Efficacy assessed in follow-ups of clinical trials: methodological conundrum

Increasingly, we see papers describing the long-term follow-up results of randomised clinical trials. Sometimes, like the article by Rantalaiho and colleagues in the previous issue of Arthritis Research & Therapy, the follow-up extends to more than 10 years. It is not uncommon that authors of such articles describe their results as a comparison of the original treatment groups in the original randomised clinical trial. Methodologically, such a comparison is fallible for several reasons. In this editorial, two important sources of bias that may jeopardise the results of such follow-up studies are discussed: confounding by indication and confounding by trial completion.     

Gel‐like inclusions of C‐terminal fragments of TDP‐43 sequester stalled proteasomes in neurons

Aggregation of the multifunctional RNA‐binding protein TDP‐43 defines large subgroups of amyotrophic lateral sclerosis and frontotemporal dementia and correlates with neurodegeneration in both diseases. In disease, characteristic C‐terminal fragments of ~25 kDa ("TDP‐25") accumulate in cytoplasmic inclusions. Here, we analyze gain‐of‐function mechanisms of TDP‐25 combining cryo‐electron tomography, proteomics, and functional assays. In neurons, cytoplasmic TDP‐25 inclusions are amorphous, and photobleaching experiments reveal gel‐like biophysical properties that are less dynamic than nuclear TDP‐43. Compared with full‐length TDP‐43, the TDP‐25 interactome is depleted of low‐complexity domain proteins. TDP‐25 inclusions are enriched in 26S proteasomes adopting exclusively substrate‐processing conformations, suggesting that inclusions sequester proteasomes, which are largely stalled and no longer undergo the cyclic conformational changes required for proteolytic activity. Reporter assays confirm that TDP‐25 impairs proteostasis, and this inhibitory function is enhanced by ALS‐causing TDP‐43 mutations. These findings support a patho‐physiological relevance of proteasome dysfunction in ALS/FTD.     

Ethyl (E)-3,5-ethano-7,11-dimethyl-2,4-dodecadienoate,A new insect growth regulator with potent juvenile hormone activity

A number of analogs of ethyl (2E,4E)-3,7,11-trimethyl-2,4-dodecadienoate were prepared and bioassayed for juvenile hormone activity on the yellow-fever mosquito (Aedes aegypti), the greater wax moth (Galleria mellonella), the yellow mealworm (Tenebrio molitor), the house fly (Musca domestica), and the tobacco budworm (Heliothis virescens). The analog ethyl (E)-3,5-ethanol-7,11-dimethyl-2,4-dodecadienoate (VI), containing a cyclopentene ring, showed remarkable potency on the above insect species. Since this compound possesses a fixed 3-s-trans-diene conformation it may provide some insight into the active conformation of bound 2,4-dienoate analogs.     

Application of stains in clinical microbiology

Stains have been used for diagnosing infectious diseases since the late 1800s. The Gram stain remains the most commonly used stain because it detects and differentiates a wide range of pathogens. The next most commonly used diagnostic technique is acid-fast staining that is used primarily to detect Mycobacterium tuberculosis and other severe infections. Many infectious agents grow slowly on culture media or may not grow at all; stains may be the only method to detect these organisms in clinical specimens. In the hands of experienced clinical microscopists, stains provide rapid and cost-effective information for preliminary diagnosis of infectious diseases. A review of the most common staining methods used in the clinical microbiology laboratory is presented here.     

Responses of male California red scale to sex pheromone isomers

The California red scale, Aonidiella aurantii (Maskell), sex pheromone components were previously identified as two independently attractive norsesquiterpenes. The four possible optical isomers of one and the four possible geometric and optical isomers of the other were synthesized and tested for male California red scale attractiveness in field tests and greenhouse bioassays. The results showed that there was enantiomeric and geometric specificity and only 1 isomer of each component was significantly more active than the others. The active isomers were (3S,6R)-3-methyl-6-isopropenyl-9 decen-1-yl acetate and (3Z,6R)-3-methyl-6-isopropenyl-3,9-decadien-1-yl acetate. The presence of other isomers, including the synthetic analogue 3-methyl-6-isopropylidene-9-decen-1-yl acetate, had no effect on trap catch.     

Data Deposition and Annotation at the Worldwide Protein Data Bank

The Protein Data Bank (PDB) is the repository for three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive is free and easily available via the Internet from any of the worldwide centers managing this global archive. These data are used by scientists, researchers, bioinformatics specialists, educators, students, and general audiences to understand biological phenomenon at a molecular level. Analysis of this structural data also inspires and facilitates new discoveries in science. This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included. Shuchismita Dutta, Kyle Burkhardt, and Ganesh J. Swaminathan have contributed equally to this work.