What is the required minimum landscape size for dispersal studies?

Among small animals dispersal parameters are mainly obtained by traditional methods using population studies of marked individuals. Dispersal studies may underestimate the rate and distance of dispersal, and be biased because of aggregated habitat patches and a small study area. The probability of observing long distance dispersal events decreases with distance travelled by the organisms. In this study a new approach is presented to solve this methodological problem. An extensive mark-release-recapture programme was performed in an area of 81 km(2) in southern Sweden. To estimate the required size of the study area for adequate dispersal measures we examined the effect of study area size on dispersal distance using empirical data and a repeated subsampling procedure. In 2003 and 2004, two species of diurnal burnet moths (Zygaenidae) were studied to explore dispersal patterns. The longest confirmed dispersal distance was 5600 m and in total 100 dispersal events were found between habitat patches for the two species. The estimated dispersal distance was strongly affected by the size of the study area and the number of marked individuals. For areas less than 10 km(2) most of the dispersal events were undetected. Realistic estimates of dispersal distance require a study area of at least 50 km(2). To obtain adequate measures of dispersal, the marked population should be large, preferably over 500 recaptured individuals. This result was evident for the mean moved distance, mean dispersal distance and maximum dispersal distance. In general, traditional dispersal studies are performed in small study areas and based on few individuals and should therefore be interpreted with care. Adequate dispersal measures for insects obtained by radio-tracking and genetic estimates (gene flow) is still a challenge for the future.     

What are the baselines for protein fold recognition?

MOTIVATION: What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein-ranging from the length of the sequence to a knowledge of its secondary structure-to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications? EXPERIMENTS PERFORMED: A number of rapid automatic methods which score similarities between protein domains were devised and tested. These methods ranged from those that incorporated no secondary structure information, such as measuring absolute differences in sequence lengths, to more complex alignments of secondary structure elements. Each method was assessed for accuracy by comparison with the Class Architecture Topology Homology (CATH) classification. Methods were rated against both a random baseline fold assignment method as a lower control and FSSP as an upper control. Similarity trees were constructed in order to evaluate the accuracy of optimum methods at producing a classification of structure. RESULTS: Using a rigorous comparison of methods with CATH, the random fold assignment method set a lower baseline of 11% true positives allowing for 3% false positives and FSSP set an upper benchmark of 47% true positives at 3% false positives. The optimum secondary structure alignment method used here achieved 27% true positives at 3% false positives. Using a less rigorous Critical Assessment of Structure Prediction (CASP)-like sensitivity measurement the random assignment achieved 6%, FSSP-59% and the optimum secondary structure alignment method-32%. Similarity trees produced by the optimum method illustrate that these methods cannot be used alone to produce a viable protein structural classification system. CONCLUSIONS: Simple methods that use perfect secondary structure information to assign folds cannot produce an accurate protein taxonomy, however they do provide useful baselines for fold recognition. In terms of a typical CASP assessment our results suggest that approximately 6% of targets with folds in the databases could be assigned correctly by randomly guessing, and as many as 32% could be recognised by trivial secondary structure comparison methods, given knowledge of their correct secondary structures.     

What is the function of protein carboxyl methylation?

The following functions of protein carboxyl methylation seem to be reasonably well established: Multiple, stoichiometric methylation of chemotactic receptors in bacteria at glutamyl residues serves as one (but not the only) adaptation mechanism of the transduction chain to constant background levels of chemotactic stimuli. Stoichiometric methylation of hormones and hormone carrier proteins plays a role in hormone storage and secretion by the pituitary gland. Substoichiometric methylation at D-aspartyl residues is involved in a repair mechanism of aged proteins. Stoichiometric methylation of calmodulin modulates the sensitivity of calmodulin-dependent processes to calcium. Research of the past 3 years has indicated that in order to demonstrate an involvement of methylation in the coupling of surface receptors to intracellular events three new criteria have to be met: (a) the cell should possess a protein carboxyl methylase with relatively narrow substrate specificity; (b) methylation should take place at L-amino acid residues; (c) the methyl accepting proteins should be methylated in a stoichiometric fashion.     

What is the total number of protein molecules per cell volume? A call to rethink some published values

Novel methods such as mass‐spectrometry enable a view of the proteomes of cells in unprecedented detail. Recently, these efforts have culminated in quantitative measurements of the number of copies per cell for most expressed proteins in organisms ranging from bacteria to mammalian cells. Here, we estimate the expected total number of proteins per unit of cell volume using known parameters related to the composition of cells such as the fraction of cell mass that is protein, and the average protein length. Using simple arguments, we estimate a range of 2–4 million proteins per cubic micron (i.e. 1 fL) in bacteria, yeast, and mammalian cells. Interestingly, we find that measured values that are reported for fission yeast and mammalian cells are often about 3–10 times lower. We discuss this apparent discrepancy and how to use the estimate as benchmark to recalibrate proteome‐wide quantitative censuses or to revisit assumptions about cell composition.     

What is the protein design alphabet?

Selecting a protein sequence that corresponds to a specific three-dimensional protein structure is known as the protein design problem. One principal bottleneck in solving this problem is our lack of knowledge of precise atomic interactions. Using a simple model of amino acid interactions, we determine three crucial factors that are important for solving the protein design problem. Among these factors is the protein alphabet-a set of sequence elements that encodes protein structure. Our model predicts that alphabet size is independent of protein length, suggesting the possibility of designing a protein of arbitrary length with the natural protein alphabet. We also find that protein alphabet size is governed by protein structural properties and the energetic properties of the protein alphabet units. We discover that the usage of average types of amino acid in proteins is less than expected if amino acids were chosen randomly with naturally occurring frequencies. We propose three possible scenarios that account for amino acid underusage in proteins. These scenarios suggest the possibility that amino acids themselves might not constitute the alphabet of natural proteins.     

Estimating the intrinsic rate of increase of Tetranychus urticae: which is the minimum number of immature individuals to consider?

The relationship between the number of immature individuals of Tetranychus urticae used to calculate life table parameters (sex ratio, development time, immature survival and the intrinsic rate of increase) and the accuracy of such determinations has been estimated. Additionally, the approach used in this paper, which considers each female offspring as a separate replicate, has allowed statistical comparison of the parameters obtained. At least the first four eggs from 16 females should be followed up to completion of their development to prevent the occurrence significant differences for the selected parameters. However, our results indicate that optimal sample sizes are different for the different life table parameters considered and should adapt to the preset level of accuracy.     

What is the role of thermodynamics on protein stability?

The most challenging and emerging field of biotechnology is the tailoring of proteins to attain the desired characteristic properties. In order to increase the stability of proteins and to study the function of proteins, the mechanism by which proteins fold and unfold should be known. It has been debated for a long time how exactly the linear form of a protein is converted into a stable 3-dimensional structure. The literature showed that many theories support the fact that protein folding is a thermodynamically controlled process. It is also possible to predict the mechanism of protein deactivation and stability to an extent from thermodynamic studies. This article reviewed various theories that have been proposed to explain the process of protein folding after its biosynthesis in ribosomes. The theories of the determination of the thermodynamic properties and the interpretation of thermodynamic data of protein stability are also discussed in this article.     

What is the shape of the distribution of protein conformations at equilibrium?

According to the thermodynamic hypothesis, the native state of proteins is that in which the free energy of the system is at its lowest, so that at normal temperature and pressure, proteins evolve to that state. We selected four proteins representative of each of the four classes, and for each protein make four simulations, one starting from the native structure and the other three starting from the structure obtained by threading the sequence of one protein onto the native backbone fold of the other three proteins. Because of their large conformational distances with respect to the native structure, the three alternative initial structures cannot be considered as local minima within the native ensemble of the corresponding protein. As expected, the initial native states are preserved in the .5?μs simulations performed here and validate the simulations. On the other hand, when the initial state is not native, an analysis of the trajectories does not reveal any evolution towards the native state, during that time. These results indicate that the distribution of protein conformations is multipeak shaped, so that apart from the peak corresponding to the native state, there are other peaks associated with average structures that are very different from the native and that can last as long as the native state.     

What is the functional role of the thalidomide binding protein cereblon?

It has been found that nonsense mutation R419X of cereblon (CRBN) is associated with autosomal recessive non-syndromic mental retardation. Further experiments showed that CRBN binds to the cytosolic C-terminus of large-conductance Ca⁺⁺ activated potassium channel (BK_Ca) α-subunit and the cytosolic C-terminus of a voltage-gated chloride channel-2 (ClC-2), suggesting that CRBN may play a role in memory and learning via regulating the assembly and surface expression of BK_Ca and ClC-2 channels. In addition, it has also been found that CRBN directly interacts with the α1 subunit of AMP-activated protein kinase (AMPK) and prevents formation of a functional holoenzyme with regulatory subunits β and γ. Since AMPK is a master sensor of energy balance that inhibits ATP-consuming anabolic pathways and increases ATP-producing catabolic pathways, binding of CRBN with α1 subunit of AMPK may play a role in these pathways by regulating the function of AMPK. Furthermore, CRBN interacts with damaged DNA binding protein 1 and forms an E3 ubiquitin ligase complex with Cullin 4 where it functions as a substrate receptor in which the proteins recognized by CRBN might be ubiquitinated and degraded by proteasomes. Proteasome-mediated degradation of unneeded or damaged proteins plays a very important role in maintaining regular function of a cell, such as cell survival, dividing, proliferation and growth. Intriguingly, a new role for CRBN has been identified, i.e, the binding of immunomodulatory drugs (IMiDs), e.g. thalidomide, to CRBN has now been associated with teratogenicity and also the cytotoxicity of IMiDs, including lenalidomide, which are widely used to treat multiple myeloma patients. CRBN likely plays an important role in binding, ubiquitination and degradation of factors involved in maintaining function of myeloma cells. These new findings regarding the role of CRBN in IMiD action will stimulate intense investigation of CRBN’s downstream factors involved in maintaining regular function of a cell.     

What is the significance of a significant TDT?

This note summarizes the development of the transmission/disequilibrium test (TDT). The initial purpose of the TDT procedure was to test for linkage between a genetic marker and a disease susceptibility locus when an association had been found between the two. An association between disease and marker had sometimes been taken to imply linkage. An association could, however, be due to population stratification even in the absence of linkage. In contrast, the outcome of the TDT is not affected by such stratification. Furthermore, when linkage is not in doubt, the TDT can, in some cases, also provide a test of association between marker and disease. We discuss these various matters in this paper.     

Is protein folding rate dependent on number of folding stages? Modeling of protein folding with ferredoxin-like fold

Statistical analysis of protein folding rates has been done for 84 proteins with available experimental data. A surprising result is that the proteins with multi-state kinetics from the size range of 50–100 amino acid residues (a.a.) fold as fast as proteins with two-state kinetics from the same size range. At the same time, the proteins with two-state kinetics from the size range 101–151 a.a. fold faster than those from the size range 50–100 a.a. Moreover, it turns out unexpectedly that usually in the group of structural homologs from the size range 50–100 a.a., proteins with multi-state kinetics fold faster than those with two-state kinetics. The protein folding for six proteins with a ferredoxin-like fold and with a similar size has been modeled using Monte Carlo simulations and dynamic programming. Good correlation between experimental folding rates, some structural parameters, and the number of Monte Carlo steps has been obtained. It is shown that a protein with multi-state kinetics actually folds three times faster than its structural homologs.     

What is the role of the transit peptide in thylakoid integration of the light-harvesting chlorophyll a/b protein?

Whereas it is widely accepted that the transit peptide of the precursor for the light-harvesting chlorophyll a/b protein (preLHCP) is responsible for targeting this polypeptide to chloroplasts, the signals which govern its intraorganellar targeting appears to be transit peptide-mediated for plastocyanin (Smeekins, S., Bauerle, C., Hageman, J., Keegstra, K., and Weisbeek, P. (1986) Cell 46, 365-375) and several other nuclear-encoded, thylakoid luminal proteins. To determine whether a similar mechanism operates for LHCP (an integral thylakoid protein), we have used oligonucleotide-directed mutagenesis to delete the proposed transit sequence from a petunia precursor of this polypeptide. Intact preLHCP and the deletion mutant product have been expressed in vitro, and their abilities to integrate into purified thylakoids have been compared. We have found that both polypeptides insert into thylakoids correctly, provided the latter are supplemented with a membrane-free stromal extract and Mg.ATP. Our results clearly demonstrate that whereas the transit peptide is required for transport into chloroplasts, thylakoid integration of preLHCP is determined by mature portions of the polypeptide. In addition, we note that transit peptide removal has little effect on the apparent solubility of the in vitro translation products.     

What is happening to the monocotyledons?

An attempt is made to elucidate some of the more pronounced departures from traditional classifications in the book The families of the monocotyledons byDahlgren and collaborators, which embodies the latest opinions of the lateRolf Dahlgren on the subject. Consideration is given to the treatment of theLiliiflorae (especiallyLiliales andAsparagales) andBromeliiflorae, and to the theory offered for the origin of the monocots which identifies theDioscoreales as the most primitive order of the subclass.Dahlgren aimed at an eclectic classification (one based on a combination of similarity criteria and phylogenetic criteria) and the results of his use of cladistic methods (in association withF. N. Rasumssen) to supply the phylogenetic input are assessed. The resulting system itself is considered in the light of the distinction drawn byJ. S. L. Gilmour between natural and artificial classifications and their respective uses.Dedicated to the memory of JohnS. L. Gilmour.     

Opinion: What is the role of protein aggregation in neurodegeneration?

Neurodegenerative diseases typically involve deposits of inclusion bodies that contain abnormal aggregated proteins. Therefore, it has been suggested that protein aggregation is pathogenic. However, several lines of evidence indicate that inclusion bodies are not the main cause of toxicity, and probably represent a cellular protective response. Aggregation is a complex multi-step process of protein conformational change and accretion. The early species in this process might be most toxic, perhaps through the exposure of buried moieties such as main chain NH and CO groups that could serve as hydrogen bond donors or acceptors in abnormal interactions with other cellular proteins. This model implies that the pathogenesis of diverse neurodegenerative diseases arises by common mechanisms, and might yield common therapeutic targets.     

What is the risk of a deadly adenovirus pandemic?

Many of us had refresher courses in virology, immunology, and epidemiology in 2020, and we were reminded of the fact that Homo sapiens, the wiliest predator on the planet, has been hunting everything that moves for millennia. These repeated interspecies contacts inherently lead to recurrent zoonosis (nonhuman to human) and anthroponosis (human to nonhuman). Given the accelerating changes in our ecosystems since the neolithic revolution, it was not surprising to see a virus that spreads via aerosolization and liquid droplets cause a pandemic in a few months. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic begs the question—which viruses could cause a global threat? In this Opinion, the characteristics that make adenoviruses a risk, which include efficient intra- and interspecies transmission, thermostable particles, persistent/latent infections in diverse hosts, and the ability to readily recombine and escape herd immunity, are discussed.     

What is the optimal number of leaves when measuring leaf area of tree species in a forest community?

植物形态性状叶面积简单易测, 能够反映植物对环境的适应与响应, 指示生态系统的功能与过程。在野外测定叶面积时, 叶片取样数量往往采用约定俗成的10-20片, 但到底采集多少叶片才是最优和最具代表性, 却少有探究。该研究以浙江金华山常绿落叶阔叶混交林的优势树种木荷(Schima superba)与枫香树(Liquidambar formosana)为研究对象, 通过对5个胸径等级植株和每个植株6个方位开展大批量叶片取样(>2 500个), 分析两个树种的叶面积变异特征, 探讨叶片取样数量为多少才能最代表该森林类型的叶片大小性状规律。结果表明, 常绿乔木木荷平均叶面积与变幅均小于落叶乔木枫香树。木荷叶面积与胸径无显著相关性, 而枫香树叶面积与胸径有较显著相关性, 但两个树种均在中胸径等级(15-20 cm)差异不显著; 两个树种的叶面积与采样方位无显著相关性, 但在东、西和底部的差异不显著。因此, 综合考虑代表性与野外可操作性, 叶片采集首选中胸径成树的底部叶片。随机抽样统计可知, 树木叶面积测定的最适叶片采集数量因物种而异, 木荷的最适叶片采集数量为40, 而枫香树最少为170片。因此, 在叶面积测定时, 叶片采集的数量应该不能只局限在10-20片, 在人力、物力和时间等条件允许的情况下, 应该尽可能多地测定较多叶片的叶面积。