Fishing for genes in hematopoiesis

Microarray experiments often reveal large numbers of differentially expressed genes, but unpacking the biological meaning of such gene lists takes additional, painstaking work. Eckfeldt et al. now show how a functional screen in zebrafish embryos can be used to decipher the output of a gene expression study of hematopoiesis. The authors began by comparing the transcriptional profiles of two populations of human cells from bone marrow and umbilical cord blood: one enriched for hematopoietic stem cells (CD34+CD33CD38Rholoc-kit+) and the other depleted of hematopoietic stem cells (CD34+CD33CD38Rhohi). Two hundred and seventy-seven genes were found to be differentially expressed (by >1.5-fold). This number was pared to 158 by eliminating genes known to be involved in hematopoiesis and several other processes. Potential orthologs in zebrafish could be identified for 86 genes, and 61 of these were chosen for in vivo screening. The screen was carried out by injecting morpholino antisense oligos against each of the tested genes into transgenic zebrafish embryos (which express a fluorescent reporter under the control of a promoter active in hematopoiesis) and looking for defects in blood-cell production by fluorescence microscopy. Sixteen of the 61 genes were shown to contribute to blood development by this assay. (PloS Biol. 3, e254, 2005) KA

Classic and molecular genetics boost rice

Researchers in China and Japan have cloned a gene whose null allele increases grain production in rice. The gene, OsCKX2, encodes an enzyme that degrades cytokinin and is one of many quantitative gene loci (QTLs) important in agricultural breeding. Ashikari et al. looked for QTLs that regulate grain number and plant height (shorter plants were important in the green revolution of 1960s) in 96 backcrosses between two rice varieties and found five for increasing grain number and four for plant height. They cloned the most effective QTL for grain production, mapped it and, using the Rice Genome Automated Annotation System, predicted its similarity to cytokinin oxidase/dehydrogenase. They showed that the OsCKX2 locus regulates cytokinin metabolism and functions in inflorescence development. A nearly isogenic line (NIL) for heavy grain production was bred with one that produced shorter plants in a strategy known as QTL pyramiding. The resulting line produced 26% more grain in the main panicle and was 18% shorter than one of the two founding varieties. Rice accounts for 23% of the calories consumed worldwide and increasing the yield of rice plants could contribute to reducing hunger. This research also provides a strategy for improvement of other crops. (Science, published online 23 June 2005, 10.1126/science.1113373, 2005) TM

New septic shock therapeutic?

Assaults from pathogens can give rise to inflammatory reactions, which, if unchecked, can lead to catastrophic consequences, sometimes even death by septic shock. Researchers from Vanderbilt University School of Medicine have developed a peptide drug based on a naturally occurring suppressor of cytokine signaling, SOCS3, which someday might provide protection against this potentially fatal complication of infection. When they attached the membrane translocation motif from fibroblast growth factor to SOCS3, they showed that the fused protein, when given intraperitoneally, penetrated blood, liver and kidney cells. Using a model of inflammation (D-galactosaminesensitized mice), they were able to show that the engineered SOCS3 blocked several inflammatory pathways and also blocked events that occurred several days into the inflammatory response. Mice receiving the SOCS3 fusion were rescued from the effects of SEB/Gal4-induced toxic shock—80% of mice given SEB/Gal4 succumbed, whereas none of the SOCS3-treated animals died. The authors suggest that cell-penetrating forms of natural inhibitors may prove more useful than gene therapy approaches to controlling inflammatory syndromes. (Nat. Med. 11, 892–898, 2005) LD

Self-cleaning microchemostats

A sophisticated new generation of microchemostats provides a powerful, biofilm-free alternative to current continuous culture systems. Quake and colleagues have developed a microfluidic device consisting of six independent, 16-nanoliter growth loops that serve as bioreactors for semi-continuously growing cells in suspension. Biofilm-free growth is achieved through an intricately choreographed series of periodic cleaning steps happening in different segments of the bioreactor loop at alternating times. To show the potential of their setup, the authors performed a series of experiments to monitor the complex growth dynamics exhibited by populations of synchronously growing cells containing a quorum sensing–based 'population control' genetic switch. The device provides a platform for very low-volume/low-wastage 'almost continuous' growth conditions that could benefit high-throughput screening of chemical compounds as well as other applications in chemical genetics and pharmaceutical discovery in general. (Science 309, 137–140, 2005) GTO

Bacterial vaccines rise from the dead

Dubensky and colleagues have developed a new class of vaccines that combines the immunogenicity of live, attenuated viruses with the safety profile of killed, whole pathogens. This innovative vaccine paradigm employs killed but metabolically active bacteria (KBMA). Using Listeria monocytogenes as a model intracellular pathogen, the authors designed bacterial nucleotide-excision-repair mutants, known to be more sensitive to photochemical treatment with a synthetic psoralen compound. Psoralen induces DNA damage when illuminated with long-wavelength ultraviolet light and ultimately leads to bacterial inactivation. The authors proposed that the nucleotide-excision-repair mutants, although inactivated by photochemical treatment and unable to proliferate and cause infection, could maintain their ability to express genes and secrete proteins that induce an effective immune response. When tested in an infectious mouse model, vaccines made from recombinant, psoraleninactivated, mutant Listeria monocytogenes elicited potent CD4+ and CD8+ T-cell responses and protected against viral challenge. In addition, KBMA vaccines engineered to express a tumor-specific antigen provided therapeutic benefit in a mouse cancer model. The KBMA vaccine approach may prove valuable as an alternative strategy for treating cancer and infectious diseases, in particular, those diseases for which vaccines from live, attenuated viruses are not suitable. (Nat. Med. 11, 3–860, 2005) NC

Research Highlights written by Kathy Aschheim, Nadia Cervoni, Laura DeFrancesco, Teresa Moogan and Gaspar Taroncher-Oldenburg.