Automated detection of remote homology

The classification of a newly identified protein as a member of a superfamily is important for focusing experiments on its most likely functions. Such classification, often performed by hand, has now been fully automated. This sophisticated new approach takes into account not only alignment scores but also a number of other computable attributes, such as functional sites deduced from sequence conservation patterns.     

Evaluation of lipophilicity and antitumour activity of parallel carboxamide libraries

Searching for molecules possessing antitumour activity, a parallel molecule library of aromatic carboxamides has been designed and synthesised. This work resulted in a "thiophene" sub-library containing a thiophene core and of a "furoyl" sub-library with a furoyl core, respectively. In both sub-libraries substitutions were carried out with six different groups resulting in six pairs of compounds differing in only the heteroatom of aromatic ring of the cores. To study the importance of the type of cores and the specific substitutions in relation to their lipophilicity and antitumour activity, lipophilicity of carboxamides was determined by chromatographical data (log k') and by software calculated parameters (CLOGP). Pairs of compounds were tested for their ability to inhibit the proliferation of the A431 cells by MTT assay. The isosteric molecule pairs were successfully separated. Our results showed that the experimentally determined (log k') and the calculated (CLOGP) lipophilicity parameters correlated well with each other. Furthermore, lipophilicity values of the thiophene sub-library were always higher than those in the furoyl sub-library. Moreover, compounds of the thiophene sub-library were more active than their respective furoyl pairs in our MTT antiproliferative assay. From these observations we can conclude that the higher the lipophilicity values the higher the antitumour activity of the carboxamides synthesised. Therefore, determination of lipophilicity by measuring the log k' or by calculating the CLOGP values of the carboxamide sub-libraries may help to predict their biological activities.     

Translocation of phosphatidylthreonine and -serine to mitochondria diminishes exponentially with increasing molecular hydrophobicity

Some cultured cells contain significant amounts of a rarely recognized phospholipid, phosphatidylthreonine. Since phosphatidylthreonine is a structural analog of phosphatidylserine, the question rises whether it is transported to mitochondria and decarboxylated to phosphatidylisopropanolamine therein. We studied this issue with hamster kidney cell-line using a novel approach, i.e. electrospray mass-spectrometry and stable isotope-labeled precursors. Scanning for a neutral loss of 155, which is characteristic for phosphatidylisopropanolamine, indicated that this lipid is indeed present. The identity of phosphatidylisopropanolamine was supported by the following: (i) it co-chromatographed with phosphatidylethanolamine; (ii) its molecular species profile was similar to that of phosphatidylethanolamine; (iii) its head group was labeled from ¹³C-threonine; and (iv) its concentration increased in parallel with phosphatidylthreonine. Tests with solubilized decarboxylase and subcellular fractionation studies indicated that the low cellular content of phosphatidylisopropanolamine is due to inefficient decarboxylation, rather than poor translocation of phosphatidylthreonine to mitochondria. Importantly, the average hydrophobicity of phosphatidylisopropanolamine molecular species was significantly less than that of phosphatidylthreonine species, indicating that hydrophilic phosphatidylthreonine species translocate to mitochondria far more rapidly than hydrophobic ones. Parallel results were obtained for phosphatidylserine. These findings imply that efflux from the ER membrane could be the rate-limiting step in the phosphatidylthreonine and -serine translocation to mitochondria.     

Detection of bacterial contamination in starch and resin-based papermaking chemicals using fluorescence techniques

Rapid fluorescence techniques were evaluated for the detection of bacterial contaminants in papermaking chemicals including starch and the resin-based sizes and starch slurries used in the paper industry. Viable and non-viable bacterial cells were visualised by fluorescent probes and detected by epifluorescence microscopy and flow cytometry. The best discrimination ability was obtained with the fluorescent probes LIVE/DEAD and SYBR Green, based on the staining of cellular nucleic acid, and ChemChrome V3, which demonstrated cellular enzymatic activity. The process samples had to be diluted and filtered before fluorescence staining and analysis because they were viscous and contained solid particles. Fluorescence microscopic counts of bacteria in highly contaminated process samples were similar to plate counts, but flow cytometric enumeration of bacterial cells in process samples yielded 2- to 10-fold lower counts compared with plate counts, depending on the consistency of the sample. The detection limits in flow cytometric analysis and in epifluorescence microscopy were 10³–10⁶ cells ml⁻¹ and 10⁵–10⁶ cells ml⁻¹, respectively. Intrinsic bacterial contamination was detectable with fluorescence techniques and highly contaminated process samples could be analysed with fluorescence methods. Electronic Publication     

Thermal inactivation of nonproteolytic Clostridium botulinum type E spores in model fish media and in vacuum-packaged hot-smoked fish products

Thermal inactivation of nonproteolytic Clostridium botulinum type E spores was investigated in rainbow trout and whitefish media at 75 to 93 degrees C. Lysozyme was applied in the recovery of spores, yielding biphasic thermal destruction curves. Approximately 0.1% of the spores were permeable to lysozyme, showing an increased measured heat resistance. Decimal reduction times for the heat-resistant spore fraction in rainbow trout medium were 255, 98, and 4.2 min at 75, 85, and 93 degrees C, respectively, and those in whitefish medium were 55 and 7.1 min at 81 and 90 degrees C, respectively. The z values were 10.4 degrees C in trout medium and 10.1 degrees C in whitefish medium. Commercial hot-smoking processes employed in five Finnish fish-smoking companies provided reduction in the numbers of spores of nonproteolytic C. botulinum of less than 10(3). An inoculated-pack study revealed that a time-temperature combination of 42 min at 85 degrees C (fish surface temperature) with >70% relative humidity (RH) prevented growth from 10(6) spores in vacuum-packaged hot-smoked rainbow trout fillets and whole whitefish stored for 5 weeks at 8 degrees C. In Finland it is recommended that hot-smoked fish be stored at or below 3 degrees C, further extending product safety. However, heating whitefish for 44 min at 85 degrees C with 10% RH resulted in growth and toxicity in 5 weeks at 8 degrees C. Moist heat thus enhanced spore thermal inactivation and is essential to an effective process. The sensory qualities of safely processed and more lightly processed whitefish were similar, while differences between the sensory qualities of safely processed and lightly processed rainbow trout were observed.     

Effects of europium ions (Eu3+) on the distribution and related biological activities of elements in Lathyrus sativus L. roots

Scanning electron microscopic and energy-dispersive X-ray analyses were used to study the distributions of different types of elements in the epidermis, exodermis, endodermis, and vascular cylinder of the fracture face in the Lathyrus sativus L. roots in the presence or absence of Eu³⁺. Some index of the biological activity related to the elements binding with protein were determined also. The results showed that the tissular distributions of elements in the fracture face are different in the presence and absence of Eu³⁺. The atomic percentages of P, S, Ca, and Mn were influenced more than those of other elements. Eu³⁺ promoted the biological activities of various kinds of element. The one possible mechanism changing the biological activities was that the reaction of Eu³⁺ Eu²⁺ would influence the electron capture or transport in elements of binding protein. Another mechanism was that CaM-Ca²⁺ becoming CaM-Eu³⁺ through Eu³⁺ instead of Ca²⁺ would affect the biological activity of elements by regulating the Ca²⁺ level in the plant cell.     

Imprint cytology in the diagnosis of Helicobacter pylori. Does imprinting damage the biopsy specimen?

OBJECTIVE: To investigate the efficacy of imprint cytology in the diagnosis of Helicobacter pylori infection and whether it damages the biopsy specimen for subsequent histologic examination. STUDY DESIGN: Two antral biopsies were taken from 76 patients with dyspeptic symptoms undergoing upper gastrointestinal endoscopy. Imprint cytology was made from the first specimen. This specimen was fixed in 10% formalin and sent for histopathologic examination. The second specimen was directly fixed in 10% formalin for routine histopathologic examination without being used for an imprint. The imprint smears were examined by cytopathologists. The biopsy specimens were examined by pathologists who did not know which specimens were used for the imprints. RESULTS: H pylori was seen in smears from 55 (72%) patients and in both biopsy specimens from the same patients. The pathologists could not recognize the biopsy specimens from which the imprints were made. Concordance between imprint cytology and histopathology was 100%. CONCLUSION: Imprint cytology is a suitable test for H pylori diagnosis, and imprints do not adversely affect the quality of the biopsy specimen.     

Kinectin-kinesin binding domains and their effects on organelle motility

Intracellular organelle motility involves motor proteins that move along microtubules or actin filaments. One of these motor proteins, kinesin, was proposed to bind to kinectin on membrane organelles during movement. Whether kinectin is the kinesin receptor on organelles with a role in organelle motility has been controversial. We have characterized the sites of interaction between human kinectin and conventional kinesin using in vivo and in vitro assays. The kinectin-binding domain on the kinesin tail partially overlaps its head-binding domain and the myosin-Va binding domain. The kinesin-binding domain on kinectin resides near the COOH terminus and enhances the microtubule-stimulated kinesin-ATPase activity, and the overexpression of the kinectin-kinesin binding domains inhibited kinesin-dependent organelle motility in vivo. These data, when combined with other studies, suggest a role for kinectin in organelle motility.     

Fibrous carrot root responses to irrigation and compaction of sandy and organic soils

Field experiments were performed in Southern Finland on fine sand and organic soil in 1990 and 1991 to study carrot roots. Fall ploughed land was loosened by rotary harrowing to a depth of 20 cm or compacted under moist conditions to a depth of 25–30 cm by three passes of adjacent wheel tracks with a tractor weighing 3 Mg, in April were contiguously applied across the plot before seed bed preparation. Sprinkler irrigation (30 mm) was applied to fine sand when moisture in the 0–15 cm range of soil depth was 50% of plant-available water capacity. For root sampling, polyvinyl chloride (PVC) cylinders (30 × 60 cm) were installed in the rows of experimental plots after sowing, and removed at harvest. Six carrot plants were grown in each of in these soil colums in situ in the field.Fine root length and width were quantified by image analysis. Root length density (RLD) per plant was 0.2–1.0 cm cm^-3 in the 0–30 cm range. The fibrous root system of one carrot had total root lengths of 130–150 m in loose fine sand and 180–200 m in compacted fine sand. More roots were observed in irrigated than non-irrigated soils. In the 0–50 cm range of organic soil, 230–250 m of root length were removed from loosened organic soils and 240–300 m from compacted soils. Specific root surface area (surface area divided by dry root weight) of a carrot fibrous root system averaged 1500–2000 cm² g^-1. Root length to weight ratios of 250–350 m g^-1 effectively compare with the ratios of other species.Fibrous root growth was stimulated by soil compaction or irrigation to a depth of 30 cm, in both the fine sand and organic soils, suggesting better soil water supply in compacted than in loosened soils. Soil compaction increased root diameters more in fine sand than it did in organic soil. Most of the root length in loosened soils (fine sand 90%, organic soil 80%) and compacted soils (fine sand 80%, organic soil 75%) was composed of roots with diameters of approximately 0.15 mm. With respect to dry weight, length, surface area and volume of the fibrous root system, all the measurements gave significant resposes to irrigation and soil compaction. Total root volumes in the 0–50 cm of soil were 4.3 cm³ and 9.8 cm³ in loosened fine sand and organic soils, respectively, and 6.7 cm³ and 13.4 cm³ in compacted sand and organic soils, respectively. In fine sand, irrigation increased the volume from 4.8 to 6.3 cm³.     

Study of the effect of lactose on the structure of sodium alginate films

The aim of this study was to evaluate the interaction between the film-forming sodium alginate and lactose monohydrate. This combination is used in the co-spray-drying technique for microencapsulation, but no respect on the structure of the film formed has not been published previously. From mechanical tests, positronium lifetime measurements and FT-IR studies on free films containing different ratios of film-former and lactose, we concluded that the mechanical strength of the sodium alginate film decreased with the increasing proportion of lactose. The free volume in the polymer matrix decreased to a minimum as the lactose content was progressively increased to 40%, but subsequently increased at higher lactose contents. The explanation of this phenomenon is the filling of the holes with the sugar. As lactose became predominant component, the structure of the polymer network weakened. These conclusions were supported by the FT-IR findings. The present results permit a clear explanation of the previously reported favourable effects of this film-forming combination on the dissolution of the active agent from the microcapsules.