A dynamic growth model of vegetative soya bean plants: model structure and behaviour under varying root temperature and nitrogen concentration

A differential equation model of vegetative growth of the soya bean plant (Glycine max (L.) Merrill cv. Ransom') was developed to account for plant growth in a phytotron system under variation of root temperature and nitrogen concentration in nutrient solution. The model was tested by comparing model outputs with data from four different experiments. Model predictions agreed fairly well with measured plant performance over a wide range of root temperatures and over a range of nitrogen concentrations in nutrient solution between 0.5 and 10.0 mmol NO3- in the phytotron environment. Sensitivity analyses revealed that the model was most sensitive to changes in parameters relating to carbohydrate concentration in the plant and nitrogen uptake rate.     

Reflections of a member of the bicentennial class on the Bicentennial Symposium

This perspective piece explores what it means to be a first-year medical student at Yale School of Medicine during its bicentennial year. At first, it seemed like a hefty burden to bear. However, upon listening to Dr. Eric Kandel speak at the Bicentennial Symposium at Yale on April 28, 2011, it became clear what it means to be a part of the future of science and medicine at Yale.     

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only ∼1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional ∼119 000 nearly full-length sequences and 28 000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life.     

The Impact of Calcium and Dairy Product Consumption on Weight Loss

Objective: Recent evidence suggests that diets high in calcium and dairy products are associated with lower body weight, particularly lower body fat levels. The purpose of this study was to compare weight and body fat loss on a calorie-restricted, low-dairy (CR) vs. high-dairy (CR+D) diet. Research Methods and Procedures: Fifty-four subjects (BMI 30 ± 2.5 kg/m², 45 ± 6.6 years, 4 men) were randomly assigned to calorie-restricted (−500 kcal/d) low-dairy calcium (n = 29; ∼1 serving dairy/d, 500 mg/d calcium) or high-dairy calcium (n = 25; 3 to 4 servings dairy/d, 1200 to 1400 mg/d calcium) diets for 12 months. Main outcome measures included change in weight (kilograms) and body fat (percentage). Results: There were no significant differences between groups at baseline. At 12 months, weight and body fat loss were not significantly different. Subjects in the CR vs. CR+D conditions lost 9.6 ± 6.5 vs. 10.8 ± 5.9 kg (p = 0.56) and 9.0 ± 3.8 vs. 10.1 ± 3.6 kg body fat (p = 0.37). Discussion: These findings suggest that a high-dairy calcium diet does not substantially improve weight loss beyond what can be achieved in a behavioral intervention.     

Haploid accumulation and translational control of phosphoglycerate kinase-2 messenger RNA during mouse spermatogenesis

The intracellular location of the mRNA for the testis-specific isozyme of phosphoglycerate kinase-2 (PGK-2) has been determined for two spermatogenic cell types. The mRNA activity for PGK-2 from the polysomal and nonpolysomal fractions of pachytene primary spermatocytes or round spermatids has been assayed by cell-free translation with the polypeptide products monitored by immunoprecipitation, followed by one-dimensional or two-dimensional electrophoresis and fluorography. The results reveal that the majority of PGK-2 mRNA activity of round spermatids was present in the polysomal fraction while the relatively less abundant PGK-2 mRNA of pachytene primary spermatocytes was present in the nonpolysomal fraction. No PGK-2 mRNA activity was observed in the cytoplasmic RNA from primitive type A spermatogonia or prepubertal Sertoli cells. These data indicate that mature PGK-2 mRNA first appears in the cytoplasm of spermatogenic cells during the prophase of meiosis and increases in amount after meiosis. Although mature PGK-2 mRNA is present in meiotic cells it is not actively translated until after meiosis has been completed. Thus, mRNA accumulation and translational mechanisms are involved in the control of phosphoglycerate kinase-2 synthesis during spermatogenesis.     

Restarted replication forks are error-prone and cause CAG repeat expansions and contractions

Disease-associated trinucleotide repeats form secondary DNA structures that interfere with replication and repair. Replication has been implicated as a mechanism that can cause repeat expansions and contractions. However, because structure-forming repeats are also replication barriers, it has been unclear whether the instability occurs due to slippage during normal replication progression through the repeat, slippage or misalignment at a replication stall caused by the repeat, or during subsequent replication of the repeat by a restarted fork that has altered properties. In this study, we have specifically addressed the fidelity of a restarted fork as it replicates through a CAG/CTG repeat tract and its effect on repeat instability. To do this, we used a well-characterized site-specific replication fork barrier (RFB) system in fission yeast that creates an inducible and highly efficient stall that is known to restart by recombination-dependent replication (RDR), in combination with long CAG repeat tracts inserted at various distances and orientations with respect to the RFB. We find that replication by the restarted fork exhibits low fidelity through repeat sequences placed 2–7 kb from the RFB, exhibiting elevated levels of Rad52- and Rad8^{ScRad5/HsHLTF}-dependent instability. CAG expansions and contractions are not elevated to the same degree when the tract is just in front or behind the barrier, suggesting that the long-traveling Polδ-Polδ restarted fork, rather than fork reversal or initial D-loop synthesis through the repeat during stalling and restart, is the greatest source of repeat instability. The switch in replication direction that occurs due to replication from a converging fork while the stalled fork is held at the barrier is also a significant contributor to the repeat instability profile. Our results shed light on a long-standing question of how fork stalling and RDR contribute to expansions and contractions of structure-forming trinucleotide repeats, and reveal that tolerance to replication stress by fork restart comes at the cost of increased instability of repetitive sequences.     

The Place of "Others" in Hunter-Gatherer Intensification

Archaeologists are interested in understanding the conditions under which hunter-gatherer intensification occurs. Typically, most models assign primacy to population pressure or social relations and address intensification as it occurs among foragers inhabiting arid or temperate environments. In this article, I explore episodes of resource intensification and "deintensification" on the subarctic island of Newfoundland. Correlating periods of resource intensification and "deintensification" with changes in the social landscape, I argue that the presence or absence of "Others" played a significant role in informing hunter-gatherer subsistence strategies and settlement patterns.     

Visualization of ATP Synthase Dimers in Mitochondria by Electron Cryo-tomography

Electron cryo-tomography is a powerful tool in structural biology, capable of visualizing the three-dimensional structure of biological samples, such as cells, organelles, membrane vesicles, or viruses at molecular detail. To achieve this, the aqueous sample is rapidly vitrified in liquid ethane, which preserves it in a close-to-native, frozen-hydrated state. In the electron microscope, tilt series are recorded at liquid nitrogen temperature, from which 3D tomograms are reconstructed. The signal-to-noise ratio of the tomographic volume is inherently low. Recognizable, recurring features are enhanced by subtomogram averaging, by which individual subvolumes are cut out, aligned and averaged to reduce noise. In this way, 3D maps with a resolution of 2 nm or better can be obtained. A fit of available high-resolution structures to the 3D volume then produces atomic models of protein complexes in their native environment. Here we show how we use electron cryo-tomography to study the in situ organization of large membrane protein complexes in mitochondria. We find that ATP synthases are organized in rows of dimers along highly curved apices of the inner membrane cristae, whereas complex I is randomly distributed in the membrane regions on either side of the rows. By subtomogram averaging we obtained a structure of the mitochondrial ATP synthase dimer within the cristae membrane.