A census of human soluble protein complexes

Cellular processes often depend on stable physical associations between proteins. Despite recent progress, knowledge of the composition of human protein complexes remains limited. To close this gap, we applied an integrative global proteomic profiling approach, based on chromatographic separation of cultured human cell extracts into more than one thousand biochemical fractions that were subsequently analyzed by quantitative tandem mass spectrometry, to systematically identify a network of 13,993 high-confidence physical interactions among 3,006 stably associated soluble human proteins. Most of the 622 putative protein complexes we report are linked to core biological processes and encompass both candidate disease genes and unannotated proteins to inform on mechanism. Strikingly, whereas larger multiprotein assemblies tend to be more extensively annotated and evolutionarily conserved, human protein complexes with five or fewer subunits are far more likely to be functionally unannotated or restricted to vertebrates, suggesting more recent functional innovations.

Protein abundances are more conserved than mRNA abundances across diverse taxa

Proteins play major roles in most biological processes; as a consequence, protein expression levels are highly regulated. While extensive post-transcriptional, translational and protein degradation control clearly influence protein concentration and functionality, it is often thought that protein abundances are primarily determined by the abundances of the corresponding mRNAs. Hence surprisingly, a recent study showed that abundances of orthologous nematode and fly proteins correlate better than their corresponding mRNA abundances. We tested if this phenomenon is general by collecting and testing matching large-scale protein and mRNA expression data sets from seven different species: two bacteria, yeast, nematode, fly, human, and rice. We find that steady-state abundances of proteins show significantly higher correlation across these diverse phylogenetic taxa than the abundances of their corresponding mRNAs (p=0.0008, paired Wilcoxon). These data support the presence of strong selective pressure to maintain protein abundances during evolution, even when mRNA abundances diverge.

Previous radiographic experience of children referred for dental extractions under general anaesthesia in the U.K

OBJECTIVE

To determine what proportion of children undergo radiographic assessment prior to referral to a dental hospital for extractions under general anaesthesia.

BASIC RESEARCH DESIGN

This prospective survey was conducted over a 6-month period. A data sheet was used to record the following information: patient's age; referrer's name and place of work (general dental practice or community dental service); teeth to be extracted (primary dentition and/or permanent dentition) and reported previous radiographic examination. Patients were excluded from the study if, following a clinical examination, radiographs were not actually deemed necessary for diagnosis and treatment planning purposes. Clinical setting A paediatric dentistry clinic within a dental hospital in the North of England. Participants 161 patients with a mean age of six years (SD = 2.2, range = 3-14 years) who were referred to the dental hospital for extractions under general anaesthesia.

RESULTS

Overall, 12.4% of children had reportedly undergone a previous radiographic assessment prior to hospital referral. A significantly greater proportion of children referred for permanent tooth extractions had been subject to radiographic examination compared to children referred for primary tooth extractions (46.2% as compared to 6.3%; P = 0.001 chi-squared test). Furthermore, patients referred from the community dental service were significantly more likely to have had previous dental radiographs than children referred from general dental practice (36.9% compared to 9.3%; P = 0.003 chi-squared test).

CONCLUSIONS

Radiographs do not appear to be routinely employed for caries diagnosis and treatment planning in young children within general dental practice in the U.K.

Characterization of Vibrio cholerae RyhB: the RyhB regulon and role of ryhB in biofilm formation

Vibrio cholerae encodes a small RNA with homology to Escherichia coli RyhB. Like E. coli ryhB, V. cholerae ryhB is negatively regulated by iron and Fur and is required for repression of genes encoding the superoxide dismutase SodB and multiple tricarboxylic acid cycle enzymes. However, V. cholerae RyhB is considerably longer (>200 nucleotides) than the E. coli RNA (90 nucleotides), and it regulates the expression of a variety of genes that are not known to be regulated by RyhB in E. coli, including genes involved in motility, chemotaxis, and biofilm formation. A mutant with a deletion in ryhB had reduced chemotactic motility in low-iron medium and was unable to form wild-type biofilms. The defect in biofilm formation was suppressed by growing the mutant in the presence of excess iron or succinate. The wild-type strain showed reduced biofilm formation in iron-deficient medium, further supporting a role for iron in normal biofilm formation. The ryhB mutant was not defective for colonization in a mouse model and appeared to be at a slight advantage when competing with the wild-type parental strain. Other genes whose expression was influenced by RyhB included those encoding the outer membrane porins OmpT and OmpU, several iron transport systems, and proteins containing heme or iron-sulfur clusters. These data indicate that V. cholerae RyhB has diverse functions, ranging from iron homeostasis to the regulation of biofilm formation.

Determination of polydextrose in foods by ion chromatography: collaborative study

Eight collaborating laboratories assayed 7 blind duplicate pairs of foods for polydextrose content. The 7 test sample pairs ranged from low (2%) to high (95%) levels. The following foods were prepared with polydextrose mixed into the other ingredients and then baked, cooked, or otherwise prepared: milk chocolate candy, iced tea, sugar cookie, grape jelly, soft jellied candy, and powdered drink mix. Collaborators received a polydextrose standard to develop a calibration curve. The method determined polydextrose by ion chromatography, after removal of interfering food components (high molecular weight solubles). Repeatability standard deviations (RSDr) ranged from 3.93 to 9.04%; reproducibility standard deviations (RSDR) ranged from 4.48 to 14.06%. The average recovery was 94%.

Studies on the effects of polydextrose intake on physiologic functions in Chinese people

BACKGROUND

Previous studies showed that polydextrose has physiologic effects similar to those of dietary fiber.

OBJECTIVE

Ingestion of 4, 8, and 12 g polydextrose/d was studied to determine the physiologic effects in Chinese subjects.

DESIGN

In a placebo-controlled, randomized, double-blind study, we evaluated the effects of polydextrose ingestion on clinical biochemistry indexes, glycated hemoglobin, glucose tolerance, the glycemic index, bowel function, stool weight and pH, short-chain fatty acid production, fecal microflora, and cecal mucosa cell proliferation.

RESULTS

Polydextrose had no significant effect on blood biochemistry indexes. Ingestion of 12 g polydextrose plus 50 g glucose resulted in a glycemic index of 89% (compared with a glycemic index of 100% after ingestion of 50 g glucose). Bowel function (frequency and ease of defecation) improved significantly and there were no reports of abdominal distention, abdominal cramps, diarrhea, or hypoglycemia. Fecal weight (wet and dry) increased and fecal pH decreased proportionally to polydextrose intake. Short-chain fatty acid production-notably that of butyrate, isobutyrate, and acetate-increased with polydextrose ingestion. There were substantial changes in fecal anaerobes after polydextrose intake. BACTEROIDES: species (B. fragilis, B. vulgatus, and B. intermedius) decreased, whereas LACTOBACILLUS: and BIFIDOBACTERIUM: species increased. The cecal mucosa whole-crypt labeling index increased, with colonocyte proliferation mainly occurring in base compartments, which provided an indirect confirmation of butyrate production in the colon.

CONCLUSION

Polydextrose ingestion had significant dietary fiber-like effects with no laxative problems.

Determination of polydextrose as dietary fiber in foods

Polydextrose (Litesse) provides physiological effects consistent with dietary fiber. However, AOAC methods for measuring total dietary fiber (TDF) in foods include an ethanol precipitation step in which polydextrose and similar carbohydrates are discarded and therefore not quantitated. This study describes a method developed to quantitate polydextrose in foods. The new method includes water extraction, centrifugal ultrafiltration, multienzyme hydrolysis, and anion exchange chromatography with electrochemical detection. Six foods were prepared with 4 levels of polydextrose to test the ruggedness of the method. Internal validation demonstrated the ruggedness of the method with recoveries ranging from 83 to 104% with an average of 95% (n = 24) and relative standard deviation of recoveries ranging from 0.7 to 13% with an average of 3.3% (n = 24). The value is added to that obtained for dietary fiber content of foods using the AOAC methods, to determine the TDF content of the food.

Patients with alcohol problems in the emergency department, part 1: improving detection. SAEM Substance Abuse Task Force. Society for Academic Emergency Medicine

Medical and social problems related to alcohol use are frequently seen in the ED. Often, the tempo of emergency medicine practice seems to preclude assessment beyond that required by the acute complaint. However, detection of ED patients with alcohol problems can occur using brief screening tools. This article was developed by members of the SAEM Substance Abuse Task Force, and describes screening tools that have been used successfully to identify at-risk and dependent drinkers. Their brevity, reproducibility, and accuracy vary somewhat, but screening can be realistically performed in the busy ED setting. The early detection of patients with alcohol problems would provide the opportunity for early intervention, and may reduce subsequent morbidity and mortality in this patient population.

Patients with alcohol problems in the emergency department, part 2: intervention and referral. SAEM Substance Abuse Task Force. Society for Academic Emergency Medicine

Early intervention and appropriate referral of patients with alcohol problems have the potential to reduce alcohol-related morbidity and mortality. Part 1 of this series introduced screening tools that can be applied in the ED to allow early detection of at-risk drinkers. This article was developed by members of the SAEM Substance Abuse Task Force and describes assessment and intervention techniques once the at-risk or dependent drinkers has been identified. Appropriate aftercare and referral of patients found to have alcohol problems are also discussed.

Emergency department management of patients with automatic implantable cardioverter-defibrillators

The case of a patient with idiopathic dilated cardiomyopathy and complex ventricular arrhythmias who underwent placement of an automatic implantable cardioverter-defibrillator (AICD) and experienced inappropriate shocks during atrial fibrillation is presented. On presentation to the emergency department, the patient had experienced approximately ten device discharges over six hours. ECG revealed atrial fibrillation with a rapid, wide complex ventricular response. Initial management consisted of IV verapamil for rate control followed by deactivation of the AICD. The patient was subsequently hospitalized for treatment of atrial fibrillation. Inappropriate device discharges, a frequently reported AICD-associated complication, are discussed.

Professional-development and continuing-education programs for pharmacists in large hospitals

Pharmacy directors at large hospitals nationwide were surveyed to determine the status of professional-development and continuing-education programs for staff pharmacists at their institutions. An 18-item questionnaire was developed and mailed in July 1987 to pharmacy directors of 445 large (bed capacity of greater than or equal to 450) hospitals. The questionnaire was designed to elicit information about who holds responsibility for the professional-development programs, the programs' frequency and format, how attendance is documented, and the types of individuals who present the programs. A total of 327 (73.5%) of the questionnaires were returned, with 256 (78.3%) of the respondents indicating that their department had some form of developmental-training program. Only 45 (17.6%) of these respondents indicated that their department employed an individual whose job title was specific for education or training functions. Hour-long lectures and videotaped programs were the most popular formats; programs were most frequently presented by pharmaceutical sales representatives or clinical or staff pharmacists. Of 251 respondents, only 90 (35.8%) indicated that an educational needs assessment of pharmacists had been conducted in the 18 months before the survey. Of 252 respondents, 138 (54.8%) indicated that their departments had no annual budget for these programs. Although program attendance was documented by 248 (97.3%) of the 256 departments, 111 (43.3%) did not require any type of certification for some programs. Evaluations were required by only 127 (49.6%) of the 256 pharmacy departments offering these programs. Inhouse programs offer opportunities for professional development, but resource allocation, program organization, and incentives for participation such as standards of performance could be improved in many of the programs explored by this survey.

The iodine-staining properties and fine structure of some mammalian and invertebrate glycogens

Glycogens from mammalian and invertebrate sources have been compared by measuring the iodine-staining spectra of the debranched polymers and the debranched beta-amylase limit dextrins. From the results, it is concluded that, whereas the interior chains of each group of glycogen are very similar, the exterior chains of the mammalian glycogens generally contain a small number of longer chains which are not found in the invertebrate glycogens.

Improved Hair-Sampling Tube for the Detection of Rare Mammals

A modified hair-sampling tube constructed from readily available PVC fittings is described. The use of aluminium screens to protect the bait source means that the hair-sampling tube remains attractive for extended periods. The hair-sampling tube has proven useful as a survey tool in the detection of iess common mammal species.

Pharmacy-based distribution system for enteral nutrition products

A hospital pharmacy department's implementation of enteral nutrition product distribution and its proposal for an enteral nutrition product admixture service are described. Responsibility for the distribution of enteral nutrition formulations was transferred from the central distribution department to the pharmacy after problems with inventory control, billing procedures, and inappropriate administration of enteral nutrition products were recognized by personnel from the central-distribution area and nutrition services. After additional problems were identified using a multi-disciplinary approach, the pharmacy department implemented an enteral nutrition product distribution system and developed an enteral nutrition product formulary. A proposal was developed for a pharmacy-based enteral nutrition admixture service, but implementation of this service was deferred because data from a cost-effectiveness evaluation and random bacteriologic monitoring did not justify adding the service. Pharmacy-based distribution and formulary control of enteral nutrition products alleviated problems with inaccurate patient charges and accumulation of stock on the nursing units. Pharmacists at this hospital hope to develop an enteral nutrition product admixture program that will result in cost savings for the institution.

Social Organization, Reproduction and Feeding Behaviour of a Population of Yellow-Bellied Gliders, Petaurus Australis (Marsupialia: Petauridae)

Population dynamics, habitat use and feeding behaviour in a small population of P. australis were studied in 190 ha of Tall Open Forest in the Victorian Central Highlands. Between October 1979 and December 1982, 13 marked individuals were trapped on 71 occasions during 1223 trap-nights. Gliders formed relatively stable family groups, each comprising a single resident pair living in a monogamous relationship with or without dependent offspring. They bred between August and October. Four females were observed with a single pouch young. Each pair occupied substantially separate ranges of between 30 and 55 ha. The maximum number of individuals estimated to be present during any month was eight. Den hollows were located only in living trees and one family group of three individuals used at least eight den trees within their home area. All sap-site trees were located mid-slope and were used mainly during the winter-spring months. Analysis of faeces and direct observation of feeding animals indicated that the bulk of this glider's diet is made up of arthropods, supplemented with insect and plant exudates. Some management implications, based on the life-history requirements of this glider, are discussed.

Lymphocyte function in experimental african trypanosomiasis: mitogenic effects of trypanosome extracts in vitro

Extracts of Trypanosoma brucei and Trypanosoma congolense were incubated in vitro with nonimmune lymphocytes of mice, rats, guinea pigs, and rabbits in order to test for mitogenic effects or for other characteristics of polyclonal B lymphocyte activators. Trypanosome extracts (TE) were not mitogenic for spleen cells of mice, rats, and guinea pigs in vitro, nor did the parasite extracts alter the mitogenic responses of lymphocytes from these animals to known B- and T-cell mitogens. TE also failed to induce polyclonal antibody synthesis in mouse spleen cell cultures in an in vitro antibody response system, in contrast to the effects of bacterial lipopolysaccharide, a known polyclonal B cell activator. Rabbit spleen cell and peripheral blood lymphocyte cultures, however, were stimulated by TE to undergo blastogenesis in vitro. Incubation of rabbit lymphocytes with phytohemagglutinin (PHA) and TE or anti-rabbit immunoglobulin serum and TE revealed an additive effect only in terms of the TE-plus-PHA culture responses; these findings suggest that a non-PHA responsive lymphocyte population, possibly B lymphocytes, is stimulated by TE in rabbits. The relationship of trypanosome-induced lymphocyte mitogenic stimulation to other immunological dysfunctions occurring in chronic African trypanosomiasis is discussed.