The benzoylarginine peptidase from Treponema denticola (strain ASLM), a human oral spirochaete: evidence for active-site carboxyl groups

The benzoylarginine peptidase of Treponema denticola (strain ASLM; a human oral spirochaete) was progressively and irreversibly inactivated by 1-(ethoxycarbonyl)-2-ethoxy-1, 2-dihydroquinoline, a carboxyl-group reagent. At acidic pH values, reaction of one mole of the modifier per active site of the enzyme resulted in total inactivation of the enzyme. Assuming that this modifier is a specific carboxyl reagent, the data suggest that the inactivation of the T. denticola benzoylarginine peptidase was caused by the modification of one carboxyl group located close to the active site of the enzyme. Results obtained with Woodward's reagent K ( N -ethyl-5-phenylisoxazolium 3’-sulphonate) supported these findings. Carbethoxylation with diethylpyrocarbonate effectively inactivated the enzyme, and addition of hydroxylamine at pH 7.0 restored the activity almost totally, suggesting that the pyrocarbonate had reacted with tyrosyl or histidyl residues.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73886/1/j.1365-2958.1990.tb00721.x.pd

The peptidolytic capacity of the spirochete system

  Relatively scant chemical information has been available on the proteinases and peptidases of spirochetes in spite of the association of spirochetes with several serious infections known to plague humans and other animal species. This situation has partly resulted from difficulties in growing some spirochetes under laboratory conditions. The cells of Treponema denticola , a spirochete suggested to be associated with periodontal infections, have turned out to be a good source of new chemical information on those enzymes. Latest studies suggest that the outer cell en-velope or the periplasmic space of T. denticola contains several novel proteinases and peptidases (hence called ``ectoenzymes'') which may contribute to the chronicity of periodontal infections. Some of the oligopeptidases discovered are specific for proline-containing host tissue peptides such as substance P, bradykinin, neurotensin, etc., and possibly small collagen fragments. The only spirochetal peptidases purified to give a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis have been obtained from T. denticola . One particular peptidase, suggested to be similar to the oligopeptidase B (EC 3.4.21.83) of Escherichia coli seems to be present in the cell envelope or in the periplasmic space at quite large concentrations. The presence of this and several other peptidases in the outer cell structures of the treponemes suggests that such enzymes are important for the nutrition of these highly motile and invasive organisms. The biological role of these enzymes can thus be envisaged in the peptidolytic processing of host tissue proteins and peptides to gradually smaller molecules to fulfill the nutritional requirements of these organisms. Although the genetic similarity between T. denticola and some other treponemes and spirochetes can be hotly debated, it is nevertheless now possible to use T. denticula enzymes as suitable objects for comparison when the chemistry of other spirochetes is studied.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42252/1/430-185-1-1_61850001.pd

Compressed Data Structures for Dynamic Sequences

We consider the problem of storing a dynamic string $S$ over an alphabet $\Sigma=\{\,1,\ldots,\sigma\,\}$ in compressed form. Our representation supports insertions and deletions of symbols and answers three fundamental queries: $\mathrm{access}(i,S)$ returns the $i$-th symbol in $S$, $\mathrm{rank}_a(i,S)$ counts how many times a symbol $a$ occurs among the first $i$ positions in $S$, and $\mathrm{select}_a(i,S)$ finds the position where a symbol $a$ occurs for the $i$-th time. We present the first fully-dynamic data structure for arbitrarily large alphabets that achieves optimal query times for all three operations and supports updates with worst-case time guarantees. Ours is also the first fully-dynamic data structure that needs only $nH_k+o(n\log\sigma)$ bits, where $H_k$ is the $k$-th order entropy and $n$ is the string length. Moreover our representation supports extraction of a substring $S[i..i+\ell]$ in optimal $O(\log n/\log\log n + \ell/\log_{\sigma}n)$ time

Screening of community-dwelling older patients by the emergency medical services : An observational retrospective registry study

Background: Inadequate nutrition, falls, and cognitive impairment are common problems among acutely ill older people and are associated with complicated and prolonged health problems and mortality. Objectives: To assess if the emergency medical services can identify patients with nutritional risk, falls risk, and cognitive impairment by using simple screening tools and to assess the prevalence of risks and rate they are reported to the emergency department. Setting: The study was carried out in Espoo, Finland to patients over the age of 70 requiring non-urgent ambulance transfer to the emergency department. Outcome measures: A set of validated electronic screening tools was used to identify patients at nutritional risk, risk of falling and having cognitive impairment. Main results: A total of 488 (8%) out of 5792 patients were screened. Of the patients 60%, (n = 292) had at least one risk: 17% (n = 81) had nutritional risk, 43% (n = 209) falls risk, and 28% (n = 137) cognitive impairment. Twenty-two (5%) were screened positive in all three categories. The observed risk was reported to the emergency department staff in 59% (n = 173) of the patients. Conclusion: The emergency medical services can be used in preventive health care to identify patients having nutritional risk, falls risk, or cognitive impairment.Peer reviewe

Saliva Stimulants and the Oral Health of Geriatric Patients

Root-surface caries (RSC) has been recognized as a specific and important dental disease. Significant advances have been made in the pathology and microbiology of RSC, and the need to standardize the guidelines for recording RSC data has been recognized. Researchers have emphasized the increasing impact RSC will have on the geriatric population, especially since the methods to treat and prevent this disease are limited. The purpose of this study was to investigate the possibility of limiting RSC in a Veterans Administration (VA) patient population, using polyol-containing saliva stimulants that were voluntarily consumed by residents of a VA Medical Center (VAMC) over a period of from six to 30 months. Another aim was to study the effect of this program on the gingival health of periodontal patients.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68278/2/10.1177_08959374950090020901.pd

Hydrolysis of the Leu-Gly bond of phenylazobenzyl-oxycarbonyl- l -Pro- l -Leu-Gly- l -Pro- D -Arg (a substrate of microbial collagenases) by treponemes isolated from the subgingival plaque of periodontitis patients

Cell extracts prepared from several oral treponemes isolated from the subgingival plaque of periodontitis patients showed high enzyme activity toward phenylazobenzyl-oxycarbonyl- l -prolyl- l -leucylglycyl- l -prolyl- d -arginine (a compound used as a substrate for microbial collagenases). One major enzyme hydrolyzing this substrate at the Leu-Gly bond only was partially purified from an unspeciated treponeme (strain US), Treponema denticola ATCC 35405, and 29 different clinical isolates of T. denticola . The Treponema US enzyme also hydrolyzed furylacryloyl- l -leucylglycyl- l -prolyl- l -alanine (another substrate of bacterial collagenases) at the Leu-Gly bond. This enzyme also hydrolyzed various collagens and collagen-derived peptides. These treponemal proteases were sensitive to metal chelators and p -chloromercury compounds. The results indicate that human oral treponemes contain enzymes that readily hydrolyze in chromogenic protease substrates the Leu-Gly bond only that is the cleavage site of these substrates also by “true” microbial collagenases.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41336/1/284_2005_Article_BF02094028.pd

Linear response of mutans streptococci to increasing frequency of xylitol chewing gum use: a randomized controlled trial [ISRCTN43479664]

BACKGROUND: Xylitol is a naturally occurring sugar substitute that has been shown to reduce the level of mutans streptococci in plaque and saliva and to reduce tooth decay. It has been suggested that the degree of reduction is dependent on both the amount and the frequency of xylitol consumption. For xylitol to be successfully and cost-effectively used in public health prevention strategies dosing and frequency guidelines should be established. This study determined the reduction in mutans streptococci levels in plaque and unstimulated saliva to increasing frequency of xylitol gum use at a fixed total daily dose of 10.32 g over five weeks. METHODS: Participants (n = 132) were randomized to either active groups (10.32 g xylitol/day) or a placebo control (9.828 g sorbitol and 0.7 g maltitol/day). All groups chewed 12 pieces of gum per day. The control group chewed 4 times/day and active groups chewed xylitol gum at a frequency of 2 times/day, 3 times/day, or 4 times/day. The 12 gum pieces were evenly divided into the frequency assigned to each group. Plaque and unstimulated saliva samples were taken at baseline and five-weeks and were cultured on modified Mitis Salivarius agar for mutans streptococci enumeration. RESULTS: There were no significant differences in mutans streptococci level among the groups at baseline. At five-weeks, mutans streptococci levels in plaque and unstimulated saliva showed a linear reduction with increasing frequency of xylitol chewing gum use at the constant daily dose. Although the difference observed for the group that chewed xylitol 2 times/day was consistent with the linear model, the difference was not significant. CONCLUSION: There was a linear reduction in mutans streptococci levels in plaque and saliva with increasing frequency of xylitol gum use at a constant daily dose. Reduction at a consumption frequency of 2 times per day was small and consistent with the linear-response line but was not statistically significant

Antiepileptic drugs and prostate cancer risk in the Finnish Randomized Study of Screening for Prostate Cancer

Antiepileptic drugs (AEDs) with histone deacetylase (HDAC) inhibitor properties decrease prostate cancer (PCa) cell proliferation in vitro. A population-based cohort of 78 615 men was used to evaluate the risk of PCa among users of AEDs. Study population was linked to the Finnish national prescription database to obtain information on individual medication reimbursements in 1996 to 2015. Cox regression with antiepileptic medication use as a time-dependent variable was used to analyze PCa risk overall, and low, medium and high-risk PCa separately. The analysis was adjusted for age, screening trial arm, and other drugs in use, including statins, antidiabetic drugs, antihypertensive drugs, aspirin, and nonsteroidal anti-inflammatory drugs. Compared to the nonusers of AEDs, overall PCa risk was decreased among AED users (hazard ratio [HR] = 0.86, 95% confidence interval [CI] = 0.76-0.96). A similar PCa risk decrease was observed among users of HDACi AEDs (HR = 0.87, 95% CI = 0.76-1.01), but no risk difference was found when comparing HDACi AED users to users of other AEDs (HR = 0.98, 95% CI = 0.76-1.27). Our study showed a decrease in overall PCa risk among men using AEDs compared to nonusers. The risk associations were similar for HDAC inhibitors as for AEDs in general.Peer reviewe

Anti-epileptic drugs and prostate cancer-specific mortality compared to non-users of anti-epileptic drugs in the Finnish Randomized Study of Screening for Prostate Cancer

Background Drugs with histone deacetylase inhibitory (HDACi) properties have shown to decrease prostate cancer (PCa) cell growth in vitro. Methods A cohort of 9261 PCa cases from the Finnish Randomized Study of Screening for Prostate Cancer (FinRSPC) was used to evaluate prostate cancer-specific mortality in men using anti-epileptic drugs (AEDs). A national subscription database was used to obtain information on medication use. Cox regression with AED use as a time-dependent variable was used to analyse prostate cancer mortality in men using AEDs compared to non-users, and in men using HDACi AEDs compared to users of other AEDs. The analysis was adjusted for age, screening trial arm, PCa risk group, primary treatment of PCa, Charlson co-morbidity score and concomitant use of other drugs. Results The use of AEDs, in general, was associated with an increased risk of PCa death. The use of HDACi AEDs was not significantly associated with decreased PCa mortality compared to use of other AEDs (HR 0.61, 95% CI 0.31-1.23). Conclusions AED usage is associated with elevated PCa mortality compared to non-users, likely reflecting the differences between men with epilepsy and those without. No benefit was observed from HDACi drugs compared to other AEDs.Peer reviewe

Storage and retrieval of individual genomes

Volume: 5541A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically huge collection is plausible using suffix trees. However, suffix tree occupies O(N log N) bits, which very soon inhibits in-memory analyses. Recent advances in full-text self-indexing reduce the space of suffix tree to O(N log σ) bits, where σ is the alphabet size. In practice, the space reduction is more than 10-fold, for example on suffix tree of Human Genome. However, this reduction factor remains constant when more sequences are added to the collection. We develop a new family of self-indexes suited for the repetitive sequence collection setting. Their expected space requirement depends only on the length n of the base sequence and the number s of variations in its repeated copies. That is, the space reduction factor is no longer constant, but depends on N / n. We believe the structures developed in this work will provide a fundamental basis for storage and retrieval of individual genomes as they become available due to rapid progress in the sequencing technologies.Peer reviewe