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Showing papers by "University of Vienna published in 1994"


Journal ArticleDOI
TL;DR: The Vienna RNA package as mentioned in this paper is based on dynamic programming algorithms and aims at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.
Abstract: Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities. An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment. All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

2,136 citations


Book ChapterDOI
TL;DR: A survey of results concerning algorithms, complexity, and applications of the maximum clique problem is presented and enumerative and exact algorithms, heuristics, and a variety of other proposed methods are discussed.
Abstract: The maximum clique problem is a classical problem in combinatorial optimization which finds important applications in different domains. In this paper we try to give a survey of results concerning algorithms, complexity, and applications of this problem, and also provide an updated bibliography. Of course, we build upon precursory works with similar goals [39, 232, 266].

1,065 citations


Journal ArticleDOI
09 Jun 1994-Nature

1,042 citations


Journal ArticleDOI
TL;DR: Using an algorithm for inverse folding, it is shown that sequences sharing the same structure are distributed randomly over sequence space, which means that finding a particular structure by mutation and selection is much simpler than expected.
Abstract: RNA folding is viewed here as a map assigning secondary structures to sequences. At fixed chain length the number of sequences far exceeds the number of structures. Frequencies of structures are highly non-uniform and follow a generalized form of Zipf's law: we find relatively few common and many rare ones. By using an algorithm for inverse folding, we show that sequences sharing the same structure are distributed randomly over sequence space. All common structures can be accessed from an arbitrary sequence by a number of mutations much smaller than the chain length. The sequence space is percolated by extensive neutral networks connecting nearest neighbours folding into identical structures. Implications for evolutionary adaptation and for applied molecular evolution are evident: finding a particular structure by mutation and selection is much simpler than expected and, even if catalytic activity should turn out to be sparse in the space of RNA structures, it can hardly be missed by evolutionary processes.

861 citations


Journal ArticleDOI
TL;DR: It is shown that STREs also mediate induction of transcription by heat shock, nitrogen starvation and oxidative stress and are also activated by low external pH, sorbate, benzoate or ethanol stress.
Abstract: The HOG signal pathway of the yeast Saccharomyces cerevisiae is defined by the PBS2 and HOG1 genes encoding members of the MAP kinase kinase and of the MAP kinase family, respectively. Mutations in this pathway (deletions of PBS2 or HOG1, or point mutations in HOG1) almost completely abolish the induction of transcription by osmotic stress that is mediated by stress response elements (STREs). We have demonstrated previously that STREs also mediate induction of transcription by heat shock, nitrogen starvation and oxidative stress. This study shows that they are also activated by low external pH, sorbate, benzoate or ethanol stress. Induction by these other stress signals appears to be HOG pathway independent. HOG1-dependent osmotic induction of transcription of the CTT1 gene encoding the cytosolic catalase T occurs in the presence of a protein synthesis inhibitor and can be detected rapidly after an increase of tyrosine phosphorylation of Hog1p triggered by high osmolarity. Consistent with a role of STREs in the induction of stress resistance, a number of other stress protein genes (e.g. HSP104) are regulated like CTT1. Furthermore, catalase T was shown to be important for viability under severe osmotic stress, and heat shock was demonstrated to provide cross-protection against osmotic stress.

509 citations


Journal ArticleDOI
TL;DR: A protein binding to a minor-group human rhinovirus (HRV2) was purified from HeLa cell culture supernatant as discussed by the authors, and amino acid sequences of tryptic peptides showed identity with the human low density lipoprotein (LDL) receptor (LDLR) mutually competed for binding sites on human fibroblasts.
Abstract: A protein binding to a minor-group human rhinovirus (HRV2) was purified from HeLa cell culture supernatant. The amino acid sequences of tryptic peptides showed identity with the human low density lipoprotein (LDL) receptor (LDLR). LDL and HRV2 mutually competed for binding sites on human fibroblasts. Cells down-regulated for LDLR expression yielded much less HRV2 upon infection than cells with up-regulated LDLR. Virus also bound to the large subunit of the alpha 2-macroglobulin receptor/LDLR-related protein (alpha 2MR/LRP). LDLR-deficient fibroblasts yielded considerably less virus in the presence of receptor-associated protein (RAP), providing evidence that alpha 2MR/LRP also acts as a minor group HRV receptor.

455 citations


Journal ArticleDOI
01 Dec 1994-Brain
TL;DR: The data indicate that the type and amount of inflammation, de- and remyelination, and of tissue damage vary between different forms of multiple sclerosis and between different stages of the disease, possibly reflecting different pathogenic mechanisms in a disease spectrum.
Abstract: Patterns of inflammation, demyelination and oligodendrocyte pathology were studied in acute multiple sclerosis and during early and late exacerbations of chronic multiple sclerosis. Cells within lesions were identified by immunocytochemistry with markers for T lymphocytes, macrophages, oligodendro-cytes and astrocytes. In addition, in situ hybridization for proteolipid protein mRNA was used to identify myelinating and myelin supporting oligodendrocytes. Degenerating cells in the lesions were detected by DNA fragmentation in cell nuclei. The inflammatory reaction in all three types of multiple sclerosis lesions was shown to be dominated by T lymphocytes and macrophages. In late chronic multiple sclerosis lesions, a significant increase in the number of immunoglobulin producing plasma cells was found in infiltrates as compared with acute and early multiple sclerosis lesions. In all three types of multiple sclerosis, confluent plaques of demyelination were found to be present. In acute multiple sclerosis, demyelination was found to be associated with extensive destruction of other tissue elements, including oligodendrocytes, astro-Acytes and axons, but even in these destructive lesions a considerable number of oligodendrocytes was preserved and at disposal therefore, for rapid remyelination. During early exacerbations of chronic multiple sclerosis, selective demyelination was associated with almost complete preservation of oligodendrocytes in the majority of cases. Correspondingly, a high number of remyelinating lesions was present at that stage of disease. In lesions developing late after onset of multiple sclerosis, demyelination generally accompanied extensive destruction and loss of oligodendrocytes. In these lesions, remyelination was sparse and restricted to lesional borders. The observed patterns of cell death suggest that in some cases oligodendrocytes, in others myelin sheaths are the primary target of the destructive process. Our data indicate that the type and amount of inflammation, de- and remyelination, and of tissue damage vary between different forms of multiple sclerosis and between different stages of the disease, possibly reflecting different pathogenic mechanisms in a disease spectrum.

406 citations


Journal ArticleDOI
TL;DR: An ultrasonography-guided approach for supraclavicular block combines the safety of axillary block with the larger extent of block of the suprAClavicular approach to investigate the effect on success rate and frequency of complications.
Abstract: We prospectively studied 40 patients (ASA grades I-III) undergoing surgery of the forearm and hand, to investigate the use of ultrasonic cannula guidance for supraclavicular brachial plexus block and its effect on success rate and frequency of complications. Patients were randomized into Group S (supraclavicular paravascular approach; n = 20) and Group A (axillary approach; n = 20). Ultrasonographic study of the plexus sheath was done. After visualization of the anatomy, the plexus sheath was penetrated using a 24-gauge cannula. Plexus block was performed using 30 mL bupivacaine 0.5%. Onset of sensory and motor block of the radial, ulnar, and median nerves was recorded in 10-min intervals for 1 h. Satisfactory surgical anesthesia was attained in 95% of both groups. In Group A, 25% showed an incomplete sensory block of the musculocutaneous nerve, whereas all patients in Group S had a block of this nerve. Complete sensory block of the radial, median, and ulnar nerves was attained after an average of 40 min without a significant difference between the two groups. Because of the direct ultrasonic view of the cervical pleura, we had no cases of pneumothorax. An accidental puncture of subclavian or axillary vessels, as well as neurologic damage, was avoided in all cases. An ultrasonography-guided approach for supraclavicular block combines the safety of axillary block with the larger extent of block of the supraclavicular approach.

393 citations


Journal ArticleDOI
TL;DR: In this article, the constitution of the titanium-aluminum-carbon ternary system was investigated combining critical evaluation of literature data with new experimental results, and a projection of the liquidus surface was given, and the reaction scheme linking this liquidus projection with the isothermal sections observed is proposed.
Abstract: The constitution of the titanium-aluminum-carbon ternary system has been investigated combining critical evaluation of literature data with new experimental results. Three ternary phases occur in this system: Ti3AlC, Ti2AlC, and newly discovered Ti3AlC2. As analyzed by wet chemistry methods, all three phases are carbon deficient with respect to their “ideal≓ stoichiometry, which is based on the crystal structure formula. Ti2AlC and Ti3AlC melt incongruently at 1625 ± 10 ‡ and 1580 ± 10 ‡, respectively. Ti3AlC2 decomposes in the solid state. The two isothermal sections at 1000 and 1300 ‡ investigated experimentally are corroborated by thermochemical calculations. A projection of the liquidus surface is given, and a reaction scheme linking this liquidus projection with the isothermal sections observed is proposed.

369 citations


Journal ArticleDOI
TL;DR: It is proposed that direct interaction of multivalent allergen with Fc epsilon RI(+)-bound IgE on mononuclear phagocytes results in cell signaling via Fc rho RI and that the biological consequences of this event may critically influence the outcome of allergic reactions.
Abstract: Suggestive evidence indicates that immunoglobulin E (IgE)-dependent activation of mononuclear phagocytes plays an important pathogenic role in allergic tissue inflammation. Prevailing opinion holds that low affinity IgE receptors are the relevant IgE-binding structures on monocytes/macrophages and that functional events occurring after cross-linking of membrane-bound IgE on these cells are mediated by these receptors. Here we demonstrate that peripheral blood monocytes can bind monomeric IgE via the high affinity IgE receptor (Fc epsilon RI) and that Fc epsilon RI expression on these cells is upregulated in atopic persons. Further, we demonstrate that, upon monocyte adherence to substrate, bridging of monocyte Fc epsilon RI is followed by cell activation. We propose that direct interaction of multivalent allergen with Fc epsilon RI(+)-bound IgE on mononuclear phagocytes results in cell signaling via Fc epsilon RI and that the biological consequences of this event may critically influence the outcome of allergic reactions.

356 citations


Journal ArticleDOI
TL;DR: In this article, a comparative analysis of the vibrational and structural properties of carbon nanotubes is presented, where the first-order Raman spectrum exhibits two lines at 1582 cm −1 and at 1350 cm−1.

Journal ArticleDOI
TL;DR: In quantification of pleural effusions, the sonographic measurement method presented is preferable to radiographic measurement.
Abstract: PURPOSE: To develop a practical method of estimating the volume of pleural effusions with sonography. MATERIALS AND METHODS: Fifty-one patients underwent sonography of the pleural space while supine. Sonographic results and results of lateral decubitus radiography were compared with actual effusion volumes. The maximum thickness of the pleural fluid layer was measured with both modalities, while actual effusion volume was determined by means of complete drainage. RESULTS: Sonographic measurements correlated statistically significantly better with actual effusion volume (r = .80) than did radiographic measurements (r = .58) (P < or = .05). With sonographic measurement, an effusion width of 20 mm had a mean volume of 380 mL +/- 130 (standard deviation), while one of 40 mm had a mean volume of 1,000 mL +/- 330. Prediction error with sonographic measurement (mean, 224 mL) was statistically significantly less (P < or = .002) than that with radiographic measurement (mean, 465 mL). CONCLUSION: In quantification ...

Journal ArticleDOI
TL;DR: The results support the idea that binge eaters might be a distinct subgroup among the obese population, and corroborate the utility of a diagnosis of BED in identifying the most disturbed obese subjects with regard to the variables tested.
Abstract: One hundred obese women with a mean age of 39.2 years, and a mean body mass index (BMI) of 35.9 kg/m2 were evaluated before entering a treatment study for weight reduction. According to the results of a structured interview, subjects were divided into four groups: (1) no overeating episodes, (2) episodic overeating episodes without the feeling of loss of control, (3) overeating plus the sense of loss of control (binge eating), and (4) full diagnostic criteria for binge eating disorder (BED). One-way analyses of variance (ANOVAs) revealed significant positive associations between binge eating and eating/weight-related characteristics such as a history of frequent weight fluctuations, the amount of time spent dieting, drive for thinness, and a tendency for disinhibition of eating. Furthermore, subjects exhibited more feelings of ineffectiveness, stronger perfectionistic attitudes, more impulsivity, less self-esteem, and less interoceptive awareness the more problems with binge eating they reported. The results support the idea that binge eaters might be a distinct subgroup among the obese population, and corroborate the utility of a diagnosis of BED in identifying the most disturbed obese subjects with regard to the variables tested.

Journal ArticleDOI
01 Jan 1994-Virology
TL;DR: Crosslinking, solubilization, and sedimentation analyses revealed the existence of prM-E heterooligomeric complexes, suggesting that the function of pr M is to protect protein E from undergoing the irreversible conformational changes in acidic compartments of the secretory pathway that are necessary for triggering fusion activity in the endosome during virus entry.

Journal ArticleDOI
TL;DR: Rational drug use, especially adequate, monitored, therapeutic administration according to strict criteria, should curb the onset and spread of resistance, but this concept may not be readily accepted by health services whose primary goal is clinical amelioration of the disease rather than the more stringent target of epidemiologically desirable results.

Journal ArticleDOI
TL;DR: In this paper, the authors consider the possibility that the subjects are simply envious and derive the implications of envy for the behaviour in ultimatum games and it will be shown that envy is a potential explanation for the most important experimental "anomalies".
Abstract: The behaviour of subjects in ultimatum bargaining experiments is very different from that predicted by standard theory. These ‘anomalies’ are frequently explained by fairness considerations. In this paper we consider the possibility that the subjects are simply envious. We derive the implications of envy for the behaviour in ultimatum games and it will be shown that envy is a potential explanation for the most important experimental ‘anomalies’. This points toward the need to set up experiments which allow to discriminate between fairness- and envy-motivated behaviour.

Journal ArticleDOI
TL;DR: Scanning with radiolabeled VIP labeled with iodine-123 for tumor localization in patients with gastrointestinal tumors was compared with computed tomography and scanning with somatostatin analogues in 79 patients with colorectal cancer, pancreatic carcinoma, gastric cancer, carcinoid tumor, or insulinoma.
Abstract: Background Intestinal adenocarcinomas and various endocrine tumors express large numbers of high-affinity receptors for vasoactive intestinal peptide (VIP). We have evaluated the usefulness of scanning with VIP labeled with iodine-123 for tumor localization in patients with gastrointestinal tumors. Methods Radioiodinated VIP was purified by high-pressure liquid chromatography and administered as a single intravenous bolus injection (300 pmol [1 microgram]). Scanning with radiolabeled VIP was compared with computed tomography and scanning with somatostatin analogues in 79 patients with colorectal cancer, pancreatic carcinoma, gastric cancer, carcinoid tumor, or insulinoma. Results Visualization of gastrointestinal tumors and metastases was obtained with radiolabeled VIP. Binding of the labeled peptide by primary tumors and metastases was visible shortly after the injection and was still demonstrable at 24 hours. In patients with colorectal adenocarcinomas, primary or recurrent tumors were visualized in 10 ...

Journal ArticleDOI
TL;DR: The long-term outcome after endoscopic thoracic sympathectomy from below D1 to D4, using a single-site access technique for primary hyperhidrosis of the upper limbs was evaluated, with particular emphasis on patient satisfaction.
Abstract: ObjectiveThis evaluated the long-term outcome after endoscopic thoracic sympathectomy (ETS) from below D1 to D4, using a single-site access technique for primary hyperhidrosis of the upper limbs.Summary Background DataPrimary hyperhidrosis of the upper limbs is a distressing and often socially disab

Journal ArticleDOI
TL;DR: The petrology and geochemistry of twentythree chondritic dust particles with masses of 1-47 μg (sizes 100-400 μm) were recovered from blue ice near Cap Prudhomme, Antarctica, and studied by INAA, ASEM, EMPA, and optical microscopy as mentioned in this paper.

Journal ArticleDOI
TL;DR: The findings indicate that the pathogenesis of demyelination may vary within different multiple sclerosis patients, and suggest that in the early course of the disease in some patients, oligodendrocytes may largely be preserved, whereas in others oligododendroglial loss is pronounced.
Abstract: The neuropathology of demyelinating lesions in multiple sclerosis was studied in specimens obtained by diagnostic needle biopsy during early stages of the disease. The lesions were characterized by a chronic inflammatory reaction dominated by lymphocytes and macrophages, plaque-like demyelination, and astroglial sclerosis. Oligodendrocytes within the lesions were studied by immunocytochemistry using antibodies against various myelin and oligodendroglia components. The expression of messenger RNA for proteolipid protein was determined by in situ hybridization. Our studies revealed that myelin-oligodendrocyte glycoprotein is a sensitive and reliable marker for identification of oligodendrocytes in demyelinated plaques. The results suggest that in the early course of the disease in some patients, oligodendrocytes may largely be preserved, whereas in others oligodendroglial loss is pronounced. Loss of oligodendrocytes was only marginally related to the stage of demyelinating activity within the lesions. These findings indicate that the pathogenesis of demyelination may vary within different multiple sclerosis patients.

Journal ArticleDOI
TL;DR: Profilin can act as a potent regulator of actin organization in living plant cells and supports a model in which organelle movements depend upon microfilaments that exist in dynamic equilibrium with the pool of monomeric actin.

Journal Article
TL;DR: It is shown that PTX exerts diverse (inhibitory) effects on cytokine release by PBMC, and appears to be exerted at the transcriptional level, since Northern blot analysis revealed reduced cytokine transcripts.
Abstract: Pentoxifylline (PTX) is a methylxanthine compound known to inhibit the production of tumour necrosis factor-alpha (TNF-alpha), which is an important inflammatory mediator. There is also recent evidence that PTX may influence other inflammatory cytokines, such as interleukin-1 (IL-1) and IL-6. Due to the therapeutic implications, the present study addressed the in vivo effects of PTX on the release of TNF-alpha, IL-1 beta, IL-6 and IL-8 by human peripheral blood mononuclear cells (PBMC). When PBMC were obtained from healthy volunteers ingesting 5 x 400 mg PTX orally for 2 days, the ability of PBMC cultured for 24 hr to release TNF-alpha was significantly reduced, while secretion of IL-1 beta, IL-6 and IL-8 was not affected. However, when PBMC were obtained from the same individuals 5 days after PTX had been stopped, the release of all four cytokines was significantly suppressed. This effect appeared to be exerted at the transcriptional level, since Northern blot analysis revealed reduced cytokine transcripts. In order to gain more insight into the effect of PTX on cytokine release, PBMC were obtained from normal volunteers, either stimulated with lipopolysaccharide (LPS) or left unstimulated, and subsequently incubated in vitro with PTX for 48 hr. Under these conditions, only TNF-alpha was found to be reduced by PTX, while IL-1 beta and IL-8 were not affected, IL-6 was even enhanced. However, when PBMC were incubated with PTX for 24 hr, PTX removed thereafter by medium change and cells further cultured, the production not only of TNF-alpha but also of IL-1 beta, IL-6 and IL-8 was reduced, demonstrating that PTX exerts diverse (inhibitory) effects on cytokine release by PBMC.

Journal ArticleDOI
TL;DR: It was shown that tissue ablation in patients with symptomatic BPH using HIFU is safe and dramatically reduces both obstructive and irritative symptoms and leads to a significant increase in uroflow and a decrease in postvoid residual volume.

Journal ArticleDOI
TL;DR: In this article, the photophysical properties and spectral shifts of 7-aminocoumarins were investigated in a combined experimental and theoretical study and the spectral shifts were found in accordance with Onsager's coatinuum model and excited state dipole moments were compared to semi-empirically calculated values.

Journal ArticleDOI
TL;DR: The characteristics of suicide and attempted suicide on the Viennese subway are discussed and appropriate guidelines for media coverage of suicidal acts are presented.

Journal ArticleDOI
TL;DR: It is concluded that ice may be useful for a variety of musculoskeletal pains, yet the evidence for its efficacy should be established more convincingly.

Journal ArticleDOI
TL;DR: Based on an analysis of the contrast behavior of spoiled gradient echo sequences, a method is described that overcomes the limitations of relative signal intensity increase measurement and introduces a parameter, called “enhancement factor” (EF), that approximates differential T1 relaxation rate.
Abstract: In previous papers relative signal intensity increase was used as a quantitative assessment parameter for contrast uptake in contrastenhanced MRI. However, relative signal intensity increase does not only reflect contrast uptake but depends also on tissue parameters (native T1 relaxation time) and sequence parameters (repetition time and flip angle); thus, the contrast uptake cannot be assessed accurately using relative signal intensity increase. Based on an analysis of the contrast behavior of spoiled gradient echo sequences, a method is described in this paper that overcomes the limitations of relative signal intensity increase measurement. A parameter, called “enhancement factor” (EF) is introduced that approximates differential T1 relaxation rate. The enhancement factor scales linearly with contrast uptake and is independent of tissue and sequence parameters. The additional measurement time involved in determining the enhancement factor is less than 1 min and computation is straightforward. The practicality of the new method was confirmed by phantom measurements using T1-weighted and proton density-weighted spoiled gradient echo sequences (FLASH-2D). Enhancing tissues were simulated by water phantoms doped with increasing concentrations of Gd-DTPA.

Journal ArticleDOI
TL;DR: Comparable sweating, vasoconstriction, and shivering thresholds during epidural and spinal anesthesia suggest that thermoregulatory processing is similar during each type of regional anesthesia, as indicated by significantly enlarged interthreshold and sweating-to-shivering ranges.
Abstract: BackgroundThere are significant physiologic differences between spinal and epidural anesthesia. Consequently, these two types of regional anesthesia may influence thermoregulatory processing differently. Accordingly, in volunteers and in patients, we tested the null hypothesis that the core-temperat

Journal ArticleDOI
TL;DR: The purification to homogeneity of the Lb form of the leader proteinase expressed in Escherichia coli is described, and the primary cleavage products of eIF-4 gamma obtained in vitro with purified leader or 2A proteinase are electrophoretically indistinguishable from those found during infection in vivo.
Abstract: Many picornaviruses cause a dramatic decrease in the translation of cellular mRNAs in the infected cell, without affecting the translation of their own RNA. Specific proteolysis of protein synthesis initiation factor eIF-4 gamma occurs during infection with rhinoviruses, enteroviruses, and aphthoviruses, apparently leading to an inability of the ribosomes to bind capped mRNAs. Cleavage of eIF-4 gamma in human rhinoviruses and enteroviruses is carried out by the viral 2A proteinase; in aphthoviruses (i.e., foot-and-mouth disease viruses), the leader proteinase is responsible for this reaction. We describe here the purification to homogeneity of the Lb form of the leader proteinase expressed in Escherichia coli. The primary cleavage products of eIF-4 gamma obtained in vitro with purified leader or 2A proteinase are electrophoretically indistinguishable from those found during infection in vivo. However, additional proteolysis products of eIF-4 gamma are observed with the leader proteinase and the human rhinovirus type 2 2A proteinase in vitro. The cleavage site of the leader proteinase in eIF-4 gamma from rabbit reticulocyte was determined by sequencing the purified C-terminal cleavage product by automated Edman degradation. The cleavage site is between Gly-479 and Arg-480 and thus differs from that of rhinovirus and enterovirus 2A proteinases, which cleave between Arg-486 and Gly-487.

Journal ArticleDOI
TL;DR: In situ hybridization was used to examine chromosome behavior at meiotic prophase in the rad50S, hop1, rad50, and spo11 mutants of Saccharomyces cerevisiae, which are defective in chromosome synapsis and recombination as mentioned in this paper.
Abstract: In situ hybridization was used to examine chromosome behavior at meiotic prophase in the rad50S, hop1, rad50, and spo11 mutants of Saccharomyces cerevisiae, which are defective in chromosome synapsis and meiotic recombination. Painting of chromosomes I and III revealed that chromosome condensation and pairing are reduced in these mutants. However, there is some residual pairing in meiosis, suggesting that homologue recognition is independent of synaptonemal complex formation and recombination. Association of homologues was observed in the rad50, rad50S, and spo11 mutants, which are defective in the formation or processing of meiotic double-strand breaks. This indicates that double-strand breaks are not an essential component of the meiotic homology searching mechanism or that there exist additional or alternative mechanisms for locating homologues.