Long-lived proteins and DNA as candidate predictive biomarkers for tissue associated diseases

Protein turnover is an important mechanism to maintain proteostasis. Long-lived proteins (LLPs) are vulnerable to lose their function due to time-accumulated damages. In this study we employed in vivo stable isotope labeling in mice from birth to postnatal day 89. Quantitative proteomics analysis of ten tissues and plasma identified 2113 LLPs, including widespread and tissue-specific ones. Interestingly, a significant percentage of LLPs was detected in plasma, implying a potential link to age-related cardiovascular diseases. LLPs identified in brains were related to neurodegenerative diseases. In addition, the relative quantification of DNA-derived deoxynucleosides from the same tissues provided information about cellular DNA renewal and showed good correlation with LLPs in the brain. The combined data reveal tissue-specific maps of mouse LLPs that may be involved in pathology due to a low renewal rate and an increased risk of damage. Tissue-derived peripheral LLPs hold promise as biomarkers for aging and age-related diseases.

MMP9 mRNA is a potential diagnostic and treatment monitoring marker for PTSD: Evidence from mice and humans

Although matrix metalloproteinase 9 (MMP9) has been found associated with various psychiatric disorders and with threat memories in humans, its role in post-traumatic stress disorder (PTSD) and related animal models is understudied. Thus, we analyzed MMP9 mRNA expression kinetics during two different stress experiments, i.e., the Trier Social Stress Test and the dexamethasone suppression test (DST), in whole blood of two independent cohorts of PTSD patients vs. non-traumatized healthy controls (HC) and, moreover, in a mouse model of PTSD and in dexamethasone-treated mice. Besides MMP9, we quantified mRNA levels of four of its regulators, i.e., interleukin (IL)-1 receptor 1 and 2 (IL1R1, IL1R2), IL-6 receptor and tumor necrosis factor receptor 1 (TNFR1) in 10 patients exposed to the DST before vs. after successful PTSD psychotherapy vs. 13 HC and, except from Il6r, also in different brain regions of the PTSD mouse model. We are the first to show that blood MMP9 mRNA concentrations were elevated after acute dexamethasone in PTSD patients, improved upon partial remission of PTSD and were, furthermore, also elevated, together with its regulator Tnfr1, in the prefrontal cortex of PTSD-like mice. In contrast, blood TNFR1 and IL1R2 were markedly underexpressed in PTSD patients. In conclusion, we found translational evidence supporting that, I, TNFR1 and MMP9 mRNA expression might be involved in PTSD pathobiology, II, might constitute potential diagnostic blood biomarkers for PTSD and, importantly, III, post-dexamethasone blood MMP9 hyperexpression, which speculatively results from post-dexamethasone underexpression of IL1R2, might serve also as potential treatment monitoring biomarker for PTSD.

Oxytocin receptor is a potential biomarker of the hyporesponsive HPA axis subtype of PTSD and might be modulated by HPA axis reactivity traits in humans and mice

This study aimed to identify yet unavailable blood biomarkers for the responsive and the hyporesponsive hypothalamic-pituitary-adrenal (HPA) axis subtypes of posttraumatic stress disorder (PTSD). As, I, we recently discovered the intranasal neuropeptide oxytocin to reduce experimentally provoked PTSD symptoms, II, expression of its receptor (OXTR) has hitherto not been assessed in PTSD patients, and III, oxytocin and OXTR have previously been related to the HPA axis, we considered both as suitable candidates. During a Trier Social Stress Test (TSST), we compared serum oxytocin and blood OXTR mRNA concentrations between female PTSD patients, their HPA axis reactivity subtypes and sex and age-matched healthy controls (HC). At baseline, both candidates differentiated the hyporesponsive HPA axis subtype from HC, however, only baseline OXTR mRNA discriminated also between subtypes. Furthermore, in the hyporesponsive HPA axis subgroup, OXTR mRNA levels correlated with PTSD symptoms and changed markedly during the TSST. To assess the influence of (traumatic) stress on the cerebral expression of oxytocin and its receptor and to test their suitability as biomarkers for the mouse PTSD-like syndrome, we then analyzed oxytocin, its mRNA (Oxt) and Oxtr mRNA in three relevant brain regions and Oxt in blood of a PTSD mouse model. To further explore the HPA axis reactivity subtype dependency of OXTR, we compared cerebral OXTR protein expression between mice exhibiting two different HPA axis reactivity traits, i.e., FK506 binding protein 51 knockout vs. wildtype mice. In summary, blood OXTR mRNA emerged as a potential biomarker of the hyporesponsive HPA axis PTSD subtype and prefrontal cortical Oxtr and Oxt of the mouse PTSD-like syndrome. Moreover, we found first translational evidence for a HPA axis responsivity trait-dependent regulation of OXTR expression. The lack of a cohort of the (relatively rare) hyporesponsive HPA axis subtype of HC is a limitation of our study.

The influence of mouth breathing on skeletal and dental features of splanchnocranium

OBJECTIVE

This study was performed to investigate changes in dentofacial characteristics associated with mouth breathing (MB) and adenoidectomy.

BACKGROUND

MB is considered to be an etiological factor of malocclusion. Adenoidectomy is supposed to have the ability to prevent the development of dentofacial deformities.

METHODS

This retrospective study included 123 patients, namely 57 nose breathers, 19 former mouth breathers, who have undergone adenoidectomy, and 47 mouth breathers. The groups were compared according to their skeletal and dental characteristics. The measurements of each individual were obtained from lateral cephalograms and dental casts. The comparison was done using one-way ANOVA, Bonferroni post-hoc, Mann-Whitney U and Kruskal-Wallis tests. The statistically significant difference was defined as p<0.05.

RESULTS

The MB group showed an increase in ArGoMe (p=0.02) angle. No difference was found in the sagittal parameters among the groups. Upper dental arch compression was positively correlated with MB(p=0.00), even in adenoidectomy cases (p=0.01).

CONCLUSION

MB alters the vertical and transverse growth of the craniofacial complex. It is associated with longer lower anterior facial height and decreased maxillary intermolar distance. However, it does not influence the sagittal parameters. Airway clearance via adenoidectomy promotes the normalization of vertical parameters (Tab. 1, Fig. 2, Ref. 20).

Do we have to reduce the recall period? Validity of a daily physical activity questionnaire (PAQ24) in young active adults

Background

Combining the strengths of physical activity (PA) diaries and questionnaires may be needed to improve the unsatisfying measurement quality of existing PA questionnaires. This study investigated the construct validity of a short PA questionnaire (Physical Activity Questionnaire for 24 h [PAQ24]) with a recall period of one day.

Methods

In this cross-sectional study, participants completed the PAQ24 on seven consecutive days while wearing an accelerometer (GENEActiv). Thereafter, the Global Physical Activity Questionnaire (GPAQ) was completed. Spearman correlation coefficients and Bland-Altman analysis were used to assess construct validity.

Results

Overall, 50 active adults (11 women, mean age = 25.1 ± 2.5) participated. Relative agreements between Total PA of PAQ24 and accelerometer were 0.37 ≤ ρ ≤ 0.72 for each day with satisfying agreement on five out of seven days. Weekly relative agreement for Total PA was moderate (ρ = 0.44). Relative agreements between PAQ24 and GPAQ were ρ = 0.43 for Total PA. Daily and weekly absolute agreements were poor indicated by wide limits of agreement.

Conclusions

In contrast to weekly Total PA, the majority of daily results of the PAQ24 showed satisfying construct validity. A short recall period may improve the measurement quality of PA questionnaires, but measurement errors and the costs of multiple administrations must be considered in future studies.

Multi-omics analysis identifies mitochondrial pathways associated with anxiety-related behavior

Stressful life events are major environmental risk factors for anxiety disorders, although not all individuals exposed to stress develop clinical anxiety. The molecular mechanisms underlying the influence of environmental effects on anxiety are largely unknown. To identify biological pathways mediating stress-related anxiety and resilience to it, we used the chronic social defeat stress (CSDS) paradigm in male mice of two inbred strains, C57BL/6NCrl (B6) and DBA/2NCrl (D2), that differ in their susceptibility to stress. Using a multi-omics approach, we identified differential mRNA, miRNA and protein expression changes in the bed nucleus of the stria terminalis (BNST) and blood cells after chronic stress. Integrative gene set enrichment analysis revealed enrichment of mitochondrial-related genes in the BNST and blood of stressed mice. To translate these results to human anxiety, we investigated blood gene expression changes associated with exposure-induced panic attacks. Remarkably, we found reduced expression of mitochondrial-related genes in D2 stress-susceptible mice and in exposure-induced panic attacks in humans, but increased expression of these genes in B6 stress-susceptible mice. Moreover, stress-susceptible vs. stress-resilient B6 mice displayed more mitochondrial cross-sections in the post-synaptic compartment after CSDS. Our findings demonstrate mitochondrial-related alterations in gene expression as an evolutionarily conserved response in stress-related behaviors and validate the use of cross-species approaches in investigating the biological mechanisms underlying anxiety disorders.

Somatic mutations in kinetochore gene KNSTRN are associated with basal proliferating actinic keratoses and cutaneous squamous cell carcinoma

BACKGROUND

Mutations in kinetochore gene KNSTRN accelerate the development of cutaneous squamous cell carcinoma (SCC) and may correlate with different histological classifications of actinic keratosis (AKs).

OBJECTIVE

To determine KNSTRN gene mutation frequency in healthy skin (HS), actinically damaged skin (ADS), in AKs with different histomorphological gradings and invasive SCCs.

METHODS

All samples were histologically evaluated. AK lesions were additionally classified according to their upwards (AK I-III) and downwards (PRO I-III) directed growth pattern. Mutation analyses of all samples were performed using the Sanger method.

RESULTS

With one exception, all detected mutations in KNSTRN gene showed an alanine-to-glutamate substitution at codon 40 (p.Ala40Glu). p.Ala40Glu mutation was found in 6.9% (2/29) of HS, in 16.1% (5/31) of ADS, in 18.3% (20/109) of AKs and in 30.0% (9/30) of invasive SCCs. Further stratification of AKs using the common AK classification of Röwert-Huber revealed the p.Ala40Glu mutation in 14.7% (5/43), 13.3% (4/30) and 24.4% (11/45) (AK I, II and III). In contrast, the new PRO classification showed a distribution of 3.6% (1/28) in PRO I, 21.7% (13/60) in PRO II and 28.6% (6/21) in PRO III. Mutation frequency in HS showed significant differences compared to AKs classified as PRO III and invasive SCCs (P < 0.05). In contrast, there were no statistically significant differences between HS and AKs when classified according to Röwert-Huber.

CONCLUSIONS

Recurrent somatic mutation p.Ala40Glu in KNSTRN gene is associated with basal proliferating AKs in accordance with invasive SCCs. This supports the impact of basal proliferative pattern in terms of progression.

The influence of different illumination parameters on protoporphyrin IX induced cell death in squamous cell carcinoma cells

BACKGROUND

Topical photodynamic therapy (PDT) is a highly effective therapy especially for extended cancerized fields of the skin. Whenever extended fields are treated pain management is advisable. Light source mediated pain management can be performed by reducing fluence rates, as long as this does not compromise efficacy.

METHODS

Two squamous cell carcinoma cell lines (A431 and SCC-13) were subjected to in vitro PDT using two different ALA concentrations and synthesis intervals and protoporphyrin IX (PpIX) synthesis was assessed. Two total light doses (6 J/cm² and 37 J/cm²) were applied at three different fluence rates and cell viability was measured using the MTS-test.

RESULTS

Both cell lines synthetized PpIX at different kinetics. A431 cells produced a maximum 28.6 nmol/l PpIX, while SCC-13 reached only a production of 8.7 nmol/l. Illumination reduced cell viability depending on PpIX content and light dose. When a lower light dose (6 J/cm²) was applied, only the combination with the highest PpIX content was effective in A431 cells and no effect could be detected in SCC-13 cells. With a light dose of 37 J/cm², lower PpIX amounts became effective in A431 and cell death could be induced in SCC-13 cells. Light fluence rate had no differential effect in this setup.

CONCLUSIONS

In both, A431 and SCC-13 cells, total light dose is a key factor for photodynamic efficacy. Additionally, our results hint towards a threshold concentration of PpIX upon which a drastic loss of viability occurs. Light fluence rate in the analyzed range is not a limiting factor of photodynamic cytotoxicity. This may allow for the clinical implementation of low fluence rate protocols for pain management without compromising efficacy.

Patient-reported health outcomes in patients with non-melanoma skin cancer and actinic keratosis: results from a large-scale observational study analysing effects of diagnoses and disease progression

BACKGROUND

Non-melanoma skin cancer (NMSC) and actinic keratosis (AK) are very common among fair-skinned individuals. A disease continuum from AK to squamous cell carcinoma (SCC) has been frequently postulated. AK and NMSC may influence quality of life (QL) of patients, and it can be suspected that disease progression entails a QL reduction. The purpose of this study was to document QL in patients with NMSC and AK using the health-outcome questionnaire EQ-5D-5L.

METHODS

The study was designed as a non-interventional, prospective, cross-sectional study. Patients with AK, SCC, basal cell carcinoma (BCC) or multiple diagnoses were enrolled in this study in 29 dermatological centres across Germany. Patients were asked to complete the EQ-5D-5L (compromising EQ Index and EQ VAS), and the dermatologists provided diagnosis, disease history and treatment data.

RESULTS

A total of 1184 patients were enrolled and diagnosed as follows: 73% AK, 49% BCC and 17% SCC. 66% had a single diagnosis, 28% two different diagnoses and 6% three different diagnoses. QL was strongly associated with patients' diagnosis. Patients with a single AK diagnosis had significantly higher mean EQ VAS (78) than patients with BCC (74), SCC (72), and BCC plus SCC (69), P < 0.050. When the effects of disease progression were calculated, patients with AK plus SCC reported significantly less mean EQ VAS (71) than patients with a single AK diagnosis (78), P < 0.011.

CONCLUSIONS

While rarely being imminently life-threatening, NMSC and AK have an impact on QL as quantified by the EQ-5D-5L. This impact is associated with diagnosis (AK vs. NMSC) and clinical progression (AK vs. AK plus SCC). Both lead to a clear decline in QL. This shows that disease progression is perceived and judged as detrimental by patients and that AK and NMSC should be diligently treated to preserve and restore QL.

A phase I/II study of KW-2478, an Hsp90 inhibitor, in combination with bortezomib in patients with relapsed/refractory multiple myeloma

Background:

KW-2478 is a novel non-ansamycin Hsp90 inhibitor with modest single-agent activity in relapsed/refractory myeloma but which shows synergistic antimyeloma activity with bortezomib (BTZ) in preclinical studies. This study determined the safety, preliminary clinical activity, and pharmacokinetics of KW-2478, an Hsp90 inhibitor, in combination with BTZ in patients with relapsed/refractory multiple myeloma (MM).

Methods:

Phase I dose escalation determined the recommended phase II dose (RP2D) of KW-2478 plus BTZ, which was then used during phase II.

Results:

The maximum tolerated dose was not reached during phase I and the RP2D was KW-2478 175 mg m⁻² plus BTZ 1.3 mg m⁻² on days 1, 4, 8, and 11 every 3 weeks. In the efficacy evaluable phase I/II population treated at the RP2D (n=79), the objective response rate was 39.2% (95% confidence interval: 28.4–50.9%), clinical benefit rate 51.9% (40.4–63.3%), median progression-free survival 6.7 (5.9-not reached (NR)) months, and median duration of response 5.5 (4.9-NR) months. In the phase I/II safety population (n=95), the most frequently observed treatment-related grade 3/4 adverse events were diarrhoea, fatigue, and neutropenia (each in 7.4% of patients), and nausea and thrombocytopenia (each in 5.3%).

Conclusions:

KW-2478 plus BTZ was well tolerated with no apparent overlapping toxicity in patients with relapsed/refractory MM. The antimyeloma activity of KW-2478 in combination with BTZ as scheduled in this trial appeared relatively modest; however, the good tolerability of the combination would support further exploration of alternate dosing schedules and combinations.

Designing and evaluating Brain Powered Games for cognitive training and rehabilitation in at-risk African children

BACKGROUND

Valid, reliable, accessible, and cost-effective computer-training approaches can be important components in scaling up educational support across resource-poor settings, such as sub-Saharan Africa. The goal of the current study was to develop a computer-based training platform, the Michigan State University Games for Entertainment and Learning laboratory's Brain Powered Games (BPG) package that would be suitable for use with at-risk children within a rural Ugandan context and then complete an initial field trial of that package.

METHODS

After game development was completed with the use of local stimuli and sounds to match the context of the games as closely as possible to the rural Ugandan setting, an initial field study was completed with 33 children (mean age = 8.55 ± 2.29 years, range 6-12 years of age) with HIV in rural Uganda. The Test of Variables of Attention (TOVA), CogState computer battery, and the Non-Verbal Index from the Kaufman Assessment Battery for Children, 2nd edition (KABC-II) were chosen as the outcome measures for pre- and post-intervention testing. The children received approximately 45 min of BPG training several days per week for 2 months (24 sessions).

RESULTS

Although some improvements in test scores were evident prior to BPG training, following training, children demonstrated clinically significant changes (significant repeated-measures outcomes with moderate to large effect sizes) on specific TOVA and CogState measures reflecting processing speed, attention, visual-motor coordination, maze learning, and problem solving.

CONCLUSIONS

Results provide preliminary support for the acceptability, feasibility, and neurocognitive benefit of BPG and its utility as a model platform for computerized cognitive training in cross-cultural low-resource settings.

Identification and characterization of HPA-axis reactivity endophenotypes in a cohort of female PTSD patients

Analysis of the function of the hypothalamic-pituitary-adrenal (HPA)-axis in patients suffering from posttraumatic stress disorder (PTSD) has hitherto produced inconsistent findings, inter alia in the Trier Social Stress Test (TSST). To address these inconsistencies, we compared a sample of 23 female PTSD patients with either early life trauma (ELT) or adult trauma (AT) or combined ELT and AT to 18 age-matched non-traumatized female healthy controls in the TSST which was preceded by intensive baseline assessments. During the TSST, we determined a variety of clinical, psychological, endocrine and cardiovascular parameters as well as expression levels of four HPA-axis related genes. Using a previously reported definition of HPA-axis responsive versus non-responsive phenotypes, we identified for the first time two clinically and biologically distinct HPA-axis reactivity subgroups of PTSD. One subgroup ("non-responders") showed a blunted HPA-axis response and distinct clinical and biological characteristics such as a higher prevalence of trauma-related dissociative symptoms and of combined AT and ELT as well as alterations in the expression kinetics of the genes encoding for the mineralocorticoid receptor (MR) and for FK506 binding protein 51 (FKBP51). Interestingly, this non-responder subgroup largely drove the relatively diminished HPA axis response of the total cohort of PTSD patients. These findings are limited by the facts that the majority of patients was medicated, by the lack of traumatized controls and by the relatively small sample size. The here for the first time identified and characterized HPA-axis reactivity endophenotypes offer an explanation for the inconsistent reports on HPA-axis function in PTSD and, moreover, suggest that most likely other factors than HPA-axis reactivity play a decisive role in determination of PTSD core symptom severity.

A role for synapsin in FKBP51 modulation of stress responsiveness: Convergent evidence from animal and human studies

Both the molecular co-chaperone FKBP51 and the presynaptic vesicle protein synapsin (alternatively spliced from SYN1-3) are intensively discussed players in the still insufficiently explored pathobiology of psychiatric disorders such as major depression, schizophrenia and posttraumatic stress disorder (PTSD). To address their still unknown interaction, we compared the expression levels of synapsin and five other neurostructural and HPA axis related marker proteins in the prefrontal cortex (PFC) and the hippocampus of restrained-stressed and unstressed Fkbp5 knockout mice and corresponding wild-type littermates. In addition, we compared and correlated the gene expression levels of SYN1, SYN2 and FKBP5 in three different online datasets comprising expression data of human healthy subjects as well as of predominantly medicated patients with different psychiatric disorders. In summary, we found that Fkbp5 deletion, which we previously demonstrated to improve stress-coping behavior in mice, prevents the stress-induced decline in prefrontal cortical (pc), but not in hippocampal synapsin expression. Accordingly, pc, but not hippocampal, synapsin protein levels correlated positively with a more active mouse stress coping behavior. Searching for an underlying mechanism, we found evidence that deletion of Fkbp5 might prevent stress-induced pc synapsin loss, at least in part, through improvement of pc Akt kinase activity. These results, together with our finding that FKBP5 and SYN1 mRNA levels were regulated in opposite directions in the PFC of schizophrenic patients, who are known for exhibiting an altered stress-coping behavior, provide the first evidence of a role for pc synapsin in FKBP51 modulation of stress responsiveness. This role might extend to other tissues, as we found FKBP5 and SYN1 levels to correlate inversely not only in human PFC samples but also in other expression sites. The main limitation of this study is the small number of individuals included in the correlation analyses. Future studies will have to verify the here-postulated role of the FKBP51-Akt kinase-synapsin pathway in stress responsiveness.

Therapeutic Action of Fluoxetine is Associated with a Reduction in Prefrontal Cortical miR-1971 Expression Levels in a Mouse Model of Posttraumatic Stress Disorder

MicroRNAs (miRNA) are a class of small non-coding RNAs that have recently emerged as epigenetic modulators of gene expression in psychiatric diseases like schizophrenia and major depression. So far, miRNAs have neither been studied in patients suffering from posttraumatic stress disorder (PTSD) nor in PTSD animal models. Here, we present the first study exploring the connection between miRNAs and PTSD. Employing our previously established PTSD mouse model, we assessed miRNA profiles in prefrontal cortices (PFCs) dissected from either fluoxetine or control-treated wildtype C57BL/6N mice 74 days after their subjection to either a single traumatic electric footshock or mock-treatment. Fluoxetine is an antidepressant known to be effective both in PTSD patients and in mice suffering from a PTSD-like syndrome. Screening for differences in the relative expression levels of all potential miRNA target sequences of miRBase 18.0 by pairwise comparison of the PFC miRNA profiles of the four mouse groups mentioned resulted in identification of five miRNA candidate molecules. Validation of these miRNA candidates by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) revealed that the therapeutic action of fluoxetine in shocked mice is associated with a significant reduction in mmu-miR-1971 expression. Furthermore, our findings suggest that traumatic stress and fluoxetine interact to cause distinct alterations in the mouse PFC miRNA signature in the long-term.

A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM

Many organisms display rhythms of physiology and behavior that are entrained to the 24-h cycle of light and darkness prevailing on Earth. Under constant conditions of illumination and temperature, these internal biological rhythms persist with a period close to 1 day ("circadian"), but it is usually not exactly 24h. Recent discoveries have uncovered stunning similarities among the molecular circuitries of circadian clocks in mice, fruit flies, and bread molds. A consensus picture is coming into focus around two proteins (called PER and TIM in fruit flies), which dimerize and then inhibit transcription of their own genes. Although this picture seems to confirm a venerable model of circadian rhythms based on time-delayed negative feedback, we suggest that just as crucial to the circadian oscillator is a positive feedback loop based on stabilization of PER upon dimerization. These ideas can be expressed in simple mathematical form (phase plane portraits), and the model accounts naturally for several hallmarks of circadian rhythms, including temperature compensation and the per(L) mutant phenotype. In addition, the model suggests how an endogenous circadian oscillator could have evolved from a more primitive, light-activated switch.

Endoplasmic reticulum retention of the gamma-secretase complex component Pen2 by Rer1

gamma-Secretase is involved in the production of amyloid beta-peptide, which is the principal component of amyloid plaques in the brains of patients with Alzheimer disease. gamma-Secretase is a complex composed of presenilin (PS), nicastrin, anterior pharynx-defective phenotype 1 (Aph1) and PS enhancer 2 (Pen2). We previously proposed a mechanism of complex assembly by which unassembled subunits are retained in the endoplasmic reticulum (ER) and only the fully assembled complex is exported from the ER. We have now identified Retention in endoplasmic reticulum 1 (Rer1) as a protein that is involved in the retention/retrieval of unassembled Pen2 to the ER. Direct binding of unassembled Pen2 to Rer1 is mediated by the first transmembrane domain of Pen2, and a conserved asparagine in this domain is required. Downregulation of Rer1 leads to increased surface localization of Pen2, whereas overexpression of Rer1 stabilizes unassembled Pen2. To our knowledge, Rer1 is the first identified interaction partner of mammalian transmembrane-based retention/retrieval signals.

Control of Peripheral Nerve Myelination by the -Secretase BACE1

Although BACE1 (beta-site amyloid precursor protein-cleaving enzyme 1) is essential for the generation of amyloid-b peptide in Alzheimer's disease, its physiological function is unclear. We found that very high levels of BACE1 were expressed at time points when peripheral nerves become myelinated. Deficiency of BACE1 resulted in the accumulation of unprocessed neuregulin 1 (NRG1), an axonally expressed factor required for glial cell development and myelination. BACE1-/- mice displayed hypomyelination of peripheral nerves and aberrant axonal segregation of small-diameter afferent fibers, very similar to that seen in mice with mutations in type III NRG1 or Schwann cell-specific ErbB2 knockouts. Thus, BACE1 is required for myelination and correct bundling of axons by Schwann cells, probably through processing of type III NRG1.

The presenilin C-terminus is required for ER-retention, nicastrin-binding and gamma-secretase activity

gamma-Secretase is an intramembrane cleaving protease involved in Alzheimer's disease. gamma-Secretase occurs as a high molecular weight complex composed of presenilin (PS1/2), nicastrin (NCT), anterior pharynx-defective phenotype 1 and PS enhancer 2. Little is known about the cellular mechanisms of gamma-secretase assembly. Here we demonstrate that the cytoplasmic tail of PS1 fulfills several functions required for complex formation, retention of unincorporated PS1 and gamma-secretase activity. The very C-terminus interacts with the transmembrane domain of NCT and may penetrate into the membrane. Deletion of the last amino acid is sufficient to completely block gamma-secretase assembly and release of PS1 from the endoplasmic reticulum (ER). This suggests that unincorporated PS1 is actively retained within the ER. We identified a hydrophobic stretch of amino acids within the cytoplasmic tail of PS1 distinct from the NCT-binding site, which is required to retain unincorporated PS1 within the ER. Deletion of the retention signal results in the release of PS1 from the ER and the assembly of a nonfunctional gamma-secretase complex, suggesting that at least a part of the retention motif may also be required for the function of PS1.

Computerized Evaluation of Mammographic Lesions:What Diagnostic Role Does the Shape of the Individual Microcalcifications Play Compared with the Geometry of the Cluster?

OBJECTIVE

The objective of this study was to compare the diagnostic role of features reflecting the geometry of clusters with features reflecting the shape of the individual microcalcification in a mammographic computer-aided diagnosis system.

MATERIALS AND METHODS

Three hundred twenty-four cases of clustered microcalcifications with biopsy-proven results were digitized at 42-microm resolution and analyzed on a computerized system. The shape factor and number of neighbors were computed for each microcalcification, and the eccentricity of the cluster was computed as well. The shape factor is related to the individual microcalcification; the average number of neighbors and the cluster eccentricity reflect the cluster geometry. Stepwise discriminant analysis was used to evaluate the contribution of the extracted features in predicting malignancy. The performance of a classifier based on the features selected by stepwise discriminant analysis was evaluated by receiver operating characteristic (ROC) analysis.

RESULTS

To obtain the best discrimination model, we used stepwise discriminant analysis to select the average number of neighbors and the shape of the individual microcalcification, but excluded cluster eccentricity. A classification scheme assigned the average number of neighbors a weighting factor, which was 1.49 times greater than that assigned to the shape factor of the individual microcalcification. A scheme based only on these two features yielded an ROC curve with an area under the curve (A(z)) of 0.87, indicating a positive predictive value of 61% for 98% sensitivity.

CONCLUSION

Computerized analysis permitted calculations reflecting the shape of individual microcalcification and the geometry of clusters of microcalcifications. For the computerized classification scheme studied, the cluster geometry was more effective in differentiating benign from malignant clusters than was the shape of individual microcalcification.

Network dynamics and cell physiology

Complex assemblies of interacting proteins carry out most of the interesting jobs in a cell, such as metabolism, DNA synthesis, movement and information processing. These physiological properties play out as a subtle molecular dance, choreographed by underlying regulatory networks. To understand this dance, a new breed of theoretical molecular biologists reproduces these networks in computers and in the mathematical language of dynamical systems.

A stochastic, molecular model of the fission yeast cell cycle: role of the nucleocytoplasmic ratio in cycle time regulation

We propose a stochastic version of a recently published, deterministic model of the molecular mechanism regulating the mitotic cell cycle of fission yeast, Schizosaccharomyces pombe. Stochasticity is introduced in two ways: (i) by considering the known asymmetry of cell division, which produces daughter cells of slightly different sizes; and (ii) by assuming that the nuclear volumes of the two newborn cells may also differ. In this model, the accumulation of cyclins in the nucleus is proportional to the ratio of cytoplasmic to nuclear volumes. We have simulated the cell-cycle statistics of populations of wild-type cells and of wee1(-) mutant cells. Our results are consistent with well known experimental observations.

Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions

In recent years, molecular biologists have uncovered a wealth of information about the proteins controlling cell growth and division in eukaryotes. The regulatory system is so complex that it defies understanding by verbal arguments alone. Quantitative tools are necessary to probe reliably into the details of cell cycle control. To this end, we convert hypothetical molecular mechanisms into sets of nonlinear ordinary differential equations and use standard analytical and numerical methods to study their solutions. First, we present a simple model of the antagonistic interactions between cyclin-dependent kinases and the anaphase promoting complex, which shows how progress through the cell cycle can be thought of as irreversible transitions (Start and Finish) between two stable states (G1 and S-G2-M) of the regulatory system. Then we add new pieces to the "puzzle" until we obtain reasonable models of the control systems in yeast cells, frog eggs, and cultured mammalian cells.

Measuring comfort in caregivers and patients during late end-of-life care

The purpose of this study was to test several formats of end-of-life comfort instruments for patients and closely involved caregivers. Kolcaba's Comfort Theory was the theoretical framework utilized. Different response formats for two end-of-life (EOL) comfort questionnaires (for patients and caregivers, respectively), and horizontal and vertical visual analog scales for total comfort (TC) lines were compared in two phases. Evaluable data were collected from both members of 38 patient-caregiver dyads in each phase. Suitable dyads were recruited from two hospice agencies in northeastern Ohio. Cronbach's alpha for the EOL comfort questionnaire (six response Likert-type format) tested during phase I for patients was .98 and for caregivers was .97. Test-retest reliability for the vertical TC line tested during phase I for patients was .64 and for caregivers was .79. The implications of this study for nursing practice and research are derived from the American Nursing Association (ANA) position statement about EOL care, which states that comfort is the goal of nursing for this population. These instruments will be useful for assessing comfort in actively dying patients and comfort of their caregivers as well as for developing evidence-based practice for this population.

Angiotensin-converting enzyme gene polymorphism in patients with systemic lupus

The renin-angiotensin-aldosterone system (RAAS) has been considered one of the probable pathophysiologic mechanisms involved in disease progression. Genetic polymorphism of the RAAS has been associated with the clinical course of renal disease. One of the genetic polymorphisms is a deletion or insertion of a 287 base pair fragment in intron 16 of the angiotensin-converting enzyme (ACE) gene. It is known that ACE gene polymorphism is present in humans and that it is associated with an increased risk of cardiovascular diseases, renal disease progression and sarcoidosis. In this study, the potential significance of ACE gene polymorphism in patients with systemic lupus erythematosus (SLE) was investigated. ACE gene polymorphism was determined in 18 patients with SLE and in 21 healthy volunteers as a control group. The mean age of patients was 38.5 years. All patients had a mean follow-up of 30.7 +/- 20.2 months (range 5-95 months). ACE genotypes were determined by the method of polymerase chain reaction. Proteinuria and creatinine were also followed. The frequency of DD, ID and II genotypes was 50%, 28% and 22% in SLE patients and 25%, 50% and 25% in healthy controls, respectively. DD genotype was more common in SLE patients than in the control group. The patients with II genotype had lower proteinuria and creatinine level than those with DD genotype (p < 0.05). The time to disease remission was shorter in patients with II genotype (p < 0.05). Study results indicated an increased frequency of D allele in SLE patients. The increased ACE activity in these patients pointed to the need of further studies of ACE gene polymorphism in SLE.

Modeling the fission yeast cell cycle: quantized cycle times in wee1- cdc25Delta mutant cells

A detailed mathematical model for the fission yeast mitotic cycle is developed based on positive and negative feedback loops by which Cdc13/Cdc2 kinase activates and inactivates itself. Positive feedbacks are created by Cdc13/Cdc2-dependent phosphorylation of specific substrates: inactivating its negative regulators (Rum1, Ste9 and Wee1/Mik1) and activating its positive regulator (Cdc25). A slow negative feedback loop is turned on during mitosis by activation of Slp1/anaphase-promoting complex (APC), which indirectly re-activates the negative regulators, leading to a drop in Cdc13/Cdc2 activity and exit from mitosis. The model explains how fission yeast cells can exit mitosis in the absence of Ste9 (Cdc13 degradation) and Rum1 (an inhibitor of Cdc13/Cdc2). We also show that, if the positive feedback loops accelerating the G(2)/M transition (through Wee1 and Cdc25) are weak, then cells can reset back to G(2) from early stages of mitosis by premature activation of the negative feedback loop. This resetting can happen more than once, resulting in a quantized distribution of cycle times, as observed experimentally in wee1(-) cdc25Delta mutant cells. Our quantitative description of these quantized cycles demonstrates the utility of mathematical modeling, because these cycles cannot be understood by intuitive arguments alone.

Optimizing parameters for computer-aided diagnosis of microcalcifications at mammography

RATIONALE AND OBJECTIVES

The purpose of this study was to optimize selection of the mammographic features most useful in discriminating benign from malignant clustered microcalcifications.

MATERIALS AND METHODS

The computer-aided diagnosis (CAD) system automatically extracted from digitized mammograms 13 quantitative features characterizing microcalcification clusters. Archival cases (n = 134; patient age range, 31-77 years; mean age, 56.8 years) with known histopathologic results (79 malignant, 55 benign) were selected. Three radiologists at three facilities independently analyzed the microcalcifications by using the CAD system. Stepwise discriminant analysis selected the features best discriminating benign from malignant microcalcifications. A classification scheme was constructed on the basis of these optimized features, and its performance was evaluated by using receiver operating characteristic (ROC) analysis.

RESULTS

Six of the 13 variables extracted by the CAD system were selected by stepwise determinant analysis for generating the classification scheme, which yielded an ROC curve with an area (Az) of 0.98, specificity of 83.64%, positive predictive value of 89.53%, and accuracy of 91.79% for 98% sensitivity. When patient age was an additional variable, the scheme's performance improved, but this was not statistically significant (Az = 0.98). The ROC curve of the classifier (without age as an additional variable) yielded a high Az of 0.96 for patients younger than 50 years and an even higher (P < .02) Az of 0.99 for those 50 years or older.

CONCLUSION

Stepwise discriminant analysis optimized performance of a classification scheme for microcalcifications by selecting six optimized features. Scheme performance was significantly (P < .02) higher for women 50 years or older, but the addition of patient age as a variable did not produce a statistically significant increase in performance.

Quantitative characterization of mass lesions on digitized mammograms for computer-assisted diagnosis

RATIONALE AND OBJECTIVES

To investigate features for discriminating benign from malignant mammographic findings by using computer-aided diagnosis (CAD) and to test the accuracy of CAD interpretations of mass lesions.

METHODS

Fifty-five sequential, mammographically detected mass lesions, referred for biopsy, were digitized for computerized reevaluation with a CAD system. Quantitative features that characterize spiculation were automatically extracted by the CAD system. Data generated by 271 known retrospective cases were used to set reference values indicating the range for malignant and benign lesions. After conventional interpretation of the 55 prospective cases, they were evaluated a second time by the radiologist using the extracted features and the reference ranges. In addition, a pattern-recognition scheme based on the extracted features was used to classify the prospective cases. Accuracy of interpretation with and without the CAD system was evaluated using receiver operating characteristic (ROC) curve analysis.

RESULTS

Sensitivity of the CAD diagnosis for the prospective cases improved from 92% to 100%. Specificity improved significantly from 26.7% to 66.7%. This was accompanied by a significant increase in the accuracy of diagnosis from 56.4% to 81.8% and in the positive predictive value from 51.1% to 71.4%. The Az for the CAD ROC curve significantly increased from 0.73 to 0.90. The performance of the classification scheme was slightly lower than that of the radiologists' interpretation with the CAD system.

CONCLUSIONS

Use of the CAD system significantly improved the accuracy of diagnosis. The findings suggest that the classification scheme may improve the radiologist's ability to differentiate benign from malignant mass lesions in the interpretation of mammograms.

Improved mammographic interpretation of masses using computer-aided diagnosis

The aim of this study was to evaluate the effectiveness of computerized image enhancement, to investigate criteria for discriminating benign from malignant mammographic findings by computer-aided diagnosis (CAD), and to test the role of quantitative analysis in improving the accuracy of interpretation of mass lesions. Forty sequential mammographically detected mass lesions referred for biopsy were digitized at high resolution for computerized evaluation. A prototype CAD system which included image enhancement algorithms was used for a better visualization of the lesions. Quantitative features which characterize the spiculation were automatically extracted by the CAD system for a user-defined region of interest (ROI). Reference ranges for malignant and benign cases were acquired from data generated by 214 known retrospective cases. The extracted parameters together with the reference ranges were presented to the radiologist for the analysis of 40 prospective cases. A pattern recognition scheme based on discriminant analysis was trained on the 214 retrospective cases, and applied to the prospective cases. Accuracy of interpretation with and without the CAD system, as well as the performance of the pattern recognition scheme, were analyzed using receiver operating characteristics (ROC) curves. A significant difference (p < 0.005) was found between features extracted by the CAD system for benign and malignant cases. Specificity of the CAD-assisted diagnosis improved significantly (p < 0.02) from 14 % for the conventional assessment to 50 %, and the positive predictive value increased from 0.47 to 0.62 (p < 0.04). The area under the ROC curve (A(z)) increased significantly (p < 0. 001) from 0.66 for the conventional assessment to 0.81 for the CAD-assisted analysis. The A(z) for the results of the pattern recognition scheme was higher (0.95). The results indicate that there is an improved accuracy of diagnosis with the use of the mammographic CAD system above that of the unassisted radiologist. Our findings suggest that objective quantitative features extracted from digitized mammographic findings may help in differentiating between benign and malignant masses, and can assist the radiologist in the interpretation of mass lesions.

Intelligent systems in medical diagnosis

From an intelligent system for a computer supported medical diagnosis it is expected to achieve high accuracy and ability to draw conclusions from a small data sets. Medical practice could takes many years to generate a large database. A new mathematical method that is able to learn on a small data set is presented.

Kinetic analysis of a molecular model of the budding yeast cell cycle

The molecular machinery of cell cycle control is known in more detail for budding yeast, Saccharomyces cerevisiae, than for any other eukaryotic organism. In recent years, many elegant experiments on budding yeast have dissected the roles of cyclin molecules (Cln1-3 and Clb1-6) in coordinating the events of DNA synthesis, bud emergence, spindle formation, nuclear division, and cell separation. These experimental clues suggest a mechanism for the principal molecular interactions controlling cyclin synthesis and degradation. Using standard techniques of biochemical kinetics, we convert the mechanism into a set of differential equations, which describe the time courses of three major classes of cyclin-dependent kinase activities. Model in hand, we examine the molecular events controlling "Start" (the commitment step to a new round of chromosome replication, bud formation, and mitosis) and "Finish" (the transition from metaphase to anaphase, when sister chromatids are pulled apart and the bud separates from the mother cell) in wild-type cells and 50 mutants. The model accounts for many details of the physiology, biochemistry, and genetics of cell cycle control in budding yeast.

The use of an interactive software program for quantitative characterization of microcalcifications on digitized film-screen mammograms

RATIONALE AND OBJECTIVES

Mammography is relatively nonspecific for the early detection of breast cancer. This study evaluates the accuracy of mammographic interpretation using quantitative features characterizing microcalcifications, which are extracted by a computerized system.

METHODS

A computer-aided diagnosis (CAD) system enabling digitization of film-screen mammograms and automatic feature extraction was developed. A classification scheme (discriminant analysis) based on these features was constructed and trained on 217 cases with known pathology. The diagnostic performance of the classification scheme was tested against the radiologist's conventional interpretation on 45 additional cases of microcalcifications, each analyzed independently by four radiologists.

RESULTS

The sensitivity of the CAD system analysis (95.7%) was significantly better than that of conventional interpretation (84.8%). The positive predictive value of interpretation increased significantly, as did the area under the receiver operating characteristic curve.

CONCLUSIONS

This classification scheme for microcalcifications, based on quantitative features characterizing the lesion, significantly improved the accuracy of mammographic interpretation.

Mitotic control in the absence of cdc25 mitotic inducer in fission yeast

Fission yeast cells tolerate the total absence of the cdc25 mitotic inducer in two cases, either in cdc2-3w or in wee1 genetic backgrounds. In the cdc2-3w cdc25Delta double mutant, the rate-limiting step leading to mitosis is reaching a critical size. However, the size control of this mutant operates in late G2, which is different from wild-type (WT) cells. This fact suggests that in WT the rate-limiting molecular process during the G2 timer is the Tyr15 dephosphorylation of cdc2, for which the cdc25 phosphatase (together with its back-up, pyp3) is dependent. In the wee1-50 cdc25Delta mutant, the population splits into different clusters, all lacking mitotic size control. This strain maintains size homeostasis by a novel method, which is random movement of the cells from one cluster to another in the successive generations. These cells should normally have a ‘minimal cycle’, a ‘timer’ with short G1 and G2 phases. However, very often the cells abort mitosis, possibly at an early event and return back to early G2, thus lengthening their cycles. The inability of these cells to start anaphase might be caused by the absence of the main mitotic regulators (wee1 and cdc25) and the improper regulation of their back-up copies (mik1 and pyp3, respectively).

Model scenarios for evolution of the eukaryotic cell cycle

Progress through the division cycle of present day eukaryotic cells is controlled by a complex network consisting of (i) cyclin-dependent kinases (CDKs) and their associated cyclins, (ii) kinases and phosphatases that regulate CDK activity, and (iii) stoichiometric inhibitors that sequester cyclin-CDK dimers. Presumably regulation of cell division in the earliest ancestors of eukaryotes was a considerably simpler affair. Nasmyth (1995) recently proposed a mechanism for control of a putative, primordial, eukaryotic cell cycle, based on antagonistic interactions between a cyclin-CDK and the anaphase promoting complex (APC) that labels the cyclin subunit for proteolysis. We recast this idea in mathematical form and show that the model exhibits hysteretic behaviour between alternative steady states: a Gl-like state (APC on, CDK activity low, DNA unreplicated and replication complexes assembled) and an S/M-like state (APC off, CDK activity high, DNA replicated and replication complexes disassembled). In our model, the transition from G1 to S/M ('Start') is driven by cell growth, and the reverse transition ('Finish') is driven by completion of DNA synthesis and proper alignment of chromosomes on the metaphase plate. This simple and effective mechanism for coupling growth and division and for accurately copying and partitioning a genome consisting of numerous chromosomes, each with multiple origins of replication, could represent the core of the eukaryotic cell cycle. Furthermore, we show how other controls could be added to this core and speculate on the reasons why stoichiometric inhibitors and CDK inhibitory phosphorylation might have been appended to the primitive alternation between cyclin accumulation and degradation.

Analysis of clustered microcalcifications by using a single numeric classifier extracted from mammographic digital images

RATIONALE AND OBJECTIVES

The authors prospectively tested the performance of a single numeric classifier constructed from a discriminative analysis classification system based on automatic computer-extracted quantitative features of clustered microcalcifications.

MATERIALS AND METHODS

Mammographically detected clustered microcalcifications in patients who had been referred for biopsy were digitized at 600 dpi with an 8-bit gray scale. A software program was developed to extract features automatically from digitized images to describe the clustered microcalcifications quantitatively. The significance of these features was evaluated by using the Wilcoxon test, the Welch modified two-sample t test, and the two-sample Kolmogorov-Smirnov test. A discriminant analysis pattern recognition system was constructed to generate a single numeric classifier for each case, based on the extracted features. This system was trained on 137 archival known reference cases and its performance tested on 24 unknown prospective cases. The results were evaluated by using receiver operating characteristic analysis.

RESULTS

Thirty-seven extracted parameters demonstrated a statistically significant difference between the values for the benign and for the malignant lesions. Seven independent factors were selected to construct the classifier and to evaluate the unknown prospective cases. The area under the receiver operating characteristic curve for the prospective cases was 0.88.

CONCLUSION

A pattern recognition classifier based on quantitative features for clustered microcalcifications at screen-film mammography was found to perform satisfactorily. The software may be of value in the interpretation of mammographically detected microcalcifications.

Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions

All events of the fission yeast cell cycle can be orchestrated by fluctuations of a single cyclin-dependent protein kinase, the Cdc13/Cdc2 heterodimer. The G1/S transition is controlled by interactions of Cdc13/Cdc2 and its stoichiometric inhibitor, Rum1. The G2/M transition is regulated by a kinase-phosphatase pair, Wee1 and Cdc25, which determine the phosphorylation state of the Tyr-15 residue of Cdc2. The meta/anaphase transition is controlled by interactions between Cdc13/Cdc2 and the anaphase promoting complex, which labels Cdc13 subunits for proteolysis. We construct a mathematical model of fission yeast growth and division that encompasses all three crucial checkpoint controls. By numerical simulations we show that the model is consistent with a broad selection of cell cycle mutants, and we predict the phenotypes of several multiple-mutant strains that have not yet been constructed.

Modeling M-phase control in Xenopus oocyte extracts: the surveillance mechanism for unreplicated DNA

Alternating phases of DNA synthesis and mitosis, during the first 12 cell divisions of frog embryos, are driven by autonomous cytoplasmic oscillations of M-phase promoting factor (MPF). Cell-free extracts of frog eggs provide a convenient preparation for studying the molecular machinery that generates MPF oscillations and the surveillance mechanism that normally prevents entry into mitosis until chromosomal DNA is fully replicated. Early experiments suggested that unreplicated DNA blocks MPF activity by inducing phosphorylation of a crucial tyrosine residue, but recent evidence implicates a stoichiometric inhibitor (an MPF binding protein) as the 'braking' agent. Using a realistic mathematical model of the mitotic control system in frog egg extracts, we suggest that both tyrosine phosphorylation and a stoichiometric inhibitors are involved in the block of MPF by unreplicated DNA. Both pathways operate by raising the cyclin threshold for MPF activation. As a bonus, in the process of analyzing these experiments, we obtain more direct and reliable estimates of the rate constants in the model.

Checkpoints in the cell cycle from a modeler's perspective

The cell division cycle is a complex process by which cells grow and divide into two viable daughter cells. So that mistakes are not made in this crucial replication process, cells stop at one or more "checkpoints" in the cycle to query their internal state and external conditions, before proceeding to the next stage of the cycle. In this paper we study some simple mathematical models of cell cycle arrest in G1 ("Start") and G2. Our models help to relate the molecular mechanisms of these checkpoints with physiological properties of the cell cycle.

Modeling the control of DNA replication in fission yeast

A central event in the eukaryotic cell cycle is the decision to commence DNA replication (S phase). Strict controls normally operate to prevent repeated rounds of DNA replication without intervening mitoses ("endoreplication") or initiation of mitosis before DNA is fully replicated ("mitotic catastrophe"). Some of the genetic interactions involved in these controls have recently been identified in yeast. From this evidence we propose a molecular mechanism of "Start" control in Schizosaccharomyces pombe. Using established principles of biochemical kinetics, we compare the properties of this model in detail with the observed behavior of various mutant strains of fission yeast: wee1(-) (size control at Start), cdc13Delta and rum1(OP) (endoreplication), and wee1(-) rum1Delta (rapid division cycles of diminishing cell size). We discuss essential features of the mechanism that are responsible for characteristic properties of Start control in fission yeast, to expose our proposal to crucial experimental tests.

The size control of fission yeast revisited

An analysis was made of cell length and cycle time in time-lapse films of the fission yeast Schizosaccharomyces pombe using wild-type (WT) cells and those of various mutants. The more important conclusions about ‘size controls’ are: (1) there is a marker in G2 in WT cells provided by a rate change point (RCP) where the linear rate of length growth increases by approximately 30%. The period before this RCP is dependent on size and can be called a ‘sizer’. The period after the RCP is nearly independent of size and can be called a ‘timer’. The achievement of a critical threshold size is at or near the RCP which is on average at about 0.3 of the cycle (halfway through G2). This is much earlier than was previously believed. (2) The RCP is at about the time when H1 histone kinase activity and the B type cyclin cdc13 start to rise in preparation for mitosis. The RCP is also associated with other metabolic changes. (3) In wee1 mutants, the mitotic size control is replaced by a G1/S size control which is as strong as the mitotic control. As in WT cells, there is a sizer which precedes the RCP followed by a timer but the RCP is at about the G1/S boundary and has a larger increase (approximately 100%) in rate. (4) cdc25 is not an essential part of the size control at mitosis or at the G1/S boundary. (5) Three further situations have been examined in which the mitotic size control has been abolished. First, induction synchronisation by block and release of cdc2 and cdc10. In the largest oversize-cells which are produced, the RCP is pushed back to the beginning of the cycle. There is no sizer period but only a timer. Second, when both the antagonists wee1 and cdc25 are absent in the double mutant wee1-50 cdc25 delta. In this interesting situation there is apparently no mitotic size control and the cycle times are quantised. Third, in rum1 delta wee1-50 where the normal long G1 in wee1 is much reduced, there is probably no size control either in G1 or in G2 causing a continuous shortening of division length from cycle to cycle.

Chemical kinetic theory: understanding cell-cycle regulation

Progress of a cell through its reproductive cycle of DNA synthesis and division is governed by a complex network of biochemical reactions controlling the activities of both M-phase- and S-phase-promoting factors. Standard chemical kinetic theory provides a disciplined method for expressing the molecular biologists' diagrams and intuition in precise mathematical form, so that qualitative and quantitative implications of our 'working models' can be derived and compared with experiment.

Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos

To contribute to a deeper understanding of M-phase control in eukaryotic cells, we have constructed a model based on the biochemistry of M-phase promoting factor (MPF) in Xenopus oocyte extracts, where there is evidence for two positive feedback loops (MPF stimulates its own production by activating Cdc25 and inhibiting Wee1) and a negative feedback loop (MPF stimulates its own destruction by indirectly activating the ubiquitin pathway that degrades its cyclin subunit). To uncover the full dynamical possibilities of the control system, we translate the regulatory network into a set of differential equations and study these equations by graphical techniques and computer simulation. The positive feedback loops in the model account for thresholds and time lags in cyclin-induced and MPF-induced activation of MPF, and the model can be fitted quantitatively to these experimental observations. The negative feedback loop is consistent with observed time lags in MPF-induced cyclin degradation. Furthermore, our model indicates that there are two possible mechanisms for autonomous oscillations. One is driven by the positive feedback loops, resulting in phosphorylation and abrupt dephosphorylation of the Cdc2 subunit at an inhibitory tyrosine residue. These oscillations are typical of oocyte extracts. The other type is driven by the negative feedback loop, involving rapid cyclin turnover and negligible phosphorylation of the tyrosine residue of Cdc2. The early mitotic cycles of intact embryos exhibit such characteristics. In addition, by assuming that unreplicated DNA interferes with M-phase initiation by activating the phosphatases that oppose MPF in the positive feedback loops, we can simulate the effect of addition of sperm nuclei to oocyte extracts, and the lengthening of cycle times at the mid-blastula transition of intact embryos.