Plucking or cutting Gelidium sesquipedale? A demographic simulation of harvest impact using a population projection matrix model.

A matrix model describes the annual dynamics of a commercial (harvested by plucking) Gelidium sesquipedale population off Cape Espichel, Portugal. Vital rates were measured from a frond population divided into size classes; annual transition probabilities among them were calculated. Transition probabilities under harvest by cutting are derived by assuming that all harvested fronds are cut to the first size class, and none are plucked. Simulations of the annual population dynamics for harvest by both plucking and cutting are used to assess which harvest strategy will optimize yields. Assuming the same efficiency for both strategies, cutting fronds to 7 cm (as mechanical harvesters do) results in a higher population growth rate ( = 1.08 to 1.35) than occurs with the plucking technique ( = 0.85). Simulations of population recovery show the number of fronds in each size class available the next harvest season will be higher when cut than plucked. This model can also optimize yields by predicting the more efficient season opening, and harvesting cutting height.     

Is the sheep a suitable model to study the mechanical alterations of disc degeneration in humans? A probabilistic finite element model study

Intervertebral disc degeneration is one major source of low back pain, which because of its complex multifactorial nature renders the treatment challenging and thus necessitates extensive research. Experimental animal models have proven valuable in improving our understanding of degenerative processes and potentially promising therapies. Currently, the sheep is the most frequently used large animal in vivo model in intervertebral disc research. However, despite its undoubted value for investigations of the complex biological and cellular aspects, to date, it is unclear whether the sheep is also suited to study the mechanical aspects of disc degeneration in humans.A parametric finite element (FE) model of the L4–5 spinal motion segment was developed. Using this model, the geometry and the material properties of both the human and the ovine spinal segment as well as different appearances of disc degeneration can be depicted. Under pure and combined loads, it was investigated whether degenerative changes to both the human and the ovine model equivalent caused the same mechanical response.Different patterns of degeneration resulted in large variations in the ranges of motion, intradiscal pressure, ligament and facet loads. In the human, but not in the ovine model, all these results differed significantly between different degrees of degeneration.This FE model study highlighted possible differences in the mechanical response to disc degeneration between human and ovine intervertebral discs and indicates the necessity of further, more detailed, investigations.     

What drives the dynamics of a soil mite population under seasonal flooding? A null model analysis

Floods can inflict high mortality on terrestrial organisms, but may also promote adaptive evolution. In seasonal floodplains, several taxa show flood-related traits that may be important for their long-term persistence, but the available evidence is conflicting. Here, we used a simulation approach to investigate the interplay between seasonal floods and submersion resistance in driving the population dynamics of the parthenogenetic soil mite Rostrozetes ovulum in an Amazonian blackwater floodplain. First, we gathered data from two flood cycles to estimate field survival rate. Next, we used further data from a submersion survival laboratory experiment and a historical flood record to build a null model for R. ovulum’s survival rate under seasonal flooding, and then tested it against field survival estimates. Floods caused marked density declines, but the two estimates of field survival rate were statistically equivalent, suggesting relatively constant survival across years. Submersion survival time varied tenfold among individuals, but its variability was within the range known for life history traits of other asexual invertebrates. Both field survival rates were consistent with the null model, supporting seasonal flooding as the main mortality factor. Surprisingly, though, average flood duration was actually larger than the average mite could survive, suggesting that population persistence relies on relatively rare, super-resistant phenotypes. Overall, the studied R. ovulum population appears to have a mainly density-independent dynamics across years, with its viability depending on mechanisms that buffer flood survival rate against temporal oscillations.     

Are interlimb interactions disturbed in patients with Parkinson’s disease? A study under unloading conditions

During natural human locomotion, neural connections are activated that are typical of regulation of the quadrupedal walking. The interaction between the neural networks generating rhythmic movements of the upper and lower limbs depends on tonic state of each of these networks regulated by motor signals from the brain. Distortion of these signals in patients with Parkinson’s disease (PD) may lead to disruption of the interlimb interactions. We examined the effect of movements of the limbs of one girdle on the parameters of the motor activity of another limb girdle at their joint cyclic movements under the conditions of arm and leg unloading in 17 patients with PD and 16 healthy subjects. We have shown that, in patients, the effect of voluntary and passive movements of arms, as well as the active movement of the distal parts of arms, on the voluntary movement of legs is weak, while in healthy subjects, the effect of arm movements on the parameters of voluntary stepping is significant. The effect of arm movements on the activation of the involuntary stepping by vibrational stimulation of-legs in patients was absent, while in healthy subjects, the motor activity of arms increased the possibility of involuntary rhythmic movements activation. Differences in the effect of leg movements on the rhythmic movements of arms were found in both patients and healthy subjects. The interlimb interaction appeared after drug administration. However, the effect of the drug was not sufficient for the recovery of normal state of the neural networks in patients. In PD patients, neural networks generating stepping rhythm have an increased tonic activity, which prevents the activation and appearance of involuntary rhythmic movements facilitating the effects of arms on legs.     

A genome-wide association study of limb bone length using a Large White?×?Minzhu intercross population

Background

In pig, limb bone length influences ham yield and body height to a great extent and has important economic implications for pig industry. In this study, an intercross population was constructed between the indigenous Chinese Minzhu pig breed and the western commercial Large White pig breed to examine the genetic basis for variation in limb bone length. The aim of this study was to detect potential genetic variants associated with porcine limb bone length.

Methods

A total of 571 F2 individuals from a Large White and Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip, and phenotyped for femur length (FL), humerus length (HL), hipbone length (HIPL), scapula length (SL), tibia length (TL), and ulna length (UL). A genome-wide association study was performed by applying the previously reported approach of genome-wide rapid association using mixed model and regression. Statistical significance of the associations was based on Bonferroni-corrected P-values.

Results

A total of 39 significant SNPs were mapped to a 11.93 Mb long region on pig chromosome 7 (SSC7). Linkage analysis of these significant SNPs revealed three haplotype blocks of 495 kb, 376 kb and 492 kb, respectively, in the 11.93 Mb region. Annotation based on the pig reference genome identified 15 genes that were located near or contained the significant SNPs in these linkage disequilibrium intervals. Conditioned analysis revealed that four SNPs, one on SSC2 and three on SSC4, showed significant associations with SL and HL, respectively.

Conclusions

Analysis of the 15 annotated genes that were identified in these three haplotype blocks indicated that HMGA1 and PPARD, which are expressed in limbs and influence chondrocyte cell growth and differentiation, could be considered as relevant biological candidates for limb bone length in pig, with potential applications in breeding programs. Our results may also be useful for the study of the mechanisms that underlie human limb length and body height.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0056-6) contains supplementary material, which is available to authorized users.     

Does natural selection promote population divergence? A comparative analysis of population structure using amplified fragment length polymorphism markers and quantitative traits

Divergent natural selection is considered an important force in plant evolution leading to phenotypic differentiation between populations exploiting different environments. Extending an earlier greenhouse study of population differentiation in the selfing annual plant Senecio vulgaris, we estimated the degree of population divergence in several quantitative traits related to growth and life history and compared these estimates with those based on presumably neutral molecular markers (amplified fragment length polymorphisms; AFLPs). This approach allowed us to disentangle the effects of divergent selection from that of other evolutionary forces (e.g. genetic drift). Five populations were examined from each of two habitat types (ruderal and agricultural habitats). We found a high proportion of total genetic variance to be among populations, both for AFLP markers (phiST = 0.49) and for quantitative traits (range of QST: 0.26-0.77). There was a strong correlation between molecular and quantitative genetic differentiation between pairs of populations (Mantel's r = 0.59). However, estimates of population differentiation in several quantitative traits exceeded the neutral expectation (estimated from AFLP data), suggesting that divergent selection contributed to phenotypic differentiation, especially between populations from ruderal and agricultural habitats. Estimates of within-population variation in AFLP markers and quantitative genetic were poorly correlated, indicating that molecular marker data may be of limited value to predict the evolutionary potential of populations of S. vulgaris.     

Biomechanical differences of Coflex-F and pedicle screw fixation combined with TLIF or ALIF – a finite element study

Lumbar interbody fusion is a common procedure for treating lower back pain related to degenerative disc diseases. The Coflex-F is a recently developed interspinous spacer, the makers of which claim that it can provide stabilisation similar to pedicle screw fixation. Therefore, this study compares the biomechanical behaviour of the Coflex-F device and pedicle screw fixation with transforaminal lumbar interbody fusion (TLIF) or anterior lumbar interbody fusion (ALIF) surgeries by using finite element analysis. The results show that the Coflex-F device combined with ALIF surgery can provide stability similar to the pedicle screw fixation combined with TLIF or ALIF surgery. Also, the posterior instrumentations (Coflex-F and pedicle screw fixation) combined with TLIF surgery had lower stability than when combined with ALIF surgery.     

Terrestrial or marine species distribution model: Why not both? A case study with seabirds

Species reliant on both the terrestrial and marine realms present a challenge for conventional species distribution models (SDMs). For such species, standard single‐realm SDMs may omit key information that could result in decreased model accuracy and performance. Existing approaches to habitat suitability modeling typically do not effectively combine information from multiple realms; this methodological gap can ultimately hamper management efforts for groups such as seabirds, seals, and turtles. This study, for the first time, jointly incorporates both terrestrial information and marine information into a single species distribution model framework. We do this by sampling nearby marine conditions for a given terrestrial point and vice versa using parameters set by each species’ mean maximum foraging distance and then use standard SDM methods to generate habitat suitability predictions; therefore, our method does not rely on post hoc combination of several different models. Using three seabird species with very different ecologies, we investigate whether this new multi‐realm approach can improve our ability to identify suitable habitats for these species. Results show that incorporating terrestrial information into marine SDMs, or vice versa, generally improves model performance, sometimes drastically. However, there is considerable variability between species in the level of improvement as well as in the particular method that produces the most improvement. Our approach provides a repeatable and transparent method to combine information from multiple ecological realms in a single SDM framework. Important advantages over existing solutions include the opportunity to, firstly, easily combine terrestrial and marine information for species that forage large distances inland or out to sea and, secondly, consider interactions between terrestrial and marine variables.     

A coupled mathematical model between bone remodeling and tumors: a study of different scenarios using Komarova’s model

This paper aims to construct a general framework of coupling tumor–bone remodeling processes in order to produce plausible outcomes of the effects of tumors on the number of osteoclasts, osteoblasts, and the frequency of the bone turnover cycle. In this document, Komarova’s model has been extended to include the effect of tumors on the bone remodeling processes. Thus, we explored three alternatives for coupling tumor presence into Komarova’s model: first, using a “damage” parameter that depends on the tumor cell concentration. A second model follows the original structure of Komarova, including the tumor presence in those equations powered up to a new parameter, called the paracrine effect of the tumor on osteoclasts and osteoblasts; the last model is replicated from Ayati and collaborators in which the impact of the tumor is included into the paracrine parameters. Through the models, we studied their stability and considered some examples that can reproduce the tumor effects seen in clinic and experimentally. Therefore, this paper has three parts: the exposition of the three models, the results and discussion (where we explore some aspects and examples of the solution of the models), and the conclusion.

     

A systematic study of labelling an α-helix in a protein with a lanthanide using IDA-SH or NTA-SH tags

The previously published IDA-SH and NTA-SH tags are small synthetic lanthanide-binding tags derived from cysteine, which afford site-specific lanthanide labelling by disulfide-bond formation with a cysteine residue of the target protein. Following attachment to a single cysteine in an α-helix, sizeable pseudocontact shifts (PCS) can be observed, if the lanthanide is immobilized by additional coordination to a negatively charged amino-acid side chain that is located in a neighboring turn of the helix. To identify the best labelling strategy for PCS measurements, we performed a systematic study, where IDA-SH or NTA-SH tags were ligated to a cysteine residue in position i of an α-helix, and aspartate or glutamate residues were placed in the positions i ? 4 or i + 4. The largest anisotropy components of the magnetic susceptibility tensor were observed for an NTA-SH tag in position i with a glutamate residue in position i ? 4. While the NTA-SH tag produced sizeable PCSs regardless of the presence of nearby carboxyl groups of the protein, the IDA-SH tag generated a good lanthanide binding site only if an aspartate was placed in position i + 4. The findings provide a firm basis for the design of site-directed mutants that are suitable for the reliable generation of PCSs in proteins with paramagnetic lanthanides.     

What is genetic differentiation,and how should we measure it—GST,D, neither or both?

Estimates of the fixation index, F_ST, have been used as measures of population differentiation for many decades. However, there have been persistent voices in the literature suggesting that these statistics do not measure true differentiation. In particular, the statistics Nei's G_ST and Wier and Cockerham's θ have been criticized for being ‘constrained’ to not equal one in some situations that seem to represent maximal differentiation. Here, we address the issue of how to evaluate exactly how much information a particular statistic contains about the process of differentiation. This criterion can be used to counter most concerns about the performance of G_ST (and related statistics), while also being reconciled with the insights of those who have proposed alternative measures of differentiation. In particular, the likelihood‐based framework that we put forward can justify the use of G_ST as an effective measure of differentiation, but also shows that in some situations G_ST is insufficient on its own and needs supplementing by another measure such as Jost's D or Hedrick's G′_ST. This approach will become increasingly important in the future, as greater emphasis is placed on analysing large data sets.     

Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits

Phylogenetic comparative methods (PCMs) provide a potentially powerful toolkit for testing hypotheses about cultural evolution. Here, we build on previous simulation work to assess the effect horizontal transmission between cultures has on the ability of both phylogenetic and non-phylogenetic methods to make inferences about trait evolution. We found that the mode of horizontal transmission of traits has important consequences for both methods. Where traits were horizontally transmitted separately, PCMs accurately reported when trait evolution was not correlated even at the highest levels of horizontal transmission. By contrast, linear regression analyses often incorrectly concluded that traits were correlated. Where simulated trait evolution was not correlated and traits were horizontally transmitted as a pair, both methods inferred increased levels of positive correlation with increasing horizontal transmission. Where simulated trait evolution was correlated, increasing rates of separate horizontal transmission led to decreasing levels of inferred correlation for both methods, but increasing rates of paired horizontal transmission did not. Furthermore, the PCM was also able to make accurate inferences about the ancestral state of traits. These results suggest that under certain conditions, PCMs can be robust to the effects of horizontal transmission. We discuss ways that future work can investigate the mode and tempo of horizontal transmission of cultural traits.     

Can self-rated health identify us women and men with low bone mineral density? a cross-sectional population study

Background: Despite its simplicity, self-rated health (SRH) is a significant dimension of health assessment, with demonstrated means to identify individuals at increased risk of morbidity and mortality.Objective: The aim of the present study was to assess whether SRH, age, and modifiable osteoporosis risk factors in a hypothetical screening situation could identify individuals with low bone mineral density (BMD).Methods: Data were analyzed from a multiethnic sample of 4905 women and men aged 50 to 79 years from the Third National Health and Nutrition Examination Survey. Low BMD was assessed according to the World Health Organization definition using gender- and race/ethnicity-specific young adult mean values to calculate T-scores. Multiple linear regression analysis was used to determine whether BMD was lower among those with poorer SRH; multiple logistic regression analysis was used to determine whether poor SRH was associated with low BMD.Results: The study population included 616 and 589 African American; 522 and 564 Mexican American; and 1312 and 1302 white women and men, respectively. The distributions of SRH responses differed for African American and Mexican American women and men compared with the distributions for samegender whites, with significantly more white women and men reporting excellent or very good health (P < 0.05) and significantly greater proportions of African American and Mexican American women and men reporting poorer health (P < 0.05). Among women and nonwhite men, there was no evidence of an association between BMD and SRH. Linear trends of decreasing BMD with declining SRH were detected for all men with low or normal body mass index (P < 0.001) and overweight men (P < 0.001). When stratified by race/ethnicity, a linear trend of decreasing BMD with declining SRH was found for nonobese white men only (P-trend: <0.001). The likelihood of having low BMD among nonobese white men who reported excellent or very good health was two-thirds that of their male counterparts with poor SRH (P < 0.001).Conclusions: Independent of age and modifiable osteoporosis risk factors, poor SRH may be a relevant risk factor for low BMD among older nonobese white men. Further research is needed to determine whether SRH may be a useful risk assessment tool for low BMD in this group of men.     

Does reproductive success increase with age or with size in species with indeterminate growth? A case study using sand lizards (Lacerta agilis)

Most data on determinants of reproductive success (RS) and reproductive tactics are correlational in nature, and hence cannot be used to infer causation. Consistent patterns-such as an increase in RS with age, as seen in many types of organisms-may result from diverse underlying mechanisms. Ontogenetic increases in RS in mammals and birds may be due largely to direct effects of age (via learning, etc.) but our analyses show that apparently analogous ontogenetic shifts in reproductive tactics and increases in RS in sand lizards (Lacerta agilis) are actually due to ontogenetic changes in body size. When size effects are removed, age exerts very little effect on either reproductive behaviour or RS in either sex. In many taxa, both age and body size may exert important effects on reproductive biology, and disentangling these effects should be a focus of further research.     

Can markers injected into a single-loop anterior cruciate ligament graft define the axes of the tibial and femoral tunnels? A cadaveric study using roentgen stereophotogrammetric analysis

Lengthening of a soft-tissue anterior cruciate ligament (ACL) graft construct over time, which leads to an increase in anterior laxity following ACL reconstruction, can result from relative motions between the graft and fixation devices and between the fixation devices and bone. To determine these relative motions using Roentgen stereophotogrammetry (RSA), it is first necessary to identify the axes of the tibial and femoral tunnels. The purpose of this in vitro study was to determine the error in using markers injected into the portions of a soft-tissue tendon graft enclosed within the tibial and femoral tunnels to define the axes of these tunnels. Markers were injected into the tibia, femur, and graft in six cadaveric legs the knees of which were reconstructed with single-loop tibialis grafts. The axes of the tunnels were defined by marker pairs that were injected into the bones on lines parallel to the walls of the tibial and femoral tunnels (i.e., standard). By using marker pairs injected into the portions of the graft enclosed within the tibial and femoral tunnels and the marker pairs aligned with the tunnel axes, the directions of vectors were determined by using RSA, while a 150 N anterior force was transmitted at the knee. The average and standard deviations of the angle between the two vectors were 5.5+/-3.3 deg. This angle translates into an average error and standard deviation of the error in lengthening quantities (i.e., relative motions along the tunnel axes) at the sites of fixation of (0.6+/-0.8)%. Identifying the axes of the tunnels by using marker pairs in the graft rather than marker pairs in the walls of the tunnels will shorten the surgical procedure by eliminating the specialized tools and time required to insert marker pairs in the tunnel walls and will simplify the data analysis in in vivo studies.     

A study of staining for electron microscopy using collagen as a model system—VI. Uranyl nitrate negative staining patterns and their correlation with sequence data

Collagen is used as a model system to study the mechanism of negative staining. Negative staining patterns from reconstituted fibrils of type I calf skin collagen (of known amino acid sequence) were compared with chemical data by a computer-aided correlation procedure. The stain used was uranyl nitrate, pH 3.2 and 4.9. The results show that the ‘bulkiness’ (average cross-sectional area or ‘plumpness’) of amino acid side chains is the dominant stain-excluding factor determining the small-scale distribution of stain along the collagen fibril. Some contribution of positive staining can also be demonstrated by the analysis described here.     

Do top-down and bottom-up controls interact to exclude nitrogen-fixing cyanobacteria from the plankton of estuaries? An exploration with a simulation model

Explaining the nearly ubiquitous absence of nitrogen fixation by planktonic organisms in strongly nitrogen-limited estuaries presents a major challenge to aquatic ecologists. In freshwater lakes of moderate productivity, nitrogen limitation is seldom maintained for long since heterocystic, nitrogen-fixing cyanobacteria bloom, fix nitrogen, and alleviate the nitrogen limitation. In marked contrast to lakes, this behavior occurs in only a few estuaries worldwide. Primary production is limited by nitrogen in most temperate estuaries, yet no measurable planktonic nitrogen fixation occurs. In this paper, we present the hypothesis that the absence of planktonic nitrogen fixers from most estuaries is due to an interaction of bottom-up and top-down controls. The availability of Mo, a trace metal required for nitrogen fixation, is lower in estuaries than in freshwater lakes. This is not an absolute physiological constraint against the occurrence of nitrogen-fixing organisms, but the lower Mo availability may slow the growth rate of these organisms. The slower growth rate makes nitrogen-fixing cyanobacteria in estuaries more sensitive to mortality from grazing by zooplankton and benthic organisms.We use a simple, mechanistically based simulation model to explore this hypothesis. The model correctly predicts the timing of the formation of heterocystic, cyanobacterial blooms in freshwater lakes and the magnitude of the rate of nitrogen fixation. The model also correctly predicts that high zooplankton biomasses in freshwaters can partially suppress blooms of nitrogen-fixing cyanobacteria, even in strongly nitrogen-limited lakes. Further, the model indicates that a relatively small and environmentally realistic decrease in Mo availability, such as that which may occur in seawater compared to freshwaters due to sulfate inhibition of Mo assimilation, can suppress blooms of heterocystic cyanobacteria and prevent planktonic nitrogen fixation. For example, the model predicts that at a zooplankton biomass of 0.2 mg l^–1, cyanobacteria will bloom and fix nitrogen in lakes but not in estuaries of full-strength seawater salinity because of the lower Mo availability. Thus, the model provides strong support for our hypothesis that bottom-up and top-down controls may interact to cause the absence of planktonic nitrogen fixation in most estuaries. The model also provides a basis for further exploration of this hypothesis in individual estuarine systems and correctly predicts that planktonic nitrogen fixation can occur in low salinity estuaries, such as the Baltic Sea, where Mo availability is greater than in higher salinity estuaries.     

Could specialization to cold‐water upwelling systems influence gene flow and population differentiation in marine organisms? A case study using the blue‐footed booby,Sula nebouxii

Aim We assessed population differentiation and gene flow across the range of the blue‐footed booby (Sula nebouxii) (1) to test the generality of the hypothesis that tropical seabirds exhibit higher levels of population genetic differentiation than their northern temperate counterparts, and (2) to determine if specialization to cold‐water upwelling systems increases dispersal, and thus gene flow, in blue‐footed boobies compared with other tropical sulids. Location Work was carried out on islands in the eastern tropical Pacific Ocean from Mexico to northern Peru. Methods We collected samples from 173 juvenile blue‐footed boobies from nine colonies spanning their breeding distribution and used molecular markers (540 base pairs of the mitochondrial control region and seven microsatellite loci) to estimate population genetic differentiation and gene flow. Our analyses included classic population genetic estimation of pairwise population differentiation, population growth, isolation by distance, associations between haplotypes and geographic locations, and analysis of molecular variance, as well as Bayesian analyses of gene flow and population differentiation. We compared our results with those for other tropical seabirds that are not specialized to cold‐water upwellings, including brown (Sula leucogaster), red‐footed (S. sula) and masked (S. dactylatra) boobies. Results Blue‐footed boobies exhibited weak global population differentiation at both mitochondrial and nuclear loci compared with all other tropical sulids. We found evidence of high levels of gene flow between colonies within Mexico and between colonies within the southern portion of the range, but reduced gene flow between these regions. We also found evidence for population growth, isolation by distance and weak phylogeographic structure. Main conclusions Tropical seabirds can exhibit weak genetic differentiation across large geographic distances, and blue‐footed boobies exhibit the weakest population differentiation of any tropical sulid studied thus far. The weak population genetic structure that we detected in blue‐footed boobies may be caused by increased dispersal, and subsequently increased gene flow, compared with other sulids. Increased dispersal by blue‐footed boobies may be the result of the selective pressures associated with cold‐water upwelling systems, to which blue‐footed boobies appear specialized. Consideration of foraging environment may be particularly important in future studies of marine biogeography.     

A study of staining for electron microscopy using collagen as a model system—IV. Phosphotungstate/tungstate negative staining patterns and their correlation with sequence data

The type I collagen fibril (for which the axial distribution of amino acid residues is known) has been used as a model system to study the mechanism of negative staining. Negative staining patterns from reconstituted fibrils were compared with chemical data by a computer-aided correlation procedure. Stains used were: phosphotungstic acid, pH 3.2 and 7.0, lithium tungstate, pH 7.2, and methylamine tungstate, pH 6.6. In all cases, the results of the correlation analyses point to the ‘bulkiness’ (average cross-sectional area or ‘plumpness’) of amino acid side chains as the dominant stain-excluding factor determining the small-scale distribution of stain along the collagen fibril. Some preferred uptake of heavy metal ions on charged side chains (a positive staining contribution) can be demonstrated by partial correlation analysis but, under the staining conditions used here, the effect is largely masked by the much greater negative staining component.