Qualitative Analysis of the Effect of Weeds Removal in Paddy Ecosystems in Fallow Season

In the paper, we introduce a differential equations model of paddy ecosystems in the fallow season to study the effect of weeds removal from the paddy fields. We found that there is an unstable equilibrium of the extinction of weeds and herbivores in the system. When the intensity of weeds removal meets certain conditions and the intrinsic growth rate of herbivores is higher than their excretion rate, there is a coexistence equilibrium state in the system. By linearizing the system and using the Routh–Hurwitz criterion, we obtained the local asymptotically stable conditions of the coexistence equilibrium state. The critical value formula of the Hopf bifurcation is presented too. The model demonstrates that weeds removal from paddy fields could largely reduce the weeds biomass in the equilibrium state, but it also decreases the herbivore biomass, which probably reduces the content of inorganic fertilizer in the soil. We found a particular intensity of weeds removal that could result in the minimum content of inorganic fertilizer, suggesting weeds removal should be kept away from this intensity

Nonlinear canonical correspondence analysis and its application

Abstract The canonical correspondence analysis (CCA) is a multivariate direct gradient analysis method performing well in many fields, however, when it comes to approximating the unimodal response of species to an environmental gradient, which still assumes that the relationship between the environment and the weighted species score is linear. In this work, we propose a nonlinear canonical correspondence analysis method (NCCA), which first determines the most appropriate nonlinear explanatory factor through two screenings by correlation and LASSO regression, and successively uses the linear regression method and the improved heuristic optimal quadratic approximation method to fit the chi-square transformation values of the response variables. Thus, our method effectively reflects the nonlinear relationship between the species and the environment factors, and a biplot is employed to visualize the effects of the later on the distribution of species. The results from applying this method over a real dataset show that the NCCA method not only maintains the advantages of the polynomial canonical correspondence analysis (PCCA) proposed by Makarenkov (2002), but also outperforms Makarenkov’s method in explaining the variance of response variables

Heterogeneity in the expression and subcellular localization of POLYOL/MONOSACCHARIDE TRANSPORTER genes in <i>Lotus japonicus</i>

<div><p>Polyols can serve as a means for the translocation of carbon skeletons and energy between source and sink organs as well as being osmoprotective solutes and antioxidants which may be involved in the resistance of some plants to biotic and abiotic stresses. Polyol/Monosaccharide transporter (PLT) proteins previously identified in plants are involved in the loading of polyols into the phloem and are reported to be located in the plasma membrane. The functions of PLT proteins in leguminous plants are not yet clear. In this study, a total of 14 putative <i>PLT</i> genes (<i>LjPLT1</i>-<i>14</i>) were identified in the genome of <i>Lotus japonicus</i> and divided into 4 clades based on phylogenetic analysis. Different patterns of expression of <i>LjPLT</i> genes in various tissues were validated by qRT-PCR analysis. Four genes (<i>LjPLT3</i>, <i>4</i>, <i>11</i>, and <i>14</i>) from clade II were expressed at much higher levels in nodule than in other tissues. Moreover, three of these genes (<i>LjPLT3</i>, <i>4</i>, and <i>14</i>) showed significantly increased expression in roots after inoculation with <i>Mesorhizobium loti</i>. Three genes (<i>LjPLT1</i>, <i>3</i>, and <i>9</i>) responded when salinity and/or osmotic stresses were applied to <i>L</i>. <i>japonicus</i>. Transient expression of GFP-LjPLT fusion constructs in Arabidopsis and <i>Nicotiana benthamiana</i> protoplasts indicated that the LjPLT1, LjPLT6 and LjPLT7 proteins are localized to the plasma membrane, but LjPLT2 (clade IV), LjPLT3, 4, 5 (clade II) and LjPLT8 (clade III) proteins possibly reside in the Golgi apparatus. The results suggest that members of the <i>LjPLT</i> gene family may be involved in different biological processes, several of which may potentially play roles in nodulation in this nitrogen-fixing legume.</p></div

Transient expression of GFP-LjPLT fusion constructs in <i>N</i>. <i>benthamiana</i> expressing a marker of the Golgi apparatus, mCherry-tagged alpha-mannosidase II (AMAN-2).

<p>(A) The proteins GFP-LjPLT2, GFP-LjPLT3, GFP-LjPLT4, GFP-LjPLT5 and GFP-LjPLT8 co-localized with mCherry-tagged AMAN-2. The images were recorded with a Leica TCS SP8 X confocal microscope, in the GFP region with time gating (gate on time: 0.0–12.0 ns) and in the mCherry region with time gating (gate on time: 0.3–11.9 ns). Scale bar, 5 μm. (B) GFP-LjPLT3 and GFP-LjPLT8 are localized in the Golgi apparatus as shown by 3-D reconstructions. 3-D Images were acquired using a Nikon A1 confocal microscope, with a 60× oil objective.</p

Expression patterns of <i>LjPLT</i> genes.

<p>The relative expression levels of the <i>LjPLTs</i> in different organs were tested by qRT-PCR. Relative expression was normalized to the reference genes <i>LjATPase</i> and <i>LjUBC</i> (internal control) and the expression level in pods was defined as “1”.</p

Transient expression of GFP-LjPLT fusion constructs in Arabidopsis protoplasts.

<p>(A) GFP-LjPLT1, GFP-LjPLT6 and GFP-LjPLT7 are localized in the plasma membrane. Scale bar, 5 μm. (B) GFP-LjPLT8 is localized both in the cytoplasm and at the plasma membrane. The images were recorded with a Leica TCS SP8 confocal microscope. Scale bar, 5 μm.</p

Comparison of the 14 LjPLT proteins.

<p>Schematic alignment of the deduced protein sequences (boxes) of LjPLT1 to LjPLT14 based on the positions of intron (arrows) in these genes. Grey boxes (I–XII) indicate the positions of transmembrane helices as predicted by the HMMTOP software package. Thin lines show small gaps in the sequences. Numbers of amino acids encoded by the different exons are indicated (white).</p

<i>Cis</i>-element analysis of putative <i>LjPLT</i> promoters related to stress responses.

<p>Different <i>cis</i>-elements with the same or similar functions are shown in the same color.</p

Phylogenetic tree of polyol transporters in different species.

<p>The tree was constructed using the neighbor-joining method with 1000 bootstrap replications. Asterisks indicate proteins of plant that have been reported to be localized to the plasma membrane. Accession numbers for the <i>PLT</i> genes are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185269#pone.0185269.s004" target="_blank">S3 Table</a>.</p

The response of <i>LjPLT</i> genes to salt and osmotic stresses applied to <i>L</i>. <i>japonicus</i>.

<p>Expression of <i>LjPLTs</i> in roots and shoots at different time points after 10% PEG and 100 mM NaCl treatments.</p