Relative expression levels of lincRNAs and their apcGenes across the three developmental stages.

<p>The X axis shows the log ratio abundance for lincRNA/apcGene determined by qPCR. The Y axis lists the pair of lincRNA and apcGene. The lists are sorted based on the log ratio abundance and divided into three groups (I, II and III). The IDs of the lincRNAs and their apcGenes are shown to the right or left of the graph. The postfixes indicate the families or pathways to which the apcGenes belong. C: CAZy protein family; P: CYP450 protein family; L: lignin degradation pathway; M: <i>mat</i>B genes; T: triterpenoid synthesis pathway. Error bars denote the standard deviations of three qPCR replicates.</p

Genome-Wide Identification and Characterization of Long Intergenic Non-Coding RNAs in <i>Ganoderma lucidum</i>

<div><p><i>Ganoderma lucidum</i> is a white-rot fungus best-known for its medicinal activities. We have previously sequenced its genome and annotated the protein coding genes. However, long non-coding RNAs in <i>G. lucidum</i> genome have not been analyzed. In this study, we have identified and characterized long intergenic non-coding RNAs (lincRNA) in <i>G. lucidum</i> systematically. We developed a computational pipeline, which was used to analyze RNA-Seq data derived from <i>G. lucidum</i> samples collected from three developmental stages. A total of 402 lincRNA candidates were identified, with an average length of 609 bp. Analysis of their adjacent protein-coding genes (apcGenes) revealed that 46 apcGenes belong to the pathways of triterpenoid biosynthesis and lignin degradation, or families of cytochrome P450, mating type B genes, and carbohydrate-active enzymes. To determine if lincRNAs and these apcGenes have any interactions, the corresponding pairs of lincRNAs and apcGenes were analyzed in detail. We developed a modified 3′ RACE method to analyze the transcriptional direction of a transcript. Among the 46 lincRNAs, 37 were found unidirectionally transcribed, and 9 were found bidirectionally transcribed. The expression profiles of 16 of these 37 lincRNAs were found to be highly correlated with those of the apcGenes across the three developmental stages. Among them, 11 are positively correlated (r>0.8) and 5 are negatively correlated (r<−0.8). The co-localization and co-expression of lincRNAs and those apcGenes playing important functions is consistent with the notion that lincRNAs might be important regulators for cellular processes. In summary, this represents the very first study to identify and characterize lincRNAs in the genomes of basidiomycetes. The results obtained here have laid the foundation for study of potential lincRNA-mediated expression regulation of genes in <i>G. lucidum</i>.</p></div

The bioinformatic pipeline used to identify the lincRNA candidates.

<p>The predicted genes, transcripts and transcript units (TUs) before and after each filtering step are shown in rectangle. The number of TUs is shown in parenthesis. The filtering process is shown next to the arrowed line above each diamond. The criterion used in each filtering step is shown in diamond.</p

Schematic representation of the MRA method.

<p>(1) Relative locations of primers F1, F2, and R on a target locus; (2) First-strand cDNA synthesis using primer UP1; (3) First-round PCR amplification. The gene-specific primer F1 or R was used as the forward primer and primer UP2 was used as the reverse primer, producing PCR products P-3a and P-3b, respectively. The relative positions of the primers on the PCR products are shown; (4) Second-round PCR amplification. The gene-specific F2 was used as the forward primer and R was used as the reverse primer, producing PCR products P-4a and P-4b, respectively. The relative positions of the primers on the PCR products are shown. For the control, the first-strand cDNAs were used as the template, producing products P-c; (5) A graphic representation of the expected electrophoresis results and the corresponding transcriptional orientation they represent. The filled rectangle indicates the presence of a band and the hollow rectangle indicates the absence of a band. The name of the PCR products are the same as described above in (3) and (4). The transcriptional direction determined based on each pattern is shown as F (Forward), R (Reverse) and F/R (bidirectional).</p

Tropical forest diversity, environmental change and species augmentation: after the intermediate disturbance hypothesis

It is not simple to predict how environmental changes may impact tropical forest species diversity. Published hypotheses are almost invariably too incomplete, too poorly specified and too dependent upon unrealistic assumptions to be useful. Ecologist have sought theoretical simplicity, and while this has provided many elegant abstract concepts, it has hindered the attainment of more practical goals. The problem is not how to judge the individual hypotheses and arguments, but rather how to build upon and combine the many hard-won facts and principles into an integrated science. Controversy is inevitable when the assumptions, definitions and applications of a given hypothesis are unclear. Elegance, as an end in itself, has too often been used to justify abstract simplification and lack of operational definition. Clarifying and combining hypotheses while avoiding assumptions provides potentially more useful, if less elegant, stand-point. An appraisal of Connell's intermediate disturbance hypothesis, and its application to long-term observations from a Ugandan forest illustrates these concerns. Current emphases encourage ecologists to exclude consideration of environmental instability and non-pristine ecosystems. In reality, many environmental changes and ecological processses contribute to both the accumulation and erosion of diversity, at all spatial and temporal scales. Site histories, contexts, long-term processes, species-pool dynamics, and the role of people require greater emphasis. These considerations reveal that many environmental changes, even those associated with degradation, can lead to transient rise in species densities. Drawing on related studies, such as forest yield prediction, suggests that the formulation and calibration of simulation models provides the most tractable means to address the complexity of real vegetation. Simulation-based approaches will become increasingly useful both in unifying the study of vegetation dynamics and in providing improved predictive capacity. Quantification of the processes, scales and sensitivities of the dynamics of tropical forest communities remains a major challeng

MOESM5 of Complete chloroplast genome of the medicinal plant Amomum compactum: gene organization, comparative analysis, and phylogenetic relationships within Zingiberales

Additional file 5: Figure S3. Chloroplast genomic alignment between A. compactum and Z. spectabile (JX088661)

MOESM4 of Complete chloroplast genome of the medicinal plant Amomum compactum: gene organization, comparative analysis, and phylogenetic relationships within Zingiberales

Additional file 4: Figure S2. Chloroplast genomic alignment between A. compactum and C. roscoeana (KF601574)

<i>rab11-null</i> follicle cells lose their polarity, delaminate from the epithelium and invade the neighboring germline cyst.

<p>(A) Schematic diagram of follicle epithelial cell polarity. Markers used in this study are highlighted [adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020180#pone.0020180-StJohnston1" target="_blank">[13]</a>]. (B–G″) Confocal images of mosaic stages 7/8 egg chambers 4–6 days ACI. The <i>rab11-null</i> clones are marked by their absence of GFP expression and are outlined with dashed lines. (B-B′″) nGFP (green), Eya (red), E-cad (blue). All of the <i>rab11-null</i> cells stain positive for Eya, consistent with an epithelial cell fate. In contrast to the strict apical expression pattern of E-cad in neighboring wildtype cells, the protein is highly enriched in intracellular compartments in the <i>rab11-null</i> cells (also see D″ and E″). (C-C′″) nGFP (green), Discs large (Dlg) (red), E-cad (blue). (D-D′″) Enlarged views of the bracketed regions shown in (C-C′″). Note that <i>rab11-null</i> cells that are still embedded in the epithelium (outlined in yellow) exhibit wildtype or near wildtype (basolateral) expression patterns for Dlg and mostly normal (mostly apical) expression pattern for E-cad. In contrast, the <i>rab11-null</i> cells that have delaminated from the epithelium (outlined in white) exhibit a vesicular staining pattern for E-cad, while Dlg is dispersed throughout the cell and /or completely absent. (E-E′″) nGFP (green), Fas2 (red), E-cad (blue). Three clusters of delaminated <i>rab11-null</i> cells are outlined. Each cluster contains two cells. None of the cells exhibit apical-basal polarity as evident by the vesicular-like staining pattern of both Fas2 and E-cad. (F-F′″) nGFP (green), ß-integrin (ß-int) (red), Rab11 (blue). Note, the donut-shape distribution pattern of ß-int, which suggest that the some of the protein is still on the cell surface. All of the other examined cell surface markers exhibit a strictly intracellular staining pattern in delaminated cells. The circled <i>rab11-null</i> clone, along with the one shown in (G) is situated in a bubble between the epithelium proper and the germline cyst, which partially accounts for the weak ß-int signal in the flanking wildtype epithelial cells. Nevertheless, the ß-int signal was reproducibly more intense in the <i>rab11-null</i> epithelial cells than in wildtype epithelial cells. (G-G′″) nGFP (green), DAPI (red), ß-int (blue). A large (>50 cells) <i>rab11-null</i> clone in the posterior portion of the egg chamber is circled. Note that the ß –int staining pattern in this clone is more vesicular in nature than that in the previous panels. Most other similarly large clones were also located in the posterior portion of the egg chamber and like the one shown wedged between the follicle cell epithelium and the oocyte.</p

<i>rab11-null</i> epithelial cells arrest differentiation early, but continue to divide through s6 or 7, while <i>sec-15 null</i> cells arrest differentiation early and are targeted for programmed cell death.

<p>(A–C) Confocal images of wildtype s9 egg chambers immunostained for (A) Rab11 (red), (B) Nuf (green), or (C) Sec15 (red). Magnified views are shown at the bottom of each panel. (D) Mosaic s6 egg chamber immunostained for nGFP (green) and Fas3 (red) 4–6 days ACI. The asterisks point to <i>rab11-null</i> cells still embedded in the epithelium. A cluster of 3 or 4 <i>rab11-null</i> cells that have delaminated from the epithelium and invaded the germline cyst is enclosed in the dashed white line. All of the <i>rab11-null</i> cells over-express Fas3 consistent with an early arrest of epithelial cell differentiation (see Text). The arrow points to a wildtype polar cell, which also over-expresses Fas3. (D′) Light micrograph of egg chamber shown in (D). (E) Mosaic s4/5 egg chamber immunostained for nGFP (green), E-cad (red) and phospho-histone 3 (PH3) (blue) 3 days ACI, with <i>rab11-null</i> cells enclosed by the dashed white lines. The asterisk marks a dividing (PH3-positive) <i>rab11-null</i> cell, while the arrows point to two dividing wildtype cells. (F) Mosaic s7 egg chamber immunostained as in (E), with <i>rab11-null</i> cells enclosed by the dashed white lines. (F′) Magnified view of the region bracketed in (F), where a pair of dividing <i>rab11-null</i> (PH3-positive) cells are clearly evident. (G) Mosaic <i>sec15-null</i> s6/7 egg chamber immunostained for nGFP (green) and Fas3 (red) 2 days ACI. All of the <i>sec15-null</i> (GFP-negative) cells over-express Fas3 again consistent with an early arrest of epithelial cell differentiation. The yellow dashed line highlights a gap in the follicle cell epithelium, presumably due to PCD of <i>sec15-null</i> cells. (H) Mosaic <i>sec15-null</i> s6/7 egg chamber immunostained for nGFP (green) and counterstained for activated caspase-3 two days (red) ACI. The arrow points to an apoptotic <i>sec15-null</i> cell.</p

<i>rab11-null</i> stalk cells fail to organize themselves into a functional stalk and are associated with fused and compound egg chambers.

<p>(A–D) Confocal images of immunostained germaria and/or egg chambers 10–12 days ACI, with <i>rab11-null</i> cells marked by the absence of nGFP. (A, A′) Two different focal planes of an s1 (germarial region 3) egg chamber fused to a compound egg chamber containing 3 germline cysts (approximate germline cyst borders outlined with white dashes) immunostained for nGFP (green), LamC (blue), and Traffic jam (Tj) (red). The arrowheads point to putative <i>rab11-null</i> stalk (LamC-positive) cell clusters. As described in the text, such clusters contain ∼6 cells each and are located at or near the junctions of fused and compound egg chambers. The arrows point to candidate <i>rab11-null</i> polar cells (see Text), while the curved arrow points to a clone of <i>rab11-null</i> pre-follicle cells, which also stain positively for Tj. (B, B′) Two different focal planes of a compound egg chamber immunostained for GFP (green) and the oocyte marker, Orb (red). (C) Fused egg chamber immunostained for nGFP (green) and E-cad (red). Anterior at bottom. (D) Massive compound egg chamber immunostained for nGFP (green) and lamC (blue). The LamC-positive nuclei correspond to germ cells and ovariole sheath cells, which are distinguishable from stalk cells by their sizes and position. (E-E′″) Enlarged confocal image of a mosaic stalk cell cluster immunostained for nGFP (green), LamC (blue), and E-cad (red) 5–6 days ACI. The borders of the flanking egg chambers are indicated with the dashed yellow line. The <i>rab11-null</i> stalk cells (enclosed in the dashed white line) are excluded from the stalk proper. (F, G) Wildtype germaria immunostained for (F) nGFP (green) and Rab11 (red), or (G) Nuf (white), a Rab11 effector protein <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020180#pone.0020180-Riggs1" target="_blank">[18]</a>. The arrow in (F) points to enriched expression of Rab11 in presumptive stalk and polar cells at the junction of germarial regions 2B and 3 (s1). The region 2b/3 (s1) junction is expanded in (G) as stalk cell formation is more advanced in this particular germarium.</p