The SBASE protein domain library, release 2.0: a collection of annotated protein sequence segments.

SBASE 2.0 is the second release of SBASE, a collection of annotated protein domain sequences. SBASE entries represent various structural, functional, ligand-binding and topogenic segments of proteins [Pongor, S. et al. (1993) Prot. Eng., in press]. This release contains 34,518 entries provided with standardized names and it is cross-referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalog of protein sequence patterns [Bairoch, A. (1992) Nucl. Acids Res., 20 suppl, 2013-2018]. SBASE can be used for establishing domain homologies using different database-search tools such as FASTA [Lipman and Pearson (1985) Science, 227, 1436-1441], FASTDB [Brutlag et al. (1990) Comp. Appl. Biosci., 6, 237-245] or BLAST3 [Altschul and Lipman (1990) Proc. Natl. Acad. Sci. USA, 87, 5509-5513] which is especially useful in the case of loosely defined domain types for which efficient consensus patterns can not be established. SBASE 2.0 and a set of search and retrieval tools are freely available on request to the authors or by anonymous 'ftp' file transfer from mean value of ftp.icgeb.trieste.it.     

Cytological localization of thePGIP genes in the embryo suspensor cells ofPhaseolus vulgavis L

Polygalacturonase-inhibiting protein (PGIP) is a cell wall protein which inhibits fungalendopolygalacturonases. A small gene family encodesPGIP in the genome of common bean, as indicated by Southernblot experiments performed at high-stringency conditions. Southern-blot analysis of DNA extracted from different cultivars ofPhaseolus vulgaris and fromPhaseolus coccineus showed length polymorphism of the hybridizing restriction fragments. The cytological localization of thePGIP genes was determined in polytene chromosomes of theP. vulgaris embryo suspensor cells. In-situ hybridization experiments using the clonedPGIP gene revealed labelling over a single region of the pericentromeric heterochromatin of chromosome pair X, next to the euchromatin, suggesting thatPGIP gene family may be clustered in one chromosomal region.     

Characterization of a new metal-mobilizing Thiobacillus isolate

A new acidophilic, mineral sulphide oreoxidizing bacterium was isolated from a uranium mine near Salamanca, Spain. Cells were rod-shaped, motile and gram-negative. They were aerobes, could grow on pyrite and use sulphur or thiosulphate as sole energy source, suggesting this new isolate belongs to the genus Thiobacillus. It could grow neither with glucose nor with yeast extract as sole substrates. It could not grow on ferrous sulphate as the only energy source, although it grew in the same medium supplemented with glucose, yeast extract or thiosulphate. It was a mesophilic and extremely acidophilic Thiobacillus, with an optimal pH of 1.5 2. The G+C content of the DNA was 58%. The new isolate could grow in cultures on pyrite where electrophoretic pattern was clearly different from those of other thiobacilli, such as T. ferrooxidans.Abbreviations G+C Guanine + Cytosine     

Vasopressin-dependent control of basolateral Na/H-exchange in highly differentiated A6-cell monolayers

We have used a well-differentiated A6-cell preparation (A6-C1) to study cellular location and vasopressin control of Na/H-exchange activity. After cell acidification, cell pH_i (measured by BCECF-fluorescence) only recovered by the addition of Na medium to the basolateral cell surface; this pH_i recovery was inhibited by dimethylamiloride (2 m) consistent with basolateral location of Na/H-exchange activity. Addition of vasopressin produced stimulation of Na/H-exchange activity and increased the affinity of the exchanger for Na⁺. Stimulation of Na/H exchange was mimicked by pharmacological activation of protein kinase A (forskolin, 8-Br-cAMP) and not by pharmacological activation of protein kinase C (TPA). It is concluded that basolaterally located Na/H-exchange in A6-C1 cells is activated by vasopressin.     

Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy.     

Thermal broadening of the Soret band in heme complexes and in heme-proteins: role of iron dynamics

We report the thermal broadening of the Soret band in heme-CO, heme-OH and protoporphyrin IX in the temperature range 300–20 K. For protoporphyrin IX the temperature dependent Gaussian line broadening follows the behavior predicted by the harmonic approximation in the entire temperature range investigated. In contrast, for heme-CO and heme-OH the harmonic behavior is obeyed only up to about 180 K and an anomalous line broadening increase is observed at higher temperatures. This effect is attributed to the onset of anharmonic motions of the iron atom with respect to the porphyrin plane. Comparison with previously reported analogous data for heme proteins enables us to suggest that the onset of substate interconversions in these latter systems can be reflected in motions of the iron atom with respect to the porphyrin plane. Correspondence to: L. Cordone     

Long-Term Responses to Loss of Renal Mass: Pathophysiological Aspects: The Influence of Age on the Response to Renal Parenchymal Loss

The effect of age on compensatory hypertrophy and functional adaptation to loss of 75 percent of renal mass was studied in canine puppies. In one group of animals the surgery was done between 1-5 days after birth and in another group, at two months of age. All animals were studied six weeks later. Shamoperated littermates served as controls. The newborn puppies in the experimental group were able to grow and maintain homeostasis as well as their controls, whereas the older experimental animals grew poorly and had significantly higher levels of plasma creatinine than their sham-operated counterparts (p < .05). The increase in mass of the remaining kidney was twice as much in the newborn as in the older dogs. Functional adaptation, as expressed by GFR, was nearly complete in the young, but reached only about 45 percent of controls in the older age group (p<.005). The intrarenal blood flow distribution was similar for experimental and control animals in both groups studied. There were, however, marked differences in the pattern of single glomerular perfusion rates: whereas in the older dogs the increase was confined to the deeper nephrons, in the newborn an increase occurred in all zones of the kidney. These studies demonstrate that compensation for massive loss of renal tissue is complete when the injury is sustained in the immediate postnatal period but only partial when it occurs later on in life. A loss in the adaptive capacity of the superficial nephrons appears to account for this age-related difference.     

CHROMOSOMAL STUDIES OF SUBGENUS TRIDENTATAE OF ARTEMISIA: EVIDENCE FOR AUTOPOLYPLOIDY

The sagebrushes (subgenus Tridentatae of Artemisia—new combination presented in the text) are western North America's most widespread and populous shrub group. Chromosome counts from 120 populations confirm the base chromosome number at x = 9 with numerous 2n = 2x = 18 diploids and 2n = 4x = 36 tetraploids. Few higher polyploids are known, and aneuploidy and supernumerary chromosomes are rare. All 11 Tridentatae species are now known cytologically. All but the narrowly endemic A. argillosa are known from at least three locations: A. arbuscula (2n = 18, 36), A. bigelovii (2n = 18, 36), A. cana (2n = 18, 36), A. longiloba (2n = 18, 36), A. nova (2n = 18, 36), A. pygmaea (2n = 18, 36), A. rigida (2n = 18, 36), A. rothrockii (2n = 18, 36, 54, ca. 72), A. tridentata (2n = 18, 36, 54), and A. tripartita (2n = 18, 36). The chromosome number of A. argillosa, reported here for the first time, is 2n = 36. Chromosome numbers of eight subspecies also have been determined. The subgenus is characterized by autopolyploidy as indicated by morphologically indistinguishable 2x and 4x plants, a few mixed ploidy populations, consistent formation of IVs in 4x PMCs, a relatively uniform 2x karyotype, and a 4x karyotype, which is approximately twice the 2x one. Karyotypic differences, if they exist at all, are on a populational level rather than a systematic taxonomic level. The Tridentatae have apparently rapidly differentiated in situ in North America under the stimulus of recurring aridic cycles since late Tertiary or early Quaternary. They likely derive from more primitive circumboreal stock originating from the Eurasian homeland of Artemisia. The differentiation of myriad forms of Tridentatae was seemingly achieved through genic rather than genomic means. Karyotypic analysis supports a position within Tridentatae of A. rigida, A. bigelovii, and A. pygmaea.