What is the minimum number of dedicated functions required for a basic cell cycle?

The genome of Escherichia coli has a coding capacity for about 4500 proteins but only a small number of these appear to be specific for the periodic events (initiation of DNA replication, chromosome partitioning and cell division) that punctuate the cell-duplication cycle: furthermore, many of these cell cycle dedicated functions are dispensible under certain conditions, although their presence undoubtedly increases the fitness of the organism to survive in a competitive environment. A simplified but effective cell replication cycle can probably operate with only a few cycle-dedicated proteins, in addition to those required for cell growth itself.     

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.     

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.     

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 upper size limit for cosmopolitan distribution in free‐living microorganisms?

A comparison of testate amoebae assemblages from the Arctic and Antarctic (areas of similar habitat a maximum distance apart) is used to try and answer the question ‘What is the upper size limit for cosmopolitan distribution in free‐living microbes?’ Species restricted to either the Arctic or Antarctic exhibited sizes up to 230 μm while the largest cosmopolitan species was 135 μm in size. Comparison of the testate assemblages using a multivariate classificatory technique (TWINSPAN ) also suggested more restricted distribution for the larger species. There was a negative relationship between species size and number of sites at which it was recorded (r_s=?0.261, P < 0.05), with all the more widespread species having a size of below 100 μm. It is suggested that for testate amoebae cosmopolitan distributions become common below 100–150 μm. This suggests that most species of testate (indeed most free‐living microbes) have low species richness because of lack of opportunities for allopatric speciation as most are below 100 μm and so geographical isolation is unlikely. It is suggested that if this is correct, only the largest free‐living microbes (> 150 μm) are likely to be of conservation concern because of their smaller ranges. However, I point out that currently different studies are giving very different answers to the question, how ubiquitous and species rich are free‐living microbes? The subject requires further work to try and reconcile these different results.     

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.