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PubMed2003

Evaluation of Cobas Integra 800 under simulated routine conditions in six laboratories.

The new selective access analyser Cobas Integra 800 from Roche Diagnostics was evaluated in an international multicentre study at six sites. Routine simulation experiments showed good performance and full functionality of the instrument and provocation of anomalous situations generated no problems. The new features on Cobas Integra 800, namely clot detection and dispensing control, worked according to specifications. The imprecision of Cobas Integra 800 fulfilled the proposed quality specifications regarding imprecision of analytical systems for clinical chemistry with few exceptions. Claims for linearity, drift, and carry-over were all within the defined specifications, except urea linearity. Interference exists in some cases, as could be expected due to the chemistries applied. Accuracy met the proposed quality specifications, except in some special cases. Method comparisons with Cobas Integra 700 showed good agreement; comparisons with other analysis systems yielded in several cases explicable deviations. Practicability of Cobas Integra 800 met or exceeded the requirements for more than 95% of all attributes rated. The strong points of the new analysis system were reagent handling, long stability of calibration curves, high number of tests on board, compatibility of the sample carrier to other Roche systems, and the sample integrity check for more reliable analytical results. The improvement of the workflow offered by the 5-position rack and STAT handling like on Cobas Integra 800 makes the instrument attractive for further consolidation in the medium-sized laboratory, for dedicated use of special analytes, and/or as back-up in the large routine laboratory.

Blood Proteins↗

PubMed2005

Felodipine-influenced gingival enlargement in an uncontrolled type 2 diabetic patient.

BACKGROUND: The potential of calcium channel blockers (CCBs) to induce gingival enlargement (GE) as well as the influence of diabetes mellitus on periodontal tissues has been well documented. This case report documents a conservative clinical approach to the management of felodipine-influenced gingival enlargement and displays a clinical and histologic case of felodipine-influenced GE in an undiagnosed type 2 diabetic patient. METHODS: At the initial examination, a medical consultation was requested and two incisional biopsies were taken for pathological evaluation. The patient was diagnosed with uncontrolled type 2 diabetes. Felodipine was withdrawn and the diabetes was controlled before dental treatment was initiated. The patient then underwent selective extractions and full-mouth scaling and root planing as well as oral hygiene instructions. No surgical therapy was indicated. RESULTS: The histological results demonstrated the presence of elongated rete pegs; fibrous hyperplasia; a low-grade chronic inflammatory infiltrate, predominantly consisting of lymphocytes; and collagen bundle groups randomly distributed. These features were similar to those present in other drug-influenced GE. Clinical results have demonstrated almost complete resolution of GE after the withdrawal of felodipine and the control of diabetes. Further improvements were seen after scaling and root planing and oral hygiene instructions. No recurrences were noted 12 months after initial therapy. CONCLUSIONS: This report demonstrated that the control of systemic factors seemed to have the most influence on success for this particular case. Since the control of diabetes was managed at the same time as the felodipine withdrawal, it remains difficult to speculate how these two factors impacted both the severity of the GE and the therapeutic results. More importantly, the conservative treatment rendered demonstrated the stability of periodontal status during maintenance phase and the avoidance of surgical interventions.

Alveolar Bone Loss↗

PubMed1993

Human monoclonal islet specific autoantibodies share features of islet cell and 64 kDa antibodies.

The first human monoclonal islet cell antibodies of the IgG class (MICA 1-6) obtained from an individual with Type 1 (insulin-dependent) diabetes mellitus were cytoplasmic islet cell antibodies selected by the indirect immunofluorescence test on pancreas sections. Surprisingly, they all recognized the 64 kDa autoantigen glutamate decarboxylase. In this study we investigated which typical features of cytoplasmic islet cell antibodies are represented by these monoclonals. We show by double immunofluorescence testing that MICA 1-6 stain pancreatic beta cells which is in agreement with the beta-cell specific expression of glutamate decarboxylase. In contrast an islet-reactive IgM monoclonal antibody obtained from a pre-diabetic individual stained all islet cells but lacked the tissue specificity of MICA 1-6 and must therefore be considered as a polyreactive IgM-antibody. We further demonstrate that MICA 1-6 revealed typical features of epitope sensitivity to biochemical treatment of the target tissue which has been demonstrated for islet cell antibodies, and which has been used to argue for a lipid rather than a protein nature of target antigens. Our results provide direct evidence that the epitopes recognized by the MICA are destroyed by methanol/chloroform treatment but reveal a high stability to Pronase digestion compared to proinsulin epitopes. Conformational protein epitopes in glutamate decarboxylase therefore show a sensitivity to biochemical treatment of sections such as ganglioside epitopes. MICA 1-6 share typical features of islet cell and 64 kDa antibodies and reveal that glutamate decarboxylase-reactive islet cell antibodies represent a subgroup of islet cell antibodies present in islet cell antibody-positive sera.

Animals↗

PubMed1992

Time-resolved ultraviolet resonance Raman studies of protein structure: application to bacteriorhodopsin.

Time-resolved ultraviolet resonance Raman spectra of bacteriorhodopsin are used to study protein structural changes on the nanosecond and millisecond time scales. Excitation at 240 nm is used to selectively enhance vibrational scattering from tyrosine so that changes in its hydrogen bonding and protonation state can be examined. Both nanosecond and millisecond UV Raman difference spectra indicate that none of the tyrosine residues change ionization state during the BR----K and BR----M transitions. However, intensity changes are observed at 1172 and 1615 cm-1 in the BR----M UV Raman difference spectra. The 1615-cm-1 feature shifts down 25 cm-1 in tyrosine-d4-labeled BR, consistent with its assignment as a tyrosine vibration. The intensity changes in the BR----M UV Raman difference spectra most likely reflect an increase in resonance enhancement that occurs when one or more tyrosine residues interact more strongly with a hydrogen-bond acceptor in M412. The frequency of the v7a feature (1172 cm-1) in the BR----M UV Raman difference spectra supports this interpretation. The proximity of Tyr-185 and Asp-212 in the retinal binding pocket suggests that deprotonation of the Schiff base in M412 causes Tyr-185 to stabilize ionized Asp-212 by forming a stronger hydrogen bond.

Bacteriorhodopsins↗

PubMed1997

[Doppler color ultrasonography with contrast media in the study of eye and orbit neoplasms].

We investigated the diagnostic efficacy of the i.v. administration of a sonography (US) contrast agent to study eye and orbit tumors at different stages. We administered Levovist (Schering), an air microbubble stabilized by fatty acid, which is specific for angiographic indications. Baseline color Doppler US was performed on 24 selected patients and tumor vascularization patterns were classified into three classes. Color Doppler signal enhancement was assessed after contrast agent administration and the signal-to-noise ratio (SNR) was improved in 70% of cases, which helped identify vascular patterns and improved flowmetric accuracy. The Doppler effect was also improved and vascular signal was always enhanced. The SNR was improved also by the postcontrast detection of small vessels missed on baseline scans. Doppler signal enhancement was proportional to precontrast vascularization and depended on tumor size, with poor results in lesions < 5 mm. In contrast, vascular signal spots with increased postcontrast echogenicity sometimes caused excessive noise affecting the results. No correlation was found between signal enhancement and lesion histotype or between signal and lesion site. Treated lesions exhibited poorer contrast agent enhancement. The examination technique must be accurate and the various parameters set optimally, especially the velocity scale, gain and filtration; the unit must feature adequate recording capabilities (mm/s). To conclude, we believe that the routine use of i.v. US contrast agents will play a major role in improving diagnostic imaging in oculistics also thanks to the lack of untoward reactions and to the ease of contrast agent preparation.

Adult↗

PubMed2004

Analysis of the thyrotropin receptor-thyrotropin interaction by comparative modeling.

We have used the most advanced programs currently available to construct the first three-domain structure of the human thyrotropin receptor (TSHR) using comparative modeling. The model consists of a leucine-rich domain (LRD; amino acids 36-281; porcine ribonuclease inhibitor used as a template for modeling), a cleavage domain (CD; amino acids 282-409; tissue inhibitor of matrix metalloproteinases 2 as template) and transmembrane domain (TMD amino acids 410-699; bovine rhodopsin as template). Models of human, porcine, and bovine TSH were also constructed (human chorionic gonadotropin [hCG] and human follicle stimulating hormone [hFSH] as templates). The LRD has a characteristic horseshoe shape with 10 tandem homologous repeats. The CD consists of beta-barrel and alpha helix structures (OB-like fold) with two disulfide bridges and the structure around these disulfide bridges remains stable after cleavage. The TMD presents the typical seven membrane-spanning helices. The TSH, LRD, CD, and TMD models were brought together in an extensive series of docking experiments. Known features of the TSH-TSHR interaction were used for selection of appropriate complexes that were then validated using a different set of experimental data. A similar approach was used to build a model of a complex between the TSHR and a monoclonal TSHR antibody with weak thyroid stimulating activity. Human thyrotropin (hTSH) alpha chains were found to make contact with many amino acids on the LRD surface and CD surface whereas no interaction between the beta chains and the CD were found. The higher affinity of bovine thyrotropin (bTSH) and porcine thyrotropin (pTSH) (relative to hTSH) for the TSHR is explained well by the models in terms of charge-charge interactions between their alpha chains and the receptor. Experimental observations showing increased sensitivity of the TSHR to hCG after mutation of TSHR Lys209 to Glu are explained well by our model. Furthermore, several mutations in the TMD that are associated with increased TSHR basal activity are predicted from our model to be caused by the formation of new interactions that stabilize the activated form of the TMD.

Animals↗

PubMed1988

Folding of collagen IV.

Collagen IV dimers of two collagen IV molecules connected by their C-terminal globular NC1 domains were isolated by limited digestion with bacterial collagenase from mouse Engelbreth-Holm-Swarm (EHS) sarcoma tissue. The collagenous domains were only 300 nm long as compared to 400 nm of intact collagen IV but the disulfide bonds in the N-terminal region of the major triple helix were retained. Unfolding of the collagenous domains as monitored by circular dichroism occurred in a temperature range of 30 to 44 degrees C with a midpoint at 37 degrees C. The transition is significantly broader than that of the continuous triple helices in collagens I, II and III, a feature which can be explained by the frequent non-collagenous interruptions in the triple-helical domain of collagen IV. Refolding at 25 degrees C following complete unfolding at 50 degrees C was monitored by circular dichroism, selective proteolytic digestion of non-refolded segments and by a newly developed method in which the recovered triple-helical segments were visualized by electron microscopy. Triple-helix formation was found to proceed in a zipper-like fashion from the C-terminal NC1 domains towards the N-terminus, indicating that this domain is essential for nucleations. For collagen IV dimers with intact NC1 domains the rate of triple-helix growth was of comparable magnitude to that of collagen III, demonstrating that the non-collagenous interruptions do not slow down the refolding process where the rate-limiting step is the cis-trans isomerization of proline peptide bonds. Refolding was near to 100% and the refolding products were similar to the starting material as judged by thermal stability and electron microscopic appearance. Removal of the NC1 domains by pepsin or dissociation of their hexametric structures by acetic acid led to a loss of the refolding ability. Instead products with randomly dispersed short triple-helical segments were formed in a slow reaction. In no case, even when the disulfide bonds in the N-terminal region of the triple-helical domain were intact, was refolding from the N- towards the C-terminus observed. Taken together with results in other collagens, this suggests that C to N directionality might be an intrinsic property of triple-helix folding.

Animals↗

PubMed1995

Predictors of response to divalproex and lithium.

Predictors of response to mood stabilizers are of interest to psychiatrists because patients want and deserve prompt improvement, need to preserve limited hospital benefits, and desire agents that are both efficacious and free of adverse effects. Clinically practical guidelines for the likelihood of lithium responsiveness include mild and uncomplicated illness, pure manic symptomatology, prior response to lithium, and infrequent episodes. Divalproex has a broader spectrum of responders and has approximately equal benefit for patients with pure mania as for those with several forms of bipolar disorder that respond poorly to lithium (e.g., mixed mania, rapid cycling, comorbid substance abuse, and secondary bipolar disorder). Carbamazepine may be effective in patients who failed to respond to lithium and is more likely to be effective as part of combined drug therapy than as monotherapy. This review points out that, although the number of firm findings regarding predictors of response and the features associated with response are few, many of these can be combined with other general clinical information about the status of the patient to provide a guide to treatment selection and implementation of a therapeutic regimen.

Bipolar Disorder↗

PubMed1991

In vitro evaluation of platinum, titanium and ruthenium metal complexes in cisplatin-sensitive and -resistant rat ovarian tumors.

The antitumor activity of eight new metal complexes (three platinum, one titanium, four ruthenium derivatives) was investigated in a cisplatin (DDP)--sensitive (O-342) and a DDP-resistant (O-342/DDP) ovarian tumor line using the bilayer soft-agar assay. A continuous exposure set up at logarithmically spaced concentrations was used to test the drugs; to uncover possible pharmacokinetic features, a short-term exposure was additionally included for selected compounds. DDP served as the reference drug. The following compounds were investigated: 18-crown-6-tetracarboxybis-diammineplatinum(II) (CTDP), cis-aminotrismethylenephosphonato-diammine-platinum(II) (ADP), cis-diamminecyclohexano-aminotrismethylenephosphonato-platin um(II) (DAP), diethoxybis(1-phenylbutane-1,3-dionato)titanium(IV) (DBT, budotitane), trans-imidazolium-bisimidazoletetrachlororuthenate(III) (ICR), trans-indazolium-tetrachlorobisindazoleruthenate(III) (IndCR), cis-triazolium-tetrachlorobis-triazoleruthenate(III) (TCR) and trans-pyrazolium-tetrachlorobispyrazoleruthenate(III) (PCR). Of the new metal complexes, CTDP was the most active compound in O-342, resulting in a percentage of control plating efficiency (+/- SE) of 1 +/- 1, 12 +/- 8 and 40 +/- 21 following continuous exposure to 10, 1 and 0.1 microM, respectively, and was thus comparable to DDP at equimolar concentrations. In the resistant line, 10 microM CTDP reduced colony growth to 18% +/- 8%, whereas an equimolar concentration of DDP effected a reduction to 26% +/- 9%. During short-term exposure. CTDP was inferior to DDP, which may be ascribed to the stability of the bis-dicarboxylate platinum ring system. The titanium compound DBT, in contrast, showed promising effects at its highest concentration (100 microM) during short-term exposure in both lines; at this concentration the activity in O-342/DDP was higher than that in O-342 (7% +/- 7% vs 34% +/- 17% of control plating efficiency at 100 microM). All ruthenium complexes showed higher activity in the resistant line O-342/DDP than in the sensitive counterpart. ICR was the most active compound. Following continuous exposure of O-342/DDP cells to 10 microM ICR, colony growth was reduced to 18% +/- 4% that of controls. Further studies should concentrate on CTDP and ICR for the following reasons; the activity of CTDP was equal to that of DDP at equimolar concentrations during continuous exposure; considering that the in vivo toxicity of DDP was 3-fold that of CTDP, an increase in the therapeutic index of CTDP would be expected. ICR showed the best effect of all ruthenium complexes; it was superior to DDP in the resistant line.

Animals↗

PubMed1995

Multiple amino acids determine the DNA binding specificity of the Msx-1 homeodomain.

This study investigates the sequence features that contribute to the differential DNA binding properties of two divergent homeodomains, Msx-1 and HoxA3. We show that these homeodomains have overlapping, but nonidentical, DNA binding site preferences. We defined the amino acid residues that contribute to the observed differences in DNA binding specificity by producing a series of mutated polypeptides in which selected residues in Msx-1 were replaced with the corresponding ones in HoxA3. These analyses show that the DNA binding specificity of Msx-1 versus HoxA3 results from the cumulative action of multiple residues in all segments of the homeodomain (i.e., the N-terminal arm and helices I, II, and III). Therefore, substitutions of residues in both helix III and the N-terminal arm (but not in either segment alone) produced an Msx-1 polypeptide whose binding site preference was indistinguishable from that of HoxA3. Residues in helices I and II also influence DNA binding activity; these oppositely charged residues (e.g., lysine 19 and glutamate 30) may mediate ionic interactions between helices I and II which stabilize DNA binding by Msx-1. These findings demonstrate a critical interplay between residues in each homeodomain segment for appropriate conformation of the protein-DNA complex.

Amino Acid Sequence↗

PubMed2006

HSP induction mediates selective clearance of tau phosphorylated at proline-directed Ser/Thr sites but not KXGS (MARK) sites.

Neurofibrillary tangles (NFTs) are a characteristic neuropathological feature of Alzheimer's disease (AD), and molecular chaperones appear to be involved in the removal of disease-associated hyperphosphorylated tau, a primary component of NFTs. Here, novel HSP90 inhibitors were used to examine the impact of chaperone elevation on clearance of different tau species in transfected cells using a unique quantitative assay. The HSP90 inhibitors reduced levels of tau phosphorylated at proline-directed Ser/Thr sites (pS202/T205, pS396/S404) and conformationally altered (MC-1) tau species, an epitope that is immeasurable by standard Western blot techniques. The selective clearance of these phospho-tau species and MC-1 tau was mediated via the proteasome, while lysosomal-mediated tau degradation seems to lack specificity for certain tau species, suggesting a more general role in total tau removal. Interestingly, tau phosphorylated at S262/S356 within the tau microtubule binding domain was minimally affected by chaperone induction. Overall, our data show that chaperone induction results in the selective clearance of specific phospho-tau and conformationally altered tau species mediated by the proteasome; however, the apparent stability of pS262/S356 tau may also explain why MARK is able to regulate normal tau function yet still be linked to the initiation of pathogenic tau hyperphosphorylation in AD.

Animals↗

PubMed2003

Widespread selection for local RNA secondary structure in coding regions of bacterial genes.

Redundancy of the genetic code dictates that a given protein can be encoded by a large collection of distinct mRNA species, potentially allowing mRNAs to simultaneously optimize desirable RNA structural features in addition to their protein-coding function. To determine whether natural mRNAs exhibit biases related to local RNA secondary structure, a new randomization procedure was developed, DicodonShuffle, which randomizes mRNA sequences while preserving the same encoded protein sequence, the same codon usage, and the same dinucleotide composition as the native message. Genes from 10 of 14 eubacterial species studied and one eukaryote, the yeast Saccharomyces cerevisiae, exhibited statistically significant biases in favor of local RNA structure as measured by folding free energy. Several significant associations suggest functional roles for mRNA structure, including stronger secondary structure bias in the coding regions of intron-containing yeast genes than in intronless genes, and significantly higher folding potential in polycistronic messages than in monocistronic messages in Escherichia coli. Potential secondary structure generally increased in genes from the 5' to the 3' end of E. coli operons, and secondary structure potential was conserved in homologous Salmonella typhi operons. These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control.

Computational Biology↗

PubMed2000

Transposon stability and a role for conjugational transfer in adaptive mutability.

Lac(+) revertants of Escherichia coli that occur after prolonged nonlethal selection display a high frequency of transposon loss when the transposon Tn10 and the reverting lacI33 allele are linked on an F'128 episome. As many as 20% of the Lac(+) revertants are sensitive to tetracycline, about half because of transposon loss, nearly all by precise excision, and the remainder because of amplification of both the transposon and the linked lac allele. Lethality of the amplified products in the presence of tetracycline is a peculiarity of the tetA gene at high gene dosage. The selective conditions on lactose medium result in 10% transposon-free revertants, whether or not a requirement for conjugal DNA transfer is imposed. In addition, a similar fraction, about 5% of Lac(-) unreverted colonies that are products of transfer between cells experiencing nonlethal selection are also tetracycline-sensitive, and all are attributable to loss of the Tn10 transposon. These results suggest the possibility that the high frequency of transposon loss is a consequence of conjugal transfer, making this loss a marker for that transfer. We suggest that conjugal DNA transfer may be a prominent feature in the mutability process that occurs during nonlethal selection and that the subset of bacteria displaying hypermutability are those that experience such transfer.

Conjugation, Genetic↗

PubMed2006

IL-9 modulated MUC4 gene and glycoprotein expression in airway epithelial cells.

Compromised epithelial cell integrity is a common feature associated with chronic lung inflammatory states such as asthma. While epithelial cell damage is largely due to sustained effects of inflammatory mediators localized to airways, the subsequent process of epithelial cell differentiation is attributed to members of the transmembrane receptor tyrosine kinase family called the ErbB's. MUC4, a large molecular weight membrane-bound glycoprotein, has recently been identified as a potential ligand for the ErbB-2 receptor. In this study, we investigated the possible role of interleukin-9 (IL-9), a Th2 cytokine, on MUC4 expression using a lung cancer cell line, NCI-H650. We determined that IL-9 up-regulates MUC4 expression in a time and concentration-dependent fashion. Nuclear run-on assays indicated transcriptional regulation of MUC4 while no post-transcriptional mRNA stabilization was observed by actinomycin D chase experiments. IL-9 also increased MUC4 glycoprotein expression as determined by Western blots using a monoclonal antibody specific for a non-tandem repeat region on ASGP-2 region of MUC4. Furthermore, a JAK3-selective inhibitor 4-(4'-hydroxyphenyl) amino-6, 7-dimethoxyquinazoline (WHI-P131), substantially reduced IL-9-induced MUC4 mRNA expression in a dose-dependent fashion. These results implicate a potential role for IL-9 upon MUC4 expression in human airway epithelial cells.

Adenocarcinoma, Bronchiolo-Alveolar↗

PubMed2006

Management of high risk metastatic prostate cancer: the case for novel therapies.

PURPOSE: We reviewed the results of preliminary studies of select novel agents for metastatic prostate cancer and discuss the potential benefit of these agents for earlier stage disease, eg biochemically recurrent prostate cancer with high risk features. MATERIALS AND METHODS: Available data on select investigational immunotherapies as well as endothelin-A receptor antagonists and survivin inhibitors were obtained and reviewed through PubMed searches, conference proceedings and unpublished proprietary information, when available. RESULTS: A large number of promising agents are in varying stages of development. Phase III results have been reported for the endothelin-A receptor antagonist atrasentan. Several immunotherapies are currently in phase II/III trials, namely the GM-CSF transduced tumor cell vaccine GVAX, the prostatic acid phosphatase loaded dendritic cell vaccine Provenge and the prostate specific antigen expressing poxvirus vaccine PROSTVAC-VF. Another immunotherapy, the prostate specific membrane antigen immunoconjugate MLN2704 (Millennium Pharmaceuticals, Cambridge, Massachusetts), is in phase I/II study. The first clinical inhibitors of survivin are in early phase I studies. Several of these agents, including atrasentan, have shown statistically significant but modest effects in the advanced disease setting in which they have been studied. CONCLUSIONS: Clinical trial design with these novel therapies presents particular challenges since most of these agents may induce disease stabilization rather than disease regression. There is a risk of false-negative results and failure to recognize a potentially efficacious agent if these cytostatic agents are studied only in men with advanced, heavily pretreated disease in whom life expectancy is measured in months. We advocate the early referral and enrollment of men with high risk prostate cancer in clinical trials.

Antineoplastic Agents↗

PubMed1996

Interaction of a DNA-threading netropsin-amsacrine combilexin with DNA and chromatin.

Combilexins are a group of DNA ligands having a sequence-specific minor groove binding element combined with an intercalating chromophore which stabilizes the DNA complex and can interfere with topoisomerases. In this study, complementary methods of spectroscopy (absorption, circular dichroism, electric linear dichroism) and biochemistry (viscometry, footprinting) have been applied to explore the nature of the complex formed between a new amsacrine-4-carboxamide-netropsin combilexin and DNA or chromatin. Collectively, the structural and kinetic data concur that the conjugate threads through the DNA double helix so as to intercalate its acridine chromophore, leaving the netropsin moiety and the methanesulfonanilino group positioned within the minor and major grooves of the double helix, respectively. The hybrid retains the AT selectivity conferred by the netropsin moiety. The threading-type intercalation process, evidenced by stopped-flow measurements, is affected when the DNA is wrapped around histones. The composite drug can bind to both the DNA linker segments and the nucleosomal cores in chromatin though, unlike its constituents, it antagonizes the salt-induced condensation of chromatin. As far as its mode of binding to DNA is concerned, the netropsin-amsacrine hybrid molecule exhibits structural features reminiscent of the antitumor antibiotics nogalamycin and pluramycin. The design of DNA-threading combilexins provides an original route for the development of sequence-specific ligands capable of forming stable complexes with DNA.

Amsacrine↗

PubMed2025

Genomic Insights Into Convergent Evolution: Adaptation to Rocky Habitats in Rock-Inhabiting Fungi.

Rock-inhabiting fungi (RIF), obligate colonizers of bare rocks, are primarily distributed across two major phylogenetic classes: Dothideomycetes and Eurotiomycetes. These fungi display striking convergence in morphology and physiology, characterized by meristematic growth, melanized cell walls, and extreme stress tolerance. However, the genomic underpinnings of this adaptive convergence remain poorly understood. Here, through comparative genomic analysis of 9 RIF and 18 non-RIF fungi, we revealed that RIF possess compact, gene-dense genomes marked by contraction of genes involved in nutrient uptake and secondary metabolism, alongside expansions in cell wall biosynthesis, lipid metabolism, and stress-responsive pathways. We identified two genes under positive selection across multiple RIF lineages: Ino80 ATPase (chromatin remodeling) and the ER chaperone BiP (protein folding). Further evidence of convergence was found in the mannosyltransferase Mnn9, a key enzyme in cell wall assembly, where two RIF-specific amino acid substitutions were predicted to enhance protein stability. Additionally, a unique Mnn9-like clade has expanded exclusively in RIF. RNAi-mediated knockdown of an Mnn9-like gene in Rachicladosporium sp. confirmed its role in cell wall mannosylation, osmotic stress response, and the transition from meristematic to filamentous growth. Our findings elucidate a set of common genomic adaptations and highlight the specialized evolution of the Mnn9 family in driving the convergent success of phylogenetically diverse RIF in rocky environments.

Phylogeny↗

PubMed1986

Microinjection studies on selective protein degradation: relationships between stability, structure, and location.

We have used two approaches to study the relationship between the structure of a protein and its intracellular stability. First, over 35 proteins for which the primary and X-ray structure are known were radiolabeled and introduced into HeLa cells by RBC-mediated microinjection. We then measured the half-life and intracellular location of each protein. Analysis of these data has shown that the role of lysosomes in degradation of injected proteins is minor and nonselective, and that the subcellular location of a protein following injection may have a significant influence on its stability. Furthermore, no correlations were found between the half-life of a protein and its size, isoelectric point, hydrophobicity, or thermostability. However, initial multiple correlative analyses suggest that the stability of an injected protein may be related to an interplay between its location and the presence of unstable amino acids and disordered structure on the protein surface. Second, we have examined the primary sequences of 10 proteins with intracellular half-lives of less than 2 h. Each rapidly degraded protein contains at least one region of 12 to 45 amino acids rich in proline, glutamic acid, serine, and threonine (PEST). These PEST regions, flanked by positively charged amino acids, can also be identified by features common in their hydropathy plots. Similar inspection of 35 more stable, structurally characterized proteins revealed that only three contained weak PEST regions. On the basis of this information, we anticipated that caseins, which contain several PEST regions, would be rapidly degraded within eukaryotic cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Enzyme Stability↗