Diversity of fish species in the trawl catches in the southeastern Barents Sea in 1980–2008

Analysis of trawl catches in the southeastern Barents Sea was performed for the period of 1980–2008. One lamprey and 48 fish species were defined, including 38 marine fish species, 8 anadromous and amphidromous species, and 1 freshwater species. The ichthyofauna of several areas of the southeastern Barents Sea was described (Cheshskaya Inlet, Pomorskiy Strait, southeastern Pechora Sea, Pechora Sea, Khaipudyrskaya Inlet and adjacent areas). Biodiversity indexes and Shannon Index were applied to describe the species diversity. Cluster analysis was applied to compare the species lists from different areas. Multiyear dynamics of ichthyofauna was studied. The tendency of geographical range expansion eastward was observed for boreal species.     

Variation in the methods leads to variation in the interpretation of biodiversity–ecosystem multifunctionality relationships

生物多样性常常和生态系统多功能性(生态系统同时提供多个生态系统功能的能力)正相关。然而,生物多样性与生态系统多功能性的关系是否依赖于生态系统功能的数目有诸多争议。其中,生物多样性对生态系统多功能性的影响或许不随生态系统功能数目的变化而变化,或者随生态系统功能数目的增多而增强。我们期望通过研究不同生态系统多功能性指数的统计原理来解决这些争议。 我们使用了模型模拟和一系列来自不同空间尺度(从局域到全球)和不同生物群系(温带和高寒草地、森林和干旱地)的经验数据。我们回顾了量化生态系统多功能性的三种方法,包括平均值法、加和法和阈值法。我们发现随着生态系统功能数目的增加,生物多样性与生态系统多功能性的关系要么不变,要么增强。这些结果可由平均和加和的多功能性指数的统计原理来解释。具体来讲,当利用生态系统功能的平均值计算多功能性指数时,由于多样性对多功能性的效应等于多样性对单个生态系统功能效应的平均值,所以不会随生态系统功能数目的变化而变化。同样的道理,当利用单个生态系统的加和值计算多功能性指数时,多样性的效应会随着生态系统功能数目的增加而增强。我们提出了一个改进的多功能性指数,将平均或加和多功能性指数转化为标准化的多功能性指数, 以便于对不同研究的结果进行比较。此外,我们提出了基于变量数值范围的标准化方法来解决阈值法的数学假象问题(多样性效应随生态系统功能数目的增加而增强)。我们的研究结果表明,量化多功能性指数的方法不同,结果也不同。因此,有必要加深对不同方法数理基础的理解。而标准化的多功能性指数为比较不同研究中的生物多样性与生态系统多功能性的关系提供了有效的方法。     

Comparison of the Higher-Severity Fire Regime in Historical (A.D. 1800s) and Modern (A.D. 1984–2009) Montane Forests Across 624,156?ha of the Colorado Front Range

There are concerns that recent fires, following a century of land uses, are burning in dry western forests in an uncharacteristic manner with large patches of higher-severity fire affecting long-term ecosystem dynamics. For example, it is well documented that a mixed-severity fire regime predominated over montane forests of the Colorado Front Range. However, much about the historical fire regime is unknown including the size, frequency, and distribution of higher-severity fires. We addressed these questions utilizing data from the original land surveyors who recorded locations of burned timber along survey lines resulting in a coarse-scale transect of fire occurrence across 624,156?ha. We reconstructed higher-severity burn patches, size distribution, and fire rotation for the 1800s (A.D. 1809–1883) and compared to the characteristics of modern fires over a recent 26-year period (A.D. 1984–2009) taken from remotely sensed data. We found the historical geometric mean higher-severity patch was 170.9?ha and the maximum patch size was 8,331?ha; the higher-severity fire rotation was 248.7?years. In addition, we confirmed that higher-severity fires were historically less common at elevations below 2,200?m. Modern fires had a geometric mean patch size of 90.0?ha (patches >20?ha) and a maximum size of 5,183?ha; the higher-severity fire rotation was 431?years. The distributions of higher-severity patches were only 63.5% similar, as the historical distribution had fewer small patches and more large patches. The mixed-severity fire regime, historically, included a significant portion of higher-severity fire and large burn patches; modern fires appear to be within the range of historical variability.     

Untangling structure–function relationships in the rhomboid family of intramembrane proteases

Rhomboid proteases are a family of integral membrane proteins that have been implicated in critical regulatory roles in a wide array of cellular processes and signaling events. The determination of crystal structures of the prokaryotic rhomboid GlpG from Escherichia coli and Haemophilus influenzae has ushered in an era of unprecedented understanding into molecular aspects of intramembrane proteolysis by this fascinating class of protein. A combination of structural studies by X-ray crystallography, and biophysical and spectroscopic analyses, combined with traditional enzymatic and functional analysis has revealed fundamental aspects of rhomboid structure, substrate recognition and the catalytic mechanism. This review summarizes these remarkable advances by examining evidence for the proposed catalytic mechanism derived from inhibitor co-crystal structures, conflicting models of rhomboid-substrate interaction, and recent work on the structure and function of rhomboid cytosolic domains. In addition to exploring progress on aspects of rhomboid structure, areas for future research and unaddressed questions are emphasized and highlighted. This article is part of a Special Issue entitled: Intramembrane Proteases.     

Tree rings reveal a growth-decline event in A.D. 1875–1883 in a Tibetan plateau juniper forest

Forest declines under global warming have received much attention in studies of forest ecology, yet such events in periods before climate warming have been less studied because of shortage in documentation of past decline events. Here we used dendroecological techniques to identify forest decline events in the past five and a half centuries for a juniper forest near Lhasa of Tibet, China. Data of tree ring-widths were obtained from 42 relatively old trees after sample collection, measurement and crossdating. Radial growth of these trees was significantly and positively correlated with total precipitation in May and June. Persistent and severe growth reductions, lasting for at least eight years, were identified for each sample. We found that greater than 35% of the trees exhibited persistent and severe growth reductions in the interval A.D. 1875–1883, suggesting a growth decline event in the forest. This growth decline was the most severe event in the past five and half centuries. The weakened Indian monsoon in A.D. 1875–1878, which would result in extreme and prolonged droughts at spatially large scale in the monsoon zone, was most likely the driving force for the forest decline event discovered in this study. Our results suggested that future risk of juniper forest declines in central Tibetan plateau will be related to extreme droughts which could be amplified by warming. The study highlighted the importance of examining growth trajectory of individual trees in assessing forest health in a long perspective.     

Isometric torque–angle relationships of the elbow flexors and extensors in the transverse plane

Maximal voluntary isometric torque–angle relationships of elbow extensors and flexors in the transverse plane (humerus elevation angle of 90°) were measured at two different horizontal adduction angles of the humerus compared to thorax: 20° and 45°. For both elbow flexors and extensors, the torque–angle relationship was insensitive to this 25° horizontal adduction of the humerus. The peak in torque–angle relationship of elbow extensors was found at 55° (0° is full extension). This is closer to full elbow extension than reported by researchers who investigated this relationship in the sagittal plane. Using actual elbow angles during contraction, as we did in this study, instead of angles set by the dynamometer, as others have done, can partly explain this difference.We also measured electromyographic activity of the biceps and triceps muscles with pairs of surface electrodes and found that electromyographic activity level of the agonistic muscles was correlated to measured net torque (elbow flexion torque: Pearson’s r = 0.21 and extension torque: Pearson’s r = 0.53). We conclude that the isometric torque–angle relationship of the elbow extensors found in this study provides a good representation of the force–length relationship and the moment arm–angle relationship of the elbow extensors, but angle dependency of neural input gives an overestimation of the steepness.     

Evaluation of the importance of roe deer fawns in the spring–summer diet of red foxes in southeastern Norway

Red fox Vulpes vulpes predation on roe deer Capreolus capreolus fawns has the potential to strongly affect prey population dynamics, but it is unclear whether this relationship is symmetrical or not. We analysed the spring–summer diet of adult foxes and of their cubs in a fragmented agricultural area of southeastern Norway, where a parallel study showed that the predator kills annually 25% of the radio-monitored roe deer fawns. The overall diet was highly varied and was dominated by small mammals (33% volume), especially Microtus agrestis, and medium-large mammals (25%), largely represented by fawns. The frequency of occurrence (FO) of fawns in the diet of adult foxes was highest in early spring, thus, supporting previous studies showing that the predator started actively hunting for fawns from the very beginning of the birth season. During the summer, the FO of both fawns and small mammals markedly declined, while that of berries and invertebrates increased. As expected for central-place foragers, cubs consumed a higher proportion of large prey items compared to adults. In particular, 25% of scats from cubs—versus 9% from adults—contained roe deer remains, suggesting a high profitability of fawns for vixens raising offspring. However, considering the wide food spectrum and the availability of several large prey items in our study area, it seems unlikely that the importance of fawns to the diet and population dynamics of red foxes could be as great as the impact of the predator on roe deer populations. This asymmetrical relationship implies that there are unlikely to be any stabilising feedback mechanisms in the predator–prey relationship.     

A preliminary fish assemblage index for a transitional river–reservoir system in southeastern Brazil

Large river–reservoir systems are some of the most difficult aquatic ecosystems to assess because: (1) they typically lack minimally disturbed reference sites; (2) the reservoirs are not natural systems to begin with; and (3) reservoirs with high exchange rates are transitional systems between rivers and lakes. These features are further complicated in Brazil where fish species taxonomy is incomplete (let alone fully described ecologically), where waters naturally have high organic and thermal loadings, and where dams and reservoirs provide most of the nation's electricity and water supplies. As a first step towards generating a biological tool for assessing the effects of reservoirs on rivers, we developed a preliminary River–Reservoir Fish Assemblage Index (RRFAI) in a transitional river–reservoir system in southeastern Brazil. To do so, we gill-netted fish monthly between October 2006 and September 2007 (excluding May and July 2007) immediately upriver of the reservoir, in the upper reservoir, in the lower reservoir, and immediately downriver of the reservoir. In developing our RRFAI we sought fish assemblage metrics to represent ecological characteristics including richness, habitat, trophic, tolerance, and resilience guilds. Despite clear differences in fish assemblage composition between river and reservoir sites, we found 9 metrics common to both systems that were nonredundant and had low sampling variability (number of native species, number of characiform species, number of siluriform species, % omnivorous individuals, % invertivorous individuals, % non-native carnivorous individuals, % intolerant individuals, % tolerant individuals, number of tolerant species). Fish assemblage condition was significantly and consistently lower in the lower reservoir. There was no significant difference between the dry and wet season in RRFAI scores, suggesting that a single season sample should usually suffice. Further research is needed along distinct disturbance gradients in multiple river–reservoir systems in Brazil to confirm the sensitivity of our preliminary RRFAI for assessing the physical and chemical habitat disturbances common to such systems.     

Structure–function relationships in the bifunctional ferrisiderophore FpvA receptor from Pseudomonas aeruginosa

FpvA is the primary outer membrane transporter required for iron acquisition via the siderophore pyoverdine (Pvd) in Pseudomonas aeruginosa. FpvA, like other ferrisiderophore transporters, consists of a membrane-spanning β-barrel occluded by a plug domain. The β-strands of the barrel are connected by large extracellular loops and periplasmic turns. Like some other TonB-dependent transporters, FpvA has a periplasmic domain involved in a signalling cascade that regulates expression of genes required for ferrisiderophore transport. Here, the structures of FpvA in different loading states are analysed in light of mutagenesis data. This analysis highlights the roles of different protein domains in Pvd-Fe uptake and the signalling cascade and reveals a strong correlation between Pvd-Fe transport and activation of the signalling cascade. It is likely that conclusions drawn for FpvA will be relevant to other TonB-dependent ferrisiderophore transport and signalling proteins.     

A preliminary reconstruction (A.D. 1635–2000) of spring precipitation using oak tree rings in the western Black Sea region of Turkey

Tree-ring data for Turkey are crucial to the understanding of the climatological effect of drought and rainfall from one era to the next. To this end, the present study reconstructed precipitation patterns in the western Black Sea region of Turkey. Tree-ring widths of oak trees were used to reconstruct March–June precipitation patterns for the years A.D. 1635–2000. According to the findings, during the past four centuries drought events in this region persisted for no more than 2 years, and extreme dry and wet events occurred generally in 1-year intervals. Historical records of droughts in Anatolia and neighboring countries corroborate the data furnished by tree-ring widths to indicate that major droughts and famine events occurred in 1725, 1757, 1887, 1890–1891, 1893–1894 and 1927–1928.     

Structure–function relationships in HIV-1 Nef

The accessory Nef protein of HIV and SIV is essential for viral pathogenesis, yet it is perplexing in its multitude of molecular functions. In this review we analyse the structure–function relationships of motifs recently proposed to play roles in aspects of Nef modification, signalling and trafficking, and thereby to impinge on the ability of the virus to survive in, and to manipulate, its cellular host. Based on the full-length structure assembly of HIV Nef, we correlate surface accessibility with secondary structure elements and sequence conservation. Motifs involved in Nef-mediated CD4 and MHC I downregulation are located in flexible regions of Nef, suggesting that the formation of the transient trafficking complexes involved in these processes depends on the recognition of primary sequences. In contrast, the interaction sites for signalling molecules that contain SH3 domains or the p21-activated kinases are associated with the well folded core domain, suggesting the recognition of highly structured protein surfaces.     

Male–male relationships in chimpanzees and the evolution of human pair bonds

The evolution of monogamy has been a central question in biological anthropology. An important avenue of research has been comparisons across “socially monogamous” mammals, but such comparisons are inappropriate for understanding human behavior because humans are not “pair living” and are only sometimes “monogamous.” It is the “pair bond” between reproductive partners that is characteristic of humans and has been considered unique to our lineage. I argue that pair bonds have been overlooked in one of our closest living relatives, chimpanzees. These pair bonds are not between mates but between male “friends” who exhibit enduring and emotional social bonds. The presence of such bonds in male–male chimpanzees raises the possibility that pair bonds emerged earlier in our evolutionary history. I suggest pair bonds first arose as “friendships” and only later, in the human lineage, were present between mates. The mechanisms for these bonds were co-opted for male-female bonds in humans.     

Species–area relationships in the Hantam-Tanqua-Roggeveld,Succulent Karoo,South Africa

The Hantam-Tanqua-Roggeveld subregion is part of the Succulent Karoo hotspot of biodiversity which stretches along the southwestern side of South Africa and Namibia. Forty Whittaker plots were surveyed in the spring of 2005, in eight vegetation associations, to gather diversity data for the Hantam, Tanqua Karoo and Roggeveld areas. Seven plot sizes were used to construct species–area curves using three different models namely: the untransformed linear function, the power function and the exponential function. In general, the power and exponential functions produced a more significant fit to the data than the untransformed linear function. Linear regressions using environmental parameters indicated that altitude, mean annual precipitation and mean annual temperature were significant predictors of species richness at the 1, 10, 100 and 1000 m² scales. To illustrate the variation in species–area curves and species richness across the landscape, a transect through the study area is discussed. The transect stretches eastwards from the Tanqua Karoo across the escarpment into the Roggeveld and crosses five different vegetation associations. Differences between associations were found in species richness in the 1000 m² plots. Each association also produced species–area curves with their own characteristics. Slope values for the samples within an association did not differ significantly, although the intercept value often did. Comparisons between associations along the transect revealed significant differences in the slope value between the associations, except for the Dicerothamnus rhinocerotis Mountain Renosterveld which did not differ significantly from the associations bordering it on either side.     

Structure–function relationships of the antigenicity of mycolic acids in tuberculosis patients

Cell wall mycolic acids (MA) from Mycobacterium tuberculosis (M.tb) are CD1b presented antigens that can be used to detect antibodies as surrogate markers of active TB, even in HIV coinfected patients. The use of the complex mixtures of natural MA is complicated by an apparent antibody cross-reactivity with cholesterol. Here firstly we report three recombinant monoclonal scFv antibody fragments in the chicken germ-line antibody repertoire, which demonstrate the possibilities for cross-reactivity: the first recognized both cholesterol and mycolic acids, the second mycolic acids but not cholesterol, and the third cholesterol but not mycolic acids. Secondly, MA structure is experimentally interrogated to try to understand the cross-reactivity. Unique synthetic mycolic acids representative of the three main functional classes show varying antigenicity against human TB patient sera, depending on the functional groups present and on their stereochemistry. Oxygenated (methoxy- and keto-) mycolic acid was found to be more antigenic than alpha-mycolic acids. Synthetic methoxy-mycolic acids were the most antigenic, one containing a trans-cyclopropane apparently being somewhat more antigenic than the natural mixture. Trans-cyclopropane-containing keto- and hydroxy-mycolic acids were also found to be the most antigenic among each of these classes. However, none of the individual synthetic mycolic acids significantly and reproducibly distinguished the pooled serum of TB positive patients from that of TB negative patients better than the natural mixture of MA. This argues against the potential to improve the specificity of serodiagnosis of TB with a defined single synthetic mycolic acid antigen from this set, although sensitivity may be facilitated by using a synthetic methoxy-mycolic acid.     

Temporally variable macroinvertebrate–stone relationships in streams

Stones were used to sample macroinvertebrates and characterise microhabitats at monthly or bimonthly intervals in six Ecuadorian streams covering a gradient in four different stability measures and other stream characteristics. The physical variables current velocity, water depth, horizontal position, embeddedness and size were measured to characterise stone microhabitats and presumed to be affected by or related to physical impact during hydrological disturbances. My first objective was to analyse how density, the number of families and a richness measure (residuals from a power regression of families vs. individuals) were related to the physical characteristics of individual stone habitats. My second objective was to quantify temporal variability in fauna–stone relationships and to analyse if such variability was related to overall stability of stream reaches. Partial Least Squares (PLS) multiple regression analyses showed high temporal variability between sampling dates in factor loadings of specific stone micro habitat variables. In spite of this, there was a clear negative effect of depth and a positive effect of current on density and number of families. Stone size was consistently negatively related to density and positively related to number of families. Patterns were less clear for richness residuals. Simple linear regressions of fauna vs. stone parameters generally confirmed the results reached by the PLS analysis, although few of the regressions were significant. For all fauna–stone regressions the variability in slopes was much higher among sampling dates within streams (temporal variability) than among streams (spatial variability), and significant slopes were even inverted on different sampling dates. Although the coefficients of variation (CV) of slopes of a given combination of fauna parameter and stone variable from different sampling dates (n=9–11) were rarely correlated to any of the measures of stream stability, this study has demonstrated high temporal variability in fauna–stone relationships (CV’s of regression slopes). Consequently, temporally un-replicated studies of such relationships do not necessarily reveal general patterns.     

A. A. Ukhtomskiĭ's ideas in studies on the cognitive activity

Experimental data on spatial and temporal organisation of the human EEG from birth to maturity, at resting and during cognitive activity, is presented. The data obtained is interpreted in light of a confirmation of the Ukhtomsky's ideas on the "functional working organ" appearing in the brain for realising cognitive processes. Role of the alpha-rhythm in formation of plastic intracortical neuronal network is elucidated. A hypothesis is advanced stating that the gradually developing brain system exerting a local regulated activating effects upon the cortical level, is a significant factor of the functional intercentre integration.     

Molecular characterization and phylogenetic relationships of a protein with potential oxygen-binding capabilities in the grasshopper embryo. A hemocyanin in insects?

Arthropodan hemocyanins, prophenoloxidases (PPOs), and insect hexamerins form a superfamily of hemolymph proteins that we propose to call the AHPH superfamily. The evolutionary and functional relationships of these proteins are illuminated by a new embryonic hemolymph protein (EHP) that is expressed during early stages of development in the grasshopper embryo. EHP is a 78-kDa soluble protein present initially in the yolk sac content, and later in the embryonic hemolymph. Protein purification and peptide sequencing were used to identify an embryonic cDNA clone coding for EHP. In situ hybridization identifies hemocytes as EHP-expressing cells. As deduced from the cDNA clone, EHP is a secreted protein with two potential glycosylation sites. Sequence analysis defines EHP as a member of the AHPH superfamily. Phylogenetic analyses with all the currently available AHPH proteins, including EHP, were performed to ascertain the evolutionary history of this protein superfamily. We used both the entire protein sequence and each of the three domains present in the AHPH proteins. The phylogenies inferred for each of the domains suggest a mosaic evolution of these protein modules. Phylogenetic and multivariate analyses consistently group EHP with crustacean hemocyanins and, less closely, with insect hexamerins, relative to cheliceratan hemocyanins and PPOs. The grasshopper protein rigorously preserves the residues involved in oxygen binding, oligomerization, and allosteric regulation of the oxygen transport proteins. Although insects were thought not to have hemocyanins, we propose that EHP functions as an oxygen transport or storage protein during embryonic development.      

A trait-based experimental approach to understand the mechanisms underlying biodiversity–ecosystem functioning relationships

Plant functional characteristics may drive plant species richness effects on ecosystem processes. Consequently, the focus of biodiversity–ecosystem functioning (BEF) experiments has expanded from the manipulation of plant species richness to manipulating functional trait composition. Involving ecophysiological plant traits in the experimental design might allow for a better understanding of how species loss alters ecosystem processes. Here we provide the theoretical background, design and first results of the ‘Trait-Based Biodiversity Experiment’ (TBE), established in 2010 that directly manipulates the trait composition of experimental plant communities.Analysis of six plant traits related to resource acquisition and use were analyzed using principal component analysis of 60 grassland species. The resulting two main axes describe gradients in functional similarity, and were used as the basis for designing plant communities with different functional and species diversity levels. Using such an approach allowed us to manipulate different levels of complementarity in spatial and temporal plant resource acquisition. In contrast to previous biodiversity experiments, the TBE is designed according to more realistic scenarios of non-random species loss along orthogonal axes of species trait dissimilarities. This allows us to tease apart the relative importance of selection and complementarity effects on multiple ecosystem processes, and to mechanistically study the consequences of plant community simplification.     

Holocene paleoenvironments in southeastern Minnesota – chasing the prairie-forest ecotone

This paper uses a multi-proxy approach involving pollen, plant macrofossils, speleothem isotopes, and alluvial history of streams to reconstruct the history of prairie expansion and contraction along the prairie-forest border of southeastern Minnesota, USA. Early Holocene forests were replaced by prairie along this border, but eastward expansion of prairie stalled for 2000 yr when the prairie-forest ecotone stabilized. Prairie invaded the area from the west 8000–9000 yr B.P., but mesic forest remained less than 100 km to the east until about 6000 yr B.P. Changes in δ¹³C values in speleothem calcite, that reflect the rise of C₄ grasses, correlate well with the presence of C₄ grass species identified in the plant macrofossil record. Periods of large floods correlate with speleothem evidence of dry summers, increased cool-season precipitation (both resulting in less plant cover to absorb moisture), and change to prairie vegetation.