Small phytoplankton and carbon export from the surface ocean

Autotrophic picoplankton dominate primary production over large oceanic regions but are believed to contribute relatively little to carbon export from surface layers. Using analyses of data from the equatorial Pacific Ocean and Arabian Sea, we show that the relative direct and indirect contribution of picoplankton to export is proportional to their total net primary production, despite their small size. We suggest that all primary producers, not just the large cells, can contribute to export from the surface layer of the ocean at rates proportional to their production rates.     

Genome streamlining in a cosmopolitan oceanic bacterium

The SAR11 clade consists of very small, heterotrophic marine alpha-proteobacteria that are found throughout the oceans, where they account for about 25% of all microbial cells. Pelagibacter ubique, the first cultured member of this clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. In contrast to parasitic bacteria and archaea with small genomes, P. ubique has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. P. ubique has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell.     

Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder

We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of lambda-phage DNA by individual bacteriophage lambda exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate DNA. By relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the DNA is the rate-limiting step in the catalytic cycle. The catalytic rate also exhibits large fluctuations independent of the sequence, which we attribute to conformational changes of the enzyme-DNA complex.     

Control of stress-dependent cardiac growth and gene expression by a microRNA

The heart responds to diverse forms of stress by hypertrophic growth accompanied by fibrosis and eventual diminution of contractility, which results from down-regulation of alpha-myosin heavy chain (alphaMHC) and up-regulation of betaMHC, the primary contractile proteins of the heart. We found that a cardiac-specific microRNA (miR-208) encoded by an intron of the alphaMHC gene is required for cardiomyocyte hypertrophy, fibrosis, and expression of betaMHC in response to stress and hypothyroidism. Thus, the alphaMHC gene, in addition to encoding a major cardiac contractile protein, regulates cardiac growth and gene expression in response to stress and hormonal signaling through miR-208.     

Start of the Wilson cycle at 3 Ga shown by diamonds from subcontinental mantle

Mineral inclusions encapsulated in diamonds are the oldest, deepest, and most pristine samples of Earth's mantle. They provide age and chemical information over a period of 3.5 billion years--a span that includes continental crustal growth, atmospheric evolution, and the initiation of plate tectonics. We compiled isotopic and bulk chemical data of silicate and sulfide inclusions and found that a compositional change occurred 3.0 billion years ago (Ga). Before 3.2 Ga, only diamonds with peridotitic compositions formed, whereas after 3.0 Ga, eclogitic diamonds became prevalent. We suggest that this resulted from the capture of eclogite and diamond-forming fluids in subcontinental mantle via subduction and continental collision, marking the onset of the Wilson cycle of plate tectonics.     

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.     

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.     

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.