Similarities In Dynamics Research Articles

Anthropogenic and tidal influences on salinity levels of the Shatt al-Arab River, Basra, Iraq

ABSTRACTUnderstanding the salinity variation caused by a combination of anthropogenic and marine sources is important for water resource management in heavily used rivers impacted by tidal influence. A quantitative analysis of intra-annual variability of salinity levels was conducted in the Shatt al-Arab River. Based on hourly records during 2014, the results showed high spatiotemporal variability in the range of 0.2–40.0 ppt. Similarities in salinity dynamics were used to divide the river course into four distinct spatial units to guide respective management actions. Salinity dynamics are influenced by different sources of saline water inflows and withdrawals associated with irrigation, industrial and municipal waste, marshes and by seawater intrusion. Adapting a simple interpolation approach, the measured distance of seawater intrusion was 80 km upstream the river mouth. Continuous monitoring of water quality can localize and assess the relative impact of the various salinity sources at different times. Managing seawater intrusion and any local effects should take into account variations in quantity and quality of irrigation return flows and wastewater discharges.

Testing the Markov hypothesis in fluid flows.

Stochastic Markov processes are used very frequently to model, for example, processes in turbulence and subsurface flow and transport. Based on the weak Chapman-Kolmogorov equation and the strong Markov condition, we present methods to test the Markov hypothesis that is at the heart of these models. We demonstrate the capabilities of our methodology by testing the Markov hypothesis for fluid and inertial particles in turbulence, and fluid particles in the heterogeneous subsurface. In the context of subsurface macrodispersion, we find that depending on the heterogeneity level, Markov models work well above a certain scale of interest for media with different log-conductivity correlation structures. Moreover, we find surprising similarities in the velocity dynamics of the different media considered.

Physical aging and structural recovery in a colloidal glass subjected to volume-fraction jump conditions.

Three important kinetic phenomena have been cataloged by Kovacs in the investigation of molecular glasses during structural recovery or physical aging. These are responses to temperature-jump histories referred to as intrinsic isotherms, asymmetry of approach, and memory effect. Here we use a thermosensitive polystyrene-poly (N-isopropylacrylamide)-poly (acrylic acid) core-shell particle-based dispersion as a colloidal model and by working at a constant number concentration of particles we use temperature changes to create volume-fraction changes. This imposes conditions similar to those defined by Kovacs on the colloidal system. We use creep experiments to probe the physical aging and structural recovery behavior of colloidal glasses in the Kovacs-type histories and compare the results with those seen in molecular glasses. We find that there are similarities in aging dynamics between molecular glasses and colloidal glasses, but differences also persist. For the intrinsic isotherms, the times t_{eq} needed for relaxing or evolving into the equilibrium (or stationary) state are relatively insensitive to the volume fraction and the values of t_{eq} are longer than the α-relaxation time τ_{α} at the same volume fraction. On the other hand, both of these times grow at least exponentially with decreasing temperature in molecular glasses. For the asymmetry of approach, similar nonlinear behavior is observed for both colloidal and molecular glasses. However, the equilibration time t_{eq} is the same for both volume-fraction up-jump and down-jump experiments, different from the finding in molecular glasses that it takes longer for the structure to evolve into equilibrium for the temperature up-jump condition than for the temperature down-jump condition. For the two-step volume-fraction jumps, a memory response is observed that is different from observations of structural recovery in two-step temperature histories in molecular glasses. The concentration dependence of the dynamics of the colloidal dispersions is also examined in the equilibrium state and we find that the dynamic fragility index m is sensitive to the degree of softness of the soft colloidal dispersion, indicating that soft colloids make stronger glasses. Finally, we compare the present results with prior findings for similar thermoresponsive systems obtained with diffusing wave spectroscopy and discuss similarities and differences.

Analiza ścieżek rozwoju gospodarczego polskich regionów

The research consists of two stages. The first provides a comparative analysis of the level of economic development of Polish voivodships for the period 2000–2013. The second evaluates how similar the paths of economic development of individual regions are. To achieve the latter end, measures of the similarity of time series were applied, particularly dynamic time warping. The starting point for this method is to compute a matrix of costs containing the distances between all the elements of the time series to be analysed (pairwise). The optimum path between the starting and the final points may then be found. This path is characterised by the minimum value of the cumulated distances. The results evidence strong similarities in dynamics and high differences in the level of economic development of Polish voivodships and can be useful for the programming of regional policy, especially for determining whether the foundations for common programmes of the cohesion policy for given groups of regions exist.

Ecosystem services in managing residential landscapes: priorities, value dimensions, and cross-regional patterns

Although ecosystem services have been intensively examined in certain domains (e.g., forests and wetlands), little research has assessed ecosystem services for the most dominant landscape type in urban ecosystems—namely, residential yards. In this paper, we report findings of a cross-site survey of homeowners in six U.S. cities to 1) examine how residents subjectively value various ecosystem services, 2) explore distinctive dimensions of those values, and 3) test the urban homogenization hypothesis. This hypothesis posits that urbanization leads to similarities in the social-ecological dynamics across cities in diverse biomes. By extension, the thesis suggests that residents’ ecosystem service priorities for residential landscapes will be similar regardless of whether residents live in the humid East or the arid West, or the warm South or the cold North. Results underscored that cultural services were of utmost importance, particularly anthropocentric values including aesthetics, low-maintenance, and personal enjoyment. Using factor analyses, distinctive dimensions of residents’ values were found to partially align with the Millennium Ecosystem Assessment’s categories (provisioning, regulating, supporting, and cultural). Finally, residents’ ecosystem service priorities exhibited significant homogenization across regions. In particular, the traditional lawn aesthetic (neat, green, weed-free yards) was similarly important across residents of diverse U.S. cities. Only a few exceptions were found across different environmental and social contexts; for example, cooling effects were more important in the warm South, where residents also valued aesthetics more than those in the North, where low-maintenance yards were a greater priority.

Enhanced visual exploration for real objects compared to pictures during free viewing in the macaque monkey

The question of whether animals perceive pictures as representation of real objects remains still unsolved. Object-picture perception is generally studied requiring animals to learn some information about real objects and transfer that knowledge to the pictorial domain, or vice versa. Here, we tackle the issue of object-picture perception from a different perspective, examining visual exploration behavior of two naïve macaque monkeys during free-viewing of objects and pictures of these objects on a computer monitor. Our main finding is that monkeys looked spontaneously longer at object rather than picture stimuli. However, we find striking similarities in temporal dynamics of gaze allocation within the time course of a single stimulus presentation, as well as in habituation rates within and across behavioral sessions. We also highlight differences between stimulus types in terms of spatial gaze patterns and looking strategies. Stimulus features that attract overt attention during spontaneous visual exploration are thus better predicted for object stimuli by a visual saliency model. Moreover, we provide evidence for a consistency in stimulus preference for objects and pictures, suggesting a correspondence of in how macaques perceive objects and their pictorial stimuli. Taken together, our data suggest that macaque monkeys exhibit evidence for correspondence between objects and pictures. This validates spontaneous visual exploration as a method for studying object-picture correspondence without a need for extensive behavioral training. We discuss the potential advantages of using object over picture stimuli in the context of studies on visual cognition.

Driven active and passive nematics

We investigate similarities in the micro-structural dynamics between externally driven and actively driven nematics. Walls, lines of strong deformations in the director field, and topological defects are characteristic features of an active nematic. Similar structures form in driven passive nematics when there are inhomogeneities in imposed velocity gradients due to nonlinear flow fields or geometrical constraints. Specifically, pressure driven flow of a tumbling passive nematic in an expanding–contracting channel produces walls and defects similar to those seen in active nematics. We also study the response of active nematics to external driving, confirming that imposed shear suppresses the hydrodynamic instabilities. We show that shear fields can lead to wall alignments and the localisation of active turbulence.

Response of planktonic cyanobacteria and periphyton assemblages to physicochemical properties of stormwater in a shallow urban lake

The aim of this study was to determine the response of planktonic cyanobacteria and periphyton assemblages (periphytic algae in the separator pipes, epilithon and epiphyton) to lamella separator-treated stormwaters in urban Lake Jeziorak Maly in 1997-2003 and 2005. Relationships between periphyton and phytoplankton assemblage and water chemistry variables were analyzed by calculating the Spearman’s rank correlation coefficient, and then with canonical correspondence analysis (CCA). The basic factors favouring the cyanobacterial growth were water temperature and iron, while high chloride concentration limited their development. Cyanobacterial abundance recorded at the separators was half that of the pelagic zone because of a lower water temperature and higher Cl concentration, indicating high algal sensitivity to the considerable velocity and disturbances caused by stormwater effluents. Higher silicon and calcium concentrations at the separators and orthophosphates at sites with stones and gravel showed connection with the growth of diatoms, especially Fragilaria leptostauron var. martyi, Diatoma vulgaris and Navicula gregaria. The richness of the dominant cyanobacteria, Aphanizomenon gracile and Limnothrix redekei, was related with the water temperature, conductivity, pH, and TN. Similarities in the periphyton dynamics in separator pipes and epilithon between the years covered by the study suggest significant influence of separator-treated stormwater on these assemblages, in contrast to epiphyton and phytoplankton in the pelagial zone, where these waters had limited influence.

Similar Crowd Behavior in Organisms of Vastly Different Body Size

Crowd behaviors can have large fitness consequences for social organisms. Here we ask if there are similarities in the crowd dynamics of organisms that differ in body size, manner of locomotion, cognitive abilities, and state of alarm. Existing models of human crowd behavior have not been tested for their generality across species and body size nor across routine and emergency movements. We explore this issue by comparing the traffic dynamics of humans and of Argentine ants (Linepithema humile) to the predictions of our own model which was designed to simulate pedestrian movement. Some parameter values in the model were directly measured on ants but others were allometrically scaled from the human values to ant values based on the body mass difference. The model, with appropriately scaled parameters, correctly predicted two important properties of crowd behaviour for both organisms in a variety of circumstances: the flow rates and the distribution of time headways between successive ants in the escape sequence. The ability of a model of human pedestrian dynamics to predict behaviours of ant aggregations through allometric scaling of some parameter values suggests that there are fundamental features of crowd behavior that transcend the biological idiosyncrasies of the organisms involved.

Structural dynamics of 4-pyrimidone in lower-lying excited States

The structural dynamics of 4-pyrimidone (4PMO) in the A- and B-band absorptions was studied by using the resonance Raman spectroscopy combined with quantum chemical calculations to better understand whether the excited state intramolecular proton-transfer (ESIPT) reaction occurs in Franck–Condon regions or not. The transition barrier for the ground state proton-transfer tautomerization reaction between 3(H) (I) and hydroxy (II) was determined to be 165 kJ·mol−1 in vacuum on the basis of the B3LYP/6-311++G(d,2p) level of theory calculations. Two ultraviolet absorption bands of 4PMO were, respectively, assigned as πHπ*L and πHπ*L+1 transitions. The vibrational assignments were done on the basis of the Fourier transform (FT)-Raman and FT-infrared (IR) measurements, the density-functional theory computations and the normal mode analysis. The A- and B-band resonance Raman spectra of 4PMO were measured in water, methanol and acetonitrile. The structural dynamics of 4PMO was obtained through the analysis of the resonance Raman intensity pattern. We discuss the similarities in the structural dynamics of 4PMO and 2-thiopyrimidone (2TPM), and the results were used to correlate to the intramolecular hydrogen-atom-transfer process as observed by matrix-isolation IR experiments for 4PMO. A variety of NH/CH bend modes + C = O stretch mode mark the hydrogen-detachment-attachment or ESIPT reaction initiated in Franck–Condon region for 4PMO and 2TPM. Copyright © 2013 John Wiley & Sons, Ltd.

Reconstitution of Innate Lymphoid Cells After Hematopoietic Stem Cell Transplantation

AbstractAbstract ▪4104▪This icon denotes a clinically relevant abstract IntroductionPatients undergoing hematopoietic stem cell transplantation (HSCT) are at increased risk of developing (severe) opportunistic infections, which can be attributed to the combination of a decimated immune system and disrupted epithelial barriers. Innate lymphoid cells (ILCs) represent a novel family of regulator and effector cells that share phenotypic and functional characteristics with both NK cells and T lymphocytes, but are non-cytotoxic and lack antigen specific receptors. ILCs serve important roles in the maintenance of epithelial integrity and - as part of the first line of defence - in protection against microbes. ILCs are mainly tissue-resident and can be identified by the absence of lineage markers (Lin-) and bright expression of the alpha chain of the IL-7 receptor (CD127). Extensive research has been carried out focussing on the relative contribution of different immune cells to immune deficiency and graft-versus-host disease (GvHD) following HSCT. However, little is known about ILCs in this context. We studied reconstitution dynamics of ILCs in order to explore their function in tissue repair and mucosal immunity following HSCT. MethodsBlood samples of adult patients (n=15) receiving an allogeneic HSCT after reduced-intensity conditioning (RIC) for acute myeloid leukemia (AML) were obtained at sequential time points during induction, consolidation and conditioning chemotherapy, at the day of HSCT and up to 6 months following HSCT. Peripheral blood ILCs were analyzed using flow cytometry and defined as Lin-CD127hi. The ILC population was further divided into various subpopulations using the markers NKp44, CRTH2 and CXCR3. ResultsInduction and consolidation chemotherapy led to a significant decline in the number of circulating ILCs. Recovery of ILCs in between chemotherapy cycles was partial as ILC numbers improved without returning to healthy control values (n=10; reference values defined as upper and lower boundaries of 95% CI), in contrast to other innate cells such as neutrophils and NK cells. Following allogeneic HSCT, recovery dynamics of ILCs parallelled those of adaptive immune cells, rather than of innate cells: recovery was relatively slow, as normal numbers of circulating ILCs had not been reached 6 months after HSCT. In addition, we observed enrichment of a particular ILC subset, defined as Lin-CD127hiCD117+NKp44+ cells, in subgroups of patients after chemotherapy and HSCT. These RORγt-dependent ILCs have been found to comprise an important innate source of IL-22 (hence referred to as ILC22s), a cytokine crucial for epithelial homeostasis and induction of epithelial antimicrobial peptides. Discussion and conclusionOur observation of a relatively slow reconstitution of ILCs is notable since innate immune cells are generally known to recover within weeks to months after HSCT. In fact, ILC reconstitution following HSCT bears resemblance to post-transplantation adaptive lymphocyte recovery dynamics. Fitting with this notion, there is a certain degree of analogy between ILCs and T helper cells as ILCs with cytokine profiles resembling those of the various T helper subsets are found, i.e. ILCs producing mainly IL-13/5, IL-22, IL-17 or IFN-γ. Furthermore, proliferation and differentiation of the ILC subpopulations stands under the control of transcription factors known to be master regulators of the different T helper subsets (i.e. GATA3, Tbet, RORγt and AHR). Hence, our data show that the analogy between the ILC and T helper systems in terms of factors that control differentiation and function is matched by their similarities in reconstitution dynamics following chemotherapy and HSCT. Interestingly, following chemotherapy and allogeneic HSCT, ILC22s, known to be primarily dedicated to the maintenance of epithelial homeostasis, were found to be enriched in subgroups of patients. Damage to mucous membranes lining the gastrointestinal tract, due to chemotherapy-induced mucositis, conditioning radiotherapy or graft-versus-host disease, is a common problem that constitutes a significant limiting factor in HSCT. Therefore, improvements in the prevention or management of such epithelial damage are eagerly awaited. Our data suggest that ILCs may be involved in protection against and/or recovery of epithelial damage in patients with a hematological malignancy receiving chemotherapy and HSCT. Disclosures:No relevant conflicts of interest to declare.

Similarities in fragmentation dynamics of molecules under various perturbations

We show experimentally, by interpretation of coincidence multiparticle momentum maps, that the evolution of an unstable molecular ion to an asymptotic many-body state occurs via pathways that are independent of the mechanism of formation of the molecular ion.

Common mechanisms of human perceptual and motor learning

The adult mammalian brain has a remarkable capacity to learn in both the perceptual and motor domains through the formation and consolidation of memories. Such practice-enabled procedural learning results in perceptual and motor skill improvements. Here, we examine evidence supporting the notion that perceptual and motor learning in humans exhibit analogous properties, including similarities in temporal dynamics and the interactions between primary cortical and higher-order brain areas. These similarities may point to the existence of a common general mechanism for learning in humans.

Impact of methylprednisolone in priming solution of cardiopulmonary bypass on anti-inflammatory CD163 receptor during cardiac surgery

We evaluated the influence of methylprednisolone in cardiopulmonary bypass fluid on scavenger receptor for hemoglobin CD163 molecule expression on monocytes of patients who underwent elective coronary artery bypass grafting with cardiopulmonary bypass with either exposure to methylprednisolone present in the cardiopulmonary bypass fluid (20 patients), or without methylprednisolone in the cardiopulmonary bypass fluid (22 patients) and operated on without cardiopulmonary bypass (42 patients). The dynamics of CD163 expression was also followed in patients operated on without cardiopulmonary bypass. This study was a retrospective analysis of a comparison of two studies. The expression of CD163 was determined quantitatively by standardized flow cytometry technique. The similarities in the dynamics of CD163 monocyte expression, comparing the patients operated on with or without cardiopulmonary bypass, were found. Compared to the preoperative level, CD163 monocyte expression was significantly elevated on the 1(st) postoperative day. Monocyte CD163 expression on the 1(st) postoperative day was evidently similar in both groups of patients operated without cardiopulmonary bypass (median value of mean fluorescence intensity (MFI) 18,896; interquartile range from 27,538 to 57,711; median value of MFI 18,863; interquartile range from 16,514 to 26,559; n.s.), suggesting high reproducibility of our flow cytometric method; the monocyte CD163 expression was significantly higher (median value of MFI 37,902; interquartile range from 27,538 to 57,711) on the 1(st) postoperative day in patients exposed to methylprednisolone compared to patients without this exposure (median value of MFI 20,995; interquartile range from 16,321 to 29,623) (p<0.001). We concluded that the expression of hemoglobin scavenger receptor CD163 on monocytes of cardiac surgical patients is induced by methylprednisolone present in cardiopulmonary bypass fluid.

ANIMAL MODELS FOR THE STUDY OF HUMAN OVARIAN FUNCTION

The study of ovarian function has been of great interest to scientists and clinicians in the human and veterinary health fields for more than 20 centuries. Initial studies of the ovaries were based on anatomical descriptions post-mortem, followed by histological and endocrinological approaches. The introduction of high-resolution ultrasonography provided a long-awaited tool to image the reproductive tissues in situ in both animals and humans. Critical studies of the characteristics and control of ovarian follicular and luteal dynamics in non-human primates, rodents, and domestic farm animals have involved frequent (i.e. daily or multiple times a day) blood sampling and ultrasonography. Studies of this nature in women are difficult, and often unethical to conduct. Differences in antral folliculogenesis between humans and animals appear to be more in detail rather than in essence, and may reflect differences in intrinsic physiology or merely differences in our ability to detect changes in a given species. In women, the presence of endometrial shedding and symmetric luteal and follicular phases are different from that observed during the estrous cycles of domestic farm animals but despite these differences, general similarities in antral follicular dynamics exist. A continuous pattern of antral follicle development was originally proposed in domestic livestock species; however, the use of frequent serial ultrasonography and simultaneous endocrine profiling in these animal species has resulted in a broad understanding of follicular wave dynamics. Follicular waves have now been described in every species in which this approach has been used, including humans. The relatively large diameters of antral follicles in cows and mares, compared to monkeys, sheep, and rodents provide greater feasibility for characterizing antral follicular dynamics ultrasonographically. Profound similarities in the dynamics of follicle development exist between the menstrual cycle in humans and the estrous cycle in cattle and horses. Despite a proportionately longer luteal phase in cows and mares, the growing phase of the dominant ovulatory follicle (defined as the time period from wave emergence to ovulation) is comparable in the human, cow, and mare. Thus, at present, cows and mares may be the most appropriate models for the study of antral follicular dynamics in women. While the use of animal models has increased our understanding of ovarian function and provides the hypothetical basis for studies in women, differences in vocabulary, culture, and research methodologies between scientists in predominantly human versus animal settings has hampered knowledge translation. These differences represent a systemic impediment to a broad understanding of ovarian function and limits progress and innovation in the development of safer and more efficacious treatments for infertility and contraception.

Interactions of Cations with RNA Loop-Loop Complexes

RNA loop-loop interactions are essential in many biological processes, including initiation of RNA folding into complex tertiary shapes, promotion of dimerization, and viral replication. In this article, we examine interactions of metal ions with five RNA loop-loop complexes of unique biological significance using explicit-solvent molecular-dynamics simulations. These simulations revealed the presence of solvent-accessible tunnels through the major groove of loop-loop interactions that attract and retain cations. Ion dynamics inside these loop-loop complexes were distinctly different from the dynamics of the counterion cloud surrounding RNA and depend on the number of basepairs between loops, purine sequence symmetry, and presence of unpaired nucleotides. The cationic uptake by kissing loops depends on the number of basepairs between loops. It is interesting that loop-loop complexes with similar functionality showed similarities in cation dynamics despite differences in sequence and loop size.

Pollen and ovule production, floral nectary structure, and nectar secretion dynamics in tristylous Lythrum salicaria L.

Lythrum salicaria L. (Lythraceae) is tristylous, each plant forming one of three floral morphs that differ in reciprocal placement of the stigma and two sets of anthers. Several reproductive traits were compared quantitatively among these morphs. Although mean pollen viability (≥93%) and total pollen per mature, indehiscent anther within a staminal level (mean CV = 11%) were constant, the patterns of mean pollen production per anther were complex, being significantly lowest in long stamens (1,490 grains) of the short-styled morph, but highest in intermediate stamens (3,590) of the long-styled morph. Overall, pollen production was greatest (38,200) in long-styled flowers and least (22,000) in short-styled ones. On the contrary, ovule quantities per ovary (mean 107) were similar among floral morphs; thus, pollen-to-ovule ratios spanned 192 (short-styled morph) to 364 (long-styled morph), relatively low values for a strictly xenogamous species. Each morph had a recessed annular nectary of similar dimensions encircling the ovary base, with equal numbers of modified stomata distributed uniformly on the nectary surface. Most stomata were solitary (94%), whereas 5% occurred in pairs and 1% of stomatal units had just one guard cell. During nectar secretion, about 16% of pores were closed plus 28% of pores were fully occluded. Similarly, nectar volumes and solute concentrations, peak rates of nectar secretion (mean 72–79 μg sugar h−1) at early afternoon, and the nectar’s sucrose prevalence [S/(G + F) ≥4.3] were not significantly different among morphs. Based on these similarities in nectary structure and nectar-secretion dynamics, traits rarely studied in tristylous species, the preferential visitation of any particular floral morph of L. salicaria during nectar foraging by insects is unlikely. Indeed, lack of discrimination among morphs by potential pollinators may be a key tenet of successful sexual reproduction in tristylous species.

A comparative study of manganese dynamics in the water column and sediments of intertidal systems of the North Sea

The dynamics of the redox-sensitive trace metal manganese (Mn) and its response to biological activity were investigated in the water column and shallow pore waters of the German Wadden Sea (southern North Sea) in 2008 and 2009. Two systems, one from the southern (backbarrier area of Spiekeroog Island) and one from the eastern part (Sylt-Rømø Wadden Sea) of the German Bight were compared. The major aim was to examine to which extent biogeochemical findings are specific for a particular tidal basin or transferable to other basins of the German Wadden Sea.Although both study areas reveal hydrodynamical, sedimentological, and ecological differences, qualitatively pronounced similarities in Mn dynamics are observed. Thus, complex cycling of dissolved Mn with increasing values in spring and late summer due to elevated biological activity as well as a depletion period in early summer were observed in both study areas. This finding suggests a seasonal behaviour of Mn being generally representative for the tidal basins of the southern North Sea. Quantitative differences are significant as the backbarrier area of Spiekeroog Island shows much higher concentrations of dissolved Mn in the water column especially during spring. We suggest that this difference is due to a larger sediment area/water volume ratio in the Spiekeroog backbarrier area combined with a higher release of dissolved Mn from the tidal flat sediments as seen in pore water profiles from surface sediments.Site-specific differences are also seen in further tidal systems of the North Frisian Wadden Sea, which are characterised by individual hydrodynamical and sedimentological conditions. Several transects leading from offshore locations towards the coast also revealed a highly variable Mn level. Overall, the North Frisian Wadden Sea most likely represents a less important source for dissolved Mn than the East Frisian Wadden Sea. Furthermore, our data suggest that site-specific properties of the different tidal basins have to be considered in budget calculations for the entire Wadden Sea.

A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network

The two retroviruses human T-lymphotropic virus type I (HTLV-I) and human immunodeficiency virus type 1 (HIV-1) are the causative agents of severe and fatal diseases including adult T-cell leukemia and the acquired immune deficiency syndrome (AIDS). Both viruses code for a protease that is essential for replication and therefore represents a key target for drugs interfering with viral infection. The retroviral proteases from HIV-1 and HTLV-I share 31% sequence identity and high structural similarities. Yet, their substrate specificities and inhibition profiles differ substantially. In this study, we performed all-atom molecular dynamics (MD) simulations for both enzymes in their ligand-free states and in complex with model substrates in order to compare their dynamic behaviors and enhance our understanding of the correlation between sequence, structure, and dynamics in this protein family. We found extensive similarities in both local and overall protein dynamics, as well as in the energetics of their interactions with model substrates. Interestingly, those residues that are important for strong ligand binding are frequently not conserved in sequence, thereby offering an explanation for the differences in binding specificity. Moreover, we identified an interaction network of contacts between conserved residues that interconnects secondary structure elements and serves as a scaffold for the protein fold. This interaction network is conformationally stable over time and may provide an explanation for the highly similar dynamic behavior of the two retroviral proteases, even in the light of their rather low overall sequence identity.

Variability and dynamics of old-growth forests in the circumboreal zone: implications for conservation, restoration and management

Due to the unprecedented loss of old-growth forests to harvesting throughout circumboreal regions an understanding of similarities and differences in old-growth dynamics is needed to design effective restoration, management and conservation efforts. This paper reviews concepts, prevalence and variability of old-growth forests across landscapes, and evaluates different stand scale dynamics at the old-growth stage across the circumboreal zone. Old-growth historically dominated many boreal forest landscapes in both Eurasia and North America. Throughout much of North America, and to some extent in western Siberia, the natural prevalence and development of old-growth forests are regulated by the occurrence of stand-replacing fires. In eastern North America and Siberia, insect outbreaks may, however, be more important. Insect outbreaks as well as recurrent non-stand replacing surface fires and windthrows, when occurring at the old-growth stage, often form stands characterized by several tree age-class cohorts. This multi age-class forest development type is common in Europe and eastern Siberia but its prevalence and importance in boreal North-America is not well documented. Similarities in successional dynamics across the circumboreal region are found in the development of mono-dominant even-aged stands, the replacement of shade intolerant tree species by shade tolerant species, as well as in all-aged stands driven by small-scale gap dynamics. The message to land managers is that the focus should not only be on setting aside remaining old-growth forests or in restoring static old-growth attributes, but also in emulating natural disturbances and successional dynamics at landscape and regional scales to maintain natural variability in old-growth attributes through time.