The genome sequence of the filamentous fungus Neurospora crassa

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.

Pathogen discovery from human tissue by sequence-based computational subtraction

We have recently reported a new pathogen discovery approach, "computational subtraction". With this approach, non-human transcripts are detected by sequencing cDNA libraries from infected tissue and eliminating those transcripts that match the human genome. We show now that this method is experimentally feasible. We generated a cDNA library from a tissue sample of post-transplant lymphoproliferative disorder (PTLD). 27,840 independent cDNA sequences were filtered by computational subtraction against the known human sequence to identify 32 nonmatching transcripts. Of these, 22 (0.1%) were found to be amplifiable from both infected and noninfected samples and were inferred to be human DNA not yet contained in the available human genome sequence. The remaining 10 sequences could be amplified only from Epstein-Barr virus (EBV)-infected tissues. All 10 corresponded to the known EBV sequence. This proof-of-principle experiment demonstrates that computational subtraction can detect pathogenic microbes in primary human-diseased tissue.

High rate of invasive fungal infections following nonmyeloablative allogeneic transplantation

Nonmyeloablative allogeneic transplantation is an emerging therapy for hematologic and solid malignancies and potentially offers patients reduced transplant-related toxicity. Data regarding infectious complications of these protocols are limited, but early studies have demonstrated little infectious morbidity, particularly low rates of invasive fungal infections (IFIs). In the present study, 31 consecutive cases of nonmyeloablative transplantation were reviewed over a 2.5-year period, with a specific focus on infectious complications. Twenty-six patients (84%) had at least 1 significant infection during the year after transplantation, and infection-related mortality was 37%. Cytomegalovirus end-organ disease was diagnosed in 3 patients (10%). Ten patients (32%) were given the diagnosis of IFI; 7 (23%) met criteria for proven IFI. Fungal-related mortality was 80% within the group of patients with IFI and accounted for a significant portion of the overall mortality in the study. Severe graft-versus-host disease, high-dose corticosteroid use, recurrent neutropenia, and relapsed or refractory disease were factors associated with development of IFI.

Initial sequencing and comparative analysis of the mouse genome

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Interpretation of atypical patterns encountered when using a flow cytometry-based method to detect residual leukocytes in leukoreduced red blood cell components

BACKGROUND

Universal leukoreduction of blood components is becoming the standard of care. Flow cytometry methods are being used for quality control of the leukoreduction process.

METHODS

We provide an atlas of atypical flow cytograms generated by a commercial LeucoCOUNT assay that was used to enumerate residual leukocytes in leukoreduced red blood cell components. Numeric results are derived from a flow cytogram generated by the assay.

RESULTS

Three types of atypical flow cytogram patterns were observed during process validation or routine quality control of leukoreduced red blood cell components. (a) Fixation artifact: Fixation of control or test samples can alter the staining intensity compared with fresh cells. (b) "Rain" pattern: Flow cytometry methods count slightly damaged leukocytes not removed during leukoreduction. Slightly damaged leukocytes appear on a flow cytogram like "rain" falling from a well-defined "cloud" of intact residual leukocytes. Discrepancies between automated flow cytometry results and subjective manual counting methods can occur. (c) Autofluorescence-debris pattern: Cell debris and age-related changes in the sample can cause shifts in the fluorescence staining pattern, resulting in erroneous test results.

CONCLUSION

Review of flow cytograms is essential for accurate reporting of flow cytometry-based methods for enumerating residual leukocytes in leukoreduced blood components.

Surgical Interbody Research Group–radiographic assessment of interbody fusion devices: fusion criteria for anterior lumbar interbody surgery

The authors present their radiographic criteria for assessing fusion of the lumbar spine after anterior interbody fusion with intradiscal implants. These criteria include the assessment of plain radiographs, dynamic motion radiographs, and thin-cut computerized tomography scans. Fusion within the instrumented spinal motion segment can be determined using radiographic evaluation to assess spinal alignment on sequential examinations, angular and translational changes on dynamic motion studies, and device–host interface, and to identify new bone formation and bone remodeling. Finally, to aid the clinician in assessing fusion, the authors describe the five zones of fusion within the intervertebral disc space.

dCtBP-dependent and -independent repression activities of the Drosophila Knirps protein

Transcriptional repressor proteins play essential roles in controlling the correct temporal and spatial patterns of gene expression in Drosophila melanogaster embryogenesis. Repressors such as Knirps, Krüppel, and Snail mediate short-range repression and interact with the dCtBP corepressor. The mechanism by which short-range repressors block transcription is not well understood; therefore, we have undertaken a detailed structure-function analysis of the Knirps protein. To provide a physiological setting for measurement of repression, the activities of endogenous or chimeric Knirps repressor proteins were assayed on integrated reporter genes in transgenic embryos. Two distinct repression functions were identified in Knirps. One repression activity depends on dCtBP binding, and this function maps to a C-terminal region of Knirps that contains a dCtBP binding motif. In addition, an N-terminal region was identified that represses in a CtBP mutant background and does not bind to the dCtBP protein in vitro. Although the dCtBP protein is important for Knirps activity on some genes, one endogenous target of the Knirps protein, the even-skipped stripe 3 enhancer, is not derepressed in a CtBP mutant. These results indicate that Knirps can utilize two different pathways to mediate transcriptional repression and suggest that the phenomenon of short-range repression may be a combination of independent activities.

Phosphorylation of the beta1 integrin cytoplasmic domain: toward an understanding of function and mechanism

As F9 stem cells differentiate into parietal endoderm they form focal adhesion sites. There is a concomitant decrease in the level of phosphorylation of S785 in the cytoplasmic domain of the beta1 integrin subunit. Previous transfection studies demonstrate that site-specific mutations at this residue, mimicking different phosphorylation states, can alter the subcellular localization of the subunit in differentiating F9 cells. We now extend these observations in an attempt to substantiate the function of beta1 phosphorylation and determine how the phosphorylation levels are regulated. We show that treatment of parietal endoderm with okadaic acid induces an increase in beta1 phosphorylation and selective loss of beta1 from focal adhesion sites. Using a PCR approach, we identify two phosphatases expressed in parietal endoderm, including PP2A. Using a crosslinking approach, where antibodies are added to live cells, we show that the catalytic subunit of PP2A co-immunoprecipitates with beta1. Immunocytochemistry shows PP2A colocalizing to focal adhesion sites with beta1. In addition integrin-linked kinase (ILK) co-immunoprecipitates with beta1 in parietal endoderm and localizes to focal adhesion sites. Okadaic acid treatment significantly decreases the level of ILK associated with beta1. A possible role for regulated beta1 phosphorylation in cell migration is discussed.

TACI and BCMA are receptors for a TNF homologue implicated in B-cell autoimmune disease

B cells are important in the development of autoimmune disorders by mechanisms involving dysregulated polyclonal B-cell activation, production of pathogenic antibodies, and co-stimulation of autoreactive T cells. zTNF4 (BLyS, BAFF, TALL-1, THANK) is a member of the tumour necrosis factor (TNF) ligand family that is a potent co-activator of B cells in vitro and in vivo. Here we identify two receptors for zTNF4 and demonstrate a relationship between zTNF4 and autoimmune disease. Transgenic animals overexpressing zTNF4 in lymphoid cells develop symptoms characteristic of systemic lupus erythaematosus (SLE) and expand a rare population of splenic B-Ia lymphocytes. In addition, circulating zTNF4 is more abundant in NZBWF1 and MRL-lpr/lpr mice during the onset and progression of SLE. We have identified two TNF receptor family members, TACI and BCMA, that bind zTNF4. Treatment of NZBWF1 mice with soluble TACI-Ig fusion protein inhibits the development of proteinuria and prolongs survival of the animals. These findings demonstrate the involvement of zTNF4 and its receptors in the development of SLE and identify TACI-Ig as a promising treatment of autoimmune disease in humans.

Use of single-frequency bioimpedance at 50 kHz to estimate total body water in patients with multiple organ failure and fluid overload

OBJECTIVE

To investigate the relationship between single-frequency bioimpedance at 50 kHz (both total body impedance and segmental impedance) and total body water, measured using tritiated water in the presence of the severe fluid retention seen in multiple organ failure.

DESIGN

Prospective, controlled study.

SETTING

General intensive care unit.

SUBJECTS

Twenty patients with multiple organ failure and 30 normal volunteers, of whom a subgroup of ten had total body water measured.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Total body water and total and segmental bioimpedance values at 50 kHz were measured using tritiated water and a Holtain body composition analyzer in 20 patients with multiple organ failure and in ten normal volunteers. An additional 20 normal volunteers also had segmental and total body impedance measured. There was no difference in the linear regression lines constructed for the patients and the volunteers, but the SEM in the patients (7.6 L) was four times that seen in the normal subjects (1.9 L). In a further seven patients, the impedance technique overestimated the change in total body water, deduced from acute changes in weight, by between 0% and 46% (median, 12%). In the patients, who were supine, the knee-ankle segment contributed significantly more to total body impedance than it did in the normal volunteers (42.5% vs. 34.4%; p < .001), who were upright and mobile immediately before the measurement.

CONCLUSIONS

Although single-frequency bioimpedance does give an indication of total body water and change in total body water, it is neither precise nor accurate enough to be the sole guide to fluid therapy. The proportion of total impedance contributed by the knee-ankle segment, which contains relatively little water, was significantly greater in the patients than in the controls, probably reflecting better drainage of fluid from the lower limb in the supine position.

Visual confrontation naming outcome after standard left anterior temporal lobectomy with sparing versus resection of the superior temporal gyrus: a randomized prospective clinical trial

PURPOSE

Intraoperative mapping of eloquent cortex during left (speech dominant) anterior temporal lobectomy has shown a significant proportion of patients to have sites on the anterior superior temporal gyrus at which visual confrontation naming can be disrupted by electrical stimulation. The purpose of this investigation was to conduct a randomized clinical trial to determine whether sparing versus resection of the superior temporal gyrus affected visual confrontation naming outcome after standard left anterior temporal lobectomy. Also examined was the degree to which inherent patient characteristics were associated with language outcome regardless of surgical technique.

METHODS

Thirty patients with intractable left temporal lobe epilepsy undergoing standard anterior temporal lobectomy were randomized in regard to whether the superior temporal gyrus was resected or spared. Patients were tested preoperatively and 6-8 months postoperatively by using two conventional tests of visual confrontation naming ability.

RESULTS

No significant differences were found between the groups in either confrontation naming or surgical outcome. Postoperative decline in nominal speech was most closely associated with later age at onset of epilepsy/absence of hippocampal sclerosis.

CONCLUSIONS

It appears that specific types of localization-related temporal lobe epilepsy are more closely associated with the risk of adverse language outcome after anterior temporal lobectomy than with the surgical variations investigated in this study.

Recommendations for incorporating palliative care education into the acute care hospital setting

This article presents recommendations for improving the education of physicians about end-of-life care in the acute care hospital setting. The authors, who have a variety of backgrounds and represent several types of institutions, formulated and reached consensus on these recommendations as members of the Acute Care Hospital Working Group, one of eight working groups convened at the National Consensus Conference on Medical Education for Care Near the End of Life in May 1997. A recently published literature review on the status of palliative care education, a summary of recent research on education about end-of-life care, and expert opinion were helpful in developing the recommendations. The authors emphasize that the acute care setting offers many opportunities for education about care at the end of life. Faculty should support learners' appreciation of the importance of end-of-life care, and convey the meaning and privilege of attending to patients and families at this difficult time. Faculty should teach students and residents to provide care that embodies attention to the control of distressing physical, physiologic, and spiritual symptoms, appropriate awareness of patients' differing cultural backgrounds and their impact upon the experience of dying, excellent communication skills, the application of bioethical principles, timely referral and smooth transition to other care settings that meet patient and family goals, and the role of the interdisciplinary team in meeting the diverse needs of dying patients and their families.

An evaluation of the pharmacokinetics of donepezil HCl in patients with moderately to severely impaired renal function

AIM

The aim of this study was to evaluate the pharmacokinetics of donepezil HCl (5 mg) in patients with moderately to severely impaired renal function (creatinine clearance: <30 ml min(-1) 1.73 m(-2)), following the administration of single oral doses.

METHODS

This was an open-label, non-randomized study in patients with compromised renal function (n=11), and in age- and gender-matched healthy controls (n =11). Each subject received a single oral dose of 5 mg donepezil. Blood samples for pharmacokinetic measurements were taken at specified intervals for 17 days post-dose. Concentrations of donepezil in plasma were measured by HPLC with UV detection.

RESULTS

There were no statistical differences between the two groups for any of the pharmacokinetic parameters evaluated (ANOVA). Cmax (mean +/- SD) was 7.7+/-1.2 ng ml(-1) in healthy subjects and 8.3+/-3.2 ng ml(-1) in renally impaired patients. AUC(0-infinity) in healthy subjects and in renally impaired patients was 539+/-115 ng h ml(-1) and 640+/-150 ng h ml(-1), respectively. The mean half-life of donepezil was 86.7+/-23.3 h in healthy subjects and 91.3+/-40.9 h in the renally impaired patients. The drug was well tolerated by all study participants. There were no clinically significant changes in vital signs, clinical chemistry or ECG parameters.

CONCLUSIONS

These findings suggest that the pharmacokinetics of donepezil do not change in patients with moderately to severely impaired renal function.

Concurrent administration of donepezil HCl and theophylline: assessment of pharmacokinetic changes following multiple-dose administration in healthy volunteers

AIM

The aim of the study was to evaluate the pharmacokinetics of theophylline administered alone, and in combination with donepezil HCl, following multiple-dose administration of both drugs in healthy volunteers.

METHODS

This was an open-label, randomized, two-period crossover study in healthy male volunteers (n=12). During each treatment period, subjects received either titrated-dose theophylline alone, or in combination with donepezil (5 mg, once daily) for 10 consecutive days. On day 10 of each treatment period, serial blood samples for the determination of theophylline concentrations in plasma were measured up to 24 h. Treatment periods were separated by a 3-week, drug-free washout. Plasma concentrations of theophylline were determined by HPLC with UV detection.

RESULTS

No statistically significant differences in theophylline pharmacokinetics (Cmax, AUC or tmax) were observed between theophylline administered alone and in combination with donepezil. No clinically significant changes in vital signs, ECG parameters or clinical laboratory tests were observed in any subject during any treatment period.

CONCLUSIONS

Concurrent administration of donepezil HCl does not alter the pharmacokinetic profile of theophylline following multiple-dose administration of both drugs in healthy volunteers. These findings suggest that donepezil may be safely co-administered with theophylline without a need for dose modification or additional monitoring procedures.