What is the minimum number of letters required to fold a protein?

Experimental studies have shown that the full sequence complexity of naturally occurring proteins is not required to generate rapidly folding and functional proteins, i.e. proteins can be designed with fewer than 20 letters. This raises the question of what is the minimum number of amino acid types required to encode complex protein folds? Here, we investigate this issue from three aspects. First, we study the minimum sequence complexity that can reserve the necessary structural information for detection of distantly related homologues. Second, we compare the ability of designing foldable model sequences over a wide range of reduced amino acid alphabets, which find the minimum number of letters that have the similar design ability as 20. Finally, we survey the lower bound of alphabet size of globular proteins in a non-redundant protein database. These different approaches give a remarkably consistent view, that the minimum number of letters required to fold a protein is around ten.     

Site-directed mutagenesis of a fungal β-1,4-endoglucanase increases the minimum size required for the substrate

Conserved regions within a family-5 β-1,4-endoglucanase (Egl1), produced by the fungus Macrophomina phaseolina, have been modified through site-directed mutagenesis, resulting in production of an enzyme with novel substrate requirements. The engineered form was generated through mutagenesis of D232A, which lies within the substrate-binding cleft of Egl1. Wild-type Egl1 requires a minimum substrate size of five glucosyl units, while the engineered form requires a minimum of six glucosyl units. Screening was facilitated by the unique ability to obtain functional expression of the fungal endoglucanase in Escherichia coli. Wild-type and mutated Egl1 have equivalent activity on cellohexaose, and both release cellobiose from the reducing end of the cellodextrin. This is the first example of protein engineering of an endoglucanase that results in a novel minimum substrate requirement for cellohexaose. This substrate specificity has not been reported for any native endoglucanases, thus the modified Egl1 may prove useful in applications requiring specific hydrolysis of complex carbohydrates such as β-glucans. Received: 10 November 1996 / Received revision: 22 March 1997 / Accepted: 13 April 1997     

When is dispersal for dispersal? Unifying marine and terrestrial perspectives

Recent syntheses on the evolutionary causes of dispersal have focused on dispersal as a direct adaptation, but many traits that influence dispersal have other functions, raising the question: when is dispersal ‘for’ dispersal? We review and critically evaluate the ecological causes of selection on traits that give rise to dispersal in marine and terrestrial organisms. In the sea, passive dispersal is relatively easy and specific morphological, behavioural, and physiological adaptations for dispersal are rare. Instead, there may often be selection to limit dispersal. On land, dispersal is relatively difficult without specific adaptations, which are relatively common. Although selection for dispersal is expected in both systems and traits leading to dispersal are often linked to fitness, systems may differ in the extent to which dispersal in nature arises from direct selection for dispersal or as a by‐product of selection on traits with other functions. Our analysis highlights incompleteness of theories that assume a simple and direct relationship between dispersal and fitness, not just insofar as they ignore a vast array of taxa in the marine realm, but also because they may be missing critically important effects of traits influencing dispersal in all realms.     

When is translocation required for the population recovery of old‐growth epiphytes in a reforested landscape?

It is often assumed that species recolonization follows from the restoration of key habitat structure. Thus, forest restoration focuses on the recovery of trees into deforested landscapes, so that a multitude of associated organisms can achieve “colonization credit” and recolonize from remnant source populations into restored habitat. This opportunity for recolonization exists because species vulnerable to habitat loss may experience an “extinction debt,” during which their remnant populations decline only slowly to equilibrium with a deforested landscape. These persistent but declining populations become propagule sources for recolonization. To test limits to “colonization credit,” this study focused on old‐growth dependent lichen epiphytes, using a simulation to identify a hypothetical threshold at which: (1) the number of remnant populations, and (2) their population sizes, are too low to achieve recolonization and population recovery, despite efforts placed into forest restoration. The results show that for a landscape scenario relevant to the industrialized temperate zone, with less than 5% of old‐growth forest remaining, and ambitions for restoration to circa 10–15% forest cover, there is a failure to achieve population recovery over long timescales (i.e. within 600 years), making translocation a necessary option. This delay represents a “colonization deficit” that may be a common feature in ecological restoration more generally.     

What is the minimum age for applying the forbes equation between body density and body fat to the elderly?

In order to determine the age above which the FORBES equation for calculating percent body fat (%BF) in the elderly is to be applied, 9 persons in their 60s, 7 persons in their 70s and 3 persons older than 80 took part in this study. %BF was measured using dual-energy X-ray absorptiometry (DEXA). In each subject, body density was measured using densitometry. %BF was then calculated by substituting body density for the Siri or FORBES equation. Based on the value of %BF measured with DEXA, the calculated %BF was criticized for each decade of subjects. It was concluded that the Siri equation should be applied to those who are younger than 80 and that the FORBES equation should be applied to those who are 80 and older.     

How early is firing required for wiring?

Activity is known to be important for the refinement of neural connections in the developing brain. In this issue of Neuron, Hanson and Landmesser provide evidence that GABA-dependent spontaneous bursting of motor neurons in the embryonic spinal cord is required for the correct execution of an early axon pathfinding decision.     

How much is a lot? Seed dispersal by white-faced capuchins and implications for disperser-based studies of seed dispersal systems

The quantity of seeds dispersed is considered one of several means to determine the dispersal effectiveness of an animal. However, there is little consistency in the manner in which quantities are measured or presented. Here, we quantify seed dispersal by white-faced capuchin monkeys (Cebus capucinus) in Santa Rosa National Park, Costa Rica by measuring: degree of frugivory, number of plant species consumed, the number of seeds consumed per unit time, the number of seeds dispersed intact per unit time, and the number of seeds dispersed intact per unit space. Forty-nine percent of C. capucinus diet is composed of the fruit of 39 species, 4 of which constitute 82% of the frugivory. Seventy-four percent of consumed fruits contain seeds that pass intact through the capuchin digestive system. Capuchins pass a mean of 15.7 seeds of a mean of 1.3 species per defecation, and defecate 25.4 times per 12-h day. These numbers are compared with extant data for C. capucinus, and possible reasons for discrepancies among results between studies are discussed. We propose a standardization of quantitative measures of seed dispersal so that quantifications of seed dispersal can be compared within species, and eventually across species.     

What is the optimal vitamin D status for health?

The most objectively substantiated health-related reason for tanning is that it improves vitamin D status. The serum 25-hydroxyvitamin D concentration (25(OH)D) is the measure of vitamin D nutrition status. Human biology was probably optimized through natural selection for a sun-rich environment that maintained serum 25(OH)D higher than 100 nmol/L. These levels are now only prevalent in people who spend an above-average amount of time outdoors, with the sun high in the sky. The best-characterized criteria for vitamin D adequacy are based on randomized clinical trials that show fracture prevention and preservation of bone mineral density. Based upon these studies, 25(OH)D concentrations should exceed 75 nmol/L. This concentration is near the upper end of the 25(OH)D reference ("normal") range for populations living in temperate climates, or for people who practice sun-avoidance, or who wear head coverings. Officially mandated nutrition guidelines restrict vitamin D intake from fortified food and supplements to less than 25 mcg/day, a dose objectively shown to raise serum 25(OH)D in adults by about 25 nmol/L. The combined effect of current nutrition guidelines and current sun-avoidance advice is to ensure that adults who follow these recommendations will have 25(OH)D concentrations lower than 75 nmol/L. Therefore, advice to avoid UVB light should be accompanied by encouragement to supplement with vitamin D in an amount that will correct for the nutrient deficit that sun-avoidance will cause.     

What is the future for cord blood stem cells?

Stem and progenitor cells are present in cord blood at a high frequency making these cells a major target population for experimental and clinical studies. Over the past decade there has been considerable developments in cord blood research and transplantation but despite the rapid progress many problems remain. The initial hope that cord blood would be an alternative source of haemopoietic cells for transplantation has been tempered by the fact that there are insufficient cells in most cord blood collections to engraft an adult of average weight. In attempts to increase the cell number, a plethora of techniques for ex-vivo expansion have been developed.These techniques have also proved useful for gene therapy. As cord blood cells possess unique properties this allows them to be utilised as suitable vehicles for gene therapy and long-term engraftment of transduced cells has been achieved. Current work examining the nature of the stem cells present in this haematological source indicates that cord blood contains not only haemopoietic stem cells but also primitive non-haemopoietic cells with high proliferative and developmental potential. As attention focuses on stem cell biology and the controversies surrounding the potential use of embryonic stem cells in treatment of disease, the properties of stem cells from other sources including cord blood are being re-appraised. The purpose of this article is to review some of the current areas of work and highlight biological problems associated with the use of cord blood cells. This revised version was published online in July 2006 with corrections to the Cover Date.     

What is mzXML good for?

mzXML (extensible markup language) is one of the pioneering data formats for mass spectrometry-based proteomics data collection. It is an open data format that has benefited and evolved as a result of the input of many groups, and it continues to evolve. Due to its dynamic history, its structure, purpose and applicability have all changed with time, meaning that groups that have looked at the standard at different points during its evolution have differing impressions of the usefulness of mzXML. In discussing mzXML, it is important to understand what mzXML is not. First, mzXML does not capture the raw data. Second, mzXML is not sufficient for regulatory submission. Third, mzXML is not optimized for computation and, finally, mzXML does not capture the experiment design. In general, it is the authors' opinion that XML is not a panacea for bioinformatics or a substitute for good data representation, and groups that want to use mzXML (or other XML-based representations) directly for data storage or computation will encounter performance and scalability problems. With these limitations in mind, the authors conclude that mzXML is, nonetheless, an indispensable data exchange format for proteomics.     

What is the Best Elective Operation for Duodenal Ulcer?

During the past 40 years, after gastroenterostomy and pyloroplasty for duodenal ulcer had been replaced by partial gastrectomy in many centres, partial gastrectomy itself gave way to combinations of vagotomy with gastroenterostomy, pyloroplasty or antrectomy. Opinions differ concerning the procedure of choice and in this paper the author examines the causes of this diversity of opinion and assesses the reliability of conclusions that can be drawn about the elective treatment of duodenal ulcer today. Most reports of results from various operations have come from retrospective studies, and the causes of variability among such reports are analyzed to point out the great difficulty in making a valid judgment about the relative worth of the various operations used to treat duodenal ulcer. Results of some of the few prospective studies with randomized operations assessed blindly are then presented and note is taken of the surprising observation that greatly different operations appear to give remarkably similar results. From the data available the author develops a logical way of approaching the choice of operation for the various problems related to duodenal ulcer that require elective surgical treatment.     

Understanding sample size: what determines the required number of microarrays for an experiment?

DNA microarray experiments have become a widely used tool for studying gene expression. An important, but difficult, part of these experiments is deciding on the appropriate number of biological replicates to use. Often, researchers will want a number of replicates that give sufficient power to recognize regulated genes while controlling the false discovery rate (FDR) at an acceptable level. Recent advances in statistical methodology can now help to resolve this issue. Before using such methods it is helpful to understand the reasoning behind them. In this Research Focus article we explain, in an intuitive way, the effect sample size has on the FDR and power, and then briefly survey some recently proposed methods in this field of research and provide an example of use.