Molecular interactions in bacterial cellulose composites studied by 1D FT-IR and dynamic 2D FT-IR spectroscopy

Specific strain-induced orientation and interactions in three Acetobacter cellulose composites: cellulose (C), cellulose/pectin (CP) and cellulose/xyloglucan (CXG) were characterized by FT-IR and dynamic 2D FT-IR spectroscopies. On the molecular level, the reorientation of the cellulose fibrils occurred in the direction of the applied mechanical strain. The cellulose-network reorientation depends on the composition of the matrix, including the water content, which lubricates the motion of macromolecules in the network. At the submolecular level, dynamic 2D FT-IR data suggested that there was no interaction between cellulose and pectin in CP and that they responded independently to a small amplitude strain, while in CXG, cellulose and xyloglucan were uniformly strained along the sample length.     

The alkaline,saline lakes of Uganda: a review

Most saline lakes in Uganda are alkaline and occur in closed basins associated with the Western Rift Valley. They are small shallow lakes exhibiting considerable temporal variation in volume and surface area. They have been categorized as maar lakes. Salinity in these lakes results from evaporative concentration of ions leached from their drainage basins. These lakes can be grouped into three broad categories: carbonate-chloride, sulphate-chloride, and chloride lakes according to the dominant anion(s). The relative amounts of ions in solution determines, in part, the limnochemical characteristics of the lakes. There is some evidence of thermal and chemical stratification in the deeper lakes. Records of the limnobiology in these lakes are scarce and not exhaustive.     

Production and Characterization of Protein Encapsulated Silver Nanoparticles by Marine Isolate Streptomyces parvulus SSNP11

Production of protein encapsulated silver nanoparticles (AgNPs) assisted by marine actinomycetes strain has been investigated. The selective isolate was identified as Streptomyces parvulus SSNP11 based on chemotaxonomic and 16S rRNA analysis. Maximum AgNPs production was observed within 24 h incubation time. The produced AgNPs are spherical in shape with monodispersive and crystalline in nature. The particle size distribution ranges from 1.66 to 11.68 nm with a mean size of 2.1 nm. The biosynthesized AgNPs revealed stretching vibrations of primary and secondary amines along with C–H and C–N, suggesting that metabolically produced proteins are involved in size regulation of reduced AgNPs. These particles possess an average negative zeta potential value of 81.5 mV with an electrophoretic mobility of 0.000628 cm²/Vs. The biosynthesized nanoparticles revealed antimicrobial property against gram negative as well as gram positive bacterial strains.     

EFFECT OF SILICATE LIMITATION ON VALVE MORPHOLOGY IN THALASSIOSIRA AND COSCINODISCUS (BACILLARIOPHYCEAE)1

Coscinodiscus radiatus Ehrenb. and Thalassiosira eccentrica (Ehrenb.) Cleve were grown in a silicate-limited chemostat at silicate concentrations below 1 μg-atoms · l^?1. The resulting abnormal valves of C. radiatus lacked a thickened ring around the foramina; their pore membranes were thinner and their loculi shallower than those in normal cells. Abnormal valves of T. eccentrica had a fasciculate areolae pattern; they lacked a silica covering over the foramina and some tangential areolae walls. Neither abnormal valve could be termed a new species.     

Use of Fourier transform infrared (FT-IR) spectroscopy as a tool for pollen identification

Airborne pollen are largely studied to obtain information about the atmospheric content of natural allergens. Aerobiological monitoring networks have been established to provide reliable data that facilitate the timely initiation of preventive actions aimed at minimizing allergic symptoms. Airborne pollen are usually identified and counted using an optical microscope, but as such procedures are extremely time-consuming, more expedient options are being explored. We have assessed the potential of Fourier transform infrared (FT-IR) spectroscopy as an alternative method for the rapid and reliable identification of allergenic pollen using six well-known allergenic pollen taxa and obtaining the respective FT-IR spectra. In doing this, a first IR spectral library has been created. The spectra of unknown pollen were compared to those of the reference library, and two pollen taxa of a mixed sample were identified.     

Pressure-tuning FT-IR spectroscopic study on the helix–coil transition of Ala-rich oligopeptide in aqueous solution

We investigated the effect of pressure on the helix–coil transition of an Ala-rich peptide (AK16: YGAAKAAAAKAAAAKA-NH₂) in aqueous solution by FT-IR spectroscopy. The spectra of the amide I' region of AK16 in aqueous solution was decomposed into some component bands using a curve fitting method. The peak at around 1635 cm ^?1 corresponding to the solvent exposed α-helix conformer increases with increasing pressures, while the peak at around 1655 cm ^?1 corresponding to the random coil conformer decreases. From the pressure dependence of the band intensities, we determined the volume change from the α-helix to random coil conformers of AK16 to be + 10.5 ± 0.3 cm³/mol. The positive volume change is different from the negative volume change generally observed in the pressure denaturation of proteins.     

Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria,bacteri-polymer mixtures and biofilms

Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis for freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at ～ 1740 cm^?1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggests that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled to composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum (amide I/carbohydrate C-O-～ 1150 cm^?1) and bacteria-poly-β-hydroxybutyrate (amide I/carbonyl ～ 1740 cm^?1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR sepectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at ～ 1740 cm^?1 was seen in FT-IR spectra of V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactioni within adherent microbial consortia.     

Developments in mid-infrared FT-IR spectroscopy of selected carbohydrates

FT-IR spectroscopy has become a powerful research tool for elucidating the structure, physical properties and interactions of carbohydrates. It provides a new interpretive and experimental framework for the study of complicated systems of natural polymers. This paper gives an overview over new infrared applications in the study of carbohydrates, both small compounds and macromolecules. These include a wide range of studies of carbohydrates in different physical states, from the crystalline solid state to aqueous solution, and special techniques, which expand the experimental framework to the in-muro studies of plant materials, and quantitative determination.     

Application of FT-IR spectroscopy for control of the medium composition during the biodegradation of nitro aromatic compounds

Previous studies showed that cabbage leaf extract (CLE) added to the growth medium can noticeably promote the degradation of nitro aromatic compounds by specific consortium of bacteria upon their growth. For further development of the approach for contaminated soil remediation it was necessary to evaluate the qualitative and/or quantitative composition of different origin CLE and their relevance on the growth of explosives-degrading bacteria. Six CLE (different by species, cultivars and harvesting time) were tested and used as additives to the growth medium. It was shown that nitro aromatic compounds can be identified in the FT-IR absorption spectra by the characteristic band at 1,527 cm⁻¹, and in CLE by the characteristic band at 1,602 cm⁻¹. The intensity of the CLE band at 1,602 cm⁻¹ correlated with the concentration of total nitrogen (R ² = 0.87) and decreased upon the growth of bacteria. The content of nitrogen in CLE differed (0.22–1.00 vol.%) and significantly influenced the content of total carbohydrates (9.50–16.00% DW) and lipids [3.90–9.90% dry weight (DW)] accumulated in bacterial cells while the content of proteins was similar in all samples. Though this study showed quantitative differences in the composition of the studied CLE and the response of bacterial cells to the composition of the growth media, and proved the potential of this additive for remediation of contaminated soil. It was shown that analysis of CLE and monitoring of the conversion of nitro aromatic compounds can be investigated by FT-IR spectroscopy as well as by conventional chemical methods.     

An alternative infrared spectroscopy assay for the quantification of polysaccharides in bacterial samples

The ability of bacteria to produce extracellular polysaccharides has been regarded as an indication of biofilm-forming capacity. Therefore, the determination of the sugar content in bacterial samples becomes a significant parameter. The colorimetric methods currently used are rather sensitive to the nature of the sugars and therefore require knowledge of the sugar types present in the samples. Unfortunately, the types of sugars present in bacteria are generally unknown and often composed of a complex mixture. In this article, we propose an alternative method based on Fourier transform infrared (FTIR) spectroscopy for the estimation of the total sugar content in bacterial samples. The method is based on a systematic treatment of FTIR spectra obtained from dried bacteria samples. It is assumed that the total sugar amount can be estimated from the area of characteristic bands between 970 and 1182 cm(-1). In parallel, the amide II band (1560-1530 cm(-1)) associated with proteins, or the C-H stretching region (2820-3020 cm(-1)) associated with the biomass, can be used for normalization purposes. Therefore, the ratio of the band area in the sugar window over that of the amide II or C-H stretching can be used to report the sugar content in bacterial samples. This method has been validated on model bacterial mixtures containing sugars, proteins, and DNA. Results with real bacterial samples are also provided and show conclusively that increased sugar contents in biofilms can be identified. The proposed FTIR approach requires minimal sample preparation and a single acquisition, is rapid, and may be applied to any kind of bacterial growth.     

Histological mapping of biochemical changes in solid tumors by FT-IR spectral imaging

Fourier-transform infrared (FT-IR) spectral imaging was used for analyzing biochemical changes in tumor cells. Metabolic parameters of human lung A549/8 adenocarcinoma and U87 glioma cells were compared under stress conditions in culture along with tumor progression after cell implantation onto the chick embryo chorio-allantoic membrane. In cell culture, glucose consumption and lactic acid release were higher in U87 cells. A549/8 cells were less sensitive to oxidative stress as observed through changes in fatty acyl chains. In vivo biochemical mapping of highly (U87) vs. poorly (A549/8) angiogenic tumors provided results comparable to culture models. Therefore, FT-IR imaging allows detecting subtle chemical changes in tumors, which might be useful for diagnosis.     

Chemical characteristics and gelling properties of agar from two Philippine Gracilaria spp. (Gracilariales, Rhodophyta)

The chemical structure of agars extracted from Philippine Gracilaria arcuata and G. tenuistipitata were determined by NMR and infrared spectroscopy. Agar with alternating 3-linked 6-O-methyl-β-D-galactopyranosyl and 4-linked 3,6-anhydro-2- O-methyl-α-L-galactopyranosyl units was isolated from G. arcuata, while the agar from G. tenuistipitata possesses the regular agarobiose repeating unit with partial methylation at the 6-position of the D-galactosyl residues. Both agars exhibit sulphate substitution at varying positions in the polymer. Chemical analyses reveal higher 3,6-anhydrogalactose and lower sulphate contents in alkali-modified than in native agar from both samples. Also, alkali modification enhanced agar gel strength and syneresis. Native G. arcuata agar produces a viscous solution (2000 cP at 75 °C) with a high gelling point (>60 °C) that forms a soft gel even after alkali modification (gel strength: <300 g cm⁻²). On the other hand, the agar from G. tenuistipitata exhibits gel qualities typical of most Gracilaria agars. This revised version was published online in June 2006 with corrections to the Cover Date.     

Nutritional studies on Chloroflexus,a filamentous photosynthetic,gliding bacterium

Nutritional studies on four different strains of Chloroflexus, a new genus of filamentous, photosynthetic bacteria are described. This organism appears to be related to several different procaryotic groups, and in particular to the green sulfur bacteria and blue-green algae. Unlike these autotrophs, however, Chloroflexus is nutritionally diverse, being able to grow aerobically as a light-independent heterotroph, and anaerobically as a photoautotroph or photoheterotroph. Numerous organic carbon sources including hexoses, amino acids, short chain fatty acids, organic acids, and some alcohols are utilized under various growth conditions. These results suggest that this organism may be among the most nutritionally versatile organisms known.     

Zonal plant distribution and edaphic and micrometeorological conditions on a coastal sand dune

Some edaphic and meteorological conditions were examined to detect environmental gradients from shoreline to inland at the Kado-ori coast, Ibaraki, Japan, in 1989. Zonal distribution patterns of coastal dune plant species, including three ubiquitous perennials,Calystegia soldanella, Carex kobomugi andIschaemum anthephoroides, were described in relation to the environmental gradients. Environmental gradients were found in water availability, evaporative demand and soil-water salinity. Water availability, evaluated by thickness of capillary water layer, increased from 10 cm at 20 m to 48 cm at 85 m from the shoreline, reflecting the percentage of fine sand. Evaporative demand, which was evaluated by the evaporation rate from a wet black filter paper, decreased with increasing distance from the shoreline. Soil-water salinity was lowest (15 mmol/L) at 85 m from the shoreline and highest (90 mmol/L) at 30m. On the coast,C. soldanella, a salt-tolerant perennial, was distributed mainly in the environmentally harsh area 40–60 m from the shoreline.Ischaemum anthephoroides andC. kobomugi, less salt-tolerant perennials, occurred mainly 70–80 m from the shoreline, where environmental conditions were more hospitable.     

Characterisation of Ca- and Al-pectate gels by thermal analysis and FT-IR spectroscopy

Thermal analysis (TG-DTA) and FT-IR spectroscopy have been performed on calcium-pectate membranes to investigate their structure and the consequent variation caused by aluminium sorption. Calcium-polygalacturonate (Ca-PG) membranes, model systems of the soil-root interface, were exposed to aluminium solutions at different concentrations (25-800 microM). Three different pHs (3.50, 4.00 and 4.50) were chosen to study the influence of different aluminium species, such as [Al(H2O)6]3+, [Al(OH)(H2O)5]2+ and [Al(OH)2(H2O)(4)]+, on the structure of the Ca-PG membrane. The DTA profiles and FT-IR spectra showed how aluminium sorption induces structural modifications leading to a reorganisation of the chain aggregates and a weakening of the structure. Higher pH, that is, 4.00 and 4.50, and thus hydrolytic aluminium species and related higher calcium content maintain a more regular structure than at pH 3.50. At pH 3.50, both the effect of [Al(H2O)6]3+ and a major calcium release had a greater impact and thus induced a greater weakening of the structure.     

Crystallization and micro FT-IR spectroscopy investigation of cytochrome bc1 complex

A simple method to obtain large red crystals of cytochrome bc1 complex from beef heart mitochondria has been developed. These crystals are very stable. Their shapes are retained for a long time in tip-sealed Pasteur pipets placed in a refrigerator. The structure of crystalline cytochrome bc1 complex by micro FT-IR spectroscopy has been investigated. Based on the IR spectra of cytochrome c, the empirical assignments of the major infrared frequencies of cytochrome bc1 complex are given. Infrared frequencies and relative intensities of variable orientation and section of crystal are significantly different. These imply that infrared spectral characterization of the membrane protein crystallization is associated with the variable symmetries and orientations of the structure. Experimental results show that phospholipid exists in the crystal of cytochrome bc1 complex. The membrane protein is probably spanned on the mitochondrial membrane and buried in phospholipid bilayer in an asymmetric manner.     

A combined FT-IR microscopy and principal component analysis on softwood cell walls

A combined FT-IR microscopy and principle component analysis was used to investigate chemical variations between softwood species as well as types of wood cell walls; latewood tracheids, earlywood tracheids and earlywood ray parenchyma cells. The method allowed us to detect small spectral differences between cell types rather than species and to predict characteristic chemical components of each cell type. The method enabled information to be obtained which allowed a evaluation of the polysaccharide composition even in lignified woody plant cell walls.     

Amino Acid Interaction with and Adsorption on Clays: FT-IR and Mössbauer Spectroscopy and X-ray Diffractometry Investigations

In the present paper, the adsorption of amino acids (Ala, Met, Gln, Cys, Asp, Lys, His) on clays (bentonite, kaolinite) was studied at different pH (3.00, 6.00, 8.00). The amino acids were dissolved in seawater, which contains the major elements. There were two main findings in this study. First, amino acids with a charged R group (Asp, Lys, His) and Cys were adsorbed on clays more than Ala, Met and Gln (uncharged R groups). However, 74% of the amino acids in the proteins of modern organisms have uncharged R groups. These results raise some questions about the role of minerals in providing a prebiotic concentration mechanism for amino acids. Several mechanisms are also discussed that could produce peptide with a greater proportion of amino acids with uncharged R groups. Second, Cys could play an important role in prebiotic chemistry besides participating in the structure of peptides/proteins. The FT-IR spectra showed that the adsorption of amino acids on the clays occurs through the amine group. However, the Cys/clay interaction occurs through the sulfhydryl and amine groups. X-ray diffractometry showed that pH affects the bentonite interlayer, and at pH 3.00 the expansion of Cys/bentonite was greater than that of the samples of ethylene glycol/bentonite saturated with Mg. The Mössbauer spectrum for the sample with absorbed Cys showed a large increase (～20%) in ferrous ions. This means that Cys was able to partially reduce iron present in bentonite. This result is similar to that which occurs with aconitase where the ferric ions are reduced to Fe 2.5.