Technological Adaptations of Abaknon Fishers In Capul, Northern Samar: How Ocean Currents Contribute To Resourcefulness And Transformation

This paper investigated the livelihood strategy of the Abaknons and its effects on the coastal subsystem.  Abaknons, the local people of the small-island of Capul, Northern Samar take advantage of the windswept and whirlpool-dotted strip of rushing sea San Bernardino Strait, hemmed in by the western current from the Pacific Ocean and the eastward current from the China Sea.  This paper examines how a traditional fishing community transforms its fishing technology by re-inventing the varied non-biodegradable discards brought by such ocean currents to the shores of Capul. The opportunities offered by these throw-aways heighten the resourcefulness of the Abaknons, resulting in other transformations triggered by this seemingly small change. Keywords: Technological adaptations, ocean currents, resourcefulness, transformatio

Variation In The Role And Coping Mechanism of 4Ps Beneficiaries In Northern Samar

This study analyzed the emerging roles and coping mechanisms of poor families in the province of Northern Samar considering the 4Ps recipients as the representatives of the poor families. It described the emergent roles of families in relation to income generation, provision of basic needs and family spending. The power patterns among poor families were also examined. It also discussed the coping mechanisms of poor families in terms of income generation, provision of basic needs and family spending. This study was conducted in the province of Northern Samar and considered one municipality from every geographical area as the major data source. The municipality of Lavezares represented the Balicuatro  area, Catarman for the central area and Pambujan for the Pacific Area. This study considered the heads of poor families in drawing out data. The recipients of the Pantawid Pamilyang Pilipino Program (4Ps) were basically the subjects of the study. They were drawn through purposive sampling technique. Among the parents’ emergent role on income generation, giving of the whole income for the family was frequently practiced while accepting immediate paid labor and leaving the major source of income was least or occasionally practiced. On the provision of basic needs the frequently performed role was the daily preparation of food by the parents and the least  frequently practiced was the provision of regular budget for food. On family spending, the frequently performed role was that the parents make the final decision, making authority and the occasionally practiced was that, the parents don’t tell the family on significant matters. Among the family power patterns, the frequently played was the voice of the father is the law in the family while the least manifested power pattern was that, the father is the head but not the breadwinner, thus obedient to the breadwinner. In terms of income generation, family coping mechanisms of poor families in Northern Samar, the frequently practiced mechanism was generally, the culture of sharing is observed in the family while the seldom practiced was a member of the family has to stop schooling and work to augment the income of the family. On the provision of basic needs, the occasionally practiced was that the father doubles his major task to support and satisfy the basic needs of the family while the seldom practiced was, the eldest child of the family has to go to an urban/city area for a job to finance the basic needs of the family. Any member of the family is consulted for decision on spending matter is the occasionally shown coping mechanism while, in all family affairs, decision on spending is always put upon the shoulders of the close friends was the seldom coping mechanism shown. Keywords: Family role, coping mechanisms, poor families

Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression

Antisense transcription through genic regions is pervasive in most genomes; however, its functional significance is still unclear. We are studying the role of antisense transcripts (COOLAIR) in the cold-induced, epigenetic silencing of Arabidopsis FLOWERING LOCUS C (FLC), a regulator of the transition to reproduction. Here we use single-molecule RNA FISH to address the mechanistic relationship of FLC and COOLAIR transcription at the cellular level. We demonstrate that while sense and antisense transcripts can co-occur in the same cell they are mutually exclusive at individual loci. Cold strongly upregulates COOLAIR transcription in an increased number of cells and through the mutually exclusive relationship facilitates shutdown of sense FLC transcription in cis. COOLAIR transcripts form dense clouds at each locus, acting to influence FLC transcription through changed H3K36me3 dynamics. These results may have general implications for other loci showing both sense and antisense transcription

Influence of Altitude on Tropical Marine Habitat Classification using Fixed-Wing UAV Imagery

Unmanned aerial vehicles (UAVs) are cost-effective remote sensing tools useful for generating very high-resolution (VHR) aerial imagery. Habitat maps generated from UAV imagery are a fundamental component of marine spatial planning, essential for the designation and governance of marine protected areas (MPAs). We investigated whether UAV survey altitude affects habitat classification performance and the classification accuracy of thematic maps from a tropical shallow water environment. We conducted repeated UAV flights at 75, 85, and 110 m, using a fixed-wing UAV on the Turneffe Atoll, Belize. Flights were ground-truthed with snorkel surveys. Images were mosaiced to form orthomosaics and transformed into thematic maps through semi-automatic object-based image analysis (OBIA). Three subset areas (4000 m2, 17000 m2 and 17000 m2) from two cayes on the atoll were selected to investigate the effect of survey altitude. A linear regression demonstrated that for every 1 m increase in survey altitude, there was a ~1% decrease in the overall classification accuracy. A low survey altitude of 75 m produced a higher classification accuracy for thematic maps and increased the representation of mangrove, seagrass, and sand. The variability in classified cover was driven by altitude, although the direction and extent of this relationship was specific to each class. For coral and sea, classified cover decreased with increased altitude. Mangrove classified cover was non-sensitive to altitude changes, demonstrating a lesser need for a consistent survey altitude. Sand and seagrass had a greater sensitivity to altitude, due to classified cover variability between altitudes. Our findings suggest that survey altitude should be minimised when classifying tropical marine environments (coral, seagrass) and, given that most fixed-wing UAVs are restricted to a minimum altitude of 70 m, we recommend an altitude of 75 m. Survey altitude should be a major consideration when targeting habitats with greater sensitivity to altitude variabilit

The Tetraodon nigroviridis reference transcriptome: Developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome

Pufferfish such as fugu and tetraodon carry the smallest genomes among all vertebrates and are ideal for studying genome evolution. However, comparative genomics using these species is hindered by the poor annotation of their genomes. We performed RNA sequencing during key stages of maternal to zygotic transition of Tetraodon nigroviridis and report its first developmental transcriptome. We assembled 61,033 transcripts (23,837 loci) representing 80% of the annotated gene models and 3816 novel coding transcripts from 2667 loci. We demonstrate the similarities of gene expression profiles between pufferfish and zebrafish during maternal to zygotic transition and annotated 1120 long non-coding RNAs (lncRNAs) many of which differentially expressed during development. The promoters for 60% of the assembled transcripts result validated by CAGE-seq. Despite the extreme compaction of the tetraodon genome and the dramatic loss of transposons, the length of lncRNA exons remain comparable to that of other vertebrates and a small set of lncRNAs appears enriched for transposable elements suggesting a selective pressure acting on lncRNAs length and composition. Finally, a set of lncRNAs are microsyntenic between teleost and vertebrates, which indicates potential regulatory interactions between lncRNAs and their flanking coding genes. Our work provides a fundamental molecular resource for vertebrate comparative genomics and embryogenesis studies

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

February 17, 2011The conversion of lineage-committed cells to induced pluripotent stem cells (iPSCs) by reprogramming is accompanied by a global remodeling of the epigenome[superscript 1, 2, 3, 4, 5], resulting in altered patterns of gene expression[superscript 2, 6, 7, 8, 9]. Here we characterize the transcriptional reorganization of large intergenic non-coding RNAs (lincRNAs)[superscript 10, 11] that occurs upon derivation of human iPSCs and identify numerous lincRNAs whose expression is linked to pluripotency. Among these, we defined ten lincRNAs whose expression was elevated in iPSCs compared with embryonic stem cells, suggesting that their activation may promote the emergence of iPSCs. Supporting this, our results indicate that these lincRNAs are direct targets of key pluripotency transcription factors. Using loss-of-function and gain-of-function approaches, we found that one such lincRNA (lincRNA-RoR) modulates reprogramming, thus providing a first demonstration for critical functions of lincRNAs in the derivation of pluripotent stem cells

Genome-wide linkage analyses of non-Hispanic white families identify novel loci for familial late-onset Alzheimer's disease

INTRODUCTION: Few high penetrance variants that explain risk in late-onset Alzheimer's disease (LOAD) families have been found. METHODS: We performed genome-wide linkage and identity-by-descent (IBD) analyses on 41 non-Hispanic white families exhibiting likely dominant inheritance of LOAD, and having no mutations at known familial Alzheimer's disease (AD) loci, and a low burden of APOE ε4 alleles. RESULTS: Two-point parametric linkage analysis identified 14 significantly linked regions, including three novel linkage regions for LOAD (5q32, 11q12.2-11q14.1, and 14q13.3), one of which replicates a genome-wide association LOAD locus, the MS4A6A-MS4A4E gene cluster at 11q12.2. Five of the 14 regions (3q25.31, 4q34.1, 8q22.3, 11q12.2-14.1, and 19q13.41) are supported by strong multipoint results (logarithm of odds [LOD*] ≥1.5). Nonparametric multipoint analyses produced an additional significant locus at 14q32.2 (LOD* = 4.18). The 1-LOD confidence interval for this region contains one gene, C14orf177, and the microRNA Mir_320, whereas IBD analyses implicates an additional gene BCL11B, a regulator of brain-derived neurotrophic signaling, a pathway associated with pathogenesis of several neurodegenerative diseases. DISCUSSION: Examination of these regions after whole-genome sequencing may identify highly penetrant variants for familial LOAD

A four-gene LincRNA expression signature predicts risk in multiple cohorts of acute myeloid leukemia patients.

Prognostic gene expression signatures have been proposed as clinical tools to clarify therapeutic options in acute myeloid leukemia (AML). However, these signatures rely on measuring large numbers of genes and often perform poorly when applied to independent cohorts or those with older patients. Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulators of cell identity and oncogenesis, but knowledge of their utility as prognostic markers in AML is limited. Here we analyze transcriptomic data from multiple cohorts of clinically annotated AML patients and report that (i) microarrays designed for coding gene expression can be repurposed to yield robust lincRNA expression data, (ii) some lincRNA genes are located in close proximity to hematopoietic coding genes and show strong expression correlations in AML, (iii) lincRNA gene expression patterns distinguish cytogenetic and molecular subtypes of AML, (iv) lincRNA signatures composed of three or four genes are independent predictors of clinical outcome and further dichotomize survival in European Leukemia Net (ELN) risk groups and (v) an analytical tool based on logistic regression analysis of quantitative PCR measurement of four lincRNA genes (LINC4) can be used to determine risk in AML

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

Although genetic lesions responsible for some mendelian disorders can be rapidly discovered through massively parallel sequencing of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1. Ultimately, only by cloning, capillary sequencing and de novo assembly did we find that each of six families with MCKD1 harbors an equivalent but apparently independently arising mutation in sequence markedly under-represented in massively parallel sequencing data: the insertion of a single cytosine in one copy (but a different copy in each family) of the repeat unit comprising the extremely long (~1.5–5 kb), GC-rich (>80%) coding variable-number tandem repeat (VNTR) sequence in the MUC1 gene encoding mucin 1. These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing.National Institutes of Health (U.S.) (Intramural Research Program)National Human Genome Research Institute (U.S.)Charles University (program UNCE 204011)Charles University (program PRVOUK-P24/LF1/3)Czech Republic. Ministry of Education, Youth, and Sports (grant NT13116-4/2012)Czech Republic. Ministry of Health (grant NT13116-4/2012)Czech Republic. Ministry of Health (grant LH12015)National Institutes of Health (U.S.) (Harvard Digestive Diseases Center, grant DK34854