High-Resolution Genomic Profiling of Chromosomal Abnormalities in Human Stem Cells Using the 135 K StemArray

Culturing stem cells for an extended period of time can lead to acquired chromosomal aberrations. Determining the copy number variant (CNV) profile of stem cell lines is critical since CNVs can have dramatic effects on gene expression and tumorigenic potential. Here, we describe an improved version of our StemArray, a stem-cell-focused comparative genomic hybridization (aCGH) microarray, which contains 135,000 probes and covers over 270 stem cell and cancer related genes at the exon level. We have dramatically increased the median probe spacing throughout the genome in order to obtain a higher resolution genetic profile of the cell lines. To illustrate the importance of using the StemArray, we describe a karyotypically normal iPSC line in which we detected acquired chromosomal variations that could affect the cellular phenotype of the cells. Identifying adaptive chromosomal aberrations in stem cell lines is essential if they are to be used in regenerative medicine

Liana abundance, diversitty and tree infestation in the Imbak Canyon conservation Area, Sabah, malaysia

We investigated the liana diversity and liana–tree relationship in lowland dipterocarp forest at Imbak Canyon, a recently designated conservation area in the heart of Sabah, Malaysia and compared the results with similar studies in the region. In the two 0.1-ha plots, a total of 23 liana species were found growing canopy-ward on trees ≥ 10 cm diameter at breast height (dbh); dipterocarps were less infested by lianas than non-dipterocarps. The liana species belonged to 12 families and 16 genera. Fabaceae followed by Annonaceae and Icacinaceae were the most abundant and species-rich families. The floristic pattern and the stem density of lianas > 1 cm dbh were similar to other studies conducted in Sabah and northern Sarawak at comparable elevation and site conditions but were distinct from other sites in tropical Asia where Annonaceae is the prevalent climber family. The dominance of species of the genus Spatholobus (Fabaceae) may be a conspicuous feature of lowland dipterocarp forests in Sabah under mesotrophic conditions

Development of forest structure and leaf area in secondary forests regenerating on abandoned pastures in Central Amazonia

The area of secondary forest (SF) regenerating from pastures is increasing in the Amazon basin; however, the return of forest and canopy structure following abandonment is not well understood. This study examined the development of leaf area index (LAI), canopy cover, aboveground biomass, stem density, diameter at breast height (DBH), and basal area ( BA) by growth form and diameter class for 10 SFs regenerating from abandoned pastures. Biomass accrual was tree dominated, constituting >= 94% of the total measured biomass in all forests abandoned >= 4 to 6 yr. Vine biomass increased with forest age, but its relative contribution to total biomass decreased with time. The forests were dominated by the tree Vismia spp. (> 50%). Tree stem density peaked after 6 to 8 yr ( 10 320 stems per hectare) before declining by 42% in the 12- to 14-yr-old SFs. Small-diameter tree stems in the 1-5-cm size class composed > 58% of the total stems for all forests. After 12 to 14 yr, there was no significant leaf area below 150-cm height. Leaf area return (LAI = 3.2 after 12 to 14 yr) relative to biomass was slower than literature-reported recovery following slash-and-burn, where LAI can reach primary forest levels ( LAI = 4 - 6) in 5 yr. After 12 to 14 yr, the colonizing vegetation returned some components of forest structure to values reported for primary forest. Basal area and LAI were 50% - 60%, canopy cover and stem density were nearly 100%, and the rapid tree-dominated biomass accrual was 25% - 50% of values reported for primary forest. Biomass accumulation may reach an asymptote earlier than expected because of even-aged, monospecific, untiered stand structure. The very slow leaf area accumulation relative to biomass and to reported values for recovery following slash-and-burn indicates a different canopy development pathway that warrants further investigation of causes ( e. g., nutrient limitations, competition) and effects on processes such as evapotranspiration and soil water uptake, which would influence long-term recovery rates and have regional implications

The neotropical reforestation hotspots : a biophysical and socioeconomic typology of contemporary forest expansion

Tropical reforestation is a significant component of global environmental change that is far less understood than tropical deforestation, despite having apparently increased widely in scale during recent decades. The regional contexts defining such reforestation have not been well described. They are likely to differ significantly from the geographical profiles outlined by site-specific observations that predominate in the literature. In response, this article determines the distribution, extent, and defining contexts of apparently spontaneous reforestation. It delineates regional ‘hotspots’ of significant net reforestation across Latin America and the Caribbean and defines a typology of these hotspots with reference to the biophysical and socioeconomic characteristics that unite and distinguish amongst them. Fifteen regional hotspots were identified on the basis of spatial criteria pertaining to the area, distribution, and rate of reforestation 2001–2014, observed using a custom continental MODIS satellite land-cover classification. Collectively, these hotspots cover 11% of Latin America and the Caribbean and they include 167,667.7 km2 of new forests. Comparisons with other remotely sensed estimates of reforestation indicate that these hotspots contain a significant amount of tropical reforestation, continentally and pantropically. The extent of reforestation as a proportion of its hotspot was relatively invariable (3–14%) given large disparities in hotspot areas and contexts. An ordination analysis defined a typology of five clusters, distinguished largely by their topographical roughness and related aspects of agro-ecological marginality, climate, population trends, and degree of urbanization: ‘Urban lowlands’, ‘Mountainous populated areas’, ‘Rural highlands’, ‘Rural humid lands’ and ‘Rural dry lands’. The typology highlights that a range of distinct, even oppositional regional biophysical, demographic, and agricultural contexts have equally given rise to significant, regional net reforestation, urging a concomitant diversification of forest transition science

Alzheimer disease models and human neuropathology: similarities and differences

Animal models aim to replicate the symptoms, the lesions or the cause(s) of Alzheimer disease. Numerous mouse transgenic lines have now succeeded in partially reproducing its lesions: the extracellular deposits of Aβ peptide and the intracellular accumulation of tau protein. Mutated human APP transgenes result in the deposition of Aβ peptide, similar but not identical to the Aβ peptide of human senile plaque. Amyloid angiopathy is common. Besides the deposition of Aβ, axon dystrophy and alteration of dendrites have been observed. All of the mutations cause an increase in Aβ 42 levels, except for the Arctic mutation, which alters the Aβ sequence itself. Overexpressing wild-type APP alone (as in the murine models of human trisomy 21) causes no Aβ deposition in most mouse lines. Doubly (APP × mutated PS1) transgenic mice develop the lesions earlier. Transgenic mice in which BACE1 has been knocked out or overexpressed have been produced, as well as lines with altered expression of neprilysin, the main degrading enzyme of Aβ. The APP transgenic mice have raised new questions concerning the mechanisms of neuronal loss, the accumulation of Aβ in the cell body of the neurons, inflammation and gliosis, and the dendritic alterations. They have allowed some insight to be gained into the kinetics of the changes. The connection between the symptoms, the lesions and the increase in Aβ oligomers has been found to be difficult to unravel. Neurofibrillary tangles are only found in mouse lines that overexpress mutated tau or human tau on a murine tau −/− background. A triply transgenic model (mutated APP, PS1 and tau) recapitulates the alterations seen in AD but its physiological relevance may be discussed. A number of modulators of Aβ or of tau accumulation have been tested. A transgenic model may be analyzed at three levels at least (symptoms, lesions, cause of the disease), and a reading key is proposed to summarize this analysis

Sustainable timber harvesting in Venezuela: a modelling approach

Reliable data on the growth and yield of logged-over forest to determinesustainable cutting cycles are widely missing for the tropics. We used theprocess-based model Formind2.0 to analyse the growth and yield of logged-overforest in Venezuela under different logging scenarios over a period of 240years and compared results with unlogged stands.The performance of the modelwas evaluated with a detailed stability and sensitivity analysis.In theabsence of further logging,the logged-over stand approached the standstructure of mature forest in terms of bole volume and basal area afterabout 50-100 years.Thirty-year cutting cycles with conventional loggingmethods and net extraction volumes of 45 and 60 m^3/(ha cycle) did not providesustainable yields under either of two minimum felling diameters(35 or 50 cm) that were applied. Only the 60-year cutting cycle providedsustainable yields under conventional and reduced-impact logging with thedi minimum felling diameters and a range of net volumes extracted(30-60 m^3/(ha cycle). With the longest cutting cycle (60 years), bole volumerecovered to levels similar to the mature unlogged stand, but the speciescomposition was very different.Scenarios with reduced-impact logging provideda significantly higher timber volume than under conventional logging. Theconservation of forest resources will only be possible with long cuttingcycles (at least 60 years) in combination with reduced-impact logging