Soybean transformation by electric discharge particle acceleration

By the use of a direct DNA-delivery system based on electric discharge particle acceleration we have been able to obtain transgenic soybean plants expressing the neomycin phosphotransferase II and the β-glucuronidase genes. Techniques for efficient introduction of foreign genes into agronomically important crop plants have been limited by the inability to regenerate fertile plants from single cells or by the limited hostrange of Agrobacterium vectors. In the case of soybean ( Glycine max ) the problem has been compounded due to the lack of a regeneration method compatible with existing transformation technology. In a commercial genetic engineering program the following points need to be considered: (a) not all crops/cultivars can be regenerated from transformed tissues, (b) long time frames are required for the regeneration of transgenic plants from callus, (c) Agrobacterium has a rather limited host specificity and (d) problems associated with somaclonal variation.     

Rapid larval growth predisposes sex change and sexual size dimorphism in a protogynous hermaphrodite, Parapercis snyderi Jordan & Starks 1905

The temporal relationship between growth history, sex-specific growth divergence and sex change was investigated in the haremic sandperch Parapercis snyderi using otolith microstructure and gonad histology. Parapercis synderi was found to display rapid near-linear growth with a maximum longevity of 303 days. All individuals matured first as female and later changed sex to become male (monandric protogynous hermaphroditism). Individual age-based growth histories obtained from otolith increment widths illustrated that males were larger than females at any given age. Males were found to diverge from the female growth trajectory during two ontogenetic periods; during the larval period and during the period that sex change took place. In addition, male otoliths contained a discontinuity, or 'check mark', associated with the rapid increase in otolith growth during the sex-change period. This microstructural feature was absent from all female otoliths. Accelerated growth in male otoliths lasted up to 25 days, following check-mark formation, after which time otolith growth returned to the pre-check-mark rate. Given the isometric relationship between otolith and somatic growth in P. synderi , and the temporal relationship between the time of check-mark formation and gonad condition, these results strongly suggest that individuals accelerate somatic growth during sex change to become the largest members of the population. Moreover, evidence suggests that the factors that determine the initial growth of larvae influence which individuals will later become males and achieve the highest reproductive success.     

香圆种子萌发特征及催芽技术

以香圆（Citrus wilsonii Tanaka）种子为实验材料,通过测定种皮透水性、种皮机械障碍、发芽温度等对种子萌发的影响从而探讨种子萌发特征;通过切割种子、热水浸种、赤霉素浸种、低温层积等处理方式探索种子的催芽方法。结果显示：香圆种皮不存在透水性障碍,但其机械障碍对种子萌发具有抑制作用,且内种皮对萌发影响较大;种子在15℃、25℃、35℃恒温及15℃/30℃变温条件下均可萌发,其最适萌发温度为25℃;采用低温层积、热水浸种、切除1/3种子等方法均可一定程度上促进种子萌发。生产中宜采用始温60℃热水浸种24h的方法对香圆种子进行催芽。     

重复+10Gz暴露对大鼠心肌自由基代谢的影响及低G预适应和茶多酚的保护作用

目的:观察重复 Gz暴露是否引起心肌自由基代谢异常以及低G预适应和天然抗氧化剂茶多酚(TP)的防护作用.方法:32只雄性Wistar大鼠随机分为4组(n=8):A组,仅受 1Gz 作用5 min; B组, 10Gz峰值暴露5 counts/d,每次30 s, 10Gz作用间隔为 1Gz 1 min,每周三天,共三周; C组,实验日先受到 2Gz 作用5 min,1 h后同B组处理;D组,实验日灌胃给予TP 200 mg/kg,1 h后同B组处理.于末次 Gz暴露的次日上午将各组大鼠断头处死,迅速取心脏用于以下指标测定:超氧化物歧化酶(SOD)活性和丙二醛(MDA)含量、免疫组化和半定量反转录PCR(RT-PCR)技术测定Cu,Zn-SOD和诱生型一氧化氮合酶(iNOS)含量和其mRNA表达.结果:与A组(对照组)相比,B组心肌线粒体MDA水平和iNOS酶含量显著增加(P<0.05),与B组相比,C组心肌线粒体SOD活性明显升高,C、D组的iNOS酶含量明显降低(P<0.05).各组Cu,Zn-SOD含量、mRNA表达和iNOS mRNA表达无明显差异.结论:重复 Gz暴露引起大鼠心肌自由基代谢异常,主要导致线粒体氧化损伤,低G预适应和TP具有一定的防护作用,其中以低G预适应的效果更佳.     

Transitions in nutation trajectory geometry in peppermint (Mentha x piperita L.) with respect to lunisolar acceleration

• Nutations of plant organs are significantly affected by the circatidal modulation in the gravitational force exerted by the Moon and Sun (lunisolar tidal acceleration, Etide). In a previous study on nutational rotations of stem apices, we observed abrupt alterations in their direction and irregularities of the recorded trajectories. Such transitions have not yet been analysed in detail.
• Peppermint plants were continuously recorded with time‐lapse photography and aligned with contemporaneous time courses of the Etide estimates. Each nutational stem tip movement path was assigned to one of two groups, depending on its geometry, as: (i) regular elliptical movements and (ii) irregular movements (with a random type of trajectory). Analyses of the correlation between the plant nutation trajectory parameters and Etide, as well as of the trajectory geometry of the individual plants were performed.
• The trajectory geometry of young mint stem apices was related to the velocity of the apex rotation and significantly affected by the gravitational force estimated from the Etide. A low velocity of nutational movement, associated with the random character of the trajectory, usually occurred simultaneously with local minima or maxima of Etide. As the mint plant ages, the transitions in the stem tip trajectory were limited; no correspondence with Etide dynamics was observed.
• The results indicate that the plant tip geometry path transitions with respect to the changing gradient of lunisolar tidal acceleration could be interpreted as manifestation of a continuous accommodation of the shoot apical part to the state of minimum energy dissipation.

     

Alternative production of Bcl-2 and Bax by tumor cells determines the rates of in vivo tumor progression: suggested mechanisms

The hypothesis tested in the study suggests that mechanisms of the earlier described delayed or accelerated tumor progression may be regulated by the antiapoptotic and proapoptotic cellular programs activated in stress reactions of transformed cells to the host normal cellular environment. Therefore, spontaneously transformed hamster cell line STHE, its bcl-2-transduced line STHE-Bcl-2, and 64 of their descendant tumor cell variants naturally selected in two in vivo regimes (local tumor growth versus dissemination) were examined. The role of Bcl-2 and the possible activation of endogenous death-signaling Bax, Ras, and HSP90/HSP70 stress proteins in STHE (Bcl-2+/-) tumor cell variants were studied in dynamics of in vivo tumor progression. The data demonstrate: (1) Immediate in vivo activation of Bax and of HSP90/HSP70 stress proteins in disseminated STHE cells on the background of accelerated tumor progression; (2) No immediate activation of Bax and the gradual downregulation of Bcl-2 in STHE-Bcl-2 cells on the background of delayed tumor progression; (3) Alternative and mutually suppressive character of Bcl-2 and Bax expression in both regimes of tumor progression; (4) In the later stages of tumor progression, the regular transit of the initial Bcl-2 antiapoptotic, Bax-suppressing program, and the delayed tumor progression towards Bcl-2 loss, activation of Bax, and acceleration of tumor progression. Thus, the delay of tumor progression is apparently determined by the ability of Bcl-2-expressing tumor cells to extinguish the cell-damaging environmental stress signals and Bax activation, while its acceleration correlates with Bcl-2 loss, activation of proapoptotic Bax, and tumor cells damage.     

The use of machine learning to detect foraging behaviour in whale sharks: a new tool in conservation

In this study we present the first attempt at modelling the feeding behaviour of whale sharks using a machine learning analytical method. A total of eight sharks were monitored with tri-axial accelerometers and their foraging behaviours were visually observed. Our results highlight that the random forest model is a valid and robust approach to predict the feeding behaviour of the whale shark. In conclusion this novel approach exposes the practicality of this method to serve as a conservation tool and the capability it offers in monitoring potential disturbances of the species.     

MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence

Background

Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it can take hours and days to map millions of reads even for bacteria genomes.

Results

We introduce a GPU program called MaxSSmap with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. Similar to most programs MaxSSmap identifies a local region of the genome followed by exact alignment. Instead of using hash tables or Burrows-Wheeler in the first part, MaxSSmap calculates maximum scoring subsequence score between the read and disjoint fragments of the genome in parallel on a GPU and selects the highest scoring fragment for exact alignment. We evaluate MaxSSmap’s accuracy and runtime when mapping simulated Illumina E.coli and human chromosome one reads of different lengths and 10% to 30% mismatches with gaps to the E.coli genome and human chromosome one. We also demonstrate applications on real data by mapping ancient horse DNA reads to modern genomes and unmapped paired reads from NA12878 in 1000 genomes.

Conclusions

We show that MaxSSmap attains comparable high accuracy and low error to fast Smith-Waterman programs yet has much lower runtimes. We show that MaxSSmap can map reads rejected by BWA and NextGenMap with high accuracy and low error much faster than if Smith-Waterman were used. On short read lengths of 36 and 51 both MaxSSmap and Smith-Waterman have lower accuracy compared to at higher lengths. On real data MaxSSmap produces many alignments with high score and mapping quality that are not given by NextGenMap and BWA. The MaxSSmap source code in CUDA and OpenCL is freely available from http://www.cs.njit.edu/usman/MaxSSmap.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-969) contains supplementary material, which is available to authorized users.     

Binding Pockets and Pathways for Dioxygen through the KijD3 N‐Oxygenase in Complex with Flavin Mononucleotide Cofactor and a 3‐Aminoglucose Substrate: Predictions from Molecular Dynamics Simulations

In this work, two protein systems, Kij3D? FMN? AKM? O₂ and Kij3D? FMN? O₂, made of KijD3 N‐oxygenase, flavin mononucleotide (FMN) cofactor, dTDP‐3‐amino‐2,3,6‐trideoxy‐4‐keto‐3‐methyl‐D ‐glucose (AKM) substrate, and dioxygen (O₂), have been assembled by adding a molecule of O₂, and removing (or not) AKM, to crystal data for the Kij3D? FMN? AKM complex. Egress of AKM and O₂ from these systems was then investigated by applying a tiny external random force, in turn, to their center of mass in the course of molecular dynamics in explicit H₂O. It turned out that the wide AKM channel, even when emptied, does not constitute the main route for O₂ egress. Other routes appear to be also viable, while various binding pockets (BPs) outside the active center are prone to trap O₂. By reversing the reasoning, these can also be considered as routes for uptake of O₂ by the protein, before or after AKM uptake, while BPs may serve as reservoirs of O₂. This shows that the small molecule O₂ is capable of permeating the protein by exploiting all nearby interstices that are created on thermal fluctuations of the protein, rather than having necessarily to look for farther, permanent channels.