Amino acid preferences for specific locations at the ends of alpha helices

A definition based on alpha-carbon positions and a sample of 215 alpha helices from 45 different globular protein structures were used to tabulate amino acid preferences for 16 individual positions relative to the helix ends. The interface residue, which is half in and half out of the helix, is called the N-cap or C-cap, whichever is appropriate. The results confirm earlier observations, such as asymmetrical charge distributions in the first and last helical turn, but several new, sharp preferences are found as well. The most striking of these are a 3.5:1 preference for Asn at the N-cap position, and a preference of 2.6:1 for Pro at N-cap + 1. The C-cap position is overwhelmingly dominated by Gly, which ends 34 percent of the helices. Hydrophobic residues peak at positions N-cap + 4 and C-cap - 4.     

The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.     

Do riparian buffer strips mitigate the impacts of clearcutting on small mammals?

We assessed the impact of clearcutting on small mammals in riparian areas and evaluated riparian buffer strips as a tool for conserving small mammals in managed forests. Over two summers, we trapped small mammals of seven species in riparian areas in southwestern British Columbia, Canada. Communities of small mammals were compared across three different habitat types: (1) clearcut to the stream bank, (2) clearcut with a 30 m riparian buffer strip, and (3) control (no logging). Species richness was significantly lower in clearcuts than in controls and buffers. On clearcut sites, creeping voles were more abundant, but red-backed voles and dusky shrews were less abundant than at the control sites. At sites with riparian buffer strips, both voles were present in numbers similar to those found in controls, but dusky shrews were less common. Significantly more deer mice and creeping voles were infested with bot flies at clearcut sites than at buffer sites, and no animals were infested at any of the control sites. Riparian reserves appear to be useful in reducing the short-term impacts of clearcutting on small mammal communities, though they do not eliminate these impacts altogether.     

Ex vivo investigation of the use of hydrothermal energy to induce chondrocyte necrosis in articular cartilage of the metacarpophalangeal and metatarsophalangeal joints of horses

OBJECTIVE: To evaluate the use of hydrothermal ablation of articular cartilage for arthrodesis in horses through investigation of the effects of joint lavage with physiologic saline (0.9% NaCI) solution (80 degrees C) for various treatment times on chondrocyte viability in the articular cartilage of the metacarpophalangeal and metatarsophalangeal joints of cadaveric horse limbs. Sample Population-7 pairs of metacarpophalangeal and 8 pairs of metatarsophalangeal joints from 8 Thoroughbreds. PROCEDURE: The horses were euthanatized for reasons unrelated to musculoskeletal disease. On a random basis, 1 joint of each pair underwent intra-articular lavage for 5, 10, or 15 minutes with heated saline solution (80 degrees C); the other joint underwent sham treatment of similar duration with saline solution at 22 degrees C (control). Cartilage samples from the distal articular surface of metacarpus III (or metatarsus III), the proximal surface of the proximal phalanx, and the lateral and medial proximal sesamoid bones were assessed for chondrocyte viability via confocal microscopy and viability staining following enzymatic digestion. RESULTS: Compared with the control joints, findings of both viability assays indicated that the percentage of sites containing viable chondrocytes in heat-treated joints was decreased.Treatment hazard ratios of 0.048 (confocal microscopy) and 0.2 (digestion assay) were estimated. Histologically, periarticular soft tissues had minimal detrimental effects after heat treatment. CONCLUSIONS AND CLINICAL RELEVANCE: Ex vivo intra-articular lavage with saline solution at 80 degrees C resulted in the death of almost all articular chondrocytes in the joint. This technique may be a satisfactory method for extensive cartilage ablation when performing arthrodesis by minimally invasive techniques.     

Subchondral lucency of the third carpal bone in Standardbred racehorses: 13 cases (1982-1988)

Thirteen Standardbreds had subchondral lucency of the third carpal bone (C3), described as single or multiple central areas of C3 bone loss in the radial fossa. Sclerosis of the radial fossa was also detected. The mean age of 9 stallions, 3 mares, and 1 gelding was 4.1 years (range, 3 to 7 years). All horses had an acute moderate to severe lameness referable to the middle carpal joint. A dorsoproximal dorsodistal (skyline) radiographic projection was most useful and identified mild (3 horses), moderate (6 horses), and severe (4 horses) subchondral lucency and sclerosis of the radial fossa. The margin of C3 was intact dorsal to the lucent areas in all horses. In 12 horses, arthroscopic surgical evaluation and curettage of the lesion were performed. Of the 9 horses monitored long enough to allow racing, 8 horses (89%) returned to racing, although only 6 (75%) raced at the same degree of competition. Subchondral lucency of C3 resulted from chronic damage to C3 with subsequent osteochondral collapse or acute C3 proximal surface osteochondral fracture.     

Arthroscopic removal of dorsoproximal chip fractures of the proximal phalanx in standing horses

OBJECTIVE: To report a technique for, and outcome after, arthroscopic removal of dorsoproximal chip fractures of a proximal phalanx in standing horses. STUDY DESIGN: Retrospective study. ANIMALS OR SAMPLE POPULATION: A total of 104 horses, 1 to 13 years of age, with a dorsoproximal chip fracture of a proximal phalanx. METHODS: Horses were restrained in standing stocks and sedated with intravenous xylazine, detomidine, or a combination of both drugs. Local analgesia was achieved with 2% mepivacaine administered intra-articularly and by subcutaneous infiltration in a crescent-shaped block dorsal to the fetlock. Sterile drapes were placed on the surgical field, and impervious drapes were used on the hoof and floor. Arthroscopic portals were created in the dorsal pouch of the metacarpophalangeal or metatarsophalangeal joints to remove chip fractures. Statistical analysis was performed on race records for all Thoroughbred racehorses and compared with previously published studies. Operative and hospitalization times were compared with those of the general hospital population, and risks associated with general anesthesia were examined. RESULTS: No major operative or postoperative complications occurred. Ninety-one percent of racehorses raced after surgery with 78% returning to race at the same or higher level. CONCLUSION: Standing arthroscopic surgery can be performed successfully to remove dorsoproximal chip fractures of the proximal phalanx. CLINICAL RELEVANCE: Standing arthroscopic surgery is a valid alternative treatment for experienced surgeons to avoid the expense and potential risks associated with general anesthesia.     

Cytopathological and histopathological diagnosis of canine splenic disorders

Objectives To determine (1) the common types of canine splenic disorders, and the breeds affected, that are diagnosed by cytopathological and histopathological examination in Sydney, Australia and (2) the accuracy of cytopathological examination compared with histopathological examination for the diagnosis of canine splenic disorders. Design 69 cytopathological and 51 histopathological diagnoses of canine splenic disorders presented to the Veterinary Pathology Diagnostic Services, The University of Sydney during 2006 and 2007 were tabulated and analysed; 17 cases examined both cytopathologically and histopathologically during 2001–07 were also analysed. Results The most common cytopathological diagnoses were benign disorders of growth, vascular disturbances and necrosis (29%), followed by no abnormalities detectable (28%), malignant neoplasms (20%), equivocal diagnoses (20%) and inflammatory disorders (3%). The most common breeds were Kelpie crosses and mixed breeds. The most common histopathological diagnoses were benign disorders of growth, vascular disturbances and necrosis (49%), followed by malignant neoplasms (43%) and inflammatory disorders (8%). The most common breeds were German Shepherd Dogs, Boxers and Maltese Terriers. Cytopathological and histopathological diagnoses were in complete agreement in 59% of cases, partial agreement in 29% and disagreement in 12%. Conclusion Benign disorders of growth, vascular disturbances and necrosis were the most commonly diagnosed canine splenic disorders, both cytopathologically and histopathologically. Kelpie crosses presented most frequently for cytopathological examination. German Shepherd Dogs were the most common breed diagnosed histopathologically with haemangiosarcoma. Although cytopathological and histopathological splenic examinations are complementary for diagnosis, this study has shown a high correlation for complete and partial agreement between the two.     

Comparison of two- and three-way rotational crossing and synthetic variety production involving inbred lines of Hereford cattle: postweaning traits

Data for this linecrossing study were the postweaning growth and weight records of calves born from 1967 through 1975. The records consisted of 264 bull (M) and 263 heifer (F) straightline (SL) calves; 108 M and 100 F two-line rotational cross (2W) calves; 130 M and 102 F three-line rotational cross (3W) calves and 58 M and 51 F synthetic variety (SV) calves, all in the Hereford breed. Average inbreeding percentages of calves and dams in Lines 1, 4, 6 and 10 were 24, 28, 34 and 28; respectively. The M calves were fed a growing-fattening diet for 196 d after a 14-d period of adjustment to postweaning environment. The F calves were fed to gain approximately .5 kg daily during winter from weaning to about 12 mo of age and were then grazed on native pasture until about 18 mo of age. For M, average percentage increases over SL by 2W, 3W and SV combined over three generations were respectively, 9.0, 11.0, 11.6 for initial weight; 5.9, 8.1, 8.8 for 140-d weight; 4.8, 7.2, 7.7 for final 196-d weight and 1.5, 4.2, 4.7 for 196-d gain. All above estimates of increased weight or gain over SL were significant except for 196-d gain in 2W. For F, average percentage increases over SL by 2W, 3W and SV, respectively, were 9.0, 10.9, 11.3 for initial weight; 8.2, 9.2, 8.4 for 12-mo weight; 7.5, 7.7, 9.1 for 18-mo weight; 5.2, 5.3, 5.7 for 18-mo score. All these estimated increases over SL were significant.(ABSTRACT TRUNCATED AT 250 WORDS)