Impact of microvariability on classification and management of peatlands in Asia

Globally, wetlands occupy about 18.96 x 106 km2, of which 2% is made up of organic soils. In Asia, about 2.2 million km2 (~ 1.0%) of the land surface comprises peat or Histosols. The current global approach to agriculture places considerable emphasis on environmental quality, conservation of biodiversity and preservation of ecosystem while striving to achieve sustainable production in agroecosystems. In Asia, land use on the peatlands is low-input subsistence-based systems. In a few countries, such as Malaysia and Indonesia, rubber and oil-palm are cultivated on a plantation scale. Subsistence-based agricultural systems, understandably, would not be able to provide the level of input required for sustainable management of peat lands. The knowledge base for such systems is highly traditional in nature and is therefore vulnerable to the uncontrolled changes that occur in the evolution of the agro-ecosystem. Commercial-based agricultural systems appear to thrive in areas dominated by shallow peat. This system is technology-based, has a greater control over changes that may occur within the system but is perhaps still not in harmony with nature. Ignorance of the functions and value of such areas has lead to many forms of degradation. Therefore, sustainable development of the peat soils requires not only a holistic approach to the management but also dictates the need for a paradigm shift in resource characterization, research trends and land use policies.The paper elaborates on the paradigm shift in sustainable land management system and advocates a holistic approach wherein agronomic factors, environmental considerations as well as the much de-emphasized socioeconomic aspects, are all integrated into new research approaches. Research strategies needed to ensure sustainable agricultural development of organic soils include the urgent need for innovative measures to characterize the resource, evaluating and monitoring soil quality, assessing the potential of peat lands to release methane and other greenhouse gases upon drainage, and assessing the integrity of the ecosystem. Issues pertaining to productivity, assisting in the design of rational policies for development, promoting preservation of heritage, inculcating the ownership concept and developing better methods to gauge the economic viability of such projects are additional important factors that ensure sustainability. The most important factor differentiating peatlands from their mineral counterparts is microvariability; this, specifically in the context of small farms had not been addressed adequately and requires innovative approaches and technologies. Conventional soil surveys must be augmented with more innovative techniques as current methods suffer from various kinds of limitations

Dust in Brown Dwarfs IV. Dust formation and driven turbulence on mesoscopic scales

Dust formation in brown dwarf atmospheres is studied by utilising a model for driven turbulence in the mesoscopic scale regime. We apply a pseudo-spectral method where waves are created and superimposed within a limited wavenumber interval. The turbulent kinetic energy distribution follows the Kolmogoroff spectrum which is assumed to be the most likely value. Such superimposed, stochastic waves may occur in a convectively active environment. They cause nucleation fronts and nucleation events and thereby initiate the dust formation process which continues until all condensible material is consumed. Small disturbances are found to have a large impact on the dust forming system. An initially dust-hostile region, which may originally be optically thin, becomes optically thick in a patchy way showing considerable variations in the dust properties during the formation process. The dust appears in lanes and curls as a result of the interaction with waves, i.e. turbulence, which form larger and larger structures with time. Aiming on a physical understanding of the variability of brown dwarfs, related to structure formation in substellar atmospheres, we work out first necessary criteria for small-scale closure models to be applied in macroscopic simulations of dust forming astrophysical systems.Comment: A&A accepted, 20 page

Impact of subsurface terric materials on the composition and behavior of histosols

Approximately 13% of the land area of Sarawak , Malaysia is covered by Histosols. Recent land and agricultural policies encourage utilization of Histosols for agricultural purposes to meet the national food requirements. Increasing stress on this ecosystem requires a better understanding of the resource and its behavior. Mineral terric substrata are common in many Histosols. A transect of 50 m at Kota Samarahan (Sarawak) was selected for this study to evaluate the impact of terric materials on the properties of the overlying organic tier. Six basic forms of subsurface discontinuities were recognized: symmetrical dome, asymmetrical dome, flat top, flat base, orthogonal and irregular. The degree of horizonation was different in all the soils. The pH of the soils was quite similar. All soils had net negative charges that increased with depth, however, the actual amounts of net charges varied between the soils. The soils had negligible amounts of exchangeable cations. The fiber contents, cation exchange capacities, FTIR spectra and Cue' adsorption studies showed critical differences. Despite the fact that these soils are mapped as one mapping unit, major differences in critical properties are expected to influence the behavior and performance. Variations in subsurface discontinuities cast some doubt on the reliability of conventional mapping techniques in such soils. The information generated is very useful to improve soil survey procedures and the subsequent use and management of these soils

Improving the value of public RNA-seq expression data by phenotype prediction.

Publicly available genomic data are a valuable resource for studying normal human variation and disease, but these data are often not well labeled or annotated. The lack of phenotype information for public genomic data severely limits their utility for addressing targeted biological questions. We develop an in silico phenotyping approach for predicting critical missing annotation directly from genomic measurements using well-annotated genomic and phenotypic data produced by consortia like TCGA and GTEx as training data. We apply in silico phenotyping to a set of 70 000 RNA-seq samples we recently processed on a common pipeline as part of the recount2 project. We use gene expression data to build and evaluate predictors for both biological phenotypes (sex, tissue, sample source) and experimental conditions (sequencing strategy). We demonstrate how these predictions can be used to study cross-sample properties of public genomic data, select genomic projects with specific characteristics, and perform downstream analyses using predicted phenotypes. The methods to perform phenotype prediction are available in the phenopredict R package and the predictions for recount2 are available from the recount R package. With data and phenotype information available for 70,000 human samples, expression data is available for use on a scale that was not previously feasible

Characterisation of the genomic landscape of CRLF2-rearranged acute lymphoblastic leukemia

Deregulated expression of the type I cytokine receptor, CRLF2, is observed in 5–15% of precursor B-cell acute lymphoblastic leukaemia (B-ALL). We aimed to determine the clinical and genetic landscape of those with IGH-CRLF2 or P2RY8-CRLF2 (CRLF2-r) using multiple genomic approaches. Clinical and demographic features of CRLF2-r patients were characteristic of B-ALL. Patients with IGH-CRLF2 were older (14 y vs. 4 y, P < .001), while the incidence of CRLF2-r among Down syndrome patients was high (50/161, 31%). CRLF2-r co-occurred with primary chromosomal rearrangements but the majority (111/161, 69%) had B-other ALL. Copy number alteration (CNA) profiles were similar to B-other ALL, although CRLF2-r patients harbored higher frequencies of IKZF1 (60/138, 43% vs. 77/1351, 24%) and BTG1 deletions (20/138, 15% vs. 3/1351, 1%). There were significant differences in CNA profiles between IGH-CRLF2 and P2RY8-CRLF2 patients: IKZF1 (25/35, 71% vs. 36/108, 33%, P < .001), BTG1 (11/35, 31% vs. 10/108, 9%, P =.004), and ADD3 deletions (9/19, 47% vs. 5/38, 13%, P =.008). A novel gene fusion, USP9X-DDX3X, was discovered in 10/54 (19%) of patients. Pathway analysis of the mutational profile revealed novel involvement for focal adhesion. Although the functional relevance of many of these abnormalities are unknown, they likely activate additional pathways, which may represent novel therapeutic targets

Statistical analysis of the mass-to-flux ratio in turbulent cores: effects of magnetic field reversals and dynamo amplification

We study the mass-to-flux ratio (M/\Phi) of clumps and cores in simulations of supersonic, magnetohydrodynamical turbulence for different initial magnetic field strengths. We investigate whether the (M/\Phi)-ratio of core and envelope, R = (M/\Phi)_{core}/(M/\Phi)_{envelope} can be used to distinguish between theories of ambipolar diffusion and turbulence-regulated star formation. We analyse R for different Lines-of-Sight (LoS) in various sub-cubes of our simulation box. We find that, 1) the average and median values of |R| for different times and initial magnetic field strengths are typically greater, but close to unity, 2) the average and median values of |R| saturate at average values of |R| ~ 1 for smaller magnetic fields, 3) values of |R| < 1 for small magnetic fields in the envelope are caused by field reversals when turbulence twists the field lines such that field components in different directions average out. Finally, we propose two mechanisms for generating values |R| ~< 1 for the weak and strong magnetic field limit in the context of a turbulent model. First, in the weak field limit, the small-scale turbulent dynamo leads to a significantly increased flux in the core and we find |R| ~< 1. Second, in the strong field limit, field reversals in the envelope also lead to values |R| ~< 1. These reversals are less likely to occur in the core region where the velocity field is more coherent and the internal velocity dispersion is typically subsonic.Comment: 12 pages, 8 figures, accepted for publication in MNRA

A set of canonical problems in sloshing. Part 0: Experimental setup and data processing

In a series of attempts to research and document relevant sloshing type phenomena, a series of experiments have been conducted. The aim of this paper is to describe the setup and data processing of such experiments. A sloshing tank is subjected to angular motion. As a result pressure registers are obtained at several locations, together with the motion data, torque and a collection of image and video information. The experimental rig and the data acquisition systems are described. Useful information for experimental sloshing research practitioners is provided. This information is related to the liquids used in the experiments, the dying techniques, tank building processes, synchronization of acquisition systems, etc. A new procedure for reconstructing experimental data, that takes into account experimental uncertainties, is presented. This procedure is based on a least squares spline approximation of the data. Based on a deterministic approach to the first sloshing wave impact event in a sloshing experiment, an uncertainty analysis procedure of the associated first pressure peak value is described

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed.MethodsTen CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system.ResultsAn average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q &lt; 0.05, fold change &gt;2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). Skipped exon was the most frequent splicing alteration in CLL specimens with 128 significant events (P-value &lt;0.05, minimum inclusion level difference &gt;0.1).ConclusionThe RNA-seq analysis of CLL specimens identifies novel DEG and alternatively spliced genes that are potential prognostic markers and therapeutic targets. High level of validation by qRT-PCR for a number of DEG genes supports the accuracy of this analysis. Global comparison of transcriptomes of B cells, IGVH non-mutated CLL (U-CLL) and mutated CLL specimens (M-CLL) with multidimensional scaling analysis was able to segregate CLL and B cell transcriptomes but the M-CLL and U-CLL transcriptomes were indistinguishable. The analysis of HTS RNA-seq data to identify alternative splicing events and other genetic abnormalities specific to CLL is an added advantage of RNA-seq that is not feasible with other genome wide analysis

Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots

Vascular cambium, a lateral plant meristem is a central producer of woody biomass. Although a few transcription factors (TFs) have been shown to regulate cambial activity1, the phenotypes of the corresponding loss-of-function mutants are relatively modest, highlighting our limited understanding of the underlying transcriptional regulation. Here, we utilize cambium cell-specific transcript profiling followed by a combination of TF network and genetic analyses to identify 62 novel TF genotypes displaying an array of cambial phenotypes. This approach culminated in virtual loss of cambial activity when both WUSCHEL-RELATED HOMEOBOX 4 (WOX4) and KNOTTED-like from Arabidopsis thaliana 1 (KNAT1; also known as BREVIPEDICELLUS (BP) were mutated, thereby unlocking the genetic redundancy in the regulation of cambium development. We also identified TFs with dual functions in cambial cell proliferation and xylem differentiation, including WOX4, SHORT VEGETATIVE PHASE (SVP) and PETAL LOSS (PTL). Using the TF network information, we combined overexpression of the cambial activator WOX4 and removal of the putative inhibitor PTL to engineer Arabidopsis for enhanced radial growth. This line also showed ectopic cambial activity, thus further highlighting the central roles of WOX4 and PTL in cambium development.This work was supported by Finnish Centre of Excellence in Molecular Biology of Primary Producers (Academy of Finland CoE program 2014-2019) decision #271832, the Gatsby Foundation (GAT3395/PR3)), the University of Helsinki (award 799992091) and the European Research Council Advanced Investigator Grant SYMDEV (No. 323052) to Y.H.; Academy of Finland (grants #132376, #266431, #271832), University of Helsinki HiLIFE fellowship to A.P.M.; National Research Foundation of Korea (2018R1A5A1023599 and 2016R1A2B2015258) to J-Y. L

Statistical Properties of Turbulence: An Overview

We present an introductory overview of several challenging problems in the statistical characterisation of turbulence. We provide examples from fluid turbulence in three and two dimensions, from the turbulent advection of passive scalars, turbulence in the one-dimensional Burgers equation, and fluid turbulence in the presence of polymer additives.Comment: 34 pages, 31 figure