factors. Mammalian selenoproteins contain single Sec residues, with the exception of selenoprotein P (SelP) that has 7-15 Sec residues depending on species. Assessing an individual's selenium status is important under various pathological conditions, which requires a reliable selenium biomarker. Due to a key role in organismal selenium homeostasis, high Sec content, regulation by dietary selenium, and availability of robust assays in human plasma, SelP has emerged as a major biomarker of selenium status. Here, we found that Cys is present in various Sec positions in human SelP. Treatment of cells expressing SelP with thiophosphate, an analog of the selenium donor for Sec synthesis, led to a nearly complete replacement of Sec with Cys, whereas supplementation of cells with selenium supported Sec insertion. SelP isolated directly from human plasma had up to 8% Cys inserted in place of Sec, depending on the Sec position. These findings suggest that a change in selenium status may be reflected in both SelP concentration and its Sec content, and that availability of the SelP-derived selenium for selenoprotein synthesis may be overestimated under conditions of low selenium status due to replacement of Sec with Cys.

New Metabolites from a Marine Sediment-Derived Fungus, Aspergillus carneus.

A new polyketide 1 and a new decaline derivative 2 were isolated from a sediment-derived fungus Aspergillus carneus Blochwitz, together with one known bisabolane sesquiterpenoid and seven known polyketide metabolites. The structures of the isolated compounds were established by HR-MS, and 1D and 2D NMR spectroscopy. The cytotoxic and antiradical activities of the isolated compounds were evaluated.

Rapid determination of total polyphenolic content in tea samples based on caffeic acid voltammetric behaviour on a disposable graphite electrode.

The present paper describes the voltammetric behaviour and the quantitative determination of caffeic acid (CA) on a disposable pencil graphite electrode (PGE). The anodic peak current of CA recorded by differential pulse voltammetry (DPV) varies linearly with CA concentration in the range 1×10(-7)-3×10(-3) M. The detection and quantification limits were 8.83×10(-8) M and 2.94×10(-7) M caffeic acid, respectively. The mean recoveries of CA from Turkish green, white and black teas were 98.30%, 99.57% and 91.46%. For these three tea types the corresponding total polyphenolic contents (TPCs) evaluated by DPV on PGE were 35.81, 34.59 and 31.21 mg caffeic acid equivalent/g tea, respectively. These TPC values were in good accordance with those obtained by the Folin-Ciocalteu method. The developed DPV on PGE method constitutes a simple and inexpensive tool for the rapid assessment of TPC of tea samples.

Paciente con notalgia parestésica y siringomielia: ¿relación o coincidencia? / A patient with notalgia paresthetica and syringomyelia: association or coincidence?

La notalgia parestésica (NP) es una neuropatía sensitiva comúnmente manifestada con prurito y aparición de una mácula hiperpigmentada a nivel del raquis dorsal en la mayoría de los casos. La fisiopatología de la NP es aún desconocida, aunque se considera su origen, por distintas causas, en una lesión producida en los nervios espinales. No existe un tratamiento definitivo para este desorden aunque son muchas las alternativas terapéuticas descritas. Presentamos el caso clínico de una paciente diagnosticada de NP y tratada satisfactoriamente con capsaicina, en quien encontramos una posible asociación etiológica con una siringomielia subclínica evidenciada en el estudio por resonancia magnética. Aunque teóricamente posible, no hemos encontrado otros artículos que asocien dichos cuadros (AU)

Notalgia paresthetica (NP) is a sensory neuropathy commonly manifested by pruritus and the appearance of a hyperpigmented macula, usually in the thoracic spine. The physiopathology of NP is unknown, although, for different reasons, its origin is considered to be an injury to the spinal nerves. There is no definitive treatment for this disorder, although many therapeutic alternatives have been used. We report the case of a patient diagnosed with notalgia paresthetica and successfully treated with capsaicin. In this patient, we found a possible etiological association with subclinical syringomyelia revealed by magnetic resonance imaging. Although this association is theoretically possible, we have found no other reports of an association between these two disorders (AU)

Inhibition of cellular methyltransferases promotes endothelial cell activation by suppressing glutathione peroxidase 1 protein expression.

S-adenosylhomocysteine (SAH) is a negative regulator of most methyltransferases and the precursor for the cardiovascular risk factor homocysteine. We have previously identified a link between the homocysteine-induced suppression of the selenoprotein glutathione peroxidase 1 (GPx-1) and endothelial dysfunction. Here we demonstrate a specific mechanism by which hypomethylation, promoted by the accumulation of the homocysteine precursor SAH, suppresses GPx-1 expression and leads to inflammatory activation of endothelial cells. The expression of GPx-1 and a subset of other selenoproteins is dependent on the methylation of the tRNA(Sec) to the Um34 form. The formation of methylated tRNA(Sec) facilitates translational incorporation of selenocysteine at a UGA codon. Our findings demonstrate that SAH accumulation in endothelial cells suppresses the expression of GPx-1 to promote oxidative stress. Hypomethylation stress, caused by SAH accumulation, inhibits the formation of the methylated isoform of the tRNA(Sec) and reduces GPx-1 expression. In contrast, under these conditions, the expression and activity of thioredoxin reductase 1, another selenoprotein, is increased. Furthermore, SAH-induced oxidative stress creates a proinflammatory activation of endothelial cells characterized by up-regulation of adhesion molecules and an augmented capacity to bind leukocytes. Taken together, these data suggest that SAH accumulation in endothelial cells can induce tRNA(Sec) hypomethylation, which alters the expression of selenoproteins such as GPx-1 to contribute to a proatherogenic endothelial phenotype.

Tonotopic morphometry of the lamina reticularis of the guinea pig cochlea with associated microstructures and related mechanical implications.

Morphometry of the lamina reticularis of the guinea pig cochlea was performed using scanning electron microscopy. Seventy-four geometrical parameters of the lamina reticularis, the bundles of stereocilia, and individual stereocilia, in all rows of hair cells and within the individual hair cells, were measured at ten equally spaced locations along the longitudinal direction of the cochlea. Variations of the parameters versus the longitudinal coordinate were statistically analyzed and fitted with polynomials (constant, linear, or quadratic). Our data show that a unique set of geometrical parameters of inner and outer hair cells is typical for every frequency-dependent position at the lamina reticularis. Morphology of the outer hair cell structures varies more than respective parameters of the inner hair cells. Mechanical modeling using the obtained geometrical parameters provides a novel glance at the mechanical characteristics with respect to the cochlear tonotopy.

Proteome-wide analysis reveals clues of complementary interactions between mRNAs and their cognate proteins as the physicochemical foundation of the genetic code.

Despite more than 50 years of effort, the origin of the genetic code remains enigmatic. Among different theories, the stereochemical hypothesis suggests that the code evolved as a consequence of direct interactions between amino acids and appropriate bases. If indeed true, such physicochemical foundation of the mRNA/protein relationship could also potentially lead to novel principles of protein-mRNA interactions in general. Inspired by this promise, we have recently explored the connection between the physicochemical properties of mRNAs and their cognate proteins at the proteome level. Using experimentally and computationally derived measures of solubility of amino acids in aqueous solutions of pyrimidine analogs together with knowledge-based interaction preferences of amino acids for different nucleobases, we have revealed a statistically significant matching between the composition of mRNA coding sequences and the base-binding preferences of their cognate protein sequences. Our findings provide strong support for the stereochemical hypothesis of genetic code's origin and suggest the possibility of direct complementary interactions between mRNAs and cognate proteins even in present-day cells.

Evidence of direct complementary interactions between messenger RNAs and their cognate proteins.

Recently, the ability to interact with messenger RNA (mRNA) has been reported for a number of known RNA-binding proteins, but surprisingly also for different proteins without recognizable RNA binding domains including several transcription factors and metabolic enzymes. Moreover, direct binding to cognate mRNAs has been detected for multiple proteins, thus creating a strong impetus to search for functional significance and basic physico-chemical principles behind such interactions. Here, we derive interaction preferences between amino acids and RNA bases by analyzing binding interfaces in the known 3D structures of protein-RNA complexes. By applying this tool to human proteome, we reveal statistically significant matching between the composition of mRNA sequences and base-binding preferences of protein sequences they code for. For example, purine density profiles of mRNA sequences mirror guanine affinity profiles of cognate protein sequences with quantitative accuracy (median Pearson correlation coefficient R = -0.80 across the entire human proteome). Notably, statistically significant anti-matching is seen only in the case of adenine. Our results provide strong evidence for the stereo-chemical foundation of the genetic code and suggest that mRNAs and cognate proteins may in general be directly complementary to each other and associate, especially if unstructured.

The central role of selenium in the biochemistry and ecology of the harmful pelagophyte, Aureococcus anophagefferens.

The trace element selenium (Se) is required for the biosynthesis of selenocysteine (Sec), the 21st amino acid in the genetic code, but its role in the ecology of harmful algal blooms (HABs) is unknown. Here, we examined the role of Se in the biology and ecology of the harmful pelagophyte, Aureococcus anophagefferens, through cell culture, genomic analyses, and ecosystem studies. This organism has the largest and the most diverse selenoproteome identified to date that consists of at least 59 selenoproteins, including known eukaryotic selenoproteins, selenoproteins previously only detected in bacteria, and novel selenoproteins. The A. anophagefferens selenoproteome was dominated by the thioredoxin fold proteins and oxidoreductase functions were assigned to the majority of detected selenoproteins. Insertion of Sec in these proteins was supported by a unique Sec insertion sequence. Se was required for the growth of A. anophagefferens as cultures grew maximally at nanomolar Se concentrations. In a coastal ecosystem, dissolved Se concentrations were elevated before and after A. anophagefferens blooms, but were reduced by >95% during the peak of blooms to 0.05 nM. Consistent with this pattern, enrichment of seawater with selenite before and after a bloom did not affect the growth of A. anophagefferens, but enrichment during the peak of the bloom significantly increased population growth rates. These findings demonstrate that Se inventories, which can be anthropogenically enriched, can support proliferation of HABs, such as A. anophagefferens through its synthesis of a large arsenal of Se-dependent oxidoreductases that fine-tune cellular redox homeostasis.

Contrasting roles of dietary selenium and selenoproteins in chemically induced hepatocarcinogenesis.

Selenium (Se) has long been known for its cancer prevention properties, but the molecular basis remains unclear. The principal questions in assessing the effect of dietary Se in cancer are whether selenoproteins, small molecule selenocompounds, or both, are involved, and under which conditions and genotypes Se may be protective. In this study, we examined diethylnitrosamine-induced hepatocarcinogenesis in mice lacking a subset of selenoproteins due to expression of a mutant selenocysteine tRNA gene (Trsp (A37G) mice). To uncouple the effects of selenocompounds and selenoproteins, these animals were examined at several levels of dietary Se. Our analysis revealed that tumorigenesis in Trsp (A37G) mice maintained on the adequate Se diet was increased. However, in the control, wild-type mice, both Se deficiency and high Se levels protected against tumorigenesis. We further found that the Se-deficient diet induced severe neurological phenotypes in Trsp A37G mice. Surprisingly, a similar phenotype could be induced in these mice at high dietary Se intake. Overall, our results show a complex role of Se in chemically induced hepatocarcinogenesis, which involves interaction among selenoproteins, selenocompounds and toxins, and depends on genotype and background of the animals.