Next-generation teaching: a template for bringing genomic and bioinformatic tools into the classroom

The recent increase in accessibility and scale of genetic data available through next-generation sequencing (NGS) technology has transformed biological inquiry. As a direct result, the application and analysis of NGS data has quickly become an important skill for future scientists. However, the steep learning curve for applying NGS technology to biological questions, including the complexity of sample preparation for sequencing and the analysis of large data sets, are deterrents to the integration of NGS into undergraduate education. Here, we present a course-based undergraduate research experience (CURE) designed to aid in overcoming these limitations through NGS investigations of prokaryotic diversity. Specifically, we use 16S rRNA sequencing to explore patterns of diversity stemming from student-directed hypothesis development. This CURE addresses three learning objectives: (1) it provides a forum for experimental design hypothesis generation, (2) it introduces modern genomic tools through a hands-on experience generating an NGS data-set, and (3) it provides students with an introductory experience in bioinformatics.     

油红O染色原代未活化胰腺星状细胞脂肪滴的实验观察

目的观察油红O染色原代培养的未活化胰腺星状细胞脂肪滴,并予鉴定。方法选取接种于6孔板中培养4天的原代未活化胰腺星状细胞,予100g/L甲醛液固定,磷酸盐缓冲液漂洗后,加入5g/L油红O饱和液染色,镜下动态观察。胞浆内的脂肪滴一旦着色,即可洗去油红,苏木素衬染胞核,漂洗分化脱色后镜下成像。结果未活化的胰腺星状细胞脂肪滴被油红0染成鲜艳的红色,大小不一的串珠样\"油珠子\"分散于胞质中,簇集成\"环状\",呈戒环样包绕在细胞核周围。结论油红染色原代未活化胰星状细胞脂肪滴是鉴定该细胞的重要方法之一。     

Time-lapse photomicrography and electron microscopy on initiation of infection of nematodes by Dactylella ellipsospora

 Infection of nematodes by two strains of Datylella ellipsospora was observed using video photomicrography and electron microscopy. By light microscopy, each cell with adhesive knobs contained a number of particles that were distributed evenly before capture of a nematode. The cytoplasmic particles moved to and fro at random. At the moment when the knob cell came into contact with a nematode, the particles accumulated at the place where the cell wall of the knob stuck firmly to the nematode cuticle and exuded adhesive at the same time. The adhesive can be seen near the point of contact between the cell wall of the knob and the cuticle of the nematode. At that point, the knob cell produced an infection peg in most cases, and the cell showed a preference to invade the body of the nematode rather than the tail and head. During capture, accumulation of cytoplasmic particles was seen until infection-bulb formation began. In electron micrographs of ultrathin sections, most of the particles could be seen as electron-dense vesicles, 0.2–0.6 μm in diameter. After attachment of the knob cell to the nematode cuticle, the vesicles were found to fuse with plasmalemma one after another to exude adhesive seen as an amorphous electron-dense substance. Received: January 30, 2002 / Accepted: April 25, 2002     

The use of histology in the study of plant tissue culture systems—Some practical comments

Summary Histological methods have contributed significantly to our understanding of in vitro culture systems. A good histological study based on anatomical and histochemical changes provides insight into cellular processes and provides clues that allow for the proposal of hypotheses for further experimentation. This article serves to draw attention to the use of a histological approach to one’s experimental system. Some of the common mistakes in the handling and processing of explants are discussed. A protocol for the plastic embedding method is detailed.     

A Functional Kinase Homology Domain Is Essential for the Activity of Photoreceptor Guanylate Cyclase 1

Phototransduction is carried out by a signaling pathway that links photoactivation of visual pigments in retinal photoreceptor cells to a change in their membrane potential. Upon photoactivation, the second messenger of phototransduction, cyclic GMP, is rapidly degraded and must be replenished during the recovery phase of phototransduction by photoreceptor guanylate cyclases (GCs) GC1 (or GC-E) and GC2 (or GC-F) to maintain vision. Here, we present data that address the role of the GC kinase homology (KH) domain in cyclic GMP production by GC1, the major cyclase in photoreceptors. First, experiments were done to test which GC1 residues undergo phosphorylation and whether such phosphorylation affects cyclase activity. Using mass spectrometry, we showed that GC1 residues Ser-530, Ser-532, Ser-533, and Ser-538, located within the KH domain, undergo light- and signal transduction-independent phosphorylation in vivo. Mutations in the putative Mg²⁺ binding site of the KH domain abolished phosphorylation, indicating that GC1 undergoes autophosphorylation. The dramatically reduced GC activity of these mutants suggests that a functional KH domain is essential for cyclic GMP production. However, evidence is presented that autophosphorylation does not regulate GC1 activity, in contrast to phosphorylation of other members of this cyclase family.     

The roles of head movements in the search and capture strategy of a tern (Aves, Laridae)

 Gull-billed terns (Gelochelidon nilotica) were video-filmed while searching for and capturing fiddler crabs. Search consists of a vertical head nystagmus, with fast upward flicks and downward slow phases made at the angular speed of the substrate in the approximate direction of the bill. The bill points down at about 60° during hunting, but is brought up to 15° from time to time, which brings the visual streak into line with the horizon; 45° roll movements of the head are consistent with alternation between the use of the temporal and central foveas to view the same object. When a crab has been detected the nystagmus is suspended, and the tern tracks the crab continuously as it manoeuvres into a catching position. This may involve tucking the head under the body so that the bill is 45° behind the vertical, and flying up and backwards for some metres, straightening up the head at the same time. Accepted: 7 November 1998