Network Analysis Performed on Transcriptomes of Parkinson's Disease Patients Reveals Dysfunction in Protein Translation

Parkinson's disease (PD) is a prevalent neurodegenerative disorder characterized by the progressive degeneration of dopaminergic neurons in the substantia nigra region of the brain. The hallmark pathological feature of PD is the accumulation of misfolded proteins, leading to the formation of intracellular aggregates known as Lewy bodies. Recent data evidenced how disruptions in protein synthesis, folding, and degradation are events commonly observed in PD and may provide information on the molecular background behind its etiopathogenesis. In the present study, we used a publicly available transcriptomic microarray dataset of peripheral blood of PD patients and healthy controls (GSE6613) to investigate the potential dysregulation of elements involved in proteostasis-related processes at the transcriptomic level. Our bioinformatics analysis revealed 375 differentially expressed genes (DEGs), of which 281 were down-regulated and 94 were up-regulated. Network analysis performed on the observed DEGs highlighted a cluster of 36 elements mainly involved in the protein synthesis processes. Different enriched ontologies were related to translation initiation and regulation, ribosome structure, and ribosome components nuclear export. Overall, this data consistently points to a generalized impairment of the translational machinery and proteostasis. Dysregulation of these mechanics has been associated with PD pathogenesis. Understanding the precise regulation of such processes may shed light on the molecular mechanisms of PD and provide potential data for early diagnosis.

The associations among executive planning, self-determination, and quality of life in adolescents with intellectual disability

BACKGROUND

Skills such as planning and problem solving that are required in self-determination can be cognitively demanding. It has not yet been examined whether executive functions and intelligence are associated with levels of self-determination in individuals with intellectual disability (ID), and how that is related to quality of life (QoL). This study examined the associations among executive functions, intelligence, self-determination, and QoL in adolescents with ID.

METHODS

Seventy-nine adolescents aged between 17 and 20 years with mild ID participated in the study. Executive functions were assessed by experimental tasks. Non-verbal IQ and survey data regarding QoL and self-determination capacity were collected from the participants.

RESULTS

In a regression model with QoL as the dependent variable, only executive planning and self-determination capacity (but not working memory, inhibition and IQ) were significant predictors of QoL. Two mediation models were tested based on the hypotheses, literature and current findings. Model 1 revealed that executive planning had a negative direct effect on QoL when the mediator, self-determination capacity, was held constant. Model 2 indicated that the significant association between self-determination and QoL was not mediated by executive planning.

CONCLUSIONS

The findings highlighted the crucial significance of self-determination, in comparison with executive functions and intelligence, for improving the QoL in adolescents with ID. Importantly, higher executive planning skill was even associated with lower QoL if self-determination was not concurrently strengthened. These findings carry implications for the design of education and intervention programmes aimed at improving QoL of adolescents with ID.

Cardiovascular events among recipients of hematopoietic stem cell transplantation-A systematic review and meta-analysis

Cardiovascular diseases are an emerging cause of mortality and morbidity in survivors of hematopoietic stem cell transplantation (HSCT); however, the incidence of cardiovascular events (CVEs) in this population is not well described. This systematic review summarizes the evidence on the incidence of CVEs in HSCT recipients. Medline and Embase were searched from inception to December 2020. Inclusion criteria were cohort studies and phase 3 randomized controlled trials that reported CVEs among adults who underwent HSCT for hematological malignancies. After reviewing 8386 citations, 57 studies were included. The incidence of CVEs at 100 days was 0.19 (95% CI: 0.17-0.21) per 100 person-days after autologous HSCT and 0.06 (95% CI: 0.05-0.07) per 100 person-days after allogeneic HSCT. This higher incidence after autologous HSCT was driven by reports of arrhythmia from one population-based study in patients with multiple myeloma. The incidence of long-term CVEs was 3.98 (95% CI; 3.44-4.63) per 1000 person-years in survivors of autologous HSCT and 3.06 (95% CI; 2.69-3.48) per 1000 person-years in survivors of allogeneic HSCT. CVEs remain an important but under-reported cause of morbidity and mortality in recipients of HSCT. Future studies are required to better understand the incidence and risk factors for CVEs in HSCT recipients.

P421 Whole-transcriptome analysis of Sporothrix brasiliensis grown in mold- and yeast-inducing conditions

Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM

 

Objectives

Sporothrix brasiliensis is an emerging Sporothrix species limited to Brazil capable of causing sporotrichosis in humans and animals, especially in cats. Like other pathogenic Sporothrix species, S. brasiliensis exhibits a temperature-dependent dimorphic switch and is therefore, able to undergo a reversible morphological transition (mold and yeast), in response to environmental thermal stimuli.

While dimorphism appears to be essential for virulence in Sporothrix spp, the molecular mechanisms involved in this phenomenon have not yet been fully elucidated.

In this study, we used the strand-specific RNA-Seq technique and bioinformatics analysis to investigate the transcriptomic signatures associated with mold and yeast phases of S. brasiliensis. Furthermore, we generated an accurate version of the S. brasiliensis genome annotation in order to perform high-quality gene expression analysis and other functional or structural genomic studies.

Methods

The whole transcriptome of S. brasiliensis ATCC-MYA-4823, grown in both yeast-inducing (YPD medium at 37°C) and mold-inducing (YPD medium at 25°C) conditions, was sequenced in this study. High-quality RNA was used to prepare Illumina TruSeq Stranded mRNA-paired-end sequencing libraries (2 × 150 bp) that were sequenced using the HiSeq-2500 platform. A total of three biological replicates were sequenced for each condition.

Before transcriptome assembly, adapters and low-quality reads (Phred-score <25) were removed. The StringTie software was used to assemble the transcriptomes imported into the Apollo webtool to manually curate the genome annotation. Transcripts were investigated using TransDecoder and CPC2 programs to determine whether a gene was potentially protein-coding or non-coding. Finally, differential gene expression analysis between yeast and mold forms of S. brasiliensis was conducted using the edgeR package.

Results

Illumina sequencing resulted in a total of ∼217 million raw reads. After quality filtering and trimming, ∼99.5% of reads were used for downstream bioinformatics analysis. The updated S. brasiliensis genome annotation consisted of a total of 14 664 genes of which 10 243 protein-coding genes, 4259 lncRNAs, 140 tRNAs, and 22 rRNAs.

Gene expression analysis revealed a total of 13 838 and 13 938 transcripts expressed in mold- and yeast-form, respectively. Of these, 192 and 292 were expressed exclusively in the mold and yeast-phase, respectively. Moreover, a total of 6802 genes (FDR <0.05) were differentially expressed between the two examined conditions. In particular, 3420 of these genes were up-regulated in the yeast-form (2450 coding, 970 non-coding), and 3382 genes in the filamentous form (2507 coding, 875 non-coding). The raw reads have been deposited into the SRA database and are available under BioProjectID: PRJNA646214.

Conclusions

The characterization of the whole-transcriptome of S. brasiliensis mycelial and yeast-like forms represents an essential starting point for investigating the molecular pathways and regulatory frameworks associated with these two morphological stages. Our results provide new insight into global gene expression profiles of S. brasiliensis, emphasizing the role of non-coding RNAs in its complex transcriptional network.

All transcriptomic data have also been integrated into the ‘Sporothrix Genome DataBase’ (www. sporothrixgenomedatabase.unime.it) in order to expand the current knowledge of Sporothrix genomics and to allow a more in-depth structural exploration of S. brasiliensis gene models, including gene expression patterns related to its saprophytic and pathogenic lifestyle.

Cardiovascular events among recipients of hematopoietic stem cell transplantation

Background

Allogeneic and autologous hematopoietic stem cell transplantation (HSCT) are potential curative treatments for several hematological malignancies (1). Survival after HSCT has improved over the last decade, but survivors remain at risk for health issues after transplantation. Cardiovascular complications after HSCT are increasingly recognized (2). Cardiovascular diseases may be an important cause of mortality and morbidity in patients after HSCT owing to the toxicities of the cancer therapies; however, the incidence of cardiovascular events (CVEs) in this population has not been completely characterized. The objective of this systematic review is to summarize the evidence on the incidence of CVEs in HSCT recipients.

Methods

Medline and Embase were searched from inception to December 2020 without language restriction. Two authors independently screened the titles and abstracts. Inclusion criteria were: cohort studies and phase 3 randomized controlled trials that reported CVEs (i.e., heart failure, arrythmias, acute coronary syndrome, and stroke) or cardiovascular death among adults who underwent HSCT for a hematological malignancy. All-cause mortality, relapse-related mortality, and non-relapse-related mortality (NRM) were also collected. Studies in which the follow up period was not started immediately after HSCT were excluded due to the risk of immortal bias.

Results

Of 8151 nonduplicate articles, 30 studies including 14019 individuals post autologous HSCT, and 22 studies including 31049 individuals post allogeneic HSCT met the inclusion criteria.

The cumulative incidence of CVEs in the first 100 days post autologous HSCT was 9% and arrhythmia (i.e., atrial fibrillation) was the most common CVE. In recipients of allogeneic HSCT, the 100-day cumulative incidence of CVEs was 3%, and heart failure (HF) was the most common reported CVE. In recipients of autologous and allogeneic HSCT, cardiovascular death was responsible for 43% and 10% of NRM within 100 days, respectively (Table 1).

The incidence of CVEs was 4.96 per 1000-person years (95% CI; 4.21–5.80) in long-term survivors (beyond 100-days) of autologous HSCT, and HF was the most common CVE in this population. In long-term survivors of allogeneic HSCT, the incidence of CVEs was 1.90 per 1000-person years (95% CI: 1.59–2.24). Cardiovascular death was the most frequently reported CVE in long-term survivors of allogeneic HSCT (Table 2).

Conclusion

CVEs remain a major cause of non relapse morbidity and mortality in recipients of HSCT, especially recipients of autologous HSCT within the first 100 days. Future studies are needed to identify the risk factors for CVEs that are specific to HSCT recipients.

Funding Acknowledgement

Type of funding sources: None.

Associations between increased body condition score, bodyweight, age and breed with urethral obstruction in male castrated cats

Identifying potential risk factors for urethral obstruction in male cats may help in disease prevention. The aims of this study were to assess whether breed, pedigree status, age, bodyweight and body condition score (BCS) are risk factors for urethral obstruction in castrated male cats using a primary care population. Within this, a specific question was whether any increase in rate of urethral obstruction in male cats due to excess body condition is because of higher bodyweight. A retrospective hospital-based matched case-control study was performed using 195 cases of urethral obstruction in castrated male cats and 195 control consultations for cats presenting to a feline-only first opinion veterinary practice in Brisbane, Australia. The incidence rate of urethral obstruction did not vary significantly with bodyweight but increased with BCS (incidence rate ratio 1.6; 95% CI 1.2-2.1; P<0.001). The effect of BCS was not due to high BCS cats having higher bodyweights. The incidence was lower in Burmese cats compared to Domestic shorthair cats (incidence rate ratio 0.1; 95% CI 0.0-0.4; P=0.001), and higher in non-pedigree cats compared to pedigree cats (incidence rate ratio 2.8; 95% CI 1.7-4.6; P<0.001). Incidence rate ratios increased with age to 2 to 4years (the ages with highest incidences) then progressively declined with each additional year of age. Further research is needed to define why there is a positive association between BCS and rate of urethral obstruction. In the interim, clinicians should encourage owners of castrated male pet cats to ensure their cat's BCS is not high.

Neutron Scattering Measurements of the Staggered Magnetization of an Antiferromagnetic Epitaxial thin Film FeF2

Elastic neutron scattering measurements performed at the NIST reactor have been used to measure the staggered magnetization near the transition temperature in a thin antiferromagnetic epitaxial film of FeF2 of thickness 0.8μm and diameter 1cm grown on a diamagnetic (001) ZnF2substrate by MBE. The use of a thin film permits extinction-free Bragg intensities, something which has proven impossible in bulk crystals. The growth techniques yield sufficient crystal quality to observed resolution limited Magnetic Bragg scattering peaks and to approach the transition within a reduced temperature of |t| = 0.003. The structure quality of this sample has been characterized using X-ray double crystal diffraction with a measured rocking curve lin ewidth of less than 30 arc sec. The sample thickness, while small enough to eliminate extinction, is sufficiently large to assure three-dimensional Ising Model critical behavior. We indeed observe critical behavior consistent with theoretical predictions. The success of the thin film experiments demonstrates the possibilities of extinction-free Bragg scattering measurements in a variety of antiferromagnetic Materials, including multilayered systems.

Congenital midline cervical cleft with an underlying bronchogenic like cyst

Congenital midline cervical cleft (CMCC) is an uncommon malformation. We report a case of a baby girl aged 3 days with a CMCC associated with a cyst reported as a bronchogenic cyst (BC). The pathology is not specific. The association of BC and CMCC is extremely rare and only five cases have been found in the literature. We report our case and review the relevant literature.

Fatal venous air embolism in a cat undergoing dental extractions

A five-year-old domestic shorthair cat underwent general anaesthesia and tooth extractions. Immediately after use of a high-speed, air-driven, water-cooled dental drill, the cat suffered cardiac arrest and attempted resuscitation was unsuccessful. Post-mortem radiographs showed air in the vena cava, right atrium, right auricle and right ventricle, hepatic and renal veins. These findings were confirmed at post-mortem examination. The cause of death was massive air embolism. There are reports of fatal venous air embolism in the human literature from the use of high-speed, air-driven, water-cooled dental drills. In this case, we believe that the air jet from the cooling system provided an enormous pressure gradient allowing air entry through an alveolar bone fracture or the inflamed gingival tissues. This is the first report of fatal venous air embolism associated with the use of a high-speed dental drill in the veterinary literature.

Apocrine adenoma of the breast: diagnosis on large core needle biopsy

Apocrine adenoma is a rare benign epithelial tumour of the breast that can radiologically present as a well-defined opacity. The clinical, radiological and pathological findings of apocrine adenoma of the breast in a 72-year-old woman are described. Histologically, the tumour is characterised by a circumscribed proliferation of metaplastic apocrine cells which may contain calcifications. Pathological assessment of the lesion is essential in making the diagnosis.

Identification of a putative effector protein for rab11 that participates in transferrin recycling

We have identified and cloned the cDNA for a 912-aa protein, rab11BP, that interacts with the GTP-containing active form of rab11, a GTP-binding protein that plays a critical role in receptor recycling. Although rab11BP is primarily cytosolic, a significant fraction colocalizes with rab11 in endosomal membranes of both the sorting and recycling subcompartments. In vitro binding of rab11 to native rab11BP requires partial denaturation of the latter to expose an internal binding site located between residues 334 and 504 that is apparently masked by the C-terminal portion of the protein, which includes six repeats known as WD40 domains. Within the cell, rab11BP must undergo a conformational change in which the rab11-binding site becomes exposed, because when coexpressed with rab11 in transfected cells the two proteins formed abundant complexes in association with membranes. Furthermore, although overexpression of rab11BP did not affect transferrin recycling, overexpression of a truncated form of the protein, rab11BP(1-504), that includes the rab11-binding site but lacks the WD40 domains inhibited recycling as strongly as does a dominant negative rab11 mutant protein that does not bind GTP. Strikingly, the inhibition caused by the truncated rab11BP was prevented completely when the cells also expressed a C-terminally deleted, nonprenylatable form of rab11 that, by itself, has no effect on recycling. We propose that rab11BP is an effector for rab11, whose association with this GTP-binding protein is dependent on the action of another membrane-associated factor that promotes the unmasking of the rab11-binding site in rab11BP.

Examination of micro-tip reversed-phase liquid chromatographic extraction of peptide pools for mass spectrometric analysis

Mass spectrometry occupies a central position in most current protein identification schemes. So-called 'mass fingerprinting' techniques rely on composite mass patterns of proteolytic fragments, or dissociation products thereof, to query databases. Keys to successful analysis of ever smaller amounts are sensitivity and complete spectral information, both of which depend for a large part on proper sample preparation. Clean-up and concentration of peptide mixtures over eppendorf gel loading tips filled with chromatographic media (i.e. 'micro-tips') are believed to be quite useful in this regard. We have studied quantitative and qualitative aspects of polypeptide extraction using these small manual devices. Optimization of sample volume and additives, micro-tip bed volume, and eluent composition and volume, all contribute to effective recovery (approximately 65-70%, on average). Improper digest conditions can, in fact, lead to far bigger losses, suggesting the need for at least trace amounts of Zwittergent 3-16. Of particular interest is our finding that partial fractionation, obtained by two-step micro-tip elution, generally results in more and better signals during subsequent mass analysis. Thus, by using optimized micro-tips, in combination with adequate sample handling and instrumentation, direct mass spectrometric identification can be routinely and successfully done in any resource facility type setting.

Identification of new mediator subunits in the RNA polymerase II holoenzyme from Saccharomyces cerevisiae

Mediator was isolated from yeast on the basis of its requirement for transcriptional activation in a fully defined system. We have now identified three new members of mediator in the low molecular mass range by peptide sequence determination. These are the products of the NUT2, CSE2, and MED11 genes. The product of the NUT1 gene is evidently a component of mediator as well. NUT1 and NUT2 were earlier identified as negative regulators of the HO promoter, whereas mutations in CSE2 affect chromosome segregation. MED11 is a previously uncharacterized gene. The existence of these proteins in the mediator complex was verified by copurification and co-immunoprecipitation with RNA polymerase II holoenzyme.

The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain

Mediator was resolved from yeast as a multiprotein complex on the basis of its requirement for transcriptional activation in a fully defined system. Three groups of mediator polypeptides could be distinguished: the products of five SRB genes, identified as suppressors of carboxy-terminal domain (CTD)-truncation mutants; products of four genes identified as global repressors; and six members of a new protein family, termed Med, thought to be primarily responsible for transcriptional activation. Notably absent from the purified mediator were Srbs 8, 9, 10, and 11, as well as members of the SWI/SNF complex. The CTD was required for function of mediator in vitro, in keeping with previous indications of involvement of the CTD in transcriptional activation in vivo. Evidence for human homologs of several mediator proteins, including Med7, points to similar mechanisms in higher cells.

The G beta gamma sensitivity of a PI3K is dependent upon a tightly associated adaptor, p101

Two highly similar, PtdIns(4,5)P2-selective, G beta gamma-activated PI3Ks were purified from pig neutrophil cytosol. Both were heterodimers, were composed of a 101 kDa protein and either a 120 kDa or a 117 kDa catalytic subunit, and were activated greater than 100-fold by G beta gammas. Peptide sequence-based oligonucleotide probes were used to clone cDNAs for the p120 and p101 species. The cDNA of p120 is highly related to p110 gamma, while the cDNA of p101 is not substantially related to anything in current databases. The proteins were expressed in and purified from insect and mammalian cells. They bound tightly to one another, both in vivo and in vitro, and in so doing, p101 amplified the effect of G beta gammas on the PI3K activity of p120 from less than 2-fold to greater than 100-fold.

Identification of Rox3 as a component of mediator and RNA polymerase II holoenzyme

Yeast Rox3 protein, implicated by genetic evidence in both negative and positive transcriptional regulation, is identified as a mediator subunit by peptide sequence determination and is shown to copurify and co-immunoprecipitate with RNA polymerase II holoenzyme.

Methodical analysis of protein-nitrocellulose interactions to design a refined digestion protocol

We have analyzed the efficacies of seven different organic solvents, 13 organic bases, and 17 detergents to dissociate electroblotted proteins from nitrocellulose. Most efficient were a 1% piperidine-40% acetonitrile mixture and 1% concentrations of either cetyltrimethylammonium bromide or several polyoxyethylene and zwitterionic detergents at pH > or = 8.5. In general, detergent-promoted elution varied with pH (8.5-->12.0) and temperature (37-->65 degrees C) in a detergent-dependent and protein-dependent manner, making for unpredictable results of any combination. However, Zwittergent 3-16, as the major exception, eluted proteins of different sizes and properties almost equally well at pH 8.5. This preferred effect is not enhanced by addition of organic solvent. In fact, detergent/acetonitrile mixtures were generally less efficient for protein elution. Zwittergent 3-16 (1% in 100 mM NH4HCO3) proved to be the most powerful additive for one-step enzymatic digestion of nitrocellulose-bound proteins, both in terms of highest recoveries (including endoproteinase Lys-C digestions) and general applicability, a major improvement over the use of Tween 80 and hydrogenated Triton X-100. The new digest procedure takes just 2 h to complete and requires 5 ng protease per 1 microliter buffer per 1 mm2 of nitrocellulose; relatively large pieces of membrane (> or = 100 mm2) can be successfully processed. The same detergent is a satisfactory additive for digestion of polyvinylidene difluoridebound proteins as well. Moreover, Zwittergent 3-16 is fully compatible with the usual downstream procedures. It is uv (OD214) transparent and does not interfere with high-performance liquid chromatography in any other way. Apparent incompatibility with direct (i.e., "prechromatography") matrix-assisted laser-desorption ionization time-of-flight mass spectrometry can be either reduced by methanol washing of the dried sample and activation of a low-mass gate or eliminated by a simple microliter cleanup procedure.

Adipocyte-specific transcription factor ARF6 is a heterodimeric complex of two nuclear hormone receptors, PPAR gamma and RXR alpha

Previously, we identified a novel transcription factor, ARF6, as a key regulator of the tissue-specific adipocyte P2 (aP2) enhancer. In order to identify the proteins which comprise the adipocyte ARF6 complex, we have purified this DNA binding activity from a cultured adipocyte cell line. We have developed a system for growth and differentiation of HIB-1B brown adipocytes in suspension culture that facilitates the production of large quantities of adipocyte nuclear extract. ARF6 was purified from HIB-1B nuclear extract by a combination of conventional and sequence-specific DNA affinity chromotography. Chemical sequencing and mass spectral analysis of tryptic peptides derived from the purified polypeptides identifies the ARF6 complex as a heterodimer of the retinoid X receptor alpha (RXR alpha) and the murine peroxisome proliferator activated receptor gamma (PPAR gamma). Of the known PPAR gamma isoforms, PPAR gamma is the predominant form expressed in adipose tissue. These results suggest that PPAR gamma 2 serves a unique function among PPAR family members as an important regulator of adipocyte-specific gene expression.

High-sensitivity sequencing of large proteins: partial structure of the rapamycin-FKBP12 target

We report on studies leading to refinements of various steps of the protein internal sequencing process. Specifically, the developments comprise (1) higher-sensitivity chemical sequencing through background reduction; (2) improved peptide recovery from rapid in situ digests of nanogram amount, nitrocellulose-bound proteins; and (3) accurate UV spectroscopic identification of Trp- and Cys-containing peptides. In addition, we describe strategies for 2-dimensional liquid chromatographic peptide isolation from complex mixtures and a multi-analytical approach to peptide sequence analysis (Edman sequencing, matrix-assisted laser desorption mass spectrometry, and UV spectroscopy). Both strategies were applied in tandem to the primary structural analysis of a gel-purified, 250-kDa protein (mammalian target of rapamycin-FKBP12 complex), available in low picomolar quantities only. More than 300-amino acids worth of sequence was obtained in mostly uninterrupted stretches, several containing Trp, Cys, His, and Ser. That information has allowed the matching of a biological function of a mammalian protein to a yeast gene product with a well-characterized mutant phenotype. The results also demonstrate that extended chemical sequencing analysis (e.g., 26 successive amino acids) is now feasible, starting with initial yields well below 1 pmol.

Metal chelates as reversible stains for detection of electroblotted proteins: application to protein microsequencing and immunoblotting

Coomassie brilliant blue and Ponceau red have traditionally been used to stain electroblotted proteins, since they are compatible with existing N-terminal and internal protein microsequencing as well as with immunoblotting procedures. With recent improvements in sequencing and immunoblotting technology, detection of significantly smaller amounts of protein has become necessary. Metal complexes were evaluated as alternatives to conventional stains. Electroblotted proteins were detected by blocking nonspecific sites with polyvinylpyrrolidone-40 followed by incubation in metal chelate solutions at acidic pH values. Two of the most promising metal chelate stains were the Ferrozine/ferrous complex and the ferrocyanide/ferric complex. Both stained a wide variety of proteins and peptides quantitatively. Dot blots and 1D and 2D electroblots were successfully stained using iron chelates. When these two stains were utilized in combination, they were of equivalent sensitivity to colloidal gold stain. The reversibility of the metal chelate stains was substantiated by incubating stained membranes at neutral to basic pH in the presence of 20 mM ethylenediaminetetraacetic acid to rapidly elute the complexes from the bound proteins. The chelate stains were determined to be fully compatible with immunoblotting, N-terminal, and in situ internal protein microsequencing.

Microbore reversed-phase high-performance liquid chromatographic purification of peptides for combined chemical sequencing-laser-desorption mass spectrometric analysis

An optimized microbore RP-HPLC system (1.0 mm I.D. columns) for the purification of low picomole amounts (< 5 pmol) of peptides is described. It is comprised of commercially available columns, instrument components and parts. These were selected on the basis of a comparative evaluation and to yield the highest resolution and most efficient peak collection. The sensitivity of this system equals, probably surpasses, that of advanced chemical microsequencing for which 2-4 pmol of peptide are minimally required. As an automated sequencer cannot be "on-line" connected with a micro-preparative HPLC system, fractions must be collected and transferred. With a typical flow of 30 microliters, efficient manual collection is possible and fractions (about 20 microliters in volume) can still be handled without unacceptable losses, albeit with great precaution. Furthermore, major difficulties were encountered to efficiently and quantitatively load low- or sub-picomole amounts of peptide mixtures onto the RP-HPLC column for separation. Discipline and rigorous adherence to sample handling protocols are thus on order when working at those levels of sensitivity. With adequate instrumentation and handling procedures in place, we demonstrate that low picomole amounts of peptides can now be routinely prepared for analysis by combined Edman-chemical sequencing-matrix-assisted laser-desorption mass spectrometry (MALDI-MS). The integrated method was applied to covalent structural characterization of minute quantities of a gel-purified protein of known biological function but unknown identity. The results allowed unambiguous identification and illustrated the power of MALDI-MS-aided interpretation of chemical sequencing data: accurate peptide masses were crucial for (i) confirmation of the results, (ii) deconvolution of mixed sequences, (iii) proposal of complete structures on the basis of partial sequences, and (iv) confirmation of protein identification (obtained by database search with a single, small stretch of peptide sequence) by "mass matching" of several more peptides with predicted proteolytic fragments.

RAFT1: a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs

The immunosuppressants rapamycin and FK506 bind to the same intracellular protein, the immunophilin FKBP12. The FKB12-FK506 complex interacts with and inhibits the Ca(2+)-activated protein phosphatase calcineurin. The target of the FKBP12-rapamycin complex has not yet been identified. We report that a protein complex containing 245 kDa and 35 kDa components, designated rapamycin and FKBP12 targets 1 and 2 (RAFT1 and RAFT2), interacts with FKBP12 in a rapamycin-dependent manner. Sequences (330 amino acids total) of tryptic peptides derived from the 245 kDa RAFT1 reveal striking homologies to the yeast TOR gene products, which were originally identified by mutations that confer rapamycin resistance in yeast. A RAFT1 cDNA was obtained and found to encode a 289 kDa protein (2549 amino acids) that is 43% and 39% identical to TOR2 and TOR1, respectively. We propose that RAFT1 is the direct target of FKBP12-rapamycin and a mammalian homolog of the TOR proteins.

Expression of key enzymes of purine and pyrimidine metabolism in a hepatocyte-derived cell line at different phases of the growth cycle

The effect of growth phase on enzymatic activities of the de novo and salvage pathways for purine and pyrimidine nucleotide synthesis was studied in a hepatocyte-derived cell line from the rat. The cells were in lag phase after plating for 36 h; log phase started at 48 h and persisted up to 120 h of culture. Then the cells stopped growing and entered into plateau phase (144 h). In non-proliferating cells (144 h of culture) the basal activities of the enzymes of purine de novo biosynthesis were 1.7- to 6.8-fold higher than in normal rat liver, those of pyrimidine de novo synthesis showed 0.6- to 30-fold increase in activity. The purine salvage enzymes were unchanged, and the pyrimidine salvage enzymes were 3.1- to 7.4-fold higher compared to normal liver. During the growth cycle all enzymes except the purine salvage enzymes, which did not change, showed a peak in activity at 72 h of culture (log phase). The increase in activity in log phase compared to plateau phase was 1.3- to 2.4-fold for purine de novo synthetic enzymes, 1.1- to 2.4-fold for pyrimidine de novo enzymes, and 1.4- to 4.7-fold for pyrimidine salvage enzymes. The specific activities of the enzymes in exponentially growing cells were comparable either to that in 24-h regenerating liver, or to that in hepatomas of low or medium growth rate. It was concluded that the enzymatic pattern and metabolic state of the cells shared some features with regenerating liver, others with tumors, although they were not tumorigenic after transplantation into athymic nude mice.

Cytogenetics of undifferentiated nasopharyngeal carcinoma xenografts from southern Chinese

Three undifferentiated nasopharyngeal carcinoma (NPC) tumour lines were successfully established from fresh biopsy material injected s.c. into athymic mice and passaged for many generations. These xenografts were found to be free of infiltrating lymphoid cells and remained undifferentiated up to passage 30. They were designated NPC/HK2117 (Xeno-1), NPC/HK1915 (Xeno-2) and NPC/HK1530 (Xeno-3), respectively. Passage 16 from Xeno-1, passage 1 from Xeno-2 and passage 14 from Xeno-3 were studied cytogenetically using G-banding with the trypsin-Giemsa method. Two xenografts were hyperdiploid with chromosome modal numbers ranging from 49 to 76, and one was hypodiploid with modal numbers ranging from 28 to 38. Five marker chromosomes have been identified with involvement of chromosomes 1, 3, 11, 12 and 17. Marker chromosomes derived from chromosomes 12q, 1q and 3q were consistent in one of the 2 xenografts successfully G-banded, and chromosomes 12, 11 and 17 were consistent in another. Three out of the 6 markers involve 12q13----qter. An abnormal chromosome 3 with most of the p arm deleted was also observed.

Establishment of a cell line (NPC/HK1) from a differentiated squamous carcinoma of the nasopharynx

A long-term cell culture epithelioid cell line was established from a recurrent squamous carcinoma of the nasopharynx of a Chinese male 17 1/2 years after radiation therapy. The cell line, designated NPC/HK1, has been passed 72 times over a period 1 year. The cells have been shown by light and electron microscopies to be of the squamous epithelial type. When they were transplanted subcutaneously into the back of athymic nude BALB/c (nu/nu) mice, tumors developed at the sites of inoculation, which on histological examination were shown to be well-differentiated squamous carcinomas, similar in morphology to the recurrent human tumor from which they were derived. Karyotypic analysis of cells from the cell line demonstrates an aneuploid human type with a modal chromosome number of 74 with both numerical and structural aberrations. Viral particles or Epstein-Barr viral nuclear antigen (EBNA) has not been demonstrated in the cells from the primary culture or several of the subcultures tested. The presence of EBNA in touch smears prepared from the biopsy tissue was inconclusive. Infection of the subcultured cells with EBV from P3HR1 and B95-8 cells was unsuccessful.

Partial reactions of aminoacyl-tRNA synthetases as functions of pH

The effect of pH on the properties of the partial reactions of arginyl-tRNA synthetase of E. coli has been investigated. V max of pyrophosphorolysis of arginyl adenylate has a pH optimum at pH 6.1, whereas V max of the transfer of arginine to tRNA has a pH optimum of 8.2. These values correlate with the pH optima of the ATP:PPi exchange and the overall esterification reaction, respectively. Only the pyrophosphorolysis reaction requires a divalent cation; transfer proceeds in the presence of EDTA. Inorganic pyrophosphate inhibits the transfer reaction to an extent independent of the concentration of tRNA; the maximum inhibition is a function of pH, corresponding to the relative rate of pyrophosphorolysis of the common intermediate compared with the rate of transfer. These results show that different groups on the enzyme participate in the rate-limiting steps of the two partial reactions and that these partial reactions have properties consistent with their participation in the overall esterification of arginine with tRNA.

Possible transformation of nasopharyngeal epithelial cells in culture with Epstein-Barr virus from B95-8 cells

Explants of fresh biopsy specimens from non-neoplastic nasopharyngeal (NP) mucosa, nasopharyngeal carcinoma (NPC), other tumours (OT) of the head and neck and freshly removed tonsils were treated with an Epstein-Barr virus (EBV) preparation from B95-8 cells and cultured. The mainly epitheloid outgrowths from these infected explants were then compared with those from their respective uninfected controls at 14 days. Growth stimulation occurred with a significantly higher frequency, and the degree of stimulation was generally higher with the infected NP explants than those of the similarly infected explants of other origins. Furthermore, after treatment with the virus preparation, several of the outgrowths from the NP explants showed growth characteristics and cellular morphology typical of those of transformed cells. Light microscopy has shown the changed NP cells to have epithelial characteristics. This is now being verified by electron microscopy, which has so far shown the presence of keratin fibrils and desmosomes in one specimen examined. They are also being examined for the presence of EBV-DNA and EBNA, and other features of transformation, including malignant tendency, by passage through athymic nude mice.