Bringing Machine-Learning Enhanced Quantum Chemistry and Microwave Spectroscopy to Conformational Landscape Exploration: the Paradigmatic Case of 4-Fluoro-Threonine

A combined experimental and theoretical study has been carried out on 4-fluoro-threonine, the only naturally occurring fluorinated amino acid. Fluorination of the methyl group significantly increases the conformational complexity with respect to the parent amino acid threonine. The conformational landscape has been characterized in great detail, with special attention given to the inter-conversion pathways between different conformers. This led to the identification of 13 stable low-energy minima. The equilibrium population of so many conformers produces a very complicated and congested rotational spectrum that could be assigned through a strategy that combines several levels of quantum chemical calculations with the principles of machine learning. Twelve conformers out of 13 could be experimentally characterized. The results obtained from the analysis of the intra-molecular interactions can be exploited to accurately model fluorine-substitution effects in biomolecules.

Unveiling the Shape of N-Acetylgalactosamine: A Cancer-Associated Sugar Derivative

In the present work, we report the first rotational study of N-acetylgalactosamine, a cancer-associated sugar derivative, by means of high-resolution rotational spectroscopy. Two different conformers have been conclusively characterized using broadband Fourier transform microwave spectroscopy coupled with a laser ablation vaporization system. Additionally, we performed a comprehensive analysis of the intramolecular interactions that govern these structures, which allowed us to both characterize the existence of intramolecular hydrogen bond networks that drive the intrinsic conformation panorama of N-acetylgalactosamine and further rationalize the biological role of this aminosugar derivative as part of the Tn antigen.

Rotational spectroscopic study and astronomical search for propiolamide in Sgr B2(N)

CONTEXT

For all the amides detected in the interstellar medium (ISM), the corresponding nitriles or isonitriles have also been detected in the ISM, some of which have relatively high abundances. Among the abundant nitriles for which the corresponding amide has not yet been detected is cyanoacetylene (HCCCN), whose amide counterpart is propiolamide (HCCC(O)NH2).

AIMS

With the aim of supporting searches for this amide in the ISM, we provide a complete rotational study of propiolamide from 6 GHz to 440 GHz.

METHODS

Time-domain Fourier transform microwave (FTMW) spectroscopy under supersonic expansion conditions between 6 GHz and 18 GHz was used to accurately measure and analyze ground-state rotational transitions with resolved hyperfine structure arising from nuclear quadrupole coupling interactions of the 14N nucleus. We combined this technique with the frequency-domain room-temperature millimeter wave and submillimeter wave spectroscopies from 75 GHz to 440 GHz in order to record and assign the rotational spectra in the ground state and in the low-lying excited vibrational states. We used the ReMoCA spectral line survey performed with the Atacama Large Millimeter/submillimeter Array toward the star-forming region Sgr B2(N) to search for propiolamide.

RESULTS

We identified and measured more than 5500 distinct frequency lines of propiolamide in the laboratory. These lines were fitted using an effective semi-rigid rotor Hamiltonian with nuclear quadrupole coupling interactions taken into consideration. We obtained accurate sets of spectroscopic parameters for the ground state and the three low-lying excited vibrational states. We report the nondetection of propiolamide toward the hot cores Sgr B2(N1S) and Sgr B2(N2). We find that propiolamide is at least 50 and 13 times less abundant than acetamide in Sgr B2(N1S) and Sgr B2(N2), respectively, indicating that the abundance difference between both amides is more pronounced by at least a factor of 8 and 2, respectively, than for their corresponding nitriles.

CONCLUSIONS

Although propiolamide has yet to be included in astrochemical modeling networks, the observed upper limit to the ratio of propiolamide to acetamide seems consistent with the ratios of related species as determined from past simulations. The comprehensive spectroscopic data presented in this paper will aid future astronomical searches.

A rotational study of the AlaAla dipeptide

Herein, we present the first rotational study of the AlaAla dipeptide, brought into the gas phase by laser ablation. Two different structures have been unveiled in the isolated environment of a supersonic expansion by Fourier transform microwave spectroscopy. These structures have been identified through their rotational and 14N quadrupole coupling constants. The flexibility of the -NH2 and -COOH ends allows the formation of strong intramolecular interactions giving rise to five- and seven-membered ring configurations.

Interstellar glycolamide: A comprehensive rotational study and an astronomical search in Sgr B2(N)

CONTEXT

Glycolamide is a glycine isomer and also one of the simplest derivatives of acetamide (e.g., one hydrogen atom is replaced with a hydroxyl group), which is a known interstellar molecule.

AIMS

In this context, the aim of our work is to provide direct experimental frequencies of the ground vibrational state of glycolamide in the centimeter-, millimeter- and submillimeter-wavelength regions in order to enable its identification in the interstellar medium.

METHODS

We employed a battery of state-of-the-art rotational spectroscopic techniques in the frequency and time domain to measure the frequencies of glycolamide. We used the spectral line survey named Exploring Molecular Complexity with ALMA (EMoCA), which was performed toward the star forming region Sgr B2(N) with ALMA to search for glycolamide in space. We also searched for glycolamide toward Sgr B2(N) with the Effelsberg radio telescope. The astronomical spectra were analyzed under the local thermodynamic equilibrium approximation. We used the gas-grain chemical kinetics model MAGICKAL to interpret the results of the astronomical observations.

RESULTS

About 1500 transitions have been newly assigned up to 460 GHz to the most stable conformer, and a precise set of spectroscopic constants was determined. Spectral features of glycolamide were then searched for in the prominent hot molecular core Sgr B2(N2). We report the nondetection of glycolamide toward this source with an abundance at least six and five times lower than that of acetamide and glycolaldehyde, respectively. Our astrochemical model suggests that glycolamide may be present in this source at a level just below the upper limit, which was derived from the EMoCA survey. We could also not detect the molecule in the region's extended molecular envelope, which was probed with the Effelsberg telescope. We find an upper limit to its column density that is similar to the column densities obtained earlier for acetamide and glycolaldehyde with the Green Bank Telescope.

Gas-Phase Conformational Map of the Amino Acid Isovaline

Four conformers of the non-proteinogenic α-amino acid isovaline, vaporized by laser ablation, are characterized by Fourier-transform microwave techniques in a supersonic expansion. The comparison between the experimental rotational and ¹⁴ N nuclear quadrupole coupling constants and the ab initio calculated ones provides conclusive evidence for the identification of the conformers. The most stable species is stabilized by an N-H⋅⋅⋅O =C intramolecular hydrogen bond and a cis-COOH interaction, whereas the higher-energy conformers exhibit an N⋅⋅⋅H-O intramolecular hydrogen bond and trans-COOH, as in other aliphatic amino acids. The spectroscopic data herein reported can be used for the astrophysical purpose in a possible detection of isovaline in space.

Elucidating the multiple structures of pipecolic acid by rotational spectroscopy

The complex conformational space of the non-proteinogenic cyclic amino acid pipecolic acid has been explored in the gas phase for the first time. Solid pipecolic acid samples were vaporized by laser ablation and expanded in a supersonic jet where the rotational spectral signatures owing to nine different conformers were observed by Fourier transform microwave spectroscopy. All species were identified by comparison of the experimental rotational and nuclear quadrupole coupling constants with those predicted theoretically. Observation of type-III conformers, leading to a difference when compared against the conformational behavior of the analog amino acid proline, has been interpreted by an increment in steric hindrance when increasing the number of carbons present in the ring.

The effect of N-methylation on the conformational landscape of alanine: the case of N-methyl-l-alanine

The non-proteinogenic amino acid N-methyl-l-alanine has been brought into the gas phase using laser ablation techniques and studied by high resolution chirped pulse and molecular-beam Fourier transform microwave spectroscopies coupled to supersonic expansion. Four conformers showing the three types of hydrogen bond interactions I (NHO[double bond, length as m-dash]C), II (OHN) and III (N-HO-H) have been unambiguously identified, based on the comparison of the experimental rotational and 14N nuclear quadrupole constants with the calculated ab initio values. The observation of a type III conformer evidences the role of methyl groups in both sides to impose the steric hindrance, precluding the relaxation from type III to type I conformers and explains the responsibility for the unique conformational landscape observed in the case of NMA.

Laboratory rotational spectrum and astronomical search for methoxyacetaldehyde

CONTEXT

Methoxyacetaldehyde belongs to a group of structural isomers with the general formula C3H6O2, of which methyl acetate and ethyl formate are known interstellar molecules. Rotational data available for methoxyacetaldehyde are limited to 40 GHz, which makes predictions at higher frequencies rather uncertain.

AIMS

The aim of this work is to provide accurate experimental frequencies of methoxyacetaldehyde in the millimeter-wave region to support its detection in the interstellar medium.

METHODS

The rotational spectrum of methoxyacetaldehyde was recorded at room-temperature from 75 to 120 GHz and from 170 to 310 GHz using the millimeter-wave spectrometer in Valladolid. Additional measurements were also performed at conditions of supersonic expansion from 6 to 18 GHz. The assigned rotational transitions were analyzed using the S -reduced semirigid-rotor Hamiltonian.

RESULTS

We newly assigned over 1000 lines for the most stable conformer of methoxyacetaldehyde in its ground state and five lowest excited vibrational states, and precise sets of spectroscopic constants were obtained. We searched for spectral features of methoxyacetaldehyde in the high-mass star-forming regions Orion KL and Sagittarius B2, as well as in the cold dark cloud Barnard 1 (B1-b). No lines belonging to methoxyacetaldehyde were detected above the detection limit of our data. We provide upper limits to the methoxyacetaldehyde colum density in these sources.

The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH2

The steric effects imposed by the isopropyl group of valine in the conformational stabilization of the capped dipeptide N-acetyl-l-valinamide (Ac-Val-NH₂) have been studied by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy.

Psychosine variants as antigens for natural killer T cells

Natural killer T (NKT) cells play a central role in the interface between innate and adaptive immunity, and alpha-galactosylceramide was recently shown to be an endogenous antigen for these cells. The source of alpha-galactosylceramide has not yet been determined; however, in vivo degradation of alpha-galactosylceramide involves generation of alpha-psychosine (alpha-galactosylsphingosine). Alpha-psychosine stimulates cytokine release from NKT cells and constitutes an endogenous antigen for these cells. Alpha-psychosine contains a single lipid chain, while most antigens for NKT cells have two lipid chains, and we have investigated if other glycolipids with one lipid chain, derived from know antigens for NKT cells, stimulate cytokine release from NKT cells. Only psychosine variants derived from the most potent NKT cell antigens cause stimulation, and this stimulation occurs in vitro as well as in vivo. Truncated forms of weak antigens for NKT cells are not stimulatory.

Noradrenaline transporter and its turnover rate are decreased in blood lymphocytes of patients with major depression

Lymphocytes possess transporters of serotonin and dopamine, and also contain monoamines. The objective of this work was to determine the presence of noradrenaline transporters, the turnover rate of noradrenaline and serotonin in lymphocytes of major depression patients, and to correlate the biochemical parameters with the severity of the disorder. Lymphocytes from peripheral blood were isolated by Ficoll/Hypaque, and noradrenaline transporter was studied by binding of [3H]nisoxetine: control group (29, age 31.52+/-1.08, 7 men) and major depression patients (35, age 36.68+/-1.69, 6 men), Hospital Vargas de Caracas. Diagnostic was done by criteria of the American Psychiatric Association and severity by Hamilton Scale for Depression. Levels of noradrenaline, serotonin, 3-methoxy-4-hydroxyphenylglycol and 5-hydroxyindoleacetic acid were determined by HPLC. Turnover rate was evaluated by the ratios of monoamines and metabolites. Correlations were done between the biochemical parameters and the severity of depression. The score of Hamilton for Depression was 22.77+/-0.51. There was a reduction in the number of transporters in lymphocytes of patients, 0.95+/-0.27 versus 4.06+/-1.67 fmol/10(6) cells. Levels of monoamines and metabolites did not significantly differ between patients and controls. However, there was a higher monoamine/metabolite ratio in lymphocytes of patients, indicating a reduction of metabolic turnover rate. Also there was a relative greater concentration of noradrenaline than serotonin in the lymphocytes of the patients, as indicated by the ratio noradrenaline/serotonin. Noradrenergic and serotonergic turnover is decreased in blood peripheral lymphocytes of major depression patients; the reduction in noradrenaline transporter could be related to changes in intracellular levels, and these modifications could result in functional changes of the immune system.

Allelic isoforms and decrease in serotonin transporter mRNA in lymphocytes of patients with major depression

Serotonin transporter, measured by the specific binding of [(3)H]paroxetine, has been reported to be reduced in circulating lymphocytes of patients with major depression. Due to this observation, the objective of the present report was to determine the levels of serotonin transporter mRNA in lymphocytes obtained from 29 major depression patients (4 men, age 33.10+/-1.63 years) and from 30 subjects included as a control group (4 men, age 37.54+/-2.18 years) using RT-PCR. The patients were diagnosed according to the criteria of the American Psychiatric Association, and had a severity of depression of 32.68+/-1.55 determined by the Hamilton Rating Scale for Depression. The DNA was submitted to polymerase chain reaction with primers for the 5' regulatory region of human serotonin transporter, which could show the long and the short allelic forms of the transporter gene for the 5 HTTLPR polymorphism. Semiquantitative analysis was performed using beta-actin as internal and external standard. Control subjects presented the two allelic forms in 9.09% and depressed patients in 8.69%. The long variant was present in 73% of controls and in 60% of patients, without significant differences. There was a significant reduction in mRNA in depressed patients expressing the long allele. The number of immunofluorescent lymphocytes, labeled with a specific antibody against serotonin transporter, was reduced in the patients, as well as CD3+ lymphocytes. Serotonin and 5-hydroxyindoleacetic acid in platelet-poor plasma or lymphocytes did not differ between depressed patients and controls. The reduction in lymphocyte serotonin transporter described in major depression might be due to a decrease in the level of its mRNA and in the number of cells expressing it. These observations might implicate that functional modifications are associated with nervous-immune interactions in depression.

In vitro susceptibility of 137 Candida sp. isolates from HIV positive patients to several antifungal drugs

Oropharyngeal candidiasis caused by various species of Candida is one of the most common infections in HIV seropositive or AIDS patients. Drug resistance among these yeasts is an increasing problem. We studied the frequency of resistance profile to fluconazole, itraconazole, ketoconazole, amphotericin B and terbinafine of 137 isolates of Candida sp. From HIV positive or AIDS patients with oropharyngeal candidiasis at Instituto de Inmunología, U.C.V. and the Hospital "Jose Ignacio Baldó", Caracas Venezuela, using the well diffusion susceptibility test (Magaldi et al.). We found that nearly 10% of C. albicans isolates were primarily fluconazole resistant, 45% of C. albicans isolates from patients with previous treatment were resistant to fluconazole, of which 93% showed cross-resistance to itraconazole, and even about 30% of C. tropicalis (n = 13) were resistant to fluconazole and/or itraconazole. To this respect, several recent reports have been described antifungal cross-resistance among azoles. Therefore, we consider that C. tropicalis should be added to the growing list of yeast in which antifungal drug resistance is common. This report could be useful for therapeutic aspect in AIDS patients with oral candidiasis.

Encephalitis caused directly by Mycoplasma pneumoniae

A case of non-fatal encephalitis in a 21-y-old immunocompetent woman is described. High titre serum antibodies against Mycoplasma pneumoniae were found. In addition, Mycoplasma pneumoniae DNA was detected in the cerebrospinal fluid by polymerase chain reaction. Neuroimaging findings by magnetic resonance and computed tomographic scanning of the brain, and laboratory investigations, including a search for serum antibodies to gangliosides, did not support an immune-mediated mechanism. No other pathogens were found. These results strongly suggest that the encephalitis was caused directly by Mycoplasma pneumoniae invasion of the central nervous system. They also indicate that such pathogenetic mechanism may sometimes be sufficient to explain neurological manifestations occurring during the course of Mycoplasma pneumoniae infection. The consequences for therapy are discussed.

Fluoxetine versus amitriptyline in the treatment of major depression with associated anxiety (anxious depression): a double-blind comparison

Although common in clinical settings, major depressive disorder with associated anxious symptoms ('anxious depression') has not been well studied in antidepressant clinical trials. The aim of this study was to compare the effects of fluoxetine versus amitriptyline in this group of patients. After a single-blind placebo run-in period of 2 weeks, patients were treated on a double-blind basis with fluoxetine or amitriptyline for 8 weeks. Assessment instruments included: 21-item Hamilton Rating Scale for Depression, Hamilton Rating Scale for Anxiety, Clinical Global Impressions, Raskin Depression Scale and Covi Anxiety Scale. A total of 157 patients were randomized to either fluoxetine or amitriptyline. Fluoxetine was given at a fixed dose of 20 mg/day and amitriptyline was given in a range of 50-250 mg/day (mean of 138.1 mg/day). Fluoxetine was comparable to amitriptyline in all efficacy measures except the HAMD sleep factor. Unwanted effects were more frequent and more severe in the amitriptyline-treated patients. Fluoxetine was comparably efficacious to amitriptyline in the treatment of major depression with associated anxiety. Since fluoxetine was far better tolerated, it is a promising alternative for this frequent and disabling condition.

Comprehensive radiographic evaluation of diffuse idiopathic skeletal hyperostosis: development and interrater reliability of a scoring system

OBJECTIVE

To develop a scoring system for radiographic findings in diffuse idiopathic skeletal hyperostosis (DISH) and to test interrater reliability.

MATERIALS AND METHODS

Fifty-five DISH patients and 35 spondylosis patients underwent two views (anteroposterior and lateral) of the cervical, thoracic, and lumbar spine, lateral views of both ankles, knees, and elbows, and anteroposterior views of the pelvis and shoulders. Two raters reviewed and scored the x-rays. Interrater reliability was assessed with the alpha statistic (alpha) for categorical variables and with the intraclass correlation coefficient (ICC) for continuous variables.

RESULTS

The agreement was similar for the three spinal segments (alpha = 0.44 to 0.71). The lower extremity agreement ranged from 0.28 to 0.76, with higher agreement at the knee (alpha > or = 0.46) and the ankle (alpha > or = 0.56) than at the pelvis (ICC < or = 0.58). The agreement at the shoulders and elbows ranged from 0.50 to 0.75. The agreement between the readers was higher with summary measurements than with single (site-by-site) measurements: for each spinal segment, the ICC was 0.83 or greater; for the lower extremity, the ICC = 0.79; and for the upper extremity, the ICC = 0.68.

CONCLUSION

We have described a comprehensive scoring system to assess the spinal and peripheral involvement of DISH.

A controlled study of diffuse idiopathic skeletal hyperostosis. Clinical features and functional status

Diffuse idiopathic skeletal hyperostosis (DISH) is a common but little-studied disorder in the elderly that is infrequently recognized by physicians. Its prevalence in adults over 40 years of age is estimated at 3.8% for men and 2.6% for women. The present case-control study evaluated the history of pain and stiffness, radicular pain and enthesitis, physical findings on the musculoskeletal examination, and level of physical and psychologic disability in 130 persons: 56 patients with DISH, 43 control patients with spondylosis of the lumbar spine, and 31 healthy control patients. DISH patients were more likely to report a past history of upper extremity pain, medial epicondylitis of the elbow, enthesitis of the patella or heel, or dysphagia than spondylosis patients. They had more extremity and spinal stiffness and pain than healthy controls. DISH patients weighed more at a young age and their body mass index was greater at the time of the clinical evaluation than either spondylosis or healthy control patients. On musculoskeletal examination, DISH patients had a greater reduction in neck rotation and thoracic movements than either spondylosis patients or healthy controls, and had a greater reduction in lumbar movement than healthy controls. DISH patients had similar levels of spinal disability and physical disability overall, as measured by standardized indices, as spondylosis patients. No differences were found among the 3 groups of patients for the laboratory tests evaluated. DISH is clearly a distinct disorder with signs and symptoms that distinguish it from other causes of spinal complaint and from healthy individuals. It has the potential to cause major disability. Future studies need to address the natural history of DISH, pursue pathogenic mechanisms, and evaluate treatment modalities.

Qualitative bacteriology and leg ulcer healing

This study investigated the bacterial profile of leg ulcers in 52 patients attending the Fremantle Hospital leg ulcer clinic. The aim was to identify whether the presence of specific bacterial groups delays healing, whether the bacterial flora changes as ulcers heal and, if so, whether these changes influence healing. The results show that the presence of any one specific bacterial group did not appear to delay healing, although the presence of four or more bacterial groups was associated with delayed healing. This was found to be statistically significant. It was noted that the bacterial flora does change as ulcers heal and that these changes were not related to changes in healing, with the exception of skin flora.

Absence of an association of rheumatoid arthritis and diffuse idiopathic skeletal hyperostosis: a case-control study

OBJECTIVE

To compare the frequency of diffuse idiopathic skeletal hyperostosis (DISH), based on an evaluation of chest radiographs, in 2 populations of patients: those with and without rheumatoid arthritis (RA).

METHODS

Cases of RA were obtained from the Wichita Arthritis Center databank and controls from a private cardiology practice. Patients with RA and controls had to be older than 50 years and have a chest radiograph available. All radiographs were read, in haphazard order, by a single reader who classified them as definitely DISH, probably DISH (these 2 categories were considered as having DISH), uncertain, probably not DISH, and definitely not DISH (these 3 groups defined the absence of DISH). Logistic regression was used to investigate the probability of DISH while controlling for age and sex. Analyses were conducted to take into account the sensitivity and specificity of chest radiographs for the diagnosis of DISH.

RESULTS

Among 748 radiographs (357 RA and 391 controls), 29 were diagnosed as DISH (21 controls and 8 RA). The mean age for the RA group was 66.2 yrs (SD = 11.9 and 108 (30.2%) were men. Control subjects had a mean age of 69.6 yrs (SD = 11.4 and 139 (35.4%) were men. The DISH patients, compared with those without DISH, were more likely to be male (p = 0.004) and older (p < 0.001). After accounting for age and sex, the relative risk of DISH in RA versus the controls was 0.40 (95% confidence interval: 0.20 to 1.01). After taking into account the sensitivity and specificity in this population, the adjusted prevalence of DISH for the RA group was 1% (95% confidence interval: 0.1 to 3.7) and 3.1% (95% confidence interval: 0.2 to 7.9) for the control group.

CONCLUSION

We confirmed the increase in frequency of DISH with increasing age and male sex, but failed to support an increased association of DISH with RA.

Chest radiographs as a screening test for diffuse idiopathic skeletal hyperostosis

OBJECTIVE

To evaluate the sensitivity, specificity, predictive value, interrater reliability and intrarater reliability of using chest radiographs as a screening tool for the diagnosis of diffuse idiopathic skeletal hyperostosis (DISH).

METHODS

After review of thoracic spine radiographs by 2 "gold standard" physicians, 45 patients with DISH meeting the criteria of Resnick and Niwayama were contrasted with 106 control patients consisting of 45 with thoracic spondylosis, 45 who lacked spondylosis and whose thoracic spine radiographs were otherwise normal for the age of the patient, and 16 with ankylosing spondylitis. The chest radiographs on the 151 subjects were placed in random order and read independently using an ordinal diagnostic certainty scale by 2 "test" radiologists, experienced in reading bone radiographs. Two months later the order of chest radiographs was rerandomized and the films reassessed by the same test radiologists.

RESULTS

The averages for the diagnostic and population test characteristics were sensitivity = 77%; specificity = 97%; positive predictive value = 91%; and, negative predictive value = 91%. The area under the receiver operating characteristic curves was 0.975 and 0.976 for the radiologists, and kappa was 0.93, demonstrating that interrater reliability was high. On rereading the chest radiographs, intrarater reliability was exceptional (weighted kappa of 0.90 and 0.96 for the two test radiologists). DISH patients whose chest radiographs were read as not demonstrating DISH had significantly less extensive disease.

CONCLUSIONS

We conclude that chest radiographs are a reliable and valid screening tool for the diagnosis of DISH.

Preservation of fungi in water (Castellani): 20 years

Five-hundred ninety-four strains of fungi were studied. They were found being preserved with Castellani's method with distilled water during 1 to 20 years. 62% of the strains (n=368) did grow when subcultured and maintained their main morphological features. 90% of the 20 years old strains of different species were viable. It is argued that the technique of introduction of the strains into the water and their optimal condition will determine survival. The Castellani's method is recommended as easy, cheap and satisfactory for preservation of most species of fungi.