REMAS: a new regression model to identify alternative splicing events from exon array data

<p>Abstract</p> <p>Background</p> <p>Alternative splicing (AS) is an important regulatory mechanism for gene expression and protein diversity in eukaryotes. Previous studies have demonstrated that it can be causative for, or specific to splicing-related diseases. Understanding the regulation of AS will be helpful for diagnostic efforts and drug discoveries on those splicing-related diseases. As a novel exon-centric microarray platform, exon array enables a comprehensive analysis of AS by investigating the expression of known and predicted exons. Identifying of AS events from exon array has raised much attention, however, new and powerful algorithms for exon array data analysis are still absent till now.</p> <p>Results</p> <p>Here, we considered identifying of AS events in the framework of variable selection and developed a regression method for AS detection (REMAS). Firstly, features of alternatively spliced exons were scaled by reasonably defined variables. Secondly, we designed a hierarchical model which can represent gene structure and transcriptional influence to exons, and the lasso type penalties were introduced in calculation because of huge variable size. Thirdly, an iterative two-step algorithm was developed to select alternatively spliced genes and exons. To avoid negative effects introduced by small sample size, we ranked genes as parameters indicating their AS capabilities in an iterative manner. After that, both simulation and real data evaluation showed that REMAS could efficiently identify potential AS events, some of which had been validated by RT-PCR or supported by literature evidence.</p> <p>Conclusion</p> <p>As a new lasso regression algorithm based on hierarchical model, REMAS has been demonstrated as a reliable and effective method to identify AS events from exon array data.</p

Primary productivity dynamics in the summer Arctic Ocean confirms broad regulation of the electron requirement for carbon fixation by light-phytoplankton community interaction

© 2019 Zhu, Suggett, Liu, He, Lin, Le, Ishizaka, Goes and Hao. Predicting conversion of photosynthetic electron transport to inorganic carbon uptake rates (the so-called electron requirement for carbon fixation, KC) is central to the broad scale deployment of Fast Repetition Rate fluorometry (FRRf) for primary productivity studies. However, reconciling variability of KC over space and time to produce robust algorithms remains challenging, given the large number of factors that influence KC. We have previously shown that light appears to be a proximal driver of Kc in several ocean regions and we therefore examined whether and how light similarly regulated KC variability in the Arctic Ocean, during a summer cruise in 2016. Sampling transited ice-free and ice-covered waters, with temperature, salinity and Chl-a concentrations all higher for the ice-free than ice covered surface waters. Micro- and pico-phytoplankton generally dominated the ice-free and ice-covered waters, respectively. Values of KC, determined from parallel measures of daily integrated electron transport rates and 14C-uptake, were overall lower for the ice-covered vs. ice-free stations. As in our previous studies, KC was strongly linearly correlated to daily PAR (r = 0.68, n = 46, p < 0.001) and this relationship could be further improved (r = 0.84, n = 46, p < 0.001) by separating samples into ice-free (micro-phytoplankton dominated) vs. ice-covered (Nano- and Pico-phytoplankton dominated water. We subsequently contrasted the PAR-KC relationship form the Arctic waters with the previous relationships from the Ariake Bay and East China Sea and revealed that these various PAR-KC relationships can be systematically explained across regions by phytoplankton community size structures. Specifically, the value of the linear slope describing PAR-KC decreases as water bodies have an increasing fraction of larger phytoplankton. We propose that this synoptic trend reflects how phytoplankton community structure integrates past and immediate environmental histories and hence may be a better broad-scale predictor of KC than specific environmental factors such as temperature and nutrients. We provide a novel algorithm that may enable broad-scale retrieval of CO2 uptake from FRRf with knowledge of light and phytoplankton community size information

Dynamics of photosynthesis in Eichhornia crassipes Solms of Jiangsu of China and their influencing factors

With LI-6400 portable photosynthesis system, the photosynthetic characteristics of artificially cultured Eichhornia crassipes in Jiangsu, China, were monitored from June 1 to November 14, 2009. Both the net photosynthetic rate (Pn) in different positions and light and temperature-response curves of the top fourth leaf were measured in an open-circuit gas channel system in June, July, and August, respectively. The top third to sixth leaves matured with a high Pn in August, 2009. The values of the maximum net photosynthesis (Pmax), light component point (LCP) and apparent quantum efficiency (AQE) of the top fourth leaf of E. crassipes were 34.5±0.72 and 20.25±3.6 μmol m-2s-1 as well as 0.0532±0.0014, respectively, significantly higher than those in rice and maize. The light-saturation point (LSP) of leaves of E. crassipes was 2358±69 μmol m-2s-1, significantly higher than that in rice and much close to that in maize. The natural light intensity and temperatures in Jiangsu are suitable for E. crassipes to rapidly grow but not good enough for it to show the maximum internal photosynthetic capacity from the perspective of photosynthetic physiology, thus resulting in its low biomass in this region.Key words: Eichhornia crassipes, photosynthetic characteristics, environmental influencing factors

Influence of heat stress on leaf morphology and nitrogen–carbohydrate metabolisms in two wucai (Brassica campestris L.) genotypes

Heat stress is a major environmental stress that limits plant growth and yield worldwide. The present study was carried out to explore the physiological mechanism of heat tolerant to provide the theoretical basis for heat-tolerant breeding. The changes of leaf morphology, anatomy, nitrogen assimilation, and carbohydrate metabolism in two wucai genotypes (WS-1, heat tolerant; WS-6, heat sensitive) grown under heat stress (40°C/30°C) for 7 days were investigated. Our results showed that heat stress hampered the plant growth and biomass accumulation in certain extent in WS-1 and WS-6. However, the inhibition extent of WS-1 was significantly smaller than WS-6. Thickness of leaf lamina, upper epidermis, and palisade mesophyll were increased by heat in WS-1, which might be contributed to the higher assimilation of photosynthates. During nitrogen assimilation, WS-1 possessed the higher nitrogen-related metabolic enzyme activities, including nitrate reductase (NR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH), which were reflected by higher photosynthetic nitrogen-use efficiency (PNUE) with respect to WS-6. The total amino acids level had no influence in WS-1, whereas it was reduced in WS-6 by heat. And the proline contents of both wucai genotypes were all increased to respond the heat stress. Additionally, among all treatments, the total soluble sugar content of WS-1 by heat got the highest level, including higher contents of sucrose, fructose, and starch than those of WS-6. Moreover, the metabolism efficiency of sucrose to starch in WS-1 was greater than WS-6 under heat stress, proved by higher activities of sucrose phosphate synthase (SPS), sucrose synthase (SuSy), acid invertase (AI), and amylase. These results demonstrated that leaf anatomical alterations resulted in higher nitrogen and carbon assimilation in heat-tolerant genotype WS-1, which exhibited a greater performance to resist heat stress

Nanoplanktonic diatom rapidly alters sinking velocity via regulating lipid content and composition in response to changing nutrient concentrations

Diatom sinking plays a crucial role in the global carbon cycle, accounting for approximately 40% of marine particulate organic carbon export. While oceanic models typically represent diatoms as microphytoplankton (&gt; 20 μm), it is important to recognize that many diatoms fall into the categories of nanophytoplankton (2-20 μm) and picophytoplankton (&lt; 2 μm). These smaller diatoms have also been found to significantly contribute to carbon export. However, our understanding of their sinking behavior and buoyancy regulation mechanisms remains limited. In this study, we investigate the sinking behavior of a nanoplanktonic diatom, Phaeodactylum tricornutum (P. tricornutum), which exhibits rapid changes in sinking behavior in response to varying nutrient concentrations. Our results demonstrate that a higher sinking rate is observed under phosphate limitation and depletion. Notably, in phosphate depletion, the sinking rate of P. tricornutum was 0.79 ± 0.03 m d-1, nearly three times that of the previously reported sinking rates for Skeletonema costatum, Ditylum brightwellii, and Chaetoceros gracile. Furthermore, during the first 6 h of phosphate spike, the sinking rate of P. tricornutum remained consistently high. After 12 h of phosphate spike, the sinking rate decreased to match that of the phosphate repletion phase, only to increase again over the next 12 hours due to phosphate depletion. This rapid sinking behavior contributes to carbon export and potentially allows diatoms to exploit nutrient-rich patches when encountering increased nutrient concentrations. We also observed a significant positive correlation (P&lt; 0.001) between sinking rate and lipid content (R = 0.91) during the phosphate depletion and spike experiment. It appears that P. tricornutum regulates its sinking rate by increasing intracellular lipid content, particularly digalactosyldiacylglycerol, hexosyl ceramide, monogalactosyldiacylglycerol, and triglycerides. Additionally, P. tricornutum replaces phospholipids with more dense membrane sulfolipids, such as sulfoquinovosyldiacylglycerol under phosphate shortage. These findings shed light on the intricate relationship between nutrient availability, sinking behavior, and lipid composition in diatoms, providing insights into their adaptive strategies for carbon export and nutrient utilization

Fifty-year climate change and its effect on annual runoff in the Tarim River Basin, China

Based on the hydrologic and meteorological data in the Tarim River basin from 1958 to 2004, the trend, characteristics and spatial variation of climate change in the upper reaches of the Tarim River were examined in the study. The long-term trend of climate change and hydrological variations were determined by using both Mann-Kendall and Mann-Whitney nonparametric tests. The results showed that the temperature and precipitation had significantly increased in the drainage basin in the mid-1980s. The climate was the warmest in 1990s among the recent 50 years. The increase of temperature in the tributaries of the Aksu River and Kaidu-Kongque River is higher than that in the tributaries of the Yarkand River and Hotan River. The streamflow at Aksu River showed a significant increasing monotonic trend. The annual runoff in the Aksu River had increased by 10.9% since 1990. The independence test of temperature and precipitation with chi(2) of the El Nino event reveals that there is no significant effect of the El Nino and La Nina events on the annual temperature and annual precipitation in the drainage basin. (C) 2008 Elsevier Ltd and INQUA. All rights reserved

Corrigendum to: The TianQin project: current progress on science and technology

In the originally published version, this manuscript included an error related to indicating the corresponding author within the author list. This has now been corrected online to reflect the fact that author Jun Luo is the corresponding author of the article