The role of miRNAs and endogenous siRNAs in maternal‐to‐zygotic reprogramming and the establishment of pluripotency

RNA silencing is a complex of mechanisms that regulate gene expression through small RNA molecules. The microRNA (miRNA) pathway is the most common of these in mammals. Genome‐encoded miRNAs suppress translation in a sequence‐specific manner and facilitate shifts in gene expression during developmental transitions. Here, we discuss the role of miRNAs in oocyte‐to‐zygote transition and in the control of pluripotency. Existing data suggest a common principle involving miRNAs in defining pluripotent and differentiated cells. RNA silencing pathways also rapidly evolve, resulting in many unique features of RNA silencing in different taxonomic groups. This is exemplified in the mouse model of oocyte‐to‐zygote transition, in which the endogenous RNA interference pathway has acquired a novel role in regulating protein‐coding genes, while the miRNA pathway has become transiently suppressed.     

The small‐scale spatiotemporal pattern of the seedbank and vegetation of a highly invasive weed,Centaurea solstitialis: strength in numbers

The dynamics of invasive plant populations are intriguing and informative of the importance of population and community‐level processes. A dominant approach to understanding and describing invasion has been the development of unique hypotheses to explain invasion. However, here we directly explore the relevance of the small‐scale, spatiotemporal pattern in seedbanks and plants of the highly invasive weed, Centaurea solstitialis, to determine whether pattern can be used to contrast predictions associated with the simple ecological hypotheses of seed versus microsite limitations. At three invaded grasslands in California, highly invaded (> 20 adult plants present), invaded (< 10 adults), and uninvaded (no C. solstitialis plants) sites were selected. The spatial pattern of the seedbank was assessed using fine‐scale, 2 cm diameter contiguous cores and geostatistical statistics, and the number of C. solstitialis seeds in the seedbank was recorded in addition to the total community seedbank density. Three of the four critical predictions associated with the seed limitation hypothesis were clearly supported as an explanation for the patterns of C. solstitialis invasion observed in the field. The density of C. solstitialis seeds decreased from high to low extents of invasion, there was no relationship between the community seedbank and C. solstitialis seeds, and the distances between C. solstitialis plants was inversely related to the density of C. solstitialis seeds. However, both the persistent and transient seedbanks of C. solstitialis were spatially aggregated with autocorrelation up to 12 cm² which suggests that aggregation is a consistent attribute of this species in the seedbank regardless of extent of invasion. This basic pattern‐based approach clearly detected an ecological signal of invasive seedbank dynamics and is thus a useful tool for subsequent studies of invasions in grasslands.     

An idealized model for tree–grass coexistence in savannas: the role of life stage structure and fire disturbances

1.  We discuss a simple implicit-space model for the competition of trees and grasses in an idealized savanna environment. The model represents patch occupancy dynamics within the habitat and introduces life stage structure in the tree population, namely adults and seedlings. A tree can be out-competed by grasses only as long as it is a seedling.
2.  The model is able to predict grassland, forest, savanna and bistability between forest and grassland, depending on the different characteristics of the ecosystem, represented by the model's parameters.
3.  The inclusion of stochastic fire disturbances significantly widens the parameter range where coexistence of trees and grasses is found. At the same time, grass-fire feedback can induce bistability between forest and grassland.
4.   Synthesis . These results suggest that tree–grass coexistence in savannas can be either deterministically stable or stabilized by random disturbances, depending on prevailing environmental conditions and on the types of plant species present in the ecosystem.     

Managing mature forest features: The production,accuracy and ecological relevance of a landscape‐scale map

Mature trees and forests contain structural features such as tree hollows, large coarse woody debris and large spreading crowns that provide critical habitat for a wide range of species. These features can take hundreds of years to develop and require careful management to ensure their continued availability. Managing these features requires spatial mapping layers to facilitate landscape‐scale management. This paper outlines how a map of mature forest habitat was developed for Tasmania, Australia. The map was produced using spatial data on vegetation type, mature crown density and senescence, a global layer of forest loss data derived from satellite imagery, a database on timber harvest plans and a spatial layer on the extent of fire. The relationship between mapped mature habitat availability (high, medium, low or negligible) and tree hollow availability in wet forest areas was explored, complementing a similar published study in dry forests. The number of large trees likely to have hollows significantly increased with mapped mature habitat availability, although there was considerable variation and overlap between map categories. Data from a fauna locality database and two radio‐tracking studies showed that three of the vertebrate hollow‐using species examined (Swift Parrot, Common Brushtail Possum and the Tasmanian Long‐eared Bat) and nest records of a species reliant on large tree crowns (the Wedge‐tailed Eagle) were all more likely to occur in areas of higher mapped mature habitat availability. It is concluded that this map reflects the relative availability of tree hollows, is ecologically meaningful and will be useful when managing mature forest habitat at large spatial scales, but the variable accuracy of the map at fine scales needs to be taken into account.     

A comparison of persistence-time estimation for discrete and continuous stochastic population models that include demographic and environmental variability

A discrete-time Markov chain model, a continuous-time Markov chain model, and a stochastic differential equation model are compared for a population experiencing demographic and environmental variability. It is assumed that the environment produces random changes in the per capita birth and death rates, which are independent from the inherent random (demographic) variations in the number of births and deaths for any time interval. An existence and uniqueness result is proved for the stochastic differential equation system. Similarities between the models are demonstrated analytically and computational results are provided to show that estimated persistence times for the three stochastic models are generally in good agreement when the models satisfy certain consistency conditions.     

Fine‐scale patterns of species and phylogenetic turnover in a global biodiversity hotspot: Implications for climate change vulnerability

Question: What is the relative importance of environmental and spatial factors for species compositional and phylogenetic turnover? Location: High‐rainfall zone of the Southwest Australian Floristic Region (SWAFR). Methods: Correlates of species compositional turnover were assessed using quadrat‐based floristic data, and establishing relationships with environmental and spatial factors using canonical correspondence analyses and Mantel tests. Between‐quadrat phylogenetic distance measures were computed and examined for correlations with environmental and spatial attributes. Processes structuring pa2t2terns of beta diversity were also evaluated within four broad floristic assemblages defined a priori. Results: Floristic diversity was strongly related to environmental attributes. A low significance of spatial variables on assemblage patterns suggested no evident effect of dispersal limitations. Species compositional turnover was especially high within the swamp and outcrop assemblage. Phylogenetic turnover was closely coupled to species compositional turnover, implying the occurrence of many locally endemic and phylogenetically relict taxa. Beta diversity patterns within assemblages were also significantly correlated with the local environment, and relevant correlates differed between floristic assemblage types. Conclusion: Phylogenetic diversity in the SWAFR high‐rainfall zone is clustered within edaphic microhabitats in a generally subdued landscape. A clustered rather than dispersed distribution of phylogenetic diversity increases the probability of significant plant diversity loss during periods of climate change. Climate change susceptibility of the region's flora is accordingly estimated to be high. We highlight the conservation significance of swamp and outcrops that are characterized by distinct hydrological properties and may provide refugial habitat for plant diversity during periods of moderate climate change.     

The ground beetle fauna (Coleoptera:Carabidae) of abandoned fields, as related to plant cover, previous management and succession stage

This study describes differences in species richness, diversity and composition of Carabidae in gradients from recently abandoned, non-grazed fields over stages of overgrowth into forest on formerly agricultural land in a large, sandy outwash plain, south Sweden. Totally 80 pitfall traps, (4 succession stages, each represented by 4 sites; 5 traps per site) installed on 29 March 2006 were emptied continuously until 1 November. Succession stages were: 7–10 y old fallows after cereals with thin and low vegetation of small perennial and annual herbs (Ia), 7–10 y old fallows abandoned as lay with a rich plant cover of broad-leaved grasses and herbs (Ib), 20–25 y old fallows with a shrub layer of colonising pine and narrow-leaved grasses (II), and ca 80 y old pine stands planted on originally cultivated ground with a rich shrub layer but lacking herbaceous plants (III). A total of 14,068 individuals of 71 carabid species were captured. Species richness was highest in stage Ib, whereas Shannon species diversity was highest in Ia. Both species richness and diversity were lowest in III, sites II being intermediate. Total number of individuals captured site⁻¹ was low in III, being highest in Ib. Mean body weight and total dry mass of species, however, increased with succession stage. Amara and Harpalus species were most common in Ia but important also in Ib, with large differences in species composition between the two stages. These genera were almost lacking in III, where Carabus spp. and Pterostichus niger dominated. The share of Calathus was highest in II, where C. fuscipes played a dominating role. P. versicolor dominated in Ib, whereas P. lepidus was quite common in all non-forest stages. Duration and intensity of capturing activity necessary to find most species of the sites are discussed. Many scarce or rare species in south Scandinavia were captured, mainly in Ib. Abandoned non-grazed fields are important hibernating and breeding refuges for many carabids. Using extensive and non-expensive management this ought to be considered as an additional alternative in environment conservation policy, which now usually recommends economically subsidised grazing on set-aside land.     

Validation of the new DSM‐5‐TR criteria for prolonged grief disorder and the PG‐13‐Revised (PG‐13‐R) scale

Although the concept of pathological grief dates back at least as far as Freud’s “Mourning and Melancholia”, there has been opposition to its recognition as a distinct mental disorder. Resistance has been overcome by evidence demonstrating that distinctive symptoms of prolonged grief disorder (PGD) – an attachment disturbance featuring yearning for the deceased, loss of meaning and identity disruption – can endure, prove distressing and disabling, and require targeted treatment. In acknowledgement of this evidence, the American Psychiatric Association Assembly has recently voted to include PGD as a new mental disorder in the DSM‐5‐TR. We tested the validity of the new DSM criteria for PGD and of an adapted version of our PG‐13 scale, the PG‐13‐Revised (PG‐13‐R), designed to map onto these criteria, using data from investigations conducted at Yale University (N=270), Utrecht University (N=163) and Oxford University (N=239). Baseline assessments were performed at 12‐24 months post‐loss; follow‐up assessments took place 5.3‐12.0 months later. Results indicated that the PG‐13‐R grief symptoms represent a unidimensional construct, with high degrees of internal consistency (Cronbach's alpha = 0.83, 0.90 and 0.93, for Yale, Utrecht and Oxford, respectively). The DSM PGD diagnosis was distinct from post‐traumatic stress disorder (phi=0.12), major depressive disorder (phi=0.25) and generalized anxiety disorder (phi=0.26) at baseline. Temporal stability was remarkable for this diagnosis (r=0.86, p<0.001). Kappa agreement between a PG‐13‐R threshold symptom summary score of 30 and the DSM symptom criterion for PGD was 0.70‐0.89 across the datasets. Both the DSM PGD diagnosis and the PG‐13‐R symptom summary score at baseline were significantly associated (p<0.05) with symptoms and diagnoses of major depressive disorder, post‐traumatic stress disorder and/or generalized anxiety disorder, suicidal ideation, worse quality of life and functional impairments at baseline and at follow‐up, in the Yale, Utrecht and Oxford datasets. Overall, the DSM‐5‐TR criteria for PGD and the PG‐13‐R both proved reliable and valid measures for the classification of bereaved individuals with maladaptive grief responses.     

The interaction of gap age and microsite for herb layer species in a near‐natural spruce forest

Question: To what degree does the regeneration of understorey forest species depend on gaps of different age and on gap‐induced and non‐gap‐induced microsites? Do species preferences for a specific microsite change with the developmental stage of the gap? How do different species in the understorey interact over time? Location: Near‐natural spruce forest on Mt. Brocken in the Harz National Park, Germany. Methods: We established 90 study plots, stratified according to different gap age classes and undisturbed forest, and including subplots with three different gap‐induced types of microsites (logs, stumps and root plates) and two non‐gap‐induced microsites (moss‐covered rocks and ordinary forest ground). Results: Significant interactions of species were encountered with gap age as well as with microsite type, light availability and competition. While shoot densities of Vaccinium myrtillus were highest at intermediate gap age, Calamagrostis villosa and Trientalis europaea showed highest densities in the oldest gaps. The species preferred different microsites but had higher densities on non‐gap‐induced microsites, and their preferences changed over time. Unexpectedly, species shoot densities were not always negatively affected by densities of competing species. Conclusion: The results confirmed the importance of gaps for regeneration of forest herb layer species, but pointed to a much higher importance of microsites that were not induced by gaps compared to gap‐induced microsites. Niche differentiation between different herb layer species can be conceived as species‐specific preferences for microsite types that change with gap age, as a result of light conditions, degree of decay of logs and root plates and presence of competitors.     

Genetic variation in herbivore resistance and tolerance: the role of plant life‐history stage and type of damage

Information of the patterns of genetic variation in plant resistance and tolerance against herbivores and genetic trade‐offs between these two defence strategies is central for our understanding of the evolution of plant defence. We found genetic variation in resistance to two specialist herbivores and in tolerance to artificial damage but not to a specialist leaf herbivore in a long‐lived perennial herb. Seedlings tended to have genetic variation in tolerance to artificial damage. Genetic variation in tolerance of adult plants to artificial damage was not consistent in time. Our results suggest that the level of genetic variation in tolerance and resistance depends on plant life‐history stage, type of damage and timing of estimating the tolerance relative to the occurrence of the damage, which might reflect the pattern of selection imposed by herbivory. Furthermore, we found no trade‐offs between resistance and tolerance, which suggests that the two defence strategies can evolve independently.     

Centennial‐scale changes to the aquatic vegetation structure of a shallow eutrophic lake and implications for restoration

1. We investigate long‐term (>200 years) changes to the composition and spatial structure of macrophyte communities in a shallow, eutrophic lake (Barton Broad, eastern England) and consider the implications for lake restoration. 2. Historical macrophyte data were assembled from a variety of sources: existing plant databases, museum herbaria, journal articles, old photographs and eyewitness accounts. Additionally, two types of sediment core sample were analysed for plant macro‐remains and pollen; bulk basal samples from multiple core sites analysed to provide information on ‘pre‐disturbance’ macrophyte communities and two whole cores analysed to determine historical change. 3. Prior to the late 1800s, macrophyte communities were diverse and included a multilayered mosaic of short‐stature submerged taxa and taller submerged and floating‐leaved species. With the progression of eutrophication after around 1900, the former community was displaced by the latter. Diversity was maintained, however, since an encroaching Schoenoplectus–nymphaeid swamp generated extensive patches of low‐energy habitat affording refugia for several macrophytes otherwise unable to withstand the hydraulic forces associated with open water conditions. When this swamp vegetation disappeared in the 1950s, many of the ‘dependent’ aquatic macrophytes also declined leaving behind a sparse, species‐poor community (as today) resilient to both eutrophication and turbulent open waters. 4. The combination of historical and palaeolimnological data sources offers considerable benefits for reconstructing past changes to the aquatic vegetation of lakes and for setting restoration goals. In this respect, our study suggests that successful restoration might often be better judged by reinstatement of the characteristic structure of plant communities than the fine detail of species lists; when nutrients are low and the structure is right, the right species will follow.     

The distribution and environmental state of vegetated islands within human‐impacted European rivers

1. Vegetated islands within river corridors are pivotal landscape features and are among the first to disappear as a consequence of flow regulation and channelisation. However, how vegetated islands vary along human‐impacted rivers is poorly understood. 2. We carried out a detailed analysis of the contemporary distribution, diversity and environmental state of vegetated islands within 12 human‐impacted European rivers, using 75 Landsat 7 ETM+ satellite images (1999–2002), historical maps, DEM data and landscape metrics. We tested whether channel fragmentation, catchment land use and the environmental state of fringing floodplains determine the spatial patterns of the islands. We also analysed the historical change of islands within selected sections of the Upper Danube, Upper Rhine and Olt rivers. 3. We identified 2771 islands in the contemporary landscape, varying from 0.06 to 9828 ha. Islands covered up to 21% of the active channel area and contributed up to 32% of the total riparian ecotone length. Island density ranged from 0.06 islands per river‐km (River Sava) to 1.6 islands per river‐km (River Tagliamento). River regulation has led to a marked loss of island density: 94% in the Upper Danube, 93% in the Upper Rhine, and 69% in the Olt. The environmental state of the islands was significantly less altered by human activity than of their fringing floodplains; 93.4% of the vegetated islands exhibited a near‐natural state, while 86% of the fringing floodplains were expansively converted to agricultural and urban land uses. 4. Our results highlight the ubiquitous presence of vegetated islands, their sensitivity to river regulation and their pivotal role for the future restoration and management of river corridors.     

Evaluation of options for harvest of a recombinant E. Coli fermentation producing a domain antibody using ultra scale‐down techniques and pilot‐scale verification

Ultra scale‐down (USD) methods operating at the millilitre scale were used to characterise full‐scale processing of E. coli fermentation broths autolysed to different extents for release of a domain antibody. The focus was on the primary clarification stages involving continuous centrifugation followed by depth filtration. The performance of this sequence was predicted by USD studies to decrease significantly with increased extents of cell lysis. The use of polyethyleneimine reagent was studied to treat the lysed cell broth by precipitation of soluble contaminants such as DNA and flocculation of cell debris material. The USD studies were used to predict the impact of this treatment on the performance and here it was found that the fermentation could be run to maximum productivity using an acceptable clarification process (e.g., a centrifugation stage operating at 0.11 L/m² equivalent gravity settling area per hour followed by a resultant required depth filter area of 0.07 m²/L supernatant). A range of USD predictions was verified at the pilot scale for centrifugation followed by depth filtration. © 2016 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 32:382–392, 2016     

Response of three lotic assemblages to riparian and catchment‐scale land use: implications for designing catchment monitoring programmes

1. Although many studies have focussed on the effects of catchment land use on lotic systems, the importance of broad (catchment) and fine (segment/reach) scale effects on stream assemblages remain poorly understood. 2. Nine biological metrics for macrophytes (498 sites), benthic macroinvertebrates (491) and fish (478) of lowland and mountain streams in four ecoregions of France and Germany were related to catchment and riparian buffer land use using partial Redundancy Analysis and Boosted Regression Trees (BRTs). 3. Lotic fauna was better correlated (mean max., r = 0.450) than flora (r = 0.277) to both scales of land use: the strongest correlations were noted for mountain streams. BRTs revealed strong non‐linear relationships between mountain assemblage metrics and land use. Correlations increased with increasing buffer lengths, suggesting the importance of near‐stream land use on biotic assemblages. 4. Several metrics changed markedly between 10–20% (mountain ecoregions) and 40–45% (lowland) of arable land use, irrespective of the buffer size. At mountain sites with >10% catchment arable land use, metric values differed between sites with <30% and sites with >30% forest in the near‐stream riparian area. 5. These findings support the role of riparian land use in catchment management; however, differences between mountain and lowland ecoregions support the need for ecoregion‐specific management.     

The role of small ground‐foraging mammals in topsoil health and biodiversity: Implications to management and restoration

Summary Many early Australian records indicate that at the time of European settlement there were extensive tracts of highly productive, and species‐rich, grassy communities and chenopod shrublands. Topsoils in many areas were soft and friable. The rapid development of livestock industries led to most changes to the environment being simplistically ascribed to domestic stock grazing, land clearance, introduced pests (such as rabbits) or changed burning practices. It has also commonly been assumed that the hoof action of domestic stock was the principal cause of the compaction and surface sealing of soils in many areas. However, the rapid soil deterioration also coincided with the dramatic decline or complete extinction of many small native ground‐foraging mammals and the consequent cessation of the soil disturbances and interactions that they created. This paper reviews the role of small mammals in disturbing soils, and implications for incorporation of organic matter, aeration, improvement in infiltration and the provision of suitable sites for seed germination and seedling establishment. This can aid topsoil formation and health by providing substrate for microorganisms, improved water balance and mineral cycles and enhanced soil structure. Seeds and mycorrhizal fungi, that are integral to the establishment and growth of many plants, are spread. Such intermittent disturbance may be an important driving force in determining the pathway of succession and lead to greater biodiversity. Further ongoing research on Australia's small mammals is needed, especially in areas where they are able to move freely in a natural environment and are protected from introduced predators.     

Towards eradication: The history and management of Bitou Bush on K'gari‐Fraser Island,Australia

Persistence and dedication over the long term has been a key to success in control of this Weed of National Significance on World Heritage Listed K'gari‐Fraser Island in Queensland, Australia. Systematic surveys and treatment show that the goal of Bitou Bush eradication is worthwhile and can inspire other such projects within the region and beyond.     

The role of Wnt/β‐catenin signaling in proliferation and regeneration of the developing basilar papilla and lateral line

Canonical Wnt/β‐catenin signaling has been implicated in multiple developmental events including the regulation of proliferation, cell fate, and differentiation. In the inner ear, Wnt/β‐catenin signaling is required from the earliest stages of otic placode specification through the formation of the mature cochlea. Within the avian inner ear, the basilar papilla (BP), many Wnt pathway components are expressed throughout development. Here, using reporter constructs for Wnt/β‐catenin signaling, we show that this pathway is active throughout the BP (E6‐E14) in both hair cells (HCs) and supporting cells. To characterize the role of Wnt/β‐catenin activity in developing HCs, we performed gain‐ and loss‐of‐function experiments in vitro and in vivo in the chick BP and zebrafish lateral line systems, respectively. Pharmacological inhibition of Wnt signaling in the BP and lateral line neuromasts during the periods of proliferation and HC differentiation resulted in reduced proliferation and decreased HC formation. Conversely, pharmacological activation of this pathway significantly increased the number of HCs in the lateral line and BP. Results demonstrated that this increase was the result of up‐regulated cell proliferation within the Sox2‐positive cells of the prosensory domains. Furthermore, Wnt/β‐catenin activation resulted in enhanced HC regeneration in the zebrafish lateral line following aminoglycoside‐induced HC loss. Combined, our data suggest that Wnt/β‐catenin signaling specifies the number of cells within the prosensory domain and subsequently the number of HCs. This ability to induce proliferation suggests that the modulation of Wnt/β‐catenin signaling could play an important role in therapeutic HC regeneration. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 74: 438–456, 2014