Use of Gliricidia sepium as a Nurse Plant to Reforest Man-made Grasslands in the Knuckles Forest Reserve, Sri Lanka

Biodiversity richness and socially beneficial watershed services are high in the KnucklesForest Reserve. However, the lower montane forest patches on the eastern slopes of the KFRare highly fragmented mainly due to anthropogenic disturbances. If these forest fragments arenot connected in the near future, they will disappear from the landscape due to their lowregeneration rates. Native tree species when used for restoration of these lands faces manydifficulties due to various biotic and abiotic stresses including harsh microclimatic conditionsand infertile soils. Therefore, usage of a nurse plant will facilitate the growth of target speciesdue to creation of favourable microclimatic conditions. Gliricidia sepium has been used as ashade plant in Sri Lanka, since colonial times. More recently it has been used for indigenousfarming practices, soil stabilization, living fences and as fuel wood, animal forage, greenmanure. In our research we investigate the potential of G. sepium as a nurse plant to establishfour native tree species on man-made grasslands in central Sri Lanka. The study wasconducted on four blocks of grasslands. Four replicates of each of the three island sizes(small 4 m2, medium 16 m2, and large 64 m2) were created inside each block. One set ofislands in each block were planted with G. sepium stakes at 2 m intervals in a grid format.The other set of islands in each block was kept as a control without planting G. sepiumstakes. Seedlings of Macaranga indica, Bhesa ceylanica, Symplocos cochinchinensis andEugenia bracteata were planted randomly in islands with and without G. sepium stakes.After three months of establishment, the survival rate of G. sepium in the four blocks wasmore than 80% and the survival rate of the G. sepium was 20% higher in the small andmedium islands than the large islands. The mean number of sprouts per stake was more thaneight in medium and large islands and less than six in small islands. The mean survival ratewas higher (5.8%) and the mean growth rates was lower (0.006%) for all the four nativespecies with G. sepium than without G. sepium after three months of planting. G. sepiumincreased the survival rates of native species after three months of establishment due tofavourable microclimatic conditions created by them. However, growth rate of the nativespecies which were planted with G. sepium was lower probably due to interspecificcompetition. Therefore, G. sepium can be used as an effective nurse plant in initial phases ofreforestation programmes to increase the survival rates of native tree species on degradedsubmontane sites in Sri Lanka.

Renormalization group approach to multiscale modelling in materials science

Dendritic growth, and the formation of material microstructure in general, necessarily involves a wide range of length scales from the atomic up to sample dimensions. The phase field approach of Langer, enhanced by optimal asymptotic methods and adaptive mesh refinement, copes with this range of scales, and provides an effective way to move phase boundaries. However, it fails to preserve memory of the underlying crystallographic anisotropy, and thus is ill-suited for problems involving defects or elasticity. The phase field crystal (PFC) equation-- a conserving analogue of the Hohenberg-Swift equation --is a phase field equation with periodic solutions that represent the atomic density. It can natively model elasticity, the formation of solid phases, and accurately reproduces the nonequilibrium dynamics of phase transitions in real materials. However, the PFC models matter at the atomic scale, rendering it unsuitable for coping with the range of length scales in problems of serious interest. Here, we show that a computationally-efficient multiscale approach to the PFC can be developed systematically by using the renormalization group or equivalent techniques to derive appropriate coarse-grained coupled phase and amplitude equations, which are suitable for solution by adaptive mesh refinement algorithms

Pattern formation in 2-frequency forced parametric waves

We present an experimental investigation of superlattice patterns generated on the surface of a fluid via parametric forcing with 2 commensurate frequencies. The spatio-temporal behavior of 4 qualitatively different types of superlattice patterns is described in detail. These states are generated via a number of different 3--wave resonant interactions. They occur either as symmetry--breaking bifurcations of hexagonal patterns composed of a single unstable mode or via nonlinear interactions between the two primary unstable modes generated by the two forcing frequencies. A coherent picture of these states together with the phase space in which they appear is presented. In addition, we describe a number of new superlattice states generated by 4--wave interactions that arise when symmetry constraints rule out 3--wave resonances.Comment: The paper contains 34 pages and 53 figures and provides an extensive review of both the theoretical and experimental work peformed in this syste

Symmetry Decomposition of Chaotic Dynamics

Discrete symmetries of dynamical flows give rise to relations between periodic orbits, reduce the dynamics to a fundamental domain, and lead to factorizations of zeta functions. These factorizations in turn reduce the labor and improve the convergence of cycle expansions for classical and quantum spectra associated with the flow. In this paper the general formalism is developed, with the $N$-disk pinball model used as a concrete example and a series of physically interesting cases worked out in detail.Comment: CYCLER Paper 93mar01

Integrated Analyses of microRNAs Demonstrate Their Widespread Influence on Gene Expression in High-Grade Serous Ovarian Carcinoma

The Cancer Genome Atlas (TCGA) Network recently comprehensively catalogued the molecular aberrations in 487 high-grade serous ovarian cancers, with much remaining to be elucidated regarding the microRNAs (miRNAs). Here, using TCGA ovarian data, we surveyed the miRNAs, in the context of their predicted gene targets.Integration of miRNA and gene patterns yielded evidence that proximal pairs of miRNAs are processed from polycistronic primary transcripts, and that intronic miRNAs and their host gene mRNAs derive from common transcripts. Patterns of miRNA expression revealed multiple tumor subtypes and a set of 34 miRNAs predictive of overall patient survival. In a global analysis, miRNA:mRNA pairs anti-correlated in expression across tumors showed a higher frequency of in silico predicted target sites in the mRNA 3'-untranslated region (with less frequency observed for coding sequence and 5'-untranslated regions). The miR-29 family and predicted target genes were among the most strongly anti-correlated miRNA:mRNA pairs; over-expression of miR-29a in vitro repressed several anti-correlated genes (including DNMT3A and DNMT3B) and substantially decreased ovarian cancer cell viability.This study establishes miRNAs as having a widespread impact on gene expression programs in ovarian cancer, further strengthening our understanding of miRNA biology as it applies to human cancer. As with gene transcripts, miRNAs exhibit high diversity reflecting the genomic heterogeneity within a clinically homogeneous disease population. Putative miRNA:mRNA interactions, as identified using integrative analysis, can be validated. TCGA data are a valuable resource for the identification of novel tumor suppressive miRNAs in ovarian as well as other cancers

The aberrant asynchronous replication — characterizing lymphocytes of cancer patients — is erased following stem cell transplantation

<p>Abstract</p> <p>Background</p> <p>Aberrations of allelic replication timing are epigenetic markers observed in peripheral blood cells of cancer patients. The aberrant markers are non-cancer-type-specific and are accompanied by increased levels of sporadic aneuploidy. The study aimed at following the epigenetic markers and aneuploidy levels in cells of patients with haematological malignancies from diagnosis to full remission, as achieved by allogeneic stem cell transplantation (alloSCT).</p> <p>Methods</p> <p><it>TP53 </it>(a tumor suppressor gene assigned to chromosome 17), <it>AML1 </it>(a gene assigned to chromosome 21 and involved in the leukaemia-abundant 8;21 translocation) and the pericentomeric satellite sequence of chromosome 17 (<it>CEN17</it>) were used for replication timing assessments. Aneuploidy was monitored by enumerating the copy numbers of chromosomes 17 and 21. Replication timing and aneuploidy were detected cytogenetically using fluorescence <it>in situ </it>hybridization (FISH) technology applied to phytohemagglutinin (PHA)-stimulated lymphocytes.</p> <p>Results</p> <p>We show that aberrant epigenetic markers are detected in patients with hematological malignancies from the time of diagnosis through to when they are scheduled to undergo alloSCT. These aberrations are unaffected by the clinical status of the disease and are displayed both during accelerated stages as well as in remission. Yet, these markers are eradicated completely following stem cell transplantation. In contrast, the increased levels of aneuploidy (irreversible genetic alterations) displayed in blood lymphocytes at various stages of disease are not eliminated following transplantation. However, they do not elevate and remain unchanged (stable state). A demethylating anti-cancer drug, 5-azacytidine, applied in vitro to lymphocytes of patients prior to transplantation mimics the effect of transplantation: the epigenetic aberrations disappear while aneuploidy stays unchanged.</p> <p>Conclusions</p> <p>The reversible nature of the replication aberrations may serve as potential epigenetic blood markers for evaluating the success of transplant or other treatments and for long-term follow up of the patients who have overcome a hematological malignancy.</p

The completion of the Mammalian Gene Collection (MGC)

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide