We have developed a new method, SOAPfuse, to identify fusion transcripts from paired-end RNA-Seq data. SOAPfuse applies an improved partial exhaustion algorithm to construct a library of fusion junction sequences, which can be used to efficiently identify fusion events, and employs a series of filters to nominate high-confidence fusion transcripts. Compared with other released tools, SOAPfuse achieves higher detection efficiency and consumed less computing resources. We applied SOAPfuse to RNA-Seq data from two bladder cancer cell lines, and confirmed 15 fusion transcripts, including several novel events common to both cell lines. SOAPfuse is available at http://soap.genomics.org.cn/soapfuse.html.

A high-resolution, 3-dimensional primitive equation model is used to investigate the crossshelf exchange in the East China Sea (ECS). Favorable comparisons between field data and model simulations from both climatological run and hindcast run for 2006 indicate that the model has essential skills in capturing the key physics of the ECS. Temporal and spatial variations of the cross-shelf exchanges are further analyzed. It was demonstrated from both observations and simulations that in 2006 high saline water could be delivered to the north of the Changjiang River mouth (near 32 N) as a result of stronger than typical cross-shelf exchanges at the shelf break and flows through the Taiwan Strait with an annual mean rate of 2.59 and 1.83 Sv, respectively. A few new places at the shelf break were also identified where persistent and vigorous onshore or offshore exchanges occur throughout the year. Cross-shelf exchange is largely determined by the along-shelf geostrophic balance with weak seasonality, which is modulated in upper layers by northeasterly monsoon from early-fall to late-spring and at seabed by bottom friction during December-January, May, and August-September. Nonlinear effect, with strong spatial variations and intraseasonal variability, is a secondary but persistent contributor to the net seaward transport, except for northeast of Taiwan where the nonlinear effect becomes significant but more varied.

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[1] Two detachment processes of low salinity water (LSW) in the Changjiang Estuary in July 2006, and the role of wind on detaching the LSW in particular, are explored with a three-dimensional numerical model. The real-case simulation and the sensitivity experiments results show that wind plays a crucial role in the detachment events and is highlighted in three aspects. First, wind is the most important dynamic factor in the two detachment processes of the LSW. Wind mixing, wind-driven northward current and wind-induced upwelling are three driving forces on detaching the LSW, which increase the salinity in the upper layer in the detachment region along the 30 m isobath and separate the offshore LSW from the nearshore main body of LSW. The diagnostic analysis further indicates that the increase of salinity in the detachment region is mainly due to northward current which transports high salinity water from the south. Second, a critical wind speed, namely a southeasterly wind above 8.0 m/s, is found to be related to the timing of the detachment events. A sensitivity experiment further confirms this critical wind speed and no detachment occurs when the wind speed is below 8.0 m/s. Third, the southwesterly wind plays a key role in the magnitude of the spatial size of the detached LSW. Before the detachment occurs, a persistent southwesterly wind induces northeastward expansion of the LSW and consequently forms larger LSW offshore after detachment, which is verified by another sensitivity experiment with modified wind direction.

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Trichodesmium is broadly distributed and occasionally blooms in the East China Sea (ECS) and southern Yellow Sea, where it contributes to local N and C budgets. However, its population structure, spatiotemporal distribution, controlling factors, and N2 fixation remain poorly documented. Here we provide high spatial resolution data sets of Trichodesmium during the four seasons of 2011–2012 using water‐ and net‐collected methods. The net‐collected method captures colonial trichomes of Trichodesmium effectively but results in an underestimation of free trichomes. Colonies are rarely observed and occur only on the ECS shelf, which are easily missed in water‐collected samples. Depth‐integrated densities of Trichodesmium were found to be significantly higher in warm seasons than in cold seasons. Maximum densities in the water column were generally found at depths of 10–50 m. Trichodesmium thrives on the oligotrophic, warm, offshore ECS shelf (controlled by the Kuroshio and Taiwan Warm Current), but restrains in the cold southern Yellow Sea and the eutrophic, inshore ECS. Seasonal and spatial variations in Trichodesmium are closely correlated with physicochemical properties (mainly temperature and P), which are primarily controlled by circulation alteration and water mass movement. The N2 fixation rates of Trichodesmium in the ECS in summer and autumn (>20°C) are roughly estimated at 17.1 and 41.7 μmol N m−2 d−1 under nonbloom conditions, which potentially contribute to 81% and 57% of biological N2 fixation, respectively. Compared with historical data since the 1970s, Trichodesmium densities have increased considerably in all seasons, and the distribution boundary has shifted northward under regional warming and hydrological changes.