On the Relation Between the Predicted Secondary Structure and the Protein Size

Accurately predicted protein secondary structure provides useful information for target selection, to analyze protein function and to predict higher dimensional structure. Existing research shows that more data + refined search = better prediction. We analyze relation between the prediction accuracy and another crucial factor, the protein size. Empirical tests performed with two secondary structure predictors on a large set of high-resolution, non-redundant proteins show that the average accuracies for small proteins (<100 residues) equal 73% and 54% for alpha-helices and beta-strands, respectively. The alpha-helix/beta-strand accuracies for very large proteins (>300 residues) equal 77%/68%, respectively. Similarly, the tests with three secondary structure content predictors show that the prediction errors for the small/very large proteins equal 0.13/0.09 and 0.09/0.06 for alpha-helix and beta-strand content, respectively. Our tests confirm that the secondary structure/content predictions for the very large proteins are characterized statistically significantly better quality than prediction for the small proteins. This is in contrast with the tertiary structure predictions in which higher accuracy is obtained for smaller proteins.     

Ectogenesis and the case against the right to the death of the foetus

Ectogenesis, or the use of an artificial womb to allow a foetus to develop, will likely become a reality within a few decades, and could significantly affect the abortion debate. We first examine the implications for Judith Jarvis Thomson’s violinist analogy, which argues for a woman’s right to withdraw life support from the foetus and so terminate her pregnancy, even if the foetus is granted full moral status. We show that on Thomson’s reasoning, there is no right to the death of the foetus, and abortion is not permissible if ectogenesis is available, provided it is safe and inexpensive. This raises the question of whether there are persuasive reasons for the right to the death of the foetus that could be exercised in the context of ectogenesis. Eric Mathison and Jeremy Davis have examined several arguments for this right, doubting that it exists, while Joona Räsänen has recently criticized their reasoning. We respond to Räsänen’s analysis, concluding that his arguments are unsuccessful, and that there is no right to the death of the foetus in these circumstances.     

感染与早产儿脑损伤临床关系探讨

目的:探讨感染与早产儿脑损伤(HIE,ICH,CWMD)的临床表现,治疗,预后和预防的关系。方法:对2000年1月-2006年10月214例早产儿进行临床分析。结果:胎膜早破32例,母亲妊高症23例,胎儿宫内窘迫33例,脐带扭转打结7人,母亲妊娠糖尿病4人,胎儿畸形4人;早产儿肺炎101人,早产儿寒冷损伤综合征7人,早产儿急性坏死性小肠结肠炎5人,低血糖症27人,低血钙症13人,早产儿缺氧缺血性脑病(HIE)76人,早产儿颅内出血(ICH)21人,早产儿脑白质损伤(CWMD)3人。早期诊断、合理抗感染治疗可减少早产儿HIE及ICH以及CWMD患儿的神经系统后遗症。结论:早产儿感染与HIE及ICH以及CWMD的关系密切,预防产前、产时、产后感染对减少或减轻早产儿脑损伤至关重要。     

Self-organization in the determination of the size of the axial structures in the embryogenesis of the clawed toad

Experiments were performed using X. laevis embryos during gastrulation and neurulation (stages 10, 11 1/2, 12 1/2, 13 1/2, 15 and 18). Part of presumptive epidermis and lateral plate mesoderm was removed, and embryos raised until stage 25. The size of axial structures (notochord, somite mesoderm, central nervous system) was determined using serial histological sections and compared with that of control embryos. In experimental embryos, the size of axial structures was decreased. Until a specific stage of development, close correlation was found between the volume of embryonic compartment corresponding to a particular, structure and the volume of presumptive epidermis and lateral plate mesoderm. This stage is individual for each axial organ: middle gastrula (stage 11 1/2) for notochord, late gastrula (stage 12 1/2) for somite mesoderm, and late neurula (stage 18) for central nervous system. This data suggest that differentiation pattern of ecto-mesodermal rudiment is subject to regulation during gastrulation-neurulation, and subdivision of ectoderm and mesoderm into axial and non-axial tissues is a self-organizing process.     

Investigating the role of the hydroxyl groups of substrate erythrose 4-phosphate in the reaction catalysed by the first enzyme of the shikimate pathway

3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) synthase catalyses the first step of the shikimate pathway, which is responsible for the biosynthesis of aromatic amino acids in microorganisms and plants. This enzyme catalyses an aldol reaction between phosphoenolpyruvate and D-erythrose 4-phosphate to generate DAH7P. Both 2-deoxyerythrose 4-phosphate and 3-deoxyerythrose 4-phosphate were synthesised and tested as alternative substrates for the enzyme. Both compounds were found to be substrates for the DAH7P synthases from Escherichia coli, Pyrococcus furiosus and Mycobacterium tuberculosis, consistent with an acyclic mechanism for the enzyme for which neither C2 nor C3 hydroxyl groups are required for catalysis. The enzymes all showed greater tolerance for the loss of the C2 hydroxyl group than the C3 hydroxyl group.     

军标菌株生活史中各阶段生长发育时间的研究

为了更好地研究军标菌在其应用中的实验周期问题 ,采用插片培养法和载片培养法对军标中 5株实验菌的生活史中各阶段生长发育所需时间进行了研究。结果表明 ,5株菌的各时期生长发育所需时间有所不同。整个生活史最长的 4940min ,如AS 3 .42 5 4。最短的 3 888min ,如AS 3 .3 95 0。孢子萌发阶段所需时间也各不相同 ,最长的需 1 5 2 0min ,如AS 3 .3 885。最短的需 640min ,如AS 3 .3 95 0。这一研究为军标中霉菌试验周期 ,即 2 8d过长而且完全可缩短试验周期的观点 ,提供了有力的证据。     

Speculations on the evolution of the genetic code IV the evolution of the aminoacyl-tRNA synthetases

An evolutionary scheme is postulated in which a primitive code, involving only guanine and cytosine, would code for glycine(GG.), alanine(GC), arginine(CG.) and proline(CC). There evolves from this primitive code families of related amino acids as the code expands. The evolution of the aminiacyl-tRNA synthetases are considered to be indicators for the evolution of the genetic code. The postulated model for the evolution of the genetic code is used to give an evolutionary interpretation to the recent work on the structure and sequences of the aminoacyl-tRNA synthetases.     

From the item to the outcome: the promising prospects of PROMIS

Evaluation of patient reported outcomes, and in particular physical function, have gained increasing importance in research and therapy of patients with rheumatic diseases. Most instruments that are used for that purpose are rigid and suffer from floor and ceiling effects when used in patients whose physical function differs from the average. A new approach to the assessment of physical function uses computerised adaptive testing, by which precision and reliability of the measurement can be achieved for most patients, while even requiring less time for the assessment. Well calibrated and tested item and large item data banks are a prerequisite for this purpose, a process that is summarised in the present report by Bruce and colleagues.     

Electroporation of the vasculature and the lung

Electroporation has proven to be a highly effective technique for the in vivo delivery of genes to a number of solid tissues. In most of the reported methods, DNA is injected into the target tissue and electrodes are placed directly on or in the tissue for application of the electric field. While this works well for solid tissues, there are many tissues and organs that are not amenable to such an approach. In this review I will focus on the development of electroporation protocols for two such tissues: the vasculature and the lung. Several methods for in vivo electroporation of the vasculature have been developed in recent years that deliver DNA to vessel segments from either the inside or outside of the vessel. The advantages and disadvantages of each are discussed, as are the applications for which they have been used. In more recent work, our laboratory has developed a novel method to deliver genes to the rodent lung that results in high level, uniform, gene expression throughout all cell types of the lung. Most importantly, this technique is safe, and causes no inflammatory response or alterations in normal physiology of the organs. Taken together, these studies demonstrate the utility of electroporation for gene transfer to non injectible tissues.     

Effect of cutting the zona pellucida on the pronuclear transplantation in the mouse

A new and reliable pronuclear transplantation procedure for the mouse egg has been developed by McGrath and Solter ('83). To overcome the technical difficulties of such a procedure, especially in uniformly preparing enucleation pipettes and in reducing damages during micromanipulation, we have examined the effect of cutting the zona pellucida of the eggs. By making a slit in the zona of an egg, the time for pipetting and exchange of pronuclei between eggs was shortened because the sharp tip of the pipette was not necessary. Although the proportion of pregnant recipients and young obtained after transfer of pronuclear transplanted eggs cultured for 1 day or 3 days was quite low, it was significantly increased (70% for pregnancy rate and 32% for the young) following transfer of eggs cultured for 4 days. These values were comparable with those after transfer of unoperated eggs cultured to morulae and blastocysts.     

Increase in the pace of the growth of the human fetus towards the end of pregnancy]

Growth velocity curves of 19 biometrical parameters were established from 490 normal fetuses or neonates, who died in the perinatal period, and from 4,507 ultrasound examinations. There was a velocity fall for numerous parameters during the third trimester of gestation, but growth rate started up again after 38 weeks for some of them (femur length, biparietal diameter, crown-rump length, head circumference ...). No acceleration was found for body weight and crown-heel length by the end of gestation.     

Making the past serve the present

Botany has been successfully introduced to environmental design students, as a foundation for ecology and horticulture, in the form of extracts from an 18th century text which students are asked to criticise and update. This historical introduction demonstrates something of both the development ofthe subject and the students ' range of knowledge in it; and is a useful prompt for study. It encourages precision in the use of words, and emphasizes the provisional nature of scientific explanations. Suggestions for the use of this approach in other subjects and more advanced studies are made.     

Freezing tolerance of the European water frogs: the good, the bad, and the ugly

Survival and some physiological responses to freezing were investigated in three European water frogs (Rana lessonae, Rana ridibunda, and their hybridogen Rana esculenta). The three species exhibited different survival times during freezing (from 10 h for R. lessonae to 20 h for R. ridibunda). The time courses of percent water frozen were similar; however, because of the huge differences in body mass among species (from 10 g for Rana lessonae to nearly 100 g for Rana ridibunda), the ice mass accumulation rate varied markedly (from 0.75 +/- 0.12 to 1.43 +/- 0.11 g ice/h, respectively) and was lowest in the terrestrial hibernator Rana lessonae. The hybrid Rana esculenta exhibited an intermediate response between the two parental species; furthermore, within-species correlation existed between body mass and ice mass accumulation rates, suggesting the occurrence of subpopulations in this species (0.84 +/- 0.08 g ice/h for small R. esculenta and 1.78 +/- 0.09 g ice/h for large ones). Biochemical analyses showed accumulation of blood glucose and lactate, liver glucose (originating from glycogen), and liver alanine in Rana lessonae and Rana esculenta but not in Rana ridibunda in response to freezing. The variation of freeze tolerance between these three closely related species could bring understanding to the physiological processes involved in the evolution of freeze tolerance in vertebrates.     

On the musculature of the forelimb of the crab-eating monkey

In this paper, the musculature of the forelimb of the crab-eating monkey was described by anatomical observation of twenty limbs and compared with that of a few other primates, especially of man andMacaca. As for the musculature of the forelimb, that of the crab-eating monkey was naturally very similar to other species of theMacaca group, except for slight differences of individual muscles.     

On the reliability of the growth rings in two species of the family Characidae in the Sudan

The scales, opercula and vertebrae from 69 Hydrocyon forskali and 63 Alestes dentex were investigated for their reliability as aging structures. In both species the scales were unreliable due to their regenerative property, in spite of the clarity of their growth rings.Back-calculated lengths from the first growth ring laid on opercula and vertebrae resulted in values that coincided with the annual growth of the two species. In H. forskali, the mean back-calculated length from the two bones were 16.2 ± 5.9 and 16.8 ± 4.4 respectively, and for A. dentex, 11.1 ± 1.7 and 12.8 ± 1.8, respectively.Predictive equations for bone radius from fish length were written for both species. In this study, reliability was maximal between the observed and back-calculated lengths for both species (r > 0.95).     

Antibody-dendrimer conjugates: the number, not the size of the dendrimers, determines the immunoreactivity

Radioimmunotherapy using antibodies with favorable tumor targeting properties and high binding affinity is increasingly applied in cancer therapy. The potential of this valuable cancer treatment modality could be further improved by increasing the specific activity of the labeled proteins. This can be done either by coupling a large number of chelators which leads to a decreased immunoreactivity or by conjugating a small number of multimeric chelators. In order to systematically investigate the influence of conjugations on immunoreactivity with respect to size and number of the conjugates, the anti-EGFR antibody hMAb425 was reacted with PAMAM dendrimers of different size containing up to 128 chelating agents per conjugation site. An improved dendrimer synthesis protocol was established to obtain compounds of high homogeneity suitable for the formation of defined protein conjugates. The quantitative derivatization of the PAMAM dendrimers with DOTA moieties and the characterization of the products by isotopic dilution titration using (111)In/(nat)In are shown. The DOTA-containing dendrimers were conjugated with high efficiency to hMAb425 by applying Sulfo-SMCC as cross-linking agent and a 10- to 25-fold excess of the thiol-containing dendrimers. The determination of the immunoreactivities of the antibody-dendrimer conjugates by FACS analysis revealed a median retained immunoreactivity of 62.3% for 1.7 derivatization sites per antibody molecule, 55.4% for 2.8, 27.9% for 5.3, and 17.1% for 10.0 derivatization sites per antibody but no significant differences in immunoreactivity for different dendrimer sizes. These results show that the dendrimer size does not influence the immunoreactivity of the derivatized antibody significantly over a wide molecular weight range, whereas the number of derivatization sites has a crucial effect.     

Maximizing the use of the abdominoplasty incision

Candidates for abdominoplasty often request multiple procedures at the time of consultation. Some of these patients have the potential opportunity to have ancillary procedures performed through the abdominoplasty incision, such as breast augmentation or suction-assisted lipectomy. Access via the abdominoplasty incision can also limit the need for distant donor sites, for instance, when autologous fillers or rib graft are necessary. The techniques described are straightforward and are based on standard principles that should be considered when ancillary procedures are performed in conjunction with abdominal contouring procedures. In a review of 70 consecutive patients undergoing abdominoplasty, 91 ancillary procedures were performed in conjunction with the abdominoplasty. Of the total number of patients undergoing abdominoplasty, 29 patients underwent 30 procedures facilitated through their abdominoplasty incision, including 23 suction-assisted lipectomies of the flanks, six breast augmentations, and one rib cartilage harvesting for rhinoplasty. A review of the author's experience and discussion for potential options afforded by this exposure are presented.     

Relationship between the time of the beginning of the anticipatory postural components and the latent period of raising the arm in the vertical posture

The relationships between the anticipatory postural components when standing subjects raised their arms and the latent period (LP) of the motor response determined by the beginning of the deltoid muscle activation were analyzed. The LP range from the least possible to 1 s was analyzed. In the case of short LPs (approximately up to 170 ms), the anticipation time for the ipsilateral biceps femoris muscle (BFM) and sacrospinalis muscle (SSM) increased linearly with the LP; at longer LPs, it did not depend on the LP and was characterized by a wide scatter. In the case of short LPs, the delay time of the beginning of activation of postural muscles in relation to the signal for movement remained constant and was approximately 100 ms for the BFM and 120 ms for the SSM. This is explained by the fact that, with short LPs of motor response, the CNS had insufficient time to complete postural adjustments before the beginning of movement, which resulted in shortening of the anticipation time of the start of change in the activity of postural muscles and, as a consequence, the appearance of an additional initial backward inclination of the body. The results obtained are discussed in the context of organizing the interaction between the regulation of maintaining the vertical posture and the system of movement control.     

Editorial: Defining the membrane precursor supporting the nucleation of the phagophore

How does the phagophore form? Which membrane acts as a platform for its biogenesis? Over the years, extensive use of microscopy techniques have led to the controversial identification of multiple potential membranes as precursors for phagophore nucleation and/or for the supply of lipids to the expanding compartment. Nevertheless, none of these studies has established a direct functional link between membrane sources and autophagosome biogenesis. Addressing this point, in a recent study highlighted by a punctum in this issue, Ge and coworkers developed an in vitro approach to determine the identity of the membranes responsible for the lipidation of LC3, thus identifying the ER-Golgi intermediate compartment (ERGIC) as a potential key determinant of phagophore biogenesis.     

On the prediction of the supercompensation phase by determining the parameters of the living functional system of the body

On the basis of the overdamped Duffing model, a technique for determining the key parameters of functional systems of the living body has been developed which characterizes its properties during recovery from standard physical load. As an example, the dynamics of restoration of pulse frequency is considered. The knowledge of these parameters allows one to predict the response of the living body to intensive external loads. This information can also be helpful for the optimization of the training process.