Researching COVID to Enhance Recovery (RECOVER) adult study protocol: Rationale, objectives, and design

IMPORTANCE

SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or other health effects after the acute phase of infection; termed post-acute sequelae of SARS-CoV-2 infection (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are ill-defined. The objectives of the Researching COVID to Enhance Recovery (RECOVER) Multi-site Observational Study of PASC in Adults (RECOVER-Adult) are to: (1) characterize PASC prevalence; (2) characterize the symptoms, organ dysfunction, natural history, and distinct phenotypes of PASC; (3) identify demographic, social and clinical risk factors for PASC onset and recovery; and (4) define the biological mechanisms underlying PASC pathogenesis.

METHODS

RECOVER-Adult is a combined prospective/retrospective cohort currently planned to enroll 14,880 adults aged ≥18 years. Eligible participants either must meet WHO criteria for suspected, probable, or confirmed infection; or must have evidence of no prior infection. Recruitment occurs at 86 sites in 33 U.S. states, Washington, DC and Puerto Rico, via facility- and community-based outreach. Participants complete quarterly questionnaires about symptoms, social determinants, vaccination status, and interim SARS-CoV-2 infections. In addition, participants contribute biospecimens and undergo physical and laboratory examinations at approximately 0, 90 and 180 days from infection or negative test date, and yearly thereafter. Some participants undergo additional testing based on specific criteria or random sampling. Patient representatives provide input on all study processes. The primary study outcome is onset of PASC, measured by signs and symptoms. A paradigm for identifying PASC cases will be defined and updated using supervised and unsupervised learning approaches with cross-validation. Logistic regression and proportional hazards regression will be conducted to investigate associations between risk factors, onset, and resolution of PASC symptoms.

DISCUSSION

RECOVER-Adult is the first national, prospective, longitudinal cohort of PASC among US adults. Results of this study are intended to inform public health, spur clinical trials, and expand treatment options.

REGISTRATION

NCT05172024.

Cost-effectiveness and safety of the molecular targeted drugs afatinib, gefitinib and erlotinib as first-line treatments for patients with advanced EGFR mutation-positive non-small-cell lung cancer

Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), including gefitinib, erlotinib and afatinib are standard first-line treatments for EGFR gene mutation-positive non-small cell lung cancer. The present study aimed to compare the cost-effectiveness of using erlotinib, afatinib or gefitinib. The safety of EGFR-TKIs was also investigated. Expected costs were calculated based on data from patients with advanced EGFR mutation-positive non-small-cell lung cancer who were treated with gefitinib, erlotinib or afatinib. Literature was collected to obtain the necessary clinical information for calculating the probability and the validity of each chemotherapy. Median survival time (MST) was used to evaluate the therapeutic effect of the regimens. The cost-effectiveness ratio was calculated using expected costs and MSTs for the three regimens. The cost-effectiveness ratio per month was JPY 386,859.4/MST for afatinib, JPY 264,788.7/MST for gefitinib and JPY 397,039.9/MST for erlotinib. Significant differences were observed between the three groups (p<0.001). The incremental cost-effectiveness ratio (ICER) of gefitinib compared with afatinib per month was JPY 122,070.7/MST. The ICER of gefitinib compared with erlotinib was JPY -69,605.9/MST. Adverse effects of Grade 3 and higher, including diarrhoea (28.6%) and paronychia (14.3%) were observed in the afatinib treatment group. Paronychia (23.1%) was observed in the erlotinib treatment group, while none were observed in the gefitinib treatment group. These findings demonstrate that gefitinib is more cost effective in comparison with the afatinib and erlotinib regimens, although the afatinib and erlotinib regimens were well-tolerated and produce sufficient effects.

Infection-related complications during treatment for childhood acute lymphoblastic leukemia

Background

Comprehensive studies on neutropenia and infection-related complications in patients with acute lymphoblastic leukemia (ALL) are lacking.

Patients and methods

We evaluated infection-related complications that were grade ≥3 on National Cancer Institute's Common Terminology Criteria for Adverse Events (version 3.0) and their risk factors in 409 children with newly diagnosed ALL throughout the treatment period.

Results

Of the 2420 infection episodes, febrile neutropenia and clinically or microbiologically documented infection were seen in 1107 and 1313 episodes, respectively. Among documented infection episodes, upper respiratory tract was the most common site (n = 389), followed by ear (n = 151), bloodstream (n = 147), and gastrointestinal tract (n = 145) infections. These episodes were more common during intensified therapy phases such as remission induction and reinduction, but respiratory and ear infections, presumably viral in origin, also occurred during continuation phases. The 3-year cumulative incidence of infection-related death was low (1.0±0.9%, n = 4), including 2 from Bacillus cereus bacteremia. There was no fungal infection-related mortality. Age 1-9.9 years at diagnosis was associated with febrile neutropenia (P = 0.002) during induction and febrile neutropenia and documented infection (both P < 0.001) during later continuation. White race was associated with documented infection (P = 0.034) during induction. Compared with low-risk patients, standard- and high-risk patients received more intensive therapy during early continuation and had higher incidences of febrile neutropenia (P < 0.001) and documented infections (P = 0.043). Furthermore, poor neutrophil surge after dexamethasone pulses during continuation, which can reflect the poor bone marrow reserve, was associated with infections (P < 0.001).

Conclusions

The incidence of infection-related death was low. However, young age, white race, intensive chemotherapy, and lack of neutrophil surge after dexamethasone treatment were associated with infection-related complications. Close monitoring for prompt administration of antibiotics and modification of chemotherapy should be considered in these patients.

Night-time communication at Stanford University Hospital: perceptions, reality and solutions

BACKGROUND

Resident work hour restrictions have led to the creation of the 'night float' to care for the patients of multiple primary teams after hours. These residents are often inundated with acute issues in the numerous patients they cover and are less able to address non-urgent issues that arise at night. Further, non-urgent pages may contribute to physician alarm fatigue and negatively impact patient outcomes.

OBJECTIVE

To delineate the burden of non-urgent paging at night and propose solutions.

METHODS

We performed a resident review and categorisation of 1820 pages to night floats between September 2014 and December 2014. Both attending and nursing review of 10% of pages was done and compared.

RESULTS

Of reviewed pages, 62.1% were urgent and 27.7% were non-urgent. Attending review of random page samples correlated well with resident review. Common reasons for non-urgent pages were non-urgent patient status updates, low-priority order requests and non-critical lab values.

CONCLUSIONS

A significant number of non-urgent pages are sent at night. These pages likely distract from acute issues that arise at night and place an unnecessary burden on night floats. Both behavioural and systemic adjustments are needed to address this issue. Possible interventions include integrating low-priority messaging into the electronic health record system and use of charge nurses to help determine urgency of issues and batch non-urgent pages.

Safety of an oral anticancer agent (trifluridine/tipiracil combination tablet) in patients with advanced and recurrent colorectal cancer

We retrospectively studied the safety of trifluridine/tipiracil combination tablet (TAS-102) monotherapy in patients with advanced and recurrent colorectal cancer. Adverse events to TAS-102 monotherapy were observed in 22 out of 23 cases (95.7%). The most frequent adverse events were neutropenia (69.6%), nausea (53.2%), and malaise (30.4%). Treatment was postponed in 54 (59.3%) out of 91 courses, and in 34 (66.7%) of these 54 courses, the delay in treatment was due to bone marrow suppression. Seven patients with peritoneal metastases suffered from nausea, whilst none of the patients without peritoneal metastases had nausea (p = 0.0139). Nausea and vomiting during a previous chemotherapy cycle was significantly associated with nausea after TAS-102 treatment (p = 0.0007), and the treatment cycles were significantly longer in patients with grade 3 or 4 neutropenia (p = 0.0061). Our results suggest that the incidence of nausea was higher in patients treated with TAS-102. Therefore, it is important to inform patients of the risk of these toxicities and to provide enhanced supportive care. Moreover, we recommend that, for patients with repeated treatment postponement due to neutropenia, the dosage should be fixed based on therapeutic efficacy and prognosis.

Improving and sustaining a reduction in iatrogenic pneumothorax through a multifaceted quality-improvement approach

BACKGROUND

The Agency for Healthcare Research and Quality has adopted iatrogenic pneumothorax (IAP) as a Patient Safety Indicator. In 2006, in response to a low performance ranking for IAP rate from the University Healthsystem Consortium (UHC), the authors established a multidisciplinary team to reduce our institution's IAP rate. Root-cause analysis found that subclavian insertion of central venous catheterization (CVC) was the most common procedure associated with IAP OBJECTIVE: Our short-term goal was a 50% reduction of both CVC-associated and all-cause IAP rates within 18 months, with long-term goals of sustained reduction.

DESIGN

Observational study.

SETTING

Academic tertiary care hospital.

PATIENTS

Consecutive inpatients from 2006 to 2014.

INTERVENTION

Our multifaceted intervention included: (1) clinical and documentation standards based on evidence, (2) cognitive aids, (3) simulation training, (4) purchase and deployment of ultrasound equipment, and (5) feedback to clinical services.

MEASUREMENTS

CVC-associated IAP, all-cause IAP rate.

RESULTS

We achieved both a short-term (years 2006 to 2008) and long-term (years 2006 to 2008-2014) reduction in our CVC-associated and all-cause IAP rates. Our short-term reduction in our CVC-associated IAP was 53% (P = 0.088), and our long-term reduction was 85% (P < 0.0001). Our short-term reduction in the all-cause IAP rate was 26% (P < 0.0001), and our long-term reduction was 61% (P < 0.0001).

CONCLUSIONS

A multidisciplinary team, focused on evidence, patient safety, and standardization, can use a set of multifaceted interventions to sustainably improve patient outcomes for several years after implementation. Our hospital was in the highest performance UHC quartile for all-cause IAP in 2012 to 2014.

The role of IL-33 and its receptor ST2 in human nasal epithelium with allergic rhinitis

BACKGROUND

Interleukin (IL)-33 is a novel member of the IL-1 cytokine family and a ligand for the orphan IL-1 family receptor ST2. The IL-33 induces T helper 2-type inflammatory responses and is considered to play a crucial rule in allergic inflammations, such as asthma and atopic dermatitis. However, the role of IL-33 and its receptor ST2 in allergic rhinitis remains unknown.

OBJECTIVE

We investigated expression of IL-33 and ST2 in the nasal epithelium of patients with allergic rhinitis and the mechanisms of the production of cytokines/chemokines induced by treatment with IL-33 using normal human nasal epithelial cells (HNECs) in vitro.

METHODS

Expression of IL-33 and ST2 in normal and allergic rhinitis nasal mucosa was evaluated by reverse transcription- and real-time polymerase chain reactions and immunohistochemical methods. The IL-33 in serum, and IL-8 and GM-CSF were measured by ELISA. For in vitro experiments, HNECs in primary culture were used.

RESULTS

The IL-33 levels in the sera of patients with allergic rhinitis were significantly higher than that in normal controls. Expression of IL-33 and ST2 was significantly elevated in the epithelium from patients with allergic rhinitis. The IL-33 mRNA in HNECs in vitro was significantly induced by treatment with IFN-γ and the toll-like receptor 9 ligand ODN2006. The IL-33-induced production of IL-8 and GM-CSF from HNECs in vitro was significantly suppressed by corticosteroid treatment and distinct signal transduction inhibitors of ERK, p38 MAPK, JNK, NF-κB and epidermal growth factor receptor.

CONCLUSIONS AND CLINICAL RELEVANCE

The IL-33 and its receptor ST2 play important roles in allergic rhinitis. The IL-33-mediated inflammatory responses via ST2 are regulated by distinct signalling pathways in HNECs and the IL-33/ST2 pathway may provide new therapeutic targets for allergic rhinitis.

Eosinophilic oesophagitis in patients presenting with dysphagia--a prospective analysis

BACKGROUND

Eosinophilic oesophagitis (EoO) may be a common finding in adults presenting with dysphagia.

AIM

To identify the risk factors and prevalence of EoO in an adult population with dysphagia.

METHODS

All patients with dysphagia referred for an upper endoscopy (EGD) were asked to participate. Patients completed a detailed questionnaire followed by EGD with four quadrant biopsies in the distal and mid-oesophagus. Primary endpoint was the prevalence of EoO; secondary endpoints included age, gender, asthma, food allergies, gastro-oesophageal reflux disease/dysphagia score and endoscopic findings.

RESULTS

Two hundred and sixty-one patients enrolled between December 2005 and January 2007. Thirty-one patients (12%) met pathological criteria for EoO. There was no difference in EoO prevalence within each gender. Mean age of EoO patients was 42 +/- 15 vs. 61 +/- 15 for non-EoO patients (P < 0.001). EoO was diagnosed in 35% of patients <50 years of age. EoO was present in 22% of asthmatics vs. 9% non-asthmatics (P < 0.01). EoO was present in 36.8% of patients with self-reported food allergies vs. 9.3% those without allergy (P < 0.001). A 13/31(42%) of EoO patients did not have the classic EGD findings (rings +/- furrows) and would have been missed without oesophageal biopsies.

CONCLUSIONS

Eosinophilic oesophagitis was diagnosed in 12% of the patients presenting with dysphagia with relative risk of 9.5 if age <50 years. Oesophageal biopsies are warranted in patients presenting with dysphagia especially in the younger population. Patients may not present with classic endoscopic findings and EoO can be missed without biopsies.

Relationship between gastroesophageal reflux disease and myocardial ischemia. Effect of reflux on temporary activity of autonomic nervous system

PURPOSE

Assessment of the gastroesophageal reflux disease (GERD) influence on myocardial ischemia and autonomic nervous system (ANS) activity.

MATERIAL AND METHODS

In 50 patients with angiographically confirmed ischemic heart disease (IHD) in I-III CCS class, simultaneous 24-hour ECG and esophageal pH-metry monitoring was performed. We assessed: (1) GERD occurrence in patients with IHD, (2) influence of pathological reflux (PR) on myocardial ischemia--number and total duration of ST depression episodes in GERD and non-GERD patients, (3) temporary activity of ANS was determined according to the dynamics of spectral HRV (Heart Rate Variability) analysis components (LF, HF, VLF, LF/HF).

RESULTS

23 patients (46%) fullfilled the GERD criteria. Patients with GERD had significantly higher number of ST depression episodes (4.13 vs 2.85, p = 0.013) as well as longer total duration of ischemia (64.73 vs 35.2 min, p = 0.034). Spectral HRV analysis showed the significant decrease of LF/HF ratio (p < 0.035), which indicates the sympathovagal balance shift towards the parasympathetic system caused by PR.

CONCLUSIONS

1. GERD is frequent condition in patients with angiographically confirmed IHD. Coexistence of GERD may predispose to the myocardial ischemia. 2. Gastroesophageal reflux may cause the shift of sympathovagal balance towards its parasympathetic component. This mechanism may induce esophago-cardiac reflex, leading to diminished myocardial perfusion.

Decreased expression of DNA-dependent protein kinase, a DNA repair protein, during human colon carcinogenesis

DNA-dependent protein kinase (DNA-PK), consisting of a catalytic subunit (DNA-PKcs) and the Ku70 and Ku86 proteins, participates in the repair of DNA double-strand breaks (DSBs). We assessed its expression immunohistochemically in normal human colon tissue, colon adenomas, colon carcinomas, and normal tissue distant from carcinomas. Normal colonocytes expressed all DNA-PK proteins. Compared with the expression in normal tissue [176.62 +/- 18.56 (the intensity of expression x the percentage of cells expressing this protein), mean + SE], the expression of Ku70 was significantly reduced in adenomas (36.62 +/- 11.09; P < 0.001) and carcinomas (85.68 +/- 15.76; P < 0.01), as was the expression of Ku86 [(113.10 +/- 10.22 versus 41.66 +/- 14.71 in adenomas (P < 0.01) or versus 85.68 +/- 15.76 in carcinomas (P < 0.05)]. The expression of DNA-PKcs was not significantly changed. The marked underexpression of Ku70 and Ku86 starting at the adenoma stage may be crucial to the development of colon cancer.

Two KaiA-binding domains of cyanobacterial circadian clock protein KaiC

kaiABC, a gene cluster, encodes KaiA, KaiB and KaiC proteins that are essential to circadian rhythms in the unicellular cyanobacterium Synechococcus sp. strain PCC 7942. Kai proteins can interact with each other in all possible combinations. This study identified two KaiA-binding domains (C(KABD1) and C(KABD2)) in KaiC at corresponding regions of its duplicated structure. Clock mutations on the two domains and kaiA altered the strength of C(KABD)-KaiA interactions assayed by the yeast two-hybrid system. Thus, interaction between KaiA and KaiC through C(KABD1) and C(KABD2) is likely important for circadian timing in the cyanobacterium.

Ecosystem impacts of three sequential hurricanes (Dennis, Floyd, and Irene) on the United States' largest lagoonal estuary, Pamlico Sound, NC

Three sequential hurricanes, Dennis, Floyd, and Irene, affected coastal North Carolina in September and October 1999. These hurricanes inundated the region with up to 1 m of rainfall, causing 50- to 500-year flooding in the watershed of the Pamlico Sound, the largest lagoonal estuary in the United States and a key West Atlantic fisheries nursery. We investigated the ecosystem-level impacts on and responses of the Sound to the floodwater discharge. Floodwaters displaced three-fourths of the volume of the Sound, depressed salinity by a similar amount, and delivered at least half of the typical annual nitrogen load to this nitrogen-sensitive ecosystem. Organic carbon concentrations in floodwaters entering Pamlico Sound via a major tributary (the Neuse River Estuary) were at least 2-fold higher than concentrations under prefloodwater conditions. A cascading set of physical, chemical, and ecological impacts followed, including strong vertical stratification, bottom water hypoxia, a sustained increase in algal biomass, displacement of many marine organisms, and a rise in fish disease. Because of the Sound's long residence time ( approximately 1 year), we hypothesize that the effects of the short-term nutrient enrichment could prove to be multiannual. A predicted increase in the frequency of hurricane activity over the next few decades may cause longer-term biogeochemical and trophic changes in this and other estuarine and coastal habitats.

Capacity of thermomonospora alba XylA to impart thermostability in family F/10 chimeric xylanases

To reveal structure-function relationships of family F/10 glycanases, an in vitro molecular level shuffling experiment was conducted to accumulate useful amino acid residues from two homologous F/10 xylanases, FXYN of Streptomyces olivaceoviridis E-86 and XylA of Thermomonospora alba ULJB1, into a single chimeric xylanase. The parent genes were shuffled by crossovers at selected module borders using self-priming Polymerase Chain Reaction (PCR)s. The shuffled constructs, designated as FXYN-M3/4-XylA, FXYN-M9/10-XylA, and FXYN-M14/15-XylA were cloned and their nucleotide sequences were confirmed. Two chimera, FXYN-M3/4-XylA and FXYN-M14/15-XylA, demonstrated activity against RBB-xylan and were over-expressed as His-tag fusion proteins under control of T5 promoter of pQE60. The homogeneously pure chimeric proteins, FXYN-M3/4-XylA and FXYN-M14/15-XylA showed improved thermal and pH profiles compared to those of one of the parents, FXYN. This was apparently due to the influence of amino acids inherited from thermophilic XylA. Measured K(m) and kcat values were closer to those of the other parent, XylA. Interestingly, a significant level of heat tolerance up to 60 degrees C, was recorded for FXYN-M3/4-XylA in comparison to only 40 degrees C for FXYN-M14/15-XylA though their temperature optima did not correlates with their thermal stability. These results indicated that the amino acid residues of the larger T. alba XylA DNA fragment present in FXYN-M3/4-XylA were responsible for inducing its thermal stability.

Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803

The relevance of pilus-related genes to motility, pilus structure on the cell surface and competency of natural transformation was studied by gene disruption analysis in the unicellular motile cyanobacterium Synechocystis: sp. PCC 6803. The genes disrupted in this study were chosen as related to the pil genes for biogenesis of the type IV pili in a Gram-negative bacterium Pseudomonas aeruginosa. It was found that motility of Synechocystis cells was lost in the mutants of slr0063, slr1274, slr1275, slr1276, slr1277 and sll1694 together with a simultaneous loss of the thick pili on the cell surface. Competency of the natural transformation was lost in the mutants listed above and slr0197-disruptant. The gene slr0197 was previously predicted as a competence gene by a search with sequence-independent DNA-binding structure [Yura et al. (1999) DNA Res. 6: 75]. It was suggested that both DNA uptake for natural transformation and motility are mediated by a specific type IV-like pilus structure, while a putative DNA-binding protein encoded by slr0197 is additionally required for the DNA uptake. Based on the homology with the pil genes in P: aeruginosa, slr0063, slr1274, slr1275, slr1276, slr1277 and sll1694 were designated pilB1, pilM, pilN, pilO, pilQ and pilA1, respectively. The gene slr0197 was designated comA.

Module shuffling of a family F/10 xylanase: replacement of modules M4 and M5 of the FXYN of Streptomyces olivaceoviridis E-86 with those of the Cex of Cellulomonas fimi

To facilitate an understanding of structure-function relationships, chimeric xylanases were constructed by module shuffling between the catalytic domains of the FXYN from Streptomyces olivaceoviridis E-86 and the Cex from Cellulomonas fimi. In the family F/10 xylanases, the modules M4 and M5 relate to substrate binding so that modules M4 and M5 of the FXYN were replaced with those of the Cex and the chimeric enzymes denoted FCF-C4, FCF-C5 and FCF-C4,5 were constructed. The k(cat) value of FCF-C5 for p-nitrophenyl-beta-D-cellobioside was similar to that of the FXYN (2.2 s(-1)); however, the k(cat) value of FCF-C4 for p-nitrophenyl-beta-D-cellobioside was significantly higher (7.0 s(-1)). The loss of the hydrogen bond between E46 and S22 or the presence of the I49W mutation would be expected to change the position of Q88, which plays a pivotal role in discriminating between glucose and xylose, resulting in the increased k(cat) value observed for FCF-C4 acting on p-nitrophenyl-beta-D-cellobioside since module M4 directly interacts with Q88. To investigate the synergistic effects of the different modules, module M10 of the FCF-C4 chimera was replaced with that of the Cex. The effects of replacement of module M4 and M10 were almost additive with regard to the K:(m) and k(cat) values.

Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis

Phycobiliproteins are basic building blocks of phycobilisomes, a supra-molecular assembly for the light-capturing function of photosynthesis in cyanobacteria and red algae. One functional form of phycobiliproteins is a trimeric form consisting of three identical units having C(3) symmetry, with each unit composed of two kinds of subunits, the alpha-subunit and beta-subunit. These subunits have similar chain folds and can be divided into either globin-like or X-Y helices domains. We studied the significance of this two-domain structure for their assembled structures and biological function (light-absorption) using a normal mode analysis to investigate dynamic aspects of their three-dimensional structures. We used C-phycocyanin (C-PC) as an example, and focused on the interactions between the two domains. The normal mode analysis was carried out for the following two cases: 1) the whole subunit, including the two domains; and 2) the globin-like domain alone. By comparing the dynamic properties, such as correlative movements between residues and the fluctuations of individual residues, we found that the X-Y helices domain plays an important role not only in the C(3) symmetry assemblies of the subunits in phycobiliproteins, but also in stabilizing the light absorption property by suppressing the fluctuation of the specific Asp residues near the chromophore. Interestingly, the conformation of the X-Y helices domain corresponds to that of a module in pyruvate phosphate dikinase (PPDK). The module in PPDK is involved in the interactions of two domains, just as the X-Y helices domain is involved in the interactions of two subunits. Finally, we discuss the mechanical construction of the C-PC subunits based on the normal mode analysis.

An investigation of the nature and function of module 10 in a family F/10 xylanase FXYN of Streptomyces olivaceoviridis E-86 by module shuffling with the Cex of Cellulomonas fimi and by site-directed mutagenesis

Although the amino acid homology in the catalytic domain of FXYN xylanase from Streptomyces olivaceoviridis E-86 and Cex xylanase from Cellulomonas fimi is only 50%, an active chimeric enzyme was obtained by replacing module 10 in FXYN with module 10 from Cex. In the family F/10 xylanases, module 10 is an important region as it includes an acid/base catalyst and a substrate binding residue. In FXYN, module 10 consists of 15 amino acid residues, while in Cex it consists of 14 amino acid residues. The Km and kcat values of the chimeric xylanase FCF-C10 for PNP-xylobioside (PNP-X2) were 10-fold less than those for FXYN. CD spectral data indicated that the structure of the chimeric enzyme was similar to that of FXYN. Based on the comparison of the amino acid sequences of FXYN and Cex in module 10, we constructed four mutants of FXYN. When D133 or S135 of FXYN was deleted, the kinetic properties were not changed from those of FXYN. By deletion of both D133 and S135, the Km value for PNP-X2 decreased from the 2.0 mM of FXYN to 0.6 mM and the kcat value decreased from the 20 s(-1) of FXYN to 8.7 s(-1). Insertion of Q140 into the doubly deleted mutant further reduced the Km value to 0.3 mM and the kcat value to 3.8 s(-1). These values are close to those for the chimeric enzyme FCF-C10. These results indicate that module 10 itself is able to accommodate changes in the sequence position of amino acids which are critical for enzyme function. Since changes of the spatial position of these amino acids would be expected to result in enzyme inactivation, module 10 must have some flexibility in its tertiary structure. The structure of module 10 itself also affects the substrate specificity of the enzyme.

Module-intron correlation and intron sliding in family F/10 xylanase genes

Xylanases are classified into two families, numbered F/10 and G/11 according to the similarity of amino acid sequences of their catalytic domain (Henrissat, B., Bairoch, A., 1993. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 293, 781-788). Three-dimensional structure of the catalytic domain of the family F/10 xylanase was reported (White, A., Withers, S.G., Gilkes, N.R., Rose, D.R., 1994. Crystal structure of the catalytic domain of the beta-1,4-glycanase Cex from Cellulomonas fimi. Biochemistry 33, 12546-12552). The domain was decomposed into 22 modules by centripetal profiles (Go, M., Nosaka, M., 1987. Protein architecture and the origin of introns. Cold Spring Harbor Symp. Quant. Biol. 52, 915-924; Noguti, T., Sakakibara, H., Go, M., 1993. Localization of hydrogen-bonds within modules in barnase. Proteins 16, 357-363). A module is a contiguous polypeptide segment of amino acid residues having a compact conformation within a globular domain. Collected 31 intron sites of the family F/10 xylanase genes from fungus were found to be correlated to module boundaries with considerable statistical force (p values <0.001). The relationship between the intron locations and protein structures provides supporting evidence for the ancient origin of introns, because such a relationship cannot be expected by random insertion of introns into eukaryotic genes, but it rather suggests pre-existence of introns in the ancestral genes of prokaryotes and eukaryotes. A phylogenetic tree of the fungal and bacterial xylanase sequences made two clusters; one includes both the bacterial and fungal genes, but the other consists of only fungal genes. The mixed cluster of bacterial genes without introns and the fungal genes with introns further supports the ancient origin of introns. Comparison of the conserved base sequences of introns indicates that sliding of a splice site occurred in Aspergillus kawachii gene by one base from the ancestral position. Substrate-binding sites of xylanase are localized on eight modules, and introns are found at both termini of six out of these functional modules. This result suggests that introns might play a functional role in shuffling the exons encoding the substrate-binding modules.

Putative mechanism of natural transformation as deduced from genome data

Genetic transformation is widely utilized in molecular biology as a tool for gene cloning in Escherichia coli and for gene mapping in Bacillus subtilis. Several strains of eubacteria can naturally take up exogenous DNA and integrate the DNA into their own genomes. Molecular details of natural transformation, however, remained to be elucidated. The complete genome of a cyanobacterium, Synechocystis sp. PCC6803, has been sequenced. This bacterium has been used to examine functions of a particular gene. The genome is considered to carry information on natural transformable characteristics of Synechocystis. The first step in genetic transformation is the uptake of exogenous DNA. Proteins with non-specific DNA binding features are required, because specificity in the exogenous DNA has not been demonstrated. Such proteins have modules interacting with the phosphate backbone of DNA, including helix-turn-helix modules. Using a consensus pattern of the phosphate-binding helix-turn-helix module, we searched through the genome data of Synechocystis for genes or open reading frame (ORF) products with the pattern in primary structures. We found that an ORF, slr0197, has the pattern in duplicate at the C-terminal region. We also found that the ORF product has a hydrophobic segment at the N-terminal region, which is followed by two internal repeats of the endonuclease domain. Based on these observations, we propose a model for the initial stage of genetic transformation. This is apparently the first report on molecular mechanisms of natural transformation.

Repetitive use of a phosphate-binding module in DNA polymerase beta, Oct-1 POU domain and phage repressors

Motifs for sequence specific-protein-DNA interactions, such as helix-turn-helix, zinc finger and leucine zipper, are now better understood as a result of extensive studies of three-dimensional (3D) structures of transcription factors. On the other hand, little attention has been paid to motifs for sequence nonspecific binding, namely DNA-phosphate binding. To address the question whether different transcription factors and DNA manipulation enzymes, that is enzymes that work on DNA, share a similar mode of phosphate binding, we surveyed interactions between DNA and protein module, a structural unit of a globular protein. We analyzed the modular organization of DNA polymerase beta and found that residues making contact with DNA phosphates were localized to five modules. Structural comparison of these phosphate-binding modules against others in transcription factors and DNA manipulation enzymes revealed that DNA polymerase beta, the Oct-1 POU domain, 434 Cro and the Arc repressor have a phosphate-binding module with 3D structures similar to one another. This newly detected module, the phosphate-binding helix-turn-helix (pbHTH) module, named for its function and 3D structure, interacts with DNA by (i) making hydrogen bonds between a DNA phosphodiester oxygen and an amino hydrogen of the main chain located at the N-terminus of a C-terminal alpha-helix, and (ii) making electrostatic interactions between DNA phosphates and side chains of lysine or arginine. Finding structurally and functionally similar phosphate-binding units in different transcription factors and DNA manipulation enzymes suggests that shuffling of modules is not limited to the DNA base-recognition motif. Phosphate-binding modules are apparently also shuffled in DNA-binding proteins.

Molecular analysis of the dnaK locus of Leptospira interrogans serovar Copenhageni

Analysis of the dnaK locus of Leptospira interrogans serovar Copenhageni identified four genes in the order hrcA, grpE, dnaK and dnaJ. This is the first time a homologue of hrcA has been identified in a spirochete. The hrcA gene and a regulatory sequence, designated CIRCE, play a significant role in the regulation of the dnaK locus of several Gram+ organisms. Their presence upstream of dnaK in Leptospira suggested a similiar regulatory mechanism. Transcriptional analysis using reverse transcriptase-PCR demonstrated transcription of all four genes and indicated that hrcA and grpE were co-transcribed, as were grpE and dnaK. Whilst hrcA, grpE and dnaK were closely linked on the chromosome, transcription terminators between dnaK and dnaJ and downstream of dnaJ suggested that this latter gene exists in its own operon. Primer extension analysis located functional promoters upstream of hrcA and grpE; however, no evidence of a functional promoter could be found for dnaJ. Moreover, transcripts encompassing the first three genes or the entire locus could not be demonstrated, suggesting that the four genes are regulated independently at the transcriptional level. These results indicate that the regulation of the dnaK locus of Leptospira differs somewhat from that observed in other organisms.

Structure—activity relationships of some indolo[3,2-c]quinolines with antimalarial activity

The synthesis, physicochemical characterization and in vitro antimalarial activity of a series of indolo[3,2-c]quinolines (9a-f) are described. There is only a poor correlation between the activity and hydrophobicity. In contrast, 33% of the observed variation in antimalarial activity can be attributed to the size of the side chain attached to position 9 of the indoloquinoline ring. An increase in the size of this dibasic side chain generally results in a reduction in activity, suggesting that it is accommodated in a site/cavity of limited size on the receptor. More significantly, the charge on the distal nitrogen (N3) on the side chain, located 10-11 A from the quinoline N, could account for 75% of the observed variation. Since a large charge on N3 is associated with improved antimalarial activity, it is suggested that N3 is protonated and functions as a H bond donor in the drug-receptor interaction.

Mechanical stability of compact modules of barnase

Globular proteins are composed of structural elements such as secondary structures and modules. Modules are compact segments consisting of 10-40 contiguous amino acid residues and are often encoded by exons. Therefore, the view that the modular organization of proteins is a result of exon-shuffling or -fusion is given support. Secondary structures such as alpha-helix and beta-sheet are stabilized by hydrogen bonds and are thus considered to be stable, structural elements of a globular domain. Since module boundaries are often located on alpha-helices or beta-sheets, it is not obvious whether the modules are mechanically stable. We carried out molecular dynamics simulations on modules of barnase, a bacterial RNase from Bacillus amyloliquefaciens, for 1 ns in vacuo and 150 ps in water. Five of six modules (M1, 1-24; M2, 25-52; M3, 53-73; M4, 74-88; M5, 89-98) retained native-like conformations during these simulations. Only the C-terminal module (M6, 99-110) was deformed; it is less compact than the other modules. As the modules are mechanically stable they are suitable as parts combined into proteins. Together with RNase activity of the three isolated modules of barnase, M2, M3 and M6, our study supports the view that modules were indeed original building blocks of proteins.

Ligase chain reaction assay for human mutations: the Sickle Cell by LCR assay

We can detect the beta-globin gene sickle cell mutation by using an assay based on the ligase chain reaction. The simultaneous amplification of the human growth hormone gene in the same reaction serves as a control for the amount of template DNA or amplification efficiency. Ligation products, which are biotinylated at one end and tagged with an arbitrary "tail" sequence at the other, are captured by hybridization to "tail"-complementary oligonucleotides immobilized on polystyrene microwells. The captured ligation products are detected colorimetrically by use of streptavidin-alkaline phosphatase conjugate. In a study of 24 subjects, the assay unequivocally discriminated among normal, carrier, and sickle cell genotypes.

Adaptive amino acid replacements accompanied by domain fusion in reverse transcriptase

Two basic processes are involved in protein evolution: One is amino acid replacement and another is reorganization of structural or functional units of proteins. Multidomain or multifunctional proteins are thought to have evolved by fusion of smaller structural units such as modules or domains. Reverse transcriptase (RT) is one of such fused proteins. The N-terminal part forms of globular domain with polymerase activity and the C-terminal part forms another globular domain with ribonuclease H activity (RNase H domain). There are single-domain enzymes which are homologous with the RNase H domain. The group of enzymes is called type I ribonuclease H (RNase HI). It is most likely that the ancestors of RNase HI and the polymerase domain were fused and became contemporary RT. At fusion, amino acid replacements presumably occurred at the interface of the domains to reinforce the interdomain interactions. Such replaced amino acid residues are conserved during evolution of the fused enzyme. We analyzed the pattern of amino acid replacement at each residue site in the free form, RNase HI group, and the integrated form, RNase H domain group. Then we compared the patterns between the two forms. Drastic fitting replacements of amino acid residues occurred at four of 29 residue sites involved in interdomain contact. Hydrophilic amino acid residues of the free form were substituted with hydrophobic or ambivalent ones in the integrated form. These substitutions aid in stabilizing the fused conformation by hydrophobic interactions at the interface of the domains. These observations imply that domain fusion could have occurred with only a relatively small number of adaptive amino acid substitutions.

Site-specific mutagenesis of Rhodobacter capsulatus ferredoxin I, FdxN, that functions in nitrogen fixation. Role of extra residues

One of the two [4Fe-4S]-type clusters of the Rhodobacter capsulatus ferredoxin I, FdxN, was modified through site-specific mutagenesis of the distinctive features of the second cluster-binding motif, Cys38-X2-Cys41-X8-Cys50-X3-Cys54-X4-Cys59. First, various mutagenized products were tested to learn whether they could rescue the decreased capacity of an fdxN-null strain MSA1 to fix nitrogen: the phenotype of MSA1 was reassessed to Nifs (slow growth by nitrogen fixation) from our previous description of Nif- (Saeki, K., Suetsugu, Y., Tokuda, K., Miyatake, Y., Young, D. A., Marrs, B. L. and Matsubara, H. (1991) J. Biol. Chem. 266, 12889-12895). Substitution of Cys59 to Ser yielded an almost fully active product, while that of Cys54 did not. Gradual deletions and deletion-substitution of the 8 residues between Cys41 and Cys50 also yielded active products. Second, three of the modified FdxN proteins were subjected to purification. Only the GA protein, whose 8 residues between positions 42 and 49 were replaced by the Gly-Ala sequence, was purified. The GA protein and the authentic FdxN showed similar optical properties. The two clusters in the former had Em values of -490 and -430 mV, while those in the latter had an identical value of -490 mV, when determined by EPR analysis. It was concluded that: 1) Cys59 is not a ligand to [4Fe-4S] clusters but is important for structural integrity, 2) the residues between positions 42 and 49 may form a "loop-out" from a structure analogous to the Peptococcus aerogenes ferredoxin, and 3) the loop-out region does not have functional significance in nitrogen fixation but may be responsible for maintaining the highly negative redox potential of one of the two clusters.

Molecular cloning, purification and characterization of two endo-1,4-beta-glucanases from Aspergillus oryzae KBN616

Two endo-1,4-beta-glucanase genes, designated celA and celB, from a shoyu koji mold Aspergillus oryzae KBN616, were cloned and characterized. The celA gene comprised 877 bp with two introns. The CelA protein consisted of 239 amino acids and was assigned to the cellulase family H. The celB gene comprised 1248 bp with no introns. The CelB protein consisted of 416 amino acids and was assigned to the cellulase family C. Both genes were overexpressed under the promoter of the A. oryzae taka-amylase A gene for purification and enzymatic characterization of CelA and CelB. CelA had a molecular mass of 31 kDa, a pH optimum of 5.0 and temperature optimum of 55 degrees C, whereas CelB had a molecular mass of 53 kDa, a pH optimum of 4.0 and temperature optimum of 45 degrees C.

Ancient divergence of long and short isoforms of adenylate kinase: molecular evolution of the nucleoside monophosphate kinase family

Adenylate kinases (AK) from vertebrates are separated into three isoforms, AK1, AK2 and AK3, based on structure, subcellular localization and substrate specificity. AK1 is the short type with the amino acid sequence being 27 residues shorter than sequences of the long types, AK2 and AK3. A phylogenetic tree prepared for the AK isozymes and other members of the nucleoside monophosphate (NMP) kinase family shows that the divergence of long and short types occurred first and then differentiation in subcellular localization or substrate specificity took place. The first step involved a drastic change in the three-dimensional structure of the LID domain. The second step was caused mainly by smaller changes in amino acid sequences.

Conversion of the coenzyme specificity of isocitrate dehydrogenase by module replacement

The coenzyme specificity of isocitrate dehydrogenase from an extreme thermophilic bacterium was converted from NADP-dependent to NAD-dependent by replacing a "module" involved in the coenzyme binding site. The conversion was not possible with the replacement of a few residues that interact with the coenzyme. In addition, the module-replaced mutant dehydrogenase was as stable as the original, wild type enzyme. The results support a previous hypothesis that a module is a structural and functional unit of a protein.

Major identity determinants in the "augmented D helix" of tRNA(Glu) from Escherichia coli

By a kinetic analysis of 59 variant transcripts of Escherichia coli tRNA(Glu) with glutamyl-tRNA synthetase (GluRS), the U11.A24 base-pair, the U13.G22..A46 base-triple, and the lack of residue 47 (delta47) were found to serve as major determinants for tRNA(Glu) identity. This is the first system for which major identity determinants are reported to be clustered in the "augmented D helix", consisting of the D stem with some neighboring residues and the variable loop. Other identity determinants are U34, U35, C36 and A37 in the anticodon loop, and G1.C72 and U2.A71 in the acceptor stem. Phosphate-group protection by GluRS from ethylnitrosourea was observed most strongly for the minor groove side of D-stem helix, indicating that GluRs tightly binds to the D stem for recognition, on the minor groove side, of the potent identity-determinant groups of the U11.A24 and U13.G22 base-pairs. A46 is not involved in direct recognition by GluRS; the U13.G22..A46 base-triple is required probably for formation of the structural features that are recognized by GluRS. In this context, the essential role of characteristic delta47 in tRNA(Glu) identity may be to maintain the U13.G22..A46 base-triple.

A three-dimensional structure model of the complex of glutamyl-tRNA synthetase and its cognate tRNA

A docking model of glutamyl-tRNA synthetase (GluRS) and tRNAGlu was constructed, on the basis of the distinguished similarity between the X-ray crystallographic three-dimensional structures of the N-terminal halves of the Thermus thermophilus GluRS in the free state and the Escherichia coli glutaminyl-tRNA synthetase in a complex with tRNAGln. The modeled structure is energetically favorable and is also well consistent with the results of site-directed mutagenesis studies. The model indicates that the GluRS-specific insertions 2 and 3 fit and bind to the acceptor stem and the D arm, respectively, of the cognate tRNA without affecting other contacts. In particular, insertion 3 strongly interacts with the two D-stem base pairs that are essential for the tRNA-GluRS recognition.

Insect prothoracicotropic hormone: a new member of the vertebrate growth factor superfamily

Prothoracicotropic hormone (PTTH) is a brain neurosecretory protein that controls insect development. PTTH of the silkmoth Bombyx mori is a homodimeric protein, the subunit of which consists of 109 amino acids. Clear-cut sequence similarity to any other proteins has not been observed. By disulfide-bond pattern analysis and modeling of the PTTH structure based on the known three-dimensional (3D) structures of growth factor family with cystine-knot motif, we propose that the PTTH protomer adopts the fold unique to the structural superfamily of the growth factors, beta-nerve growth factor (beta-NGF), transforming growth factor-beta 2 (TGF-beta 2), and platelet-derived growth factor-BB (PDGF-BB). The insect neurohormone PTTH appears to be a member of the growth factor superfamily, sharing a common ancestral gene with the three vertebrate growth factors, beta-NGF, TGF-beta 2 and PDGF-BB.

Inositol 1,4,5-trisphosphate 3-kinase activity in FRTL-5 cells: regulation of the enzyme activity by TSH

Inositol 1,4,5-trisphosphate (InsP3) 3-kinase phosphorylates the Ca(2+)-mobilizing second messenger InsP3 to inositol 1,3,4,5-tetrakisphosphate (InsP4). InsP3 5-phosphatase dephosphorylates InsP3 to inositol 1,4-bisphosphate (InsP2). We compared the effects of TSH added to a culture of FRTL-5 thyroid cells on the activity of InsP3 5-phosphatase and InsP3 3-kinase. InsP3 3-kinase activity was decreased at a physiological concentration of TSH. Inhibition of this activity started after 3 h of incubation with TSH and was maximal after 24 h. In contrast, InsP3 5-phosphatase activity was not affected by TSH under the same conditions. The inhibitory effect of TSH on InsP3 3-kinase was characterized as follows: a) inhibition of activity was mimicked by both dibutyryl cyclic AMP and forskolin; b) activity obtained by mixing lysates of TSH-stimulated and non-stimulated cells was the sum of each activity measured separately; c) inhibition persisted after a crude lysate of TSH-stimulated cells had been subjected to SDS/polyacrylamide gel electrophoresis and the extraction of InsP3 3-kinase activity. The data suggest that TSH reduced the activity of InsP3 3-kinase in FRTL-5 cells either by a phosphorylation/dephosphorylation mechanism, or by affecting expression of the enzyme.

[A case of central pontine myelinolysis and extrapontine myelinolysis during rapid correction of hypernatremia]

A 69-year-old woman was admitted because of severe dehydration due to anorexia. Consciousness disturbance was found to be due to severe abnormalities of serum electrolyte balance, but recovered quickly by correcting the hyperosmolality. While the initial serum sodium value of 186 mEq/L was corrected to 139 mEq/L in 5 days, locked-in syndrome, bilateral hand tremor and tetraparesis appeared. Brain magnetic resonance imaging (MRI) revealed symmetrically high signal intensity areas on T2-weighted images and low signal intensity areas on T1-weighted images in central part of pons and bilateral middle cerebellar peduncles. One and a half month later, these neurologic symptoms were improved and the MRI abnormalities also disappeared. Auditory brain stem responses which showed prolongations of III to V wave peak to peak latency at the onset returned to normal. It is noted in this case that central pontine myelinolysis (CPM) and extrapontine myelipolysis (EPM) appeared during the period of rapid correction of hypernatremia. Although it is known CPM and EPM are caused by hypernatremia or the rapid correction of hyponatremia, there has been reported only one case of CPM and EPM after rapid correction of hypernatremia. According to the hypothesis of Norenberg, rapid rise in serum sodium may cause CPM and EPM, but if CPM and EPM are caused by the rapid correction of hypernatremia in this case, CPM and EPM may be caused by another pathogenesis of the disorder.

Structure of the human CCG1 gene: relationship between the exons/introns and functional domain/modules of the protein

The human CCG1 gene, encoding CCG1/TAFII250/p250, was isolated by complementing tsBN462, a mutant BHK21 cell line that shows cell-cycle arrest at high temperature. Using the cDNA as a probe, the locations of exon-intron junctions were determined in the genomic DNA. Thirty-eight exons ranging from 68 to 219 bp in size were found. All the exon-intron junctions followed the GT-AG rule. Using a newly developed method, we performed a module analysis of the CCG1 protein. The functional domain previously predicted in CCG1 was further confirmed to be encoded in a single predicted module that is the minimal functional unit in the protein. The boundaries of the predicted modules show a close correlation to the intron/exon junction of CCG1. The entire gene, at least 110 kb long, has been recovered in a YAC, which provides a route to the further study of module function.

[Ultrafiltration failure in a peritoneal dialysis patient due to a marked increase in lymphatic absorption a case report]

A peritoneal dialysis patient was reported who had ultrafiltration loss due to a marked increase in lymphatic absorption and peritoneal membrane permeability. A 33-year-old male was transferred from hemodialysis to peritoneal dialysis because of acute subdural hematoma. His complicated history included left testicular tumor with retroperitoneal lymph node metastasis in 1982. He was treated with CDDP, Etoposide, Bleomycin, Vinblastine sulfate and Vincristine and received operation of retroperitoneal lymph node dissection in 1982. He had been on hemodialysis since 1983 due to cisplatinum nephropaty. Ultrafiltration failure was found immediately following the insertion of Tenckhoff catheter without malfunction of peritoneal catheter. Peritoneal equilibrate test and lymphatic absorption measurement showed a high permeability peritoneum with a marked increase in lymphatic absorption rate (3.7 ml/min). These two factors were thought to result in ultrafiltration loss. CAPD with 4-6 times exchange daily did not maintain ultrafiltration, because it gave approximately 2000 ml negative water balance every day. He was well maintained on a short time exchange intermittent peritoneal dialysis (IPD) with cycler using 18 L for 8 hours. We concluded that increased lymphatic absorption is one of the important factors for ultrafiltration fafilure and IPD with frequent exchange by cycler is suitable for the patient with ultrafiltration loss.

Evolutionary clustering and functional similarity of RNA-binding proteins

RNA-binding proteins (RNPs) involved in splicing, processing and translation regulation contain one to four RNA-binding domains. We constructed a phylogenetic tree for the RNA-binding domains, including those of poly(A)-binding protein (PABP), splicing factors, chloroplast RNPs, hnRNPs, snRNP U1-70K, nucleolin and Drosophila sex determinants. Proteins with similar functions were found to have closely related RNA-binding domains and common domain organizations. In light of these observation, one can assume the function of an RNA-binding protein, based on the evolutionary relationship between its RNA-binding domain(s) and domain organization, as compared with other RNPs.

Long-term impact of conservative management on localized prostate cancer. A twenty-year experience in Japan

The clinical outcome of 107 patients with localized prostate cancers over the past twenty years was analyzed retrospectively. Immediate endocrine therapy was administered in 55 patients after diagnosis. The other group of 52 patients did not receive any anti-tumor treatment until progression. Overall, 22 patients (21%) died of prostate cancer, while 45 (42%) died of other known causes. During a mean observation period of thirty-seven months, 27 (25%) experienced progression of the disease (local in 9, distant metastasis in 25, and both in 7 patients). The cancer-specific survival rates for these 107 patients were 78 percent at five years and 71 percent at ten years. The timing of endocrine therapy and age at diagnosis did not influence patient's prognosis. Tumor stage failed to demonstrate any prognostic significance after being controlled for other factors including tumor grade. Poorly differentiated histology appeared to be the sole and the strongest predictor for both tumor progression and cancer death. Prostate cancer may not differ significantly among races once it becomes clinically manifest. Expectant management for localized prostate cancer in well and moderately differentiated cancer may be justified because of the higher probability of dying of other intercurrent causes especially in the elderly group of patients. However, definitive forms of therapy should be considered for the group of patients with poorly differentiated tumor who have reasonably long life expectancy.

Inositol 1,4,5-trisphosphate 3-kinase highest levels in the dendritic spines of cerebellar Purkinje cells and hippocampal CA1 pyramidal cells. A pre- and post-embedding immunoelectron microscopic study

Inositol 1,4,5-trisphosphate 3-kinase (InsP3 3-kinase) plays a crucial role in calcium homeostasis by regulating InsP3 levels. We have reported the highest concentrations of InsP3 3-kinase in the dendrites of cerebellar Purkinje cells and hippocampal pyramidal cells of the CA1 sector of the Ammon's horn. We here investigate its subcellular localization by pre- and post-embedding immunoelectron microscopic study. In both populations of neurons, the major structure expressing a high level of InsP3 3-kinase is the dendritic spines.

Localization of hydrogen-bonds within modules in barnase

Proteins in eukaryotes are composed of structural units, each encoded by discrete exons. The protein module is one such structural unit; it has been defined as the least extended or the most compact contiguous segment in a globular domain. To elucidate roles of modules in protein evolution and folding, we examined roles of hydrogen bonds and hydrophobic cores, as related to the stability of these modules. For this purpose we studied barnase, a bacterial RNase from Bacillus amylolique-faciens. Barnase is decomposed into at least six modules, M1-M6; the module boundaries are identified at amino acid residues 24, 52, 73, 88, and 98. Hydrogen bonds are localized mainly within each of the modules, with only a few between them, thereby indicating that their locations are designed to primarily stabilize each individual module. To obtain support for this notion, an analysis was made of hypothetical modules defined as segments starting at a center of one module and ending at the center of the following one. We found that the hydrogen bonds did not localize in each hypothetical module and that many formed between the hypothetical modules. The native conformations of modules of barnase may be specified predominantly by interactions within the modules.

Repeat of a helix-turn-helix module in DNA-binding proteins

Helix-turn-helix motif is one of the common motifs observed in DNA-binding proteins. The motif interacts with DNA double helix and recognizes specific base sequences. It is assumed that the helix-turn-helix motif appears only once in seven prokaryotic transcriptional repressors of which 3-D structures have been determined by X-ray crystallographic studies. These prokaryotic repressors consist of several alpha-helices connected with turns. We report here that these repressors are decomposable into helix-turn-helix modules and their connectors. A module is defined as a compact structural unit with consecutive amino acid residues in a globular protein. Each of the helix-turn-helix motifs in the seven proteins corresponds approximately to a single helix-turn-helix module consisting of approximately 13 amino acids. Identification of modules of seven prokaryotic repressors and comparisons of their tertiary structures led to the conclusion that three of these DNA-binding proteins contain more than one helix-turn-helix module with a structure similar to the helix-turn-helix motif. The difference in module organization of these DNA-binding proteins paves the way for further classification of the DNA-binding proteins with the helix-turn-helix motif. The structural repertoire of these transcriptional regulators was increased through different utilizations in the number of helix-turn-helix and other modules. The difference in DNA base recognition ability in these helix-turn-helix modules is ascribed to a difference in size of a side chain at the fifth residue from Gly, on the turn.

Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation

Proteins consist of structural units such as globular domains, secondary structures, and modules. Modules were originally defined by partitioning a globular domain into compact regions, each of which is a contiguous polypeptide segment having a compact conformation. Since modules show close correlations with the intron positions of genes, they are regarded as primordial polypeptide pieces encoded by exons and shuffled, leading to yield new combination of them in early biological evolution. Do modules maintain their native conformations in solution when they are excised at their boundaries? In order to find answers to this question, we have synthesized modules of barnase, one of the bacterial RNases, and studied the solution structures of modules M2 (amino acid residues 24-52) and M3 (52-73) by 2D NMR studies. Some local secondary structures, alpha-helix, and beta-turns in M2 and beta-turns in M3, were observed in the modules at the similar positions to those in the intact barnase but the overall state seems to be in a mixture of random and native conformations. The present result shows that the excised modules have propensity to form similar secondary structures to those of the intact barnase.

[Prognosis of incidental (stage A) prostatic cancer]

Incidentally discovered prostatic cancer can pursue a benign clinical course or it can rapidly progress. For the purpose of this study, we summarized pathological and clinical results of 107 (5.3%) stage A prostatic cancer patients in 2008 transurethral resection of the prostate for clinically diagnosed benign prostatic hyperplasia. For each patient, 3.9 slides, 13.6 tissue chips per slide and 52.5 tissue chips per patient (from 16 to 140 chips) were examined microscopically. The survival rates of patient with well, moderately and poorly differentiated groups were 62, 37 and 12% at 10 years, and those with Gleason score 2 to 4, 5 to 7 and 8 to 10 group were 63, 42 and 0% respectively. The survival rates in stage A1 (well differentiated or Gleason score 4 or less in less than 5% of the tissue removed during transurethral resection of the prostate) and stage A2 (anything other than stage A1) were 63 and 41% at 10 years, respectively. And cancer specific survival rates in stage A1 and stage A2 were 96% and 64% at 10 years, respectively. The number of cancer specific death were 1 in 30 (3.3%) in stage A1 group and 14 in 77 (18.2%) in stage A2 group. Our results indicated that tumors with low potential for aggressive behavior had a volume extent of less than 5% and a well differentiated group. Aggressive treatments should be recommended to all patients who were diagnosed stage A2 prostatic cancer.