Clearing-induced tisssue shrinkage: A novel observation of a thickness size effect.

The use of clearing agents has provided new insights in various fields of medical research (developmental biology, neurology) by enabling examination of tissue architecture in 3D. One of the challenges is that clearing agents induce tissue shrinkage and the shrinkage rates reported in the literature are incoherent. Here, we report that for a classical clearing agent, benzyl-alcohol benzyl-benzoate (BABB), the shrinkage decreases significantly with increasing sample size, and present an analytical formula describing this.

Attributing the hydrological impact of different land use types and their long-term dynamics through combining parsimonious hydrological modelling, alteration analysis and PLSR analysis.

Understanding the relationship between hydrological processes and environmental changes is important for improved water management. The Geba catchment in Ethiopia, forming the headwaters of Tekeze-Atbara basin, was known for its severe land degradation before the recent success in integrated watershed management. This study analyses the hydrological response attributed to land management change using an integrated approach composed of (i) simulating the hydrological response of Land Use/Cover (LULC) changes; (ii) assessing the alteration of streamflow using Alteration of Hydrological Indicators (IHA); and (iii) quantifying the contribution of individual LULC types to the hydrology using Partial Least Square Regression model (PLSR). The results show that the expansion of agricultural and grazing land at the expense of natural vegetation has increased the surface runoff 77% and decreased dry season flow by 30% in the 1990s compared to 1970s. However, natural vegetation started to recover from the late 1990s and dry season flows increased by 16%, while surface runoff declined by 19%. More pronounced changes of the streamflow were noticed at sub-catchment level, mainly associated with the uneven spatial distribution of land degradation and rehabilitation. However, the rate of increase of low-flow halted in the 2010s, most probably due to an increase of water withdrawals for irrigation. Fluctuations in hydrological alteration parameters are in agreement with the observed LULC change. The PLSR analysis demonstrates that most LULC types showed a strong association with all hydrological components. These findings demonstrate that changing water conditions are attributed to the observed LULC change dynamics. The combined analysis of rainfall-runoff modelling, alteration indicators and PLSR is able to assess the impact of environmental change on the hydrology of complex catchments. The IHA tool is robust to assess the magnitude of streamflow alterations obtained from the hydrological model while the PLSR method is useful to zoom into which LULC is responsible for this alteration.

Sensitive detection of mitochondrial DNA variants for analysis of mitochondrial DNA-enriched extracts from frozen tumor tissue.

Large variation exists in mitochondrial DNA (mtDNA) not only between but also within individuals. Also in human cancer, tumor-specific mtDNA variation exists. In this work, we describe the comparison of four methods to extract mtDNA as pure as possible from frozen tumor tissue. Also, three state-of-the-art methods for sensitive detection of mtDNA variants were evaluated. The main aim was to develop a procedure to detect low-frequent single-nucleotide mtDNA-specific variants in frozen tumor tissue. We show that of the methods evaluated, DNA extracted from cytosol fractions following exonuclease treatment results in highest mtDNA yield and purity from frozen tumor tissue (270-fold mtDNA enrichment). Next, we demonstrate the sensitivity of detection of low-frequent single-nucleotide mtDNA variants (≤1% allele frequency) in breast cancer cell lines MDA-MB-231 and MCF-7 by single-molecule real-time (SMRT) sequencing, UltraSEEK chemistry based mass spectrometry, and digital PCR. We also show de novo detection and allelic phasing of variants by SMRT sequencing. We conclude that our sensitive procedure to detect low-frequent single-nucleotide mtDNA variants from frozen tumor tissue is based on extraction of DNA from cytosol fractions followed by exonuclease treatment to obtain high mtDNA purity, and subsequent SMRT sequencing for (de novo) detection and allelic phasing of variants.

Quantifying longitudinal land use change from land degradation to rehabilitation in the headwaters of Tekeze-Atbara Basin, Ethiopia.

The spatiotemporal variability of the Land Use/Cover (LULC) is a strong influence on the land management and hydrological processes of a river basin. In particular in semi-arid regions like the Tekeze-Atbara (T-A) basin, accurate information about LULC change is a prerequisite for improved land and water management. The human-induced landscape transformations in the T-A basin, one of the main tributaries of the Nile River, were investigated for the last four decades (1972-2014). Separate LULC maps for the years 1972, 1989, 2001, and 2014 were developed based on satellite images, Geographic Information System (GIS) and ground information. Change detection analysis based on the transitional probability matrix was applied to identify systematic transitions among the LULC categories. The results show that >72% of the landscape has changed its category during the past 43years. LULC in the basin experienced significant shifts from one category to other categories by 61%, 47%, and 45%, in 1972-1989, 1989-2001, and 2001-2014, respectively. Although both net and swap (simultaneous gain and loss of a given LULC during a certain period) change occurred, the latter is more dominant. Natural vegetation cover, including forests, reduced drastically with the rapid expansion of crops, grazing areas and bare lands during the first two decades. However, vegetation started to recover since the 1990s, when some of the agricultural and bare lands have turned into vegetated areas. Forest land showed a continuous decreasing pattern, however, it has increased by 28% in the last period (2001-2014). In contrast, plantation trees have increased by 254% in the last three decades. The increase of vegetation cover is a result of intensive watershed management programs during the last two decades. The driving forces of changes were also discussed and rapid population growth and changing government policies were found to be the most important.

Complete sequence-based pathway analysis by differential on-chip DNA and RNA extraction from a single cell.

We demonstrate on-chip, differential DNA and RNA extraction from a single cell using a microfluidic chip and a two-stage lysis protocol. This method enables direct use of the whole extract, without additional washing steps, reducing sample loss. Using this method, the tumor driving pathway in individual cells from a colorectal cancer cell line was determined by applying a Bayesian computational pathway model to sequences obtained from the RNA fraction of a single cell and, the mutations driving the pathway were determined by analyzing sequences obtained from the DNA fraction of the same single cell. This combined functional and mutational pathway assessment of a single cell could be of significant value for dissecting cellular heterogeneity in tumors and analyzing single circulating tumor cells.

Improving DNA capture on microarrays by integrated repeated denaturing.

Hybridization of nucleic acids to microarrays is a crucial step for several biological and biomedical applications. However, the poor efficiency and resulting long incubation times are major drawbacks. In addition to diffusion limitation, back hybridization to complementary strands in solution is shown to be an important cause of the low efficiency. In this paper, repeated denaturing in an integrated device has been investigated in order to increase the efficiency of microarray hybridization. The sample solution is circulated from the microarray chamber over a denaturing zone and back in a closed loop. In addition to the improved binding rate due to flow, repeated denaturing significantly increases the total amount of molecules bound. Our results demonstrate that cyclic repeated denaturing improves the efficiency of hybridization by up to an order of magnitude over a broad range of concentrations studied (1 pM to 100 nM).

Using a priori knowledge to align sequencing reads to their exact genomic position.

The use of a priori knowledge in the alignment of targeted sequencing data is investigated using computational experiments. Adapting a Needleman-Wunsch algorithm to incorporate the genomic position information from the targeted capture, we demonstrate that alignment can be done to just the target region of interest. When in addition use is made of direct string comparison, an improvement of up to a factor of 8 in alignment speed compared to the fastest conventional aligner (Bowtie) is obtained. This results in a total alignment time in targeted sequencing of around 7 min for aligning approximately 56 million captured reads. For conventional aligners such as Bowtie, BWA or MAQ, alignment to just the target region is not feasible as experiments show that this leads to an additional 88% SNP calls, the vast majority of which are false positives (≈ 92%).

Targeted enrichment of genomic DNA regions for next-generation sequencing.

In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings.

Integrating wastewater reuse in water resources management for hotels in arid coastal regions - Case Study of Sharm El Sheikh, Egypt.

Hotels in arid coastal areas use mainly desalinated water (using reverse osmosis) for their domestic water supply, and treated wastewater for irrigating green areas. Private water companies supply these hotels with their potable and non-potable water needs. There is normally a contractual agreement stating a minimum amount of water that has to be supplied by the water company and that the hotel management has to pay for regardless of its actual consumption ("contracted-for water supply"). Hotels have to carefully analyse their water requirements in order to determine which percentage of the hotel's peak water demand should be used in the contract in order to reduce water costs and avoid the risk of water shortage. This paper describes a model to optimise the contracted-for irrigation water supply with the objective function to minimise total water cost to hotels. It analyses what the contracted-for irrigation water supply of a given hotel should be, based on the size of the green irrigated area on one hand and the unit prices of the different types of water on the other hand. An example from an arid coastal tourism-dominated city is presented: Sharm El Sheikh (Sharm), Egypt. This paper presents costs of wastewater treatment using waste stabilisation ponds, which is the prevailing treatment mechanism in the case study area for centralised plants, as well as aerobic/anaerobic treatment used for decentralised wastewater treatment plants in the case study area. There is only one centralised wastewater treatment plant available in the city exerting monopoly and selling treated wastewater to hotels at a much higher price than the actual cost that a hotel would bear if it treated its own wastewater. Contracting for full peak irrigation demand is the highest total cost option. Contracting for a portion of the peak irrigation demand and complementing the rest from desalination water is a cheaper option. A better option still is to complement the excess irrigation demand from the company that treats and sells wastewater, if available or from another wastewater treatment company at a higher cost (but at a cost cheaper than that of desalination water) mainly due to the high demand season and the additional cost of trucking. In some cases, however, like in Sharm, the amount of treated wastewater is limited and variable during the year and some hotels have no choice but to partially use desalination water for irrigation. A conscious strategy for water management should rely solely on treated wastewater on-site. This can be achieved by: increasing the efficiency of the irrigation system, reducing the area of high-water consuming plantation (e.g. turf grass) and/or shifting to drought resistant plants including less water-consuming or salt tolerant turf grass.

The effect of temperature and dot size on the spectral properties of colloidal InP/ZnS core-shell quantum dots.

Visual color changes between 300 and 510 K were observed in the photoluminescence (PL) of colloidal InP/ZnS core-shell nanocrystals. A subsequent study of PL spectra in the range 2-510 K and fitting the temperature dependent line shift and line width to theoretical models show that the dominant (dephasing) interaction is due to scattering by acoustic phonons of about 23 meV. Low temperature photoluminescence excitation measurements show that the excitonic band gap depends approximately inversely linearly on the quantum dot size d, which is distinctly weaker than the dependence predicted by current theories.

Optimum contracted-for water supply for hotels in arid coastal regions.

Hotels in arid coastal areas use mainly desalinated water for their domestic water demands, and treated wastewater for irrigating green areas. Private water companies supply these hotels with their domestic water needs. There is normally a contractual agreement stating a minimum requirement that has to be supplied by the water company and that the hotel management has to pay for regardless of its actual consumption ("contracted-for water supply"). This paper describes a model to determine what value a hotel should choose for its contracted-for water supply in order to minimize its total annual water costs. An example from an arid coastal tourism-dominated city is presented: Sharm El Sheikh, Egypt.The managers of hotels with expected high occupancy rates (74% and above) can contract for more than 80%. On the other hand, hotels with expected lower occupancy rates (60% and less) can contract for less than 70% of the peak daily domestic water demand. With a green area ratio of 40 m(2)/room or less, an on-site wastewater treatment plant can satisfy the required irrigation demand for an occupancy rate as low as 42%. Increasing the ratio of green irrigated area to 100 m(2)/room does not affect the contracted-for water supply at occupancy rates above 72%; at lower occupancy rates, however, on-site treated wastewater is insufficient for irrigating the green areas. Increasing the green irrigated area to 120 m(2)/room increases the need for additional water, either from externally sourced treated wastewater or potable water. The cost of the former is much lower than the latter (0.58 versus 1.52 to 2.14 US$/m(3) in the case study area).

Link between perpendicular coupling and exchange biasing in Fe(3)O(4)/CoOMultilayers.

In studying well-characterized, exchange-biased Fe(3)O(4)/CoO superlattices, we demonstrate a causal link between the exchange bias effect and the perpendicular coupling of the ferrimagnetic and antiferromagnetic spins. Neutron diffraction studies reveal that for thin CoO layers the onset temperature for exchange biasing T(B) matches the onset of locked-in, preferential perpendicular coupling of the spins, rather than the antiferromagnetic ordering temperature T(N). The results are explained by considering the role of anisotropic exchange first proposed by Dzyaloshinsky and Moriya and developing a model based purely on information on structural defects and exchange for these oxides. The devised mechanism provides a general explanation of biasing in systems with perpendicular coupling.

Difference between blocking and Néel temperatures in the exchange biased Fe3O4/CoO system.

The blocking temperature T(B) has been determined as a function of the antiferromagnetic layer thickness in the Fe3O4/CoO exchange biased system. For CoO layers thinner than 50 A, T(B) is reduced below the Néel temperature T(N) of bulk CoO (291 K), independent of crystallographic orientation or film substrate ( alpha-Al2O3, SrTiO3, and MgO). Neutron diffraction studies show that T(B) does not track the CoO ordering temperature and, hence, that this reduction in T(B) does not arise from finite-size scaling. Instead, the ordering temperature of the CoO layers is enhanced above the bulk T(N) for layer thicknesses approximately less than or equal to 100 A due to the proximity of magnetic Fe3O4 layers.