A theoretical limit to coding space in chromosomes of bacteria

A mathematical model of cluster patterns for mapped genes with known phenotypes in Escherichia coli predicted thatfunctional genes may account for a maximum of two-thirds of the total chromosomal space. The corollary prediction was that one-third of the chromosome comprised noncoding space. Open reading frame (ORF) analyses for 15 phylogenetically diverse bacterial genomes and for 30 fully sequenced prokaryotic genomes supported the gene cluster model prediction of a two-thirds tendency for coding space. Our results suggest that only 3-4% of unassigned ORFs in E. coli represent genes with potential phenotype and that ORFs marking novel genes in prokaryotes are far fewer than previously thought.     

A State Space Transformation Can Yield Identifiable Models for Tracer Kinetic Studies with Enrichment Data

Tracer studies are analyzed almost universally by multicompartmental models where the state variables are tracer amounts or activities in the different pools. The model parameters are rate constants, defined naturally by expressing fluxes as fractions of the source pools. We consider an alternative state space with tracer enrichments or specific activities as the state variables, with the rate constants redefined by expressing fluxes as fractions of the destination pools. Although the redefinition may seem unphysiological, the commonly computed fractional synthetic rate actually expresses synthetic flux as a fraction of the product mass (destination pool). We show that, for a variety of structures, provided the structure is linear and stationary, the model in the enrichment state space has fewer parameters than that in the activities state space, and is hence better both to study identifiability and to estimate parameters. The superiority of enrichment modeling is shown for structures where activity model unidentifiability is caused by multiple exit pathways; on the other hand, with a single exit pathway but with multiple untraced entry pathways, activity modeling is shown to be superior. With the present-day emphasis on mass isotopes, the tracer in human studies is often of a precursor, labeling most or all entry pathways. It is shown that for these tracer studies, models in the activities state space are always unidentifiable when there are multiple exit pathways, even if the enrichment in every pool is observed; on the other hand, the corresponding models in the enrichment state space have fewer parameters and are more often identifiable. Our results suggest that studies with labeled precursors are modeled best with enrichments.     

Propagation of endangered birds in US institutions: How much space is there?

Captive breeding is often touted as a way to preserve species disappearing in the wild. Zoos and related institutions have limited space for animals, however, and use of what space exists may be restricted by conflicting demands of entertainment, education, and propagation. Curators of US bird collections sponsored an analysis of space available for long-term captive management. Seventy-three collections responded to a survey, providing data on 3,174 exhibits and holding areas under their control. The most optimistic analysis indicates room for fewer than 141 long-term management programs. To use space resources optimally for conservation, there is a strong need to develop priorities within management groups. New models and strategies for using captive propagation as a short-term tool to bolster wild populations should be created. Immediate attention should be paid to the most effective and efficient ways of improving husbandry and management techniques for birds. © 1995 Wiley-Liss, Inc.     

Miniaturization of nervous systems and neurons

Miniaturized species have evolved in many animal lineages, including insects and vertebrates. Consequently, their nervous systems are constrained to fit within tiny volumes. These miniaturized nervous systems face two major challenges for information processing: noise and energy consumption. Fewer or smaller neurons with fewer molecular components will increase noise, affecting information processing and transmission. Smaller, more densely-packed neural processes will increase the density of energy consumption whilst reducing the space available for mitochondria, which supply energy. Although miniaturized nervous systems benefit from smaller distances between neurons, thus saving time, space and energy, they have also increased the space available for neural processing by expanding and contorting their nervous systems to fill any available space, sometimes at the expense of other structures. Other adaptations, such as multifunctional neurons or matched filters, may further alleviate the pressures on space within miniaturized nervous systems. Despite these adaptations, we argue that limitations on information processing are likely to affect the behaviour generated by miniaturized nervous systems.     

Feeder design and available feeding space influence the feeding behaviour of hens

This paper describes a study of the influences of feeder design and available feeding space on the feeding behaviour of laying hens.When feeders were partitioned, feeding rates and the number of feeding bouts were higher than when the feeders were unpartitioned, but feed consumption was lower and the duration of feeding was shorter. Increased feeding space led to longer feeding times with fewer but longer feeding bouts. These results are discussed in relation to animal welfare, with particular reference to feather-pecking.     

基于CLUE-S模型的县域生产-生活-生态空间冲突动态模拟及特征分析

随着经济、社会发展速度不断加快,多功能空间之间的竞争不断增强,国土空间的协调与稳定受到严重影响。因此,模拟生产、生活和生态空间(简称"三生"空间)冲突格局,并分析其演变特征,对于科学利用国土空间,实现区域发展格局优化有着重要意义。以昌黎县为研究区,以2005和2015年土地利用现状数据为基础,采用CLUE-S模型预测研究区2025年土地利用格局;基于土地利用主导功能和次要功能将国土空间划分为生活生产空间、生产生态空间、生态生产空间及生态空间,依据景观生态指数构建空间冲突测度模型,测算昌黎县2005—2025年三期"三生"空间冲突变化趋势。结果表明:①2005—2025年昌黎县以生产生态空间为主。2015年末,生活生产空间、生产生态空间大量占用生态生产空间和生态空间,尤其是河流附近,空间转换更加显著;到2025年,各空间类型转变较少,但生活生产空间转入量仍相对较大。②2005—2025年昌黎县空间冲突水平呈上升趋势,到2025年,空间冲突逐渐以较强空间冲突为主。这主要是由于生产生态空间、生活生产空间不断向外扩张。随着城镇化、产业发展速度的加快,生活生产空间、生产生态空间向外扩张强度逐渐增大,生态生产空间、生态空间将面临威胁。     

A comparison of genotype-phenotype maps for RNA and proteins

The relationship between the genotype (sequence) and the phenotype (structure) of macromolecules affects their ability to evolve new structures and functions. We here compare the genotype space organization of proteins and RNA molecules to identify differences that may affect this ability. To this end, we computationally study the genotype-phenotype relationship for short RNA and lattice proteins of a reduced monomer alphabet size, to make exhaustive analysis and direct comparison of their genotype spaces feasible. We find that many fewer protein molecules than RNA molecules fold, but they fold into many more structures than RNA. In consequence, protein phenotypes have smaller genotype networks whose member genotypes tend to be more similar than for RNA phenotypes. Neighborhoods in sequence space of a given radius around an RNA molecule contain more novel structures than for protein molecules. We compare this property to evidence from natural RNA and protein molecules, and conclude that RNA genotype space may be more conducive to the evolution of new structure phenotypes.     

Comparative efficiency of different regimens of locomotor training in prolonged space flights as estimated from the data on biomechanical and electromyographic parameters of walking

Biomechanical and electromyographic characteristics of locomotion were studied before and after a space flight on days 3, 7, and 10 after landing in 18 participants of prolonged space missions on board the International Space Station. It has been shown that microgravity causes significant changes in biomechanical and electromyographic characteristics of walking, such as a decrease in the amplitude of angular displacement in leg joints, a decrease in the double step length, and an increase in the electromyographic costs of locomotion. It has been also shown that interval locomotor physical training, such as alternation of running and walking, in prolonged space flights prevents an increase in the physiological costs of locomototions after a space flight and provides more efficient maintenance of the neuromuscular system’s performance after a flight. Cosmonauts who performed interval locomotor training had fewer changes in biomechanical and electromyographic characteristics of walking.     

DF++ : an adaptive buffer-aware probabilistic delegation forwarding protocol for Delay Tolerant Network

The delegated forwarding (DF) curb transmissions by forwarding the message to a node that holds high quality value seen by the message. However, DF assumes infinite buffer space that is not possible in real time applications. In addition, quality value computation considers the encountering history and does not account for additional network parameters such as aging and transitive connectivity. In this paper, we have proposed a routing protocol called as DF++ that compute quality value based on probabilistic model used in PRoPHET protocol and forwards the message to current node by adaptive computation of available buffer space. We have compared performance of DF++ with DF, Epidemic and PRoPHET routing protocols. The proposed DF++ has higher delivery probability and fewer message drop and transmissions.     

Statistical analysis of RNA backbone

Local conformation is an important determinant of RNA catalysis and binding. The analysis of RNA conformation is particularly difficult due to the large number of degrees of freedom (torsion angles) per residue. Proteins, by comparison, have many fewer degrees of freedom per residue. In this work, we use and extend classical tools from statistics and signal processing to search for clusters in RNA conformational space. Results are reported both for scalar analysis, where each torsion angle is separately studied, and for vectorial analysis, where several angles are simultaneously clustered. Adapting techniques from vector quantization and clustering to the RNA structure, we find torsion angle clusters and RNA conformational motifs. We validate the technique using well-known conformational motifs, showing that the simultaneous study of the total torsion angle space leads to results consistent with known motifs reported in the literature and also to the finding of new ones.     

Variations in renal corpuscular morphology with adaptation to sea water in the rainbow trout, Salmo gairdneri Richardson

The kidneys of similar sized rainbow trout from freshwater and seawater environments were examined and several parameters of renal corpuscular morphology were measured, The glomeruli of the seawater trout were significantly smaller and contained significantly fewer red blood cells than those of the freshwater fish. There was also some evidence of a decreased number of renal corpuscles per unit area, and an increased proportion with no apparent capsular space in the seawater trout.     

Behavior and Welfare of Domestic Cats Housed in Cages Larger than U.S. Norm

The effect of providing additional floor space on cat behavior and welfare is not well documented. This study involved replication of an investigation of cats’ responses to enhanced cage and room environments using cages of 0.56 m² with the same methodology but an increased space allowance of 1.1 m². Singly housed adult cats (n = 59) were randomly assigned to a treatment group that was a combination of a managed or unmanaged room and an enriched or unenriched cage environment. Cats were observed for 2 days for maintenance, affiliative, and avoidant behaviors using scan sampling and 5-min, continuous focal sampling. At the end of Day 2, cats’ reactions to the approach of an unfamiliar person were assessed. Cats housed in enriched/managed environments exhibited more maintenance and affiliative behaviors and fewer avoidant behaviors than cats in unmanaged/unenriched environments, suggesting that macro and micro environments may be equally relevant to the cat. Increased space did not enhance the cats’ welfare outcomes, suggesting that the provision of additional cage space may not be as important to the cat as a managed housing environment.     

The phenotypic and genetic covariance structure of drosphilid wings

Evolutionary constraint results from the interaction between the distribution of available genetic variation and the position of selective optima. The availability of genetic variance in multitrait systems, as described by the additive genetic variance-covariance matrix (G), has been the subject of recent attempts to assess the prevalence of genetic constraints. However, evolutionary constraints have not yet been considered from the perspective of the phenotypes available to multivariate selection, and whether genetic variance is present in all phenotypes potentially under selection. Determining the rank of the phenotypic variance-covariance matrix (P) to characterize the phenotypes available to selection, and contrasting it with the rank of G, may provide a general approach to determining the prevalence of genetic constraints. In a study of a laboratory population of Drosophila bunnanda from northern Australia we applied factor-analytic modeling to repeated measures of individual wing phenotypes to determine the dimensionality of the phenotypic space described by P. The phenotypic space spanned by the 10 wing traits had 10 statistically supported dimensions. In contrast, factor-analytic modeling of G estimated for the same 10 traits from a paternal half-sibling breeding design suggested G had fewer dimensions than traits. Statistical support was found for only five and two genetic dimensions, describing a total of 99% and 72% of genetic variance in wing morphology in females and males, respectively. The observed mismatch in dimensionality between P and G suggests that although selection might act to shift the intragenerational population mean toward any trait combination, evolution may be restricted to fewer dimensions.     

MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance

MOTIVATION: Existing algorithms for automated protein structure alignment generate contradictory results and are difficult to interpret. An algorithm which can provide a context for interpreting the alignment and uses a simple method to characterize protein structure similarity is needed. RESULTS: We describe a heuristic for limiting the search space for structure alignment comparisons between two proteins, and an algorithm for finding minimal root-mean-squared-distance (RMSD) alignments as a function of the number of matching residue pairs within this limited search space. Our alignment algorithm uses coordinates of alpha-carbon atoms to represent each amino acid residue and requires a total computation time of O(m(3) n(2)), where m and n denote the lengths of the protein sequences. This makes our method fast enough for comparisons of moderate-size proteins (fewer than approximately 800 residues) on current workstation-class computers and therefore addresses the need for a systematic analysis of multiple plausible shape similarities between two proteins using a widely accepted comparison metric.     

Enhanced root production in Haplopappus gracilis grown under spaceflight conditions

The production and growth of roots in two aseptically maintained clonal populations of Haplopappus gracilis (family Compositae), each with a distinctive pattern of root production, were studied after they had been exposed to space for 5 days aboard a NASA Space Shuttle. Total root production of both populations was 67-95% greater when compared with their Earth-grown controls. Roots were generated: (1) laterally from pre-formed roots, the tips of which had been severed at the time of plantlet insertion into a "horticultural foam" substrate supplied with a nutrient solution; (2) adventitiously from the basal or cut-end portion of shoots; (3) de novo, i.e. from primordial which were non-existent at the outset of the experiment. Roots grew in all directions in space but were uniformly positively gravitropic in ground controls. In space and on Earth, both clonal populations maintained their clone-specific root formation and growth characteristics and produced an equivalent amount of tissue when compared to each other. As on Earth, and as expected, there were fewer and shorter roots on plantlets that formed floral buds. The significance of altered moisture distribution in the "horticultural foam" substrate in space for root growth and the significance of our findings for growing plants in altered gravity environments are discussed.     

Regeneration of canopy trees in tropical wet forests

The most diverse tree communities on earth, the tropical wet forests, to a large degree remain ecological enigmas. What accounts for the coexistence of 100 or more tree species per hectare, compared to the 15 or fewer found in most temperate forests? What are the lifespans of tropical forest trees? What factors control their populations through time and space? Do the different species have highly individual regeneration patterns, or are many in fact ecological equivalents? Although we are far from having satisfactory answers to these questions, recent studies of regeneration processes are leading toward new interpretations of these complex communities.     

ERα regulates lipid metabolism in bone through ATGL and perilipin

A decrease in bone mineral density during menopause is accompanied by an increase in adipocytes in the bone marrow space. Ovariectomy also leads to accumulation of fat in the bone marrow. Herein we show increased lipid accumulation in bone marrow from estrogen receptor alpha (ERα) knockout (ERαKO) mice compared to wild‐type (WT) mice or estrogen receptor beta (ERβ) knockout (ERβKO) mice. Similarly, bone marrow cells from ERαKO mice differentiated to adipocytes in culture also have increased lipid accumulation compared to cells from WT mice or ERβKO mice. Analysis of individual adipocytes shows that WT mice have fewer, but larger, lipid droplets per cell than adipocytes from ERαKO or ERβKO animals. Furthermore, higher levels of adipose triglyceride lipase (ATGL) protein in WT adipocytes correlate with increased lipolysis and fewer lipid droplets per cell and treatment with 17β‐estradiol (E2) potentiates this response. In contrast, cells from ERαKO mice display higher perilipin protein levels, promoting lipogenesis. Together these results demonstrate that E2 signals via ERα to regulate lipid droplet size and total lipid accumulation in the bone marrow space in vivo. J. Cell. Biochem. 114: 1306–1314, 2013. © 2012 Wiley Periodicals, Inc.     

Life history influences rates of climatic niche evolution in flowering plants

Across angiosperms, variable rates of molecular substitution are linked with life-history attributes associated with woody and herbaceous growth forms. As the number of generations per unit time is correlated with molecular substitution rates, it is expected that rates of phenotypic evolution would also be influenced by differences in generation times. Here, we make the first broad-scale comparison of growth-form-dependent rates of niche evolution. We examined the climatic niches of species on large time-calibrated phylogenies of five angiosperm clades and found that woody lineages have accumulated fewer changes per million years in climatic niche space than related herbaceous lineages. Also, climate space explored by woody lineages is consistently smaller than sister lineages composed mainly of herbaceous taxa. This pattern is probably linked to differences in the rate of climatic niche evolution. These results have implications for niche conservatism; in particular, the role of niche conservatism in the distribution of plant biodiversity. The consistent differences in the rate of climatic niche evolution also emphasize the need to incorporate models of phenotypic evolution that allow for rate heterogeneity when examining large datasets.     

Seasonality and reproduction in aphids

Aphids are short-lived and occupy habitats which vary in quality in both time and space. They exploit their ephemerally nutritious habitats by rapidly producing many small offspring when conditions are good, and fewer, larger offspring when conditions are poor, at which time they also divert more of their resources into fat storage. Aphids of each of the generations which make up a life cycle have specific reproductive strategies adapted to the conditions they are most likely to encounter, that is they anticipate the predictable seasonal trends in habitat quality.     

The first twelve amino acids (less than half of the pre-sequence) of an imported mitochondrial protein can direct mouse cytosolic dihydrofolate reductase into the yeast mitochondrial matrix.

Yeast cytochrome c oxidase subunit IV (an imported mitochondrial protein) is made as a larger precursor with a transient pre-sequence of 25 amino acids. If this pre-sequence is fused to the amino terminus of mouse dihydrofolate reductase (a cytosolic protein) the resulting fusion protein is imported into the matrix space, and cleaved to a smaller size, by isolated yeast mitochondria. We have now fused progressively shorter amino-terminal segments of the subunit IV pre-sequence to dihydrofolate reductase and tested each fusion protein for import into the matrix space and cleavage by the matrix-located processing protease. The first 12 amino acids of the subunit IV pre-sequence were sufficient to direct dihydrofolate reductase into the mitochondrial matrix, both in vitro and in vivo. However, import of the corresponding fusion protein into the matrix was no longer accompanied by proteolytic processing. Fusion proteins containing fewer than nine amino-terminal residues from the subunit IV pre-piece were not imported into isolated mitochondria. The information for transporting attached mouse dihydrofolate reductase into mitochondria is thus contained within the first 12 amino acids of the subunit IV pre-sequence.