Vibrational analysis and spectra of orotic acid

The IR and Raman spectra of polycrystalline anhydrous orotic acid and its N1, N3, and O12 trideuterated isotopomer are recorded in the 4000-40 cm(-1) spectral interval as part of a series of vibrational analyses of nucleosides, nucleotides, and related compounds carried out in our laboratory. The frequencies of the fundamental transitions and the potential energy distributions of the 39 normal modes of orotic acid and its isotopomer are calculated by an ab initio density functional theory Becke3P86/6-311G** treatment. Assignments of the vibrational modes are proposed that consider the results of these calculations and the observed spectra. The results of the ab initio treatment are related to crystallographic and spectral data, and they are compared with previous assignments for similar molecules.     

Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase

The Escherichia coli inducible lysine decarboxylase, LdcI/CadA, together with the inner-membrane lysine-cadaverine antiporter, CadB, provide cells with protection against mild acidic conditions (pH～5). To gain a better understanding of the molecular processes underlying the acid stress response, the X-ray crystal structure of LdcI was determined. The structure revealed that the protein is an oligomer of five dimers that associate to form a decamer. Surprisingly, LdcI was found to co-crystallize with the stringent response effector molecule ppGpp, also known as the alarmone, with 10 ppGpp molecules in the decamer. ppGpp is known to mediate the stringent response, which occurs in response to nutrient deprivation. The alarmone strongly inhibited LdcI enzymatic activity. This inhibition is important for modulating the consumption of lysine in cells during acid stress under nutrient limiting conditions. Hence, our data provide direct evidence for a link between the bacterial acid stress and stringent responses.     

Determination of dipicolinic acid in bacterial spores by derivative spectroscopy

Dipicolinic acid was extracted from approximately 0.1 mg spores or 0.5 ml of sporulating culture with 20 mM HCl for 10 min at 100 degrees C. The suspension was diluted with 5 mM Ca2+, 100 mM Tris, pH 7.6, centrifuged, and the first derivative of the uv absorbance spectrum recorded from 275 nm to 285 nm. DPA concentration was determined from the difference between the maximum at 276.6 nm and the minimum at 280 nm. The use of the difference between two first derivative values removed possible interference from sloping baselines. Turbidity, nucleic acids, and bacteriological media did not interfere. Analysis time for four extracts was 4 min using a spectrophotometer reading at 0.1-nm intervals. Dipicolinate at 0.1 mM gave 0.184 absorbance/nm at 25 degrees C. The coefficient of variation was 1.5%, and the detection limit 1 microM.     

Blood plasma resonance Raman spectroscopy combined with multivariate analysis for esophageal cancer detection

We herein report a novel, reliable and inexpensive method for detecting esophageal cancer using blood plasma resonance Raman spectroscopy combined with multivariate analysis methods. The blood plasma samples were divided into late stage cancer group (n = 164), early stage cancer group (n = 35) and normal group (n = 135) based on clinical pathological diagnosis. Using a specially designed quartz capillary tube as sample holder, we obtained higher quality resonance Raman spectra of blood plasma than existing method. The study demonstrated that the carotenoids levels in blood plasma were reduced in esophageal cancer patients. The area under the receiver operating characteristic curve (and 95% confidence interval) calculated by wavenumber selection and principal component analysis combined with linear discriminant analysis (PC-LDA) algorithm were 0.894 (0.858-0.929), 0.901 (0.841-0.960) and 0.871 (0.799-0.942) for differentiating late cancer from normal, late cancer from early cancer, and early cancer from normal respectively. The contribution from the two carotenoids wavenumber regions of 1155 and 1515 cm⁻¹ were more than 84.2%. The results show that the plasma carotenoids could be a potential biomarker for screening esophageal cancer using resonance Raman spectroscopy combined with wavenumber selection and PC-LDA algorithms.      

Vibrational spectroscopy of biopolymers under mechanical stress: processing cellulose spectra using bandshift difference integrals

Mechanical stretching of covalent bonds, for example when a fibrous polymer is loaded in tension, results in their stretching vibrational bands in the infrared or Raman spectrum being shifted to lower frequency. Conversely stretching a hydrogen bond shifts the stretching vibrational mode of the donor covalent X-H bond to higher frequency. These band shifts are small and difficult to detect in complex regions of the spectrum where differently affected bands overlap. This paper describes a method of integrating the difference spectra (spectrum under tensile strain minus spectrum at zero tensile strain) to recover the shape of the bands that are shifted and the spectral variation in bandshift. The application of this method to two sets of vibrational spectra of cellulose under tension is described. In one example, C-O-C stretching bands of highly crystalline tunicate cellulose were observed to shift to lower frequency under axial strain. In the other example, a group of overlapping O-D stretching bands in partially deuterated cellulose showed varied bandshifts under axial strain, some bandshifts being positive as expected due to extension of axially oriented hydrogen bonds while others were negative. The possibility of constructing spectral plots of bandshift has the potential to clarify the interpretation of overlapped, shifting bands in the vibrational spectra of polymers under tension.     

Physiological responses of Daphnia pulex to acid stress

Background  

Acidity exerts a determining influence on the composition and diversity of freshwater faunas. While the physiological implications of freshwater acidification have been intensively studied in teleost fish and crayfish, much less is known about the acid-stress physiology of ecologically important groups such as cladoceran zooplankton. This study analyzed the extracellular acid-base state and CO₂ partial pressure (P _CO2), circulation and ventilation, as well as the respiration rate of Daphnia pulex acclimated to acidic (pH 5.5 and 6.0) and circumneutral (pH 7.8) conditions.     

Microarray analysis of bacterial gene expression: towards the regulome

Microarray technology allows co-regulated genes to be identified. In order to identify genes that are controlled by specific regulators, gene expression can be compared in mutant and wild-type bacteria. However, there are a number of pitfalls with this approach; in particular, the regulator may not be active under the conditions in which the wild-type strain is cultured. Once co-regulated genes have been identified, proteinbinding motifs can be identified. By combining these data with a map of promoters, or operons (the operome), the regulatory networks in the cell (the regulome) can start to be built up.     

Jasmonic acid interacts with abscisic acid to regulate plant responses to water stress conditions

Phytohormones are key players in signaling environmental stress conditions. Hormone profiling together with proline accumulation were studied in leaves and roots of different mutant lines of Arabidopsis. Regulation of proline accumulation in this system seems complex and JA-deficient (jar1-1) and JA-insensitive (jai1) lines accumulating high levels of proline despite their very low ABA levels seems to discard an ABA-dependent response. However, the pattern of proline accumulation in jai1 seedlings parallels that of ABA. Under stress conditions, there is an opposite pattern of ABA accumulation in roots of jar1-1/coi1-16 (in which ABA only slightly increase) and jai1 (in which ABA increase is even higher than in WT plants). This also makes JA-ABA crosstalk complex and discards any lineal pathway that could explain this hormonal interaction.