Structure of yeast hexokinase. II. A 6 angstrom resolution electron density map showing molecular shape and heterologous interaction of subunits

An electron density map of yeast hexokinase has been calculated at 6 Å resolution using six heavy atom derivatives. The map shows each of the enzyme's two 51,000 molecular weight subunits to consist of two separate lobes connected by a narrow bridge of density. Furthermore, these two subunits are related to each other in the asymmetric unit of the crystal by a quasi-2-fold rather than a true 2-fold axis. That is, they are related by a rotation of 180 ° plus a relative translation of 3.6 Å along the symmetry axis. This gives rise to a heterologous subunit interaction and a possibility of non-identical structure and function for these chemically identical subunits. The molecule is quite asymmetric, having dimensions of 150 Å × 45 Å × 55 Å. Each subunit is about 80 Å × 40 Å × 50 Å.A portion of an electron density map at 3 Å resolution has been also calculated, based on phases from two heavy atom derivatives. Polypeptide backbone and side chains are visible in this map.     

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.     

Mitochondrion-rich cells in the embryonic yolk sac of Oreochromis mossambicus

By removing a small amount of yolk, tilapia embryos were dechorionated successfully as early as 30 h after fertilization. Using DASPEI, a mitochondrion-specific fluorescent stain, we were able to determine the first appearance of the mitochondrion rich cells on the surface of the yolk sac 26 h after fertilization ( c. 2 h after the beginning of gastrula stage). However, with scanning electron microscopy examination, no apical crypt could be found until 48 h after fertilization.     

Phosphorylation of Ran-binding protein-1 by Polo-like kinase-1 is required for interaction with Ran and early mitotic progression

Polo-like kinase-1 (Plk1) is essential for progression of mitosis and localizes to centrosomes, central spindles, midbody, and kinetochore. Ran, a small GTPase of the Ras superfamily, plays a role in microtubule dynamics and chromosome segregation during mitosis. Although Ran-binding protein-1 (RanBP1) has been reported as a regulator of RanGTPase for its mitotic functions, the action mechanism between Ran and RanBP1 during mitosis is still unknown. Here, we demonstrated in vitro and in vivo phosphorylation of RanBP1 by Plk1 as well as the importance of phosphorylation of RanBP1 in the interaction between Plk1 and Ran during early mitosis. Both phosphorylation-defective and N-terminal deletion mutant constructs of RanBP1 disrupted the interaction with Ran, and depletion of Plk1 also disrupted the formation of a complex between Ran and RanBP1. In addition, the results from both ectopic expression of phosphorylation-defective mutant construct and a functional complementation on RanBP1 deficiency with this mutant indicated that phosphorylation of RanBP1 by Plk1 might be crucial to microtubule nucleation and spindle assembly during mitosis.     

Fluid Overload,Pulse Wave Velocity,and Ratio of Brachial Pre-Ejection Period to Ejection Time in Diabetic and Non-Diabetic Chronic Kidney Disease

Fluid overload is one of the characteristics in chronic kidney disease (CKD). Changes in extracellular fluid volume are associated with progression of diabetic nephropathy. Not only diabetes but also fluid overload is associated with cardiovascular risk factors The aim of the study was to assess the interaction between fluid overload, diabetes, and cardiovascular risk factors, including arterial stiffness and left ventricular function in 480 patients with stages 4–5 CKD. Fluid status was determined by bioimpedance spectroscopy method, Body Composition Monitor. Brachial-ankle pulse wave velocity (baPWV), as a good parameter of arterial stiffness, and brachial pre-ejection period (bPEP)/brachial ejection time (bET), correlated with impaired left ventricular function were measured by ankle-brachial index (ABI)-form device. Of all patients, 207 (43.9%) were diabetic and 240 (50%) had fluid overload. For non-diabetic CKD, fluid overload was associated with being female (β = –2.87, P = 0.003), heart disease (β = 2.69, P = 0.04), high baPWV (β = 0.27, P = 0.04), low hemoglobin (β = –1.10, P<0.001), and low serum albumin (β = –5.21, P<0.001) in multivariate analysis. For diabetic CKD, fluid overload was associated with diuretics use (β = 3.69, P = 0.003), high mean arterial pressure (β = 0.14, P = 0.01), low bPEP/ET (β = –0.19, P = 0.03), low hemoglobin (β = –1.55, P = 0.001), and low serum albumin (β = –9.46, P<0.001). In conclusion, baPWV is associated with fluid overload in non-diabetic CKD and bPEP/bET is associated with fluid overload in diabetic CKD. Early and accurate assessment of these associated cardiovascular risk factors may improve the effects of entire care in late CKD.     

Cleft lip nose correction with onlay calvarial bone graft and suture suspension in Oriental patients

To correct the secondary cleft lip nose deformity in Oriental patients, many alar cartilage mobilization and suspension techniques have been developed. However, these techniques have critical limitations. One of the limitations is the suspension vector, and another is suspension power. The suspension vector is from inferior to superior and from the deformed alar cartilage to the normal alar cartilage. Thus, the vector is not suitable for normal nasal tip projection. The suspension power is not satisfactory because Oriental people have underdeveloped, thin alar cartilages and thick skin. So, the suspended, deformed alar cartilage may relapse and pull the normal alar cartilage to the deformed side. To overcome these limitations, the authors use the cantilever calvarial bone graft for tip projection; it also serves as a strong, rigid framework for cartilage and soft-tissue suspension. Using these techniques, the authors can create normal nasal tip projection and a normal looking nasal aperture.     

Immunization of cultured juvenile rockfish Sebastes schlegeli against Microcotyle sebastis (Monogenea)

To determine whether immunization with Microcotyle sebastis antigen could induce protection against the parasite's establishment, naive juvenile rockfish were immunized by injection or immersion with whole worm antigen of M. sebastis. The infestation intensities of immunized groups following a challenge (2 wk after boosting) with 5000 M. sebastis eyed-eggs were significantly lower than those of control groups, when determined 7 wk postinfection. The fish in the groups boosted with M. sebastis antigen showed stronger protection than unboosted groups. The control group injected with FCA only showed a significantly smaller number of worms than the control group, which was immersed in PBS containing seawater. The results strongly suggest that both specific and nonspecific immune factors participate in the protection of rockfish against M. sebastis establishment.     

Enhanced nitrite build-up in proportion to increasing alklinity/NH4+ ratio of influent in biofilm reactor

When the alkalinity/NH₄ ⁺ratio increased from 4.1 to 9.4, the ammonium removal rate increased from 45 to 90 mg NO_x-N l^–1 h^–1. An increase in alkalinity/NH₄ ⁺ratio was a major reason for higher pH and free ammonia (FA) concentration in the reactor. The high concentration of FA showed a selective inhibition for Nitrobacter, which caused enhanced nitrite build-up in a biofilm reactor.     

Comparison of the Effects of Cuprizone on Demyelination in the Corpus Callosum and Hippocampal Progenitors in Young Adult and Aged Mice

Neurochemical Research - Cuprizone is commonly used to induce neuronal demyelination in mice. In the present study, we compared the cuprizone-induced demyelination in the corpus callosum and...