No Fluke

Tropical diseases may have been neglected in the past, but increasing attention is now being paid to conditions such as schistosomiasis, which is caused by a parasitic worm. Vaccine efforts demand the development of new methods for studying fluke-host interactions. To date, tracking migration of schistosomes through the host has relied on tissue histology or radioactive labeling followed by whole-animal “squashes.” Although transgenic strategies have been successful in other parasites such as Leishmania, similar efforts have been disappointing in schistosomes. Writing in the FASEB Journal, Krautz-Peterson et al. offer an alternative based on fluorescence molecular tomography (FMT). The authors inject protease-activated fluorochromes intravascularly into mice; because schistosomes feed on blood, the probe should be activated by cathepsins in the parasite's gut. As expected, intense areas of schistosome accumulation are visible in the digestive tract of infected mice. Furthermore, microscopic analysis of isolated worms shows that they're no different in appearance or behavior than unlabeled controls. In other evidence that the fluorochromes do not interfere with normal schistosome biology, treatment of infected mice with the standard drug therapy results in profound reduction of fluorescence. Because the level of fluorescence correlates with fluke number, this in vivo test system should help uncover compounds with potential anti-schistosome activity. Hopes are high that this FMT-based imaging strategy will soon yield advances against parasitic infections that for too long have afflicted the developing world.

Krautz-Peterson et al. Imaging schistosomes in vivo. FASEB J [Epub ahead of print, April 3, 2009; doi: 10.1096/fj.08-127738].

The Future Is Not Flat

Regardless of what might be envisioned for the global economy, the viability of stem cell research rests on moving away from a two-dimensional (2-D) worldview, because making the transition to suspension culture would allow for meaningful scale-up. Although human embryonic stem cells (hESCs) are grown in suspension (as embryoid bodies) for differentiation, long-term propagation of undifferentiated hESCs in suspension has not succeeded beyond a several-week period. In a paper in Stem Cell Research, Oh et al. reveal that matrigel-coated rod-shaped cellulose microcarriers can serve as a substrate for extended culture. To make their case, the authors first show that expression levels of stemness markers Oct4, SSEA4, and TRA-1-60 are preserved. Genomic stability is evidenced by normal karyo-types after 25 passages (equivalent to about 6 months); in addition, the cells retain the ability to differentiate into cells indicative of endoderm, mesoderm, and ectoderm. Cell densities are 2–4× higher than 2-D cultures, depending on whether the hESCs are in static or spinner suspension cultures. Cell handling remains straightforward: cells can be passaged after dispersal by enzymatic means or by use of a pipet and mesh cell strainer, and serum-free defined media can be used. As in any fast-moving field, this study won't be the final word, but it does offer a glimpse at a future in which bioreactor-scale propagation of hESCs will be possible, and, in the nearer term, a world in which researchers will view long-term, efficient hESC culture as routine.

Oh et al. Long-term microcarrier suspension cultures of human embryonic stem cells. Stem Cell Res [Epub ahead of print, March 4, 2009; doi: 10.1016/j.scr.2009.02.005].

Consider the Alternatives

Any chagrin felt at the realization of just how few genes are in the human genome has been dissipated by the growing appreciation of the complexities enabled by alternative transcription (AT) and alternative splicing (AS). In fact, the expression possibilities are so extensive that it is difficult to keep track of just how many isoforms even a single gene may have. Part of the problem is the fact that this information is dispersed over several databases: for instance, online sources may list different numbers of RNA isoforms for a single gene, with little way to determine if these sets are overlapping or not. Matters get even more complicated when trying to pin down differences in AT/AS events between organisms in order to trace a gene's functional or evolutionary significance. In a new Genomics article, Bhasi et al. offer their solution to this frustrating situation, in the form of a Web-based tool called AspAlt. The interface is built from Ensembl, RefSeq, and AceView (a transcriptome database) and includes 2.1 million AT/AS annotations from 46 eukaryotes. A color-coded, visual display helps users quickly distinguish exons arising from alternative splice donors/acceptors (or both), alternative transcription initiation or termination sites, exon skipping, etc. Another view allows users to select organisms for cross-species comparisons of alternative transcription and processing features for a gene of interest. In another variation, different isoforms of related genes from a single organism can be viewed together. Interactivity is further facilitated by opportunities to submit customized annotations or download data files for additional analysis. Researchers wishing to sample the variety may access the tool at http://66.170.16.154/AspAlt.

Bhasi et al. AspAlt: A tool for inter-database, inter-genomic and user-specific comparative analysis of alternative transcription and alternative splicing in 46 eukaryotes. Genomics [Epub ahead of print, March 11, 2009; doi: 10.1016/j.ygeno.2009.02.006].