Saturday, November 25, 2006

Modeling terror: botulism in milk

Gnome writes "What if the milk from a single processing plant were poisoned with botulism? Poisoning cold drinks with botulinum toxin is one of the 3 “greatest threats to humans” (along with smallpox and airborne anthrax attacks) according to some experts. Authors Wein and Liu analyzed this question mathematically using the supply-chain values of the California dairy industry (which produces >20% of the milk in the US). With “enough” toxin and without “timely” diagnosis, they predict a catastrophe. For example, <1 g of toxin could cause 100,000 poisonings. Ten grams could kill over a half million people. Particularly chilling is that “due to children's higher consumption rate and greater toxin sensitivity”, they estimate 61% of the dead would be children (1 g). They recommend testing and perhaps altered heat pasteurization to inactivate the toxin at a total cost of less than 1 cent per gallon. The publication of this paper was controversial. Ironically, the full editorial on the balance between openness and secrecy, which discusses the decision to publish this paper, is not freely available.
FullandFree Wein and Liu PNAS July 12, 2005 vol. 102:9984 Analyzing a bioterror attack on the food supply: The case of botulinum toxin in milk"

Genes induced by SARS infection

drj writes "SARS (severe acute respiratory syndrome) is a form of pneumonia with a mortality rate of ~10%. No new cases have been diagnosed since mid-2004, quelling fears of a pandemic. It remains unclear why this coronavirus was is so infectious and deadly. Here, Reghunathan and colleagues analyzed the genes induced in peripheral blood mononuclear cells (PBMC) of 10 SARS patients. They report that 186 genes are expressed at different levels in the PBMC of SARS-infected people compared to PBMC from uninfected people. Several genes are strongly induced, including those encoding lactotransferrin (LTF), a marker of neutrophil degranulation, the calcium binding protein S100A9, which regulates monocyte and neutrophil migration, and the pro-apoptotic protein lipocalin 2 (Lcn2). Surprisingly, genes encoding inflammatory cytokines (such as the interferons) and other immune-related genes (such as HLA class I) are not induced. This unusual response to viral infection may contribute to the pathogenesis of SARS. FullandFree Reghunathan et al. BMC Immunology 2005, 6:2 Expression profile of immune response genes in patients with Severe Acute Respiratory Syndrome"

Neutrophil DNA traps pathogens

drj writes "Most white blood cells are neutrophils, which are small, very short lived (hours-days) cells that are crucial in immune defense. Once triggered, they leave the bloodstream and enter inflamed tissues where they engulf and kill bacteria and fungi with hydrogen peroxide and protein toxins. Now, Brinkmann and colleagues show that stimulated neutrophils also produce DNA-containing fibers that can trap and kill bacteria. They suggest these fibers, which they named neutrophil extracellular traps (NETs), are key mediators of anti-bacterial activity. Dead and dying neutrophils are major constituents of pus, from which DNA (‘nuclein’) was discovered in 1869 by Friedreich Meisher.
PubMed Brinkmann et al. Science. 2004 Mar 5;303(5663):1532-5. Neutrophil extracellular traps kill bacteria"

Bird song’s genetic key

PubMed drj writes "Canary (Serinus canaria) songs consist of arranged phrases, themselves composed of repeated, shorter tonal whistles called syllables. Syllables are learned and then arranged into sequences that are unique to each species. This structure is found even in birds raised in isolation, though their repertoire of syllables is smaller. If tutored, isolated birds can instead learn songs without such structure. Gardner et al. now show that imitated songs are remixed into the innate canary song structure as tutored male birds develop into adults. Testosterone accelerated the song restructuring and sexual maturity. The authors provide this maxim: freedom in youth, rules in adulthood . The songs of the juveniles, adults, tutor, and tutored birds are in the on-line supplementary materials.
PubMed Gardner et al. Science 308:1046, 13 May 2005 "Freedom and Rules: The Acquisition and Reprogramming of a Bird's Learned Song"

Chemokine levels influence virus infection

drj writes "HIV-1 infects cells by binding to CCR5, a cell surface receptor for the immune-signaling protein (chemokine) CCL3L1 (MIP-1alpha). One allele (version) of the CCR5 gene has a 32-bp deletion (CCR5delta32). People with two copies of CCR5delta32 are relatively resistant to HIV-1 infection and even one copy delays progression to AIDS. A relatively high frequency of the CCR5delta32 allele in people of European origin (10%) might be due to selection by plague or hemorrhagic fever. Now, Gonzalez and colleagues show that variation in the copies of the gene encoding CCL3L1 is also important. People with more copies of the CCL3L1 gene are more resistant to HIV and AIDS. (This correlation may not hold in some populations.) The simple explanation is that CCL3L1 competes with HIV-1 for binding to CCR5. It's surprising that a receptor can be occupied enough to make a difference. CCR5 is already a target for therapy with small molecule inhibitors. Unfortunately, HIV-1 has demonstrated its ability to develop resistance to some small molecule inhibitors of CCR5.
PubMed Gonzalez et al. Science. 2005 307(5714):1434-40. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility.

Multi-pathway cancer inhibition

Gnome writes "Non-small cell lung cancer (NSCLC) accounts for about 85% of all lung cancers, the leading cause of death due to cancer. A growth factor (TGF-alpha) is thought to promote NSCLC proliferation through binding to the epidermal growth factor receptor (EGFR), which is found at high levels on the tumor cell surface. A competitive inhibitor of EGFR, gefitinib (trade name “Iressa”), failed in clinical trials but physicians reported dramatic improvement in ~10% of patients. Surprisingly, further investigation revealed that these patients’ tumors nearly all carried mutations around the ATP-binding site of EGFR, precisely the target of the drug. Several different mutations were detected. [This contrasts with a similar drug imatinib (STI-571, Gleevec), where mutations or amplifications of the target kinase reduce drug efficacy against leukemias (CML)]. Unfortunately, the benefit of gefitinib is transient (average 7 months) because additional EGFR mutations arise. Here, Kwak and colleagues show that gefitinib-resistant mutants are sensitive to non-competitive (irreversible) EGFR inhibitors named HKI-272, HKI-357, and EKB-569. These inhibitors alter the movement of EGFR in the cell.  Although these studies must be extended to animals, targeting several pathways is well established, successful strategy in anti-viral treatment.
PubMed Kwak et al. PNAS 102:7665 (2005) Irreversible inhibitors of the EGF receptor may circumvent acquired resistance to gefitinib"

Wednesday, November 22, 2006

Chemotherapy for Poxvirus

BioDefense Anonymous Coward writes "Antiviral medications typically target enzymes encoded by the virus, such as reverse transcriptase or proteases. Now, viral dependence on host cell functions is being exploited. Poxviruses, the largest known animal viruses (~200 genes), encode growth factors that bind cellular receptors and increase virulence. For example, the smallpox growth factor tightly binds ErbB-1 (0.14 nM), the cell's epidermal growth factor receptor that also binds smallpox itself. Yang et al. now report the identification of a small molecule inhibitor of the ErbB-1 protein tyrosine kinase. The inhibitor is a synthetic molecule, called CI-1033, that blocks the ATP-binding site of ErbB-1 (IC50 = 0.8 nM). Although CI-1033 did not inhibit replication of a related poxvirus, vaccinia virus, it reduced ErbB-1 activity and intercellular spreading. The most convincing proof of principle came from mice treated with CI-1033 before exposure. They were protected from an otherwise fatal pneumonia following infection with vaccinia. The window of protection is narrow and protection required continuous treatment.
Most human tumors possess ErbB abnormalities, a fact that has promoted the development of orally-administered, small molecule inhibitors for cancer therapy (Gleevec, Iressa). This paper suggests a potential dual use for these medications. Fauci and Challberg provide a comprehensive introduction. See also the thorough review of poxviruses growth and antivirals from Harrison et al.
Full Text Yang et al. J. Clin. Invest. 115:379-387 "Antiviral chemotherapy facilitates control of poxvirus infections through inhibition of cellular signal transduction".

"Down Syndrome Critical Region" isn't?

Gnome writes "Down syndrome (DS) results from the most common viable human chromosomal abnormality, occurring in 1 out of 700 live births. In addition to an entire extra chromosome 21 (free trisomy), DS is also caused by translocated or duplicated portions of chromosome 21. In 1987, the "Down Syndrome Critical Region" (DSCR) was mapped to the short arm of chromosome 21 using quantitative Southern blots of genomes of DS patients and rare patients with ostensibly normal karyotypes. The DSCR was later refined as a 5.4 megabase region around 21q22.3. Known genes in the DSCR are highly conserved between humans and mice (on chromosome 16). Chimeric mice containing a human chromosome 21 exhibit learning deficits and cardiac defects reminiscent of Down syndrome. Even the fruit fly homolog of the DSCR regulates learning. Now, investigators generated transgenic mice with precise DSCR trisomy or monosomy by clever use of asymmetric Cre-Lox sites. They report that mice with three copies of the DSCR do not show the same facial skeletal abnormalities found in mice with larger duplicated regions. Surprisingly, trisomic DSCR mice are larger and monosomic DSCR are smaller than normal, though mice trisomic through a ~3-fold larger, overlapping region are smaller than normal. The authors state that these results refute the predictions of the nearly 3 decade old hypothesis that DS is caused by dose effects of genes within the DSCR."
PubMed Olson et al. Science 2004 Oct 22;306(5696):687-90
A Chromosome 21 Critical Region Does Not Cause Specific Down Syndrome Phenotype

Brain wiring patterns

Gnome writes "Complex electronic circuits designed by humans are composed of many repeated, simpler modules such as amplifiers or logic gates. Does the brain have a similar organization? Reigl and colleagues looked for such patterns in C. elegans, a worm whose nervous system wiring of its 302 neurons could be analyzed from electron micrographs of serial sections. Here, they analyzed the frequency of connection patterns up to 5 neurons. [They concede that their analysis would miss singular circuits, such as a crucial “rectifier in a power supply” (returning to the electronic analogy).] Nevertheless, they found that certain connection patterns between 2, 3, and 4 but not 5 neurons occurred more often than chance. For example, a triplet where 1 neuron stimulates 2 neurons, one of which stimulates the other, occurs much more often than expected. They conclude that these motifs could perform stereotypical functions in the worm nervous system. Many useful circuits need many more connections.
Full&Free Reigl et al., BMC Biology 2004, 2:25
Search for computational modules in the C. elegans brain

Mitochondria and Cardiovascular disease

Gnome writes "Aerobic capacity (fitness) correlates with less cardiovascular disease. Is aerobic capacity inherited? Here, rats from a genetically “heterogeneous” stock were selected for endurance running. Low and high capacity lines were bred. Investigators measured a 3.5-fold difference in aerobic capacity after 11 generations. Capacity of both lines changed through the generations, from the starting average 355 m to exhaustion to a low of 191 m and a high of 853 m. Poor runners had higher blood pressure, higher serum triglycerides, and lower glucose tolerance than good runners. Training didn't help poor runners much. Several mitochondrial proteins are much lower in poor runners and the authors attribute heritable decreases in fitness to decreased mitochondia function. Since mitochondria are maternally inherited, it would be interesting to compare the offspring of high capacity mothers with low capacity fathers and vice versa.
PubMedWisloff et al. Science 2005 Jan 21;307(5708):418-20
Cardiovascular risk factors emerge after artificial selection for low aerobic capacity.

Monday, November 20, 2006

Mouse Lupus prevented with FcgRIIB

drj writes "Mice from some lupus-prone strains make less of an inhibitory antibody receptor (FcgRIIB). Here, mice from these strains were given bone marrow cells that express more FcgRIIB. They lived longer, did not develop as many autoantibodies, and did not develop kidney inflammation (glomerularnephritis). In these experiments, the bone marrow cells from mice representing 3 different lupus models (NZM, BXSB, and B6 FcgRIIB-knockout) were infected (transduced) with retroviruses encoding FcgRIIB. Only about 40% of the B cells made FcgRIIB and the actual increase in expression was "modest" (~43% on B cells; on knockout B cells the increase was presumably qualitative). FcgRIIB may prevent lupus by limiting the development of autoantibodies. Human variations (polymorphisms) that predispose to lupus have been identified in FcgRIIA and FcgRIIIA (review), suggesting a role in human disease. It remains to be seen whether in addition to preventing the onset, retroviral transduction could cure lupus (gene therapy)."
PubMed McGaha et al., Science 307:590-593, Jan. 2005 "Restoration of Tolerance in Lupus by Targeted Inhibitory Receptor Expression".

TRAIL-R attenuates innate immunity

drj writes: "TRAIL, officially known as TNFSF10, induces apoptosis of virus-infected or transformed cells but not normal cells, suggesting a potentially "magic bullet" therapeutic. TRAIL expression is inducible on immune effector cells: Natural Killers (NK) and T cells, macrophages, and dendritic cells. TRAIL knockout mice are more susceptible to tumor metastasis and chemical carcinogenesis. TRAIL-R (receptor) expression is apparently induced by transformation or infection.
Here, Diehl and collegues describe the generation and characterization of TRAIL-R knockout (TRAIL-R-KO) mice. (Mice have only one signaling receptor; humans have two: TNFRSF10A, B.) TRAIL-R-KO mice have normal lymphocyte populations but produce more of the cytokines IL-12, IFN-alpha, and IFN-gamma and clear cytomegalovirus more rapidly. TRAIL-R-KO macrophages stimulated with pathogen-derived molecules (e.g., LPS) though the Toll-like receptors show increased TRAIL expression and enhanced cytokine production. Although early signaling is normal, activation of the transciption factor NF-kB and degradation of its inhibitor IkB-a is prolonged (12 h).
What is the point of inhibiting the innate response? Unlike the adaptive response, there are no expanded populations of cells to inactivate and remove." PubMed Diehl et al., Immunity 21:877-889, December, 2004
TRAIL-R as a Negative Regulator of Innate Immune Cell Responses

Interleukin-7, T cells, and Rheumatoid Arthritis

drj writes "Transient lymphocyte depletion is an effective therapy for some autoimmune diseases, including
juvenile rheumatoid arthritis and multiple sclerosis (MS). Lymphocytes are usually replenished by treatment with growth factors after depletion or with stem cells after ablation. However, CD4 T cells remain depleted for extended periods following therapy of rheumatoid arthritis (RA). Ponchel and colleagues now demonstrate significantly reduced levels of circulating interleukin-7 (IL-7), a T cell growth factor , in the sera of RA patients. Serum IL-7 increased transiently in cancer patients but not RA patients following lymphocyte depletion and autologous stem cell reconstitution.
It would be relatively easy to supplement RA treatment with recombinant IL-7. As the authors acknowledge, however, this would require careful monitoring since IL-7 has been implicated in MS, lymphoma and other cancers."
Ponchel et al., Arthr. Res. & Ther. 7, 2005
"Interleukin-7 deficiency in rheumatoid arthritis: consequences for therapy-induced lymphopenia"

Tuesday, November 7, 2006

Gut check time?

drj writes "Dieters complain about growing fatter despite eating less and exercising more. Backhed and colleagues now provide surprising support for half this claim. Germ-free mice “conventionalized” with microorganisms from the guts of normal mice increase their body fat 60% in just 2 weeks despite eating less. Activity levels were not reported. The bacteria were transmitted by spreading the contents of the distal intestine from normal mice onto the fur of germ-free mice. The microorganisms apparently act by increasing the uptake of sugars from the gut into the bloodstream. Adaptive immunity is not involved in this response because conventionalized Rag1-knockout animals behave similarly. The authors propose that Western diets may predispose to obesity by promoting certain gut microorganisms.
Will obesity, like ulcers caused by Helicobacter pylori, now be understood as having a key microbiological component? Is there a market for bugs from skinny people?"
PNAS "The gut microbiota as an environmental factor that regulates fat storage" Fredrik Backhed, Hao Ding, Ting Wang, Lora V. Hooper, Gou Young Koh, Andras Nagy, Clay F. Semenkovich, and Jeffrey I. Gordon. Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15718-23. PMID: 15505215

Deamidation & Deimination in Disease

Julian Banerji writes "Deamidation of ASN residues in Bcl-xl may regulate apoptosis (Zhao). Deimination of histones can regulate their activity (Cuthbert and Wang.) Deiminated ARG in Fibronectin is the target of some autoantibodies in RA (Hida). The involvement of Peptidylarginine deimidase (PAD) in disease is explored in Vossenaar. The location of PAD is characterized in synovial tissue by Chang. A Japanese group has found polymorphisms in PAD linked to RA (Suzuki). The stories speak for themselves. Something else that's pretty cool: large scale unfolding of chromatin by estrogen receptor (Carpenter) "

Pecking Ordered

drj writes "Darwin found on the Galapagos Islands 14 species of finches with different beak shapes. He proposed that their different beaks allowed them to exploit different foods – short and wide for cracking seeds vs. long and narrow for reaching into flowers. Abzhanov et al. now show that expression of the bone morphogenic protein 4 gene (Bmp4) is higher in the upper beak epithelium of embryonic chicks growing shorter, stronger beaks, suggesting that BMP4 shapes beaks. Expression of Bmp2 and Bmp4 message, in contrast, correlated with the size of the beak. Surprisingly, expression of Bmp4 in the lower beak epithelium does not vary despite shape differences that are comparable to those in the upper beak. Infection with a virus expressing BMP4 protein produced shorter, wider beaks whereas infection with a virus expressing Noggin, which antagonizes BMP2/4/7 activity, produced longer, narrower beaks. The authors are also “tempted to speculate” that Sonic hedgehog (shh) and Fibroblast growth factor 8 (fgf8) are the nuclear factors driving expression of bmp4. The accompanying article by Wu et al. also concludes that BMP4 shapes beaks. Who regulates the regulators (ssh, fgf8)?
PubMed Bmp4 and Morphological Variation of Beaks in Darwin’s Finches Arhat Abzhanov, Meredith Protas, B. Rosemary Grant, Peter R. Grant, Clifford J. Tabin. Science 305:1462, September 3, 2004

J Exp Med Classics online

drj writes "The Journal of Experimental Medicine has produced pdf (Acrobat) versions of all papers they've published since 1896! Now you can peruse the classic 1944 Avery, MacLeod, and McCarty paper that first showed “desoxyribonucleic acid” (DNA) was the “transforming substance”. Or, one of their follow-up papers, for example an "Improved Method for the Isolation of the Transforming Substance”, very early in a very long string of DNA methods papers. Or here’s one of my favorites, the genetic regulation of the immune response. For a glance backward at less memorable papers, try the I-J era. Three cheers and much appreciation to the publisher, the
Rockefeller University Press, with support from The Medical Library Center of New York. This stuff is too old for PubMed (which covers back to the mid-1960s) and even for OLDMEDLINE, which currently goes back to 1951. You’ve got to seek and find it on your own. Search here for your favorite classics (old and new).
What's your favorite J Exp Med paper?"

Monday, November 6, 2006

Synthetic prions

carbonbasedunit writes "In the 20 years since Prusiner popularized Griffith’s suggestion that infectious protein causes Creutzfeld-Jacob disease, the "protein-only" hypothesis has matured from radical to conventional. The hardy doubters not cowed by the 1997 Nobel prize still argued that the infectious agent in brain preparations had not been proven to be protein but could instead be contaminating nucleic acids (review).
Now Legname et al. show that when polymerized into amyloid fibrils and injected into the brains of mice, recombinant mouse prion protein produced in bacteria induces neurologic disease. They previously showed that disease was accelerated in disease-prone mice treated with a synthetic 55 amino acid peptide matching a fragment of a mutant (P101L) human prion that causes spontaneous disease in younger adults. Here, they produced fibrils from a recombinant, truncated mouse prion in mice that do not develop the disease spontaneously. Rather than having fortuitously refolded in vitro a natural prion form, the authors instead suggest based on histology that a novel strain of prion was created. Is there a potential Pandora’s box of prions?
PubMed Synthetic mammalian prions. Legname G, Baskakov IV, Nguyen HO, Riesner D, Cohen FE, DeArmond SJ, Prusiner SB. Science. 2004 Jul 30;305(5684):673-6.

Innate + Adaptive = Immunity

drj writes "Innate immunity is initiated by host cells recognizing stable molecular patterns associated with pathogenic microbes and viruses. These molecular patterns are thought to be reliable triggers because they are required for the life of the pathogen. Here, French et al. show that viruses can change these patterns and evade innate immunity in mice deficient in adaptive immune responses. Early infection by murine cytomegalovirus is controlled by natural killer (NK) cells, which use one form of Ly49H to recognize a viral protein, m157, that is expressed on infected cells. Mice possessing a form of Ly49H that is not activated by this virus die in 6 days. Recombinase-deficient mice without adaptive immunity efficiently suppress viral replication for only about 3 weeks, when they succumb. Viruses recovered from these mice do not trigger Ly49H+ NK cells and nearly all possess mutations in m157, probably allowing them to resist innate immunity. This paper demonstrates an essential role for adaptive immunity in clearing virus, thereby reducing the risk of a mutant evading the innate immune system. Even for this double-stranded DNA virus, mutations occur frequently enough to present a serious health risk. The authors suggest that cytomegalovirus disease, which develops more than a month after transplant in some immune suppressed recipients, may be due to a similar selection of mutant viruses escaping the innate immune response.
PubMed Escape of Mutant Double-Stranded DNA Virus from Innate Immune Control Anthony R. French, Jeanette T. Pingel, Markus Wagner, Ivan Bubic, Liping Yang, Sungjin Kim,Ulrich Koszinowski, Stipan Jonjic, and Wayne M. Yokoyama. Immunity, Vol. 20, 747–756, June, 2004

Asthma – the Chitin hypothesis

drj writes "Chitin is a polysaccharide that forms fungal cell walls and the exoskeleton of insects and crustacea. Some 'lower' organisms use enzymes that degrade chitin, chitinases, for defense. Chitinases are also found in mammals but their function is unknown. Here, Zhu et al. show that acidic mammalian chitinase (AMCase) accumulates in the lung epithelium of human asthmatics and in mice treated to induce asthma. In mice, the accumulation depended on "type 2" (allergic) helper T lymphocytes and their characteristic cytokines, IL-4 and IL-13. Most promising was the reduction in inflammation caused by blocking AMCase with specific antibodies, suggesting it is a good target for therapy. The authors discuss the potential links between chitin-containing insects, hygiene, and asthma."
PubMed Acidic Mammalian Chitinase in Asthmatic Th2 Inflammation and IL-13 Pathway Activation Zhou Zhu, Tao Zheng, Robert J. Homer, Yoon-Keun Kim, Ning Yuan Chen, Lauren Cohn, Qutayba Hamid, Jack A. EliasScience304: 1678-82 Zhu et al., Science 304:1678-82, April 2004

Splice and die!

drj writes "Cytotoxic T lymphocytes (CTL) are triggered by short peptides (8-10 amino acids) held by MHC class I molecules on the target cell. Peptides often derive from cleaved and trimmed full-length proteins but an
earlier report described a spliced peptide that flanks a 40 amino acid deletion within the protein fibroblast growth factor-5 (FGF-5). Vigneron et al. now report the second example of a spliced peptide, a 4 amino acid deletion within a melanocyte glycoprotein 100 (gp100) peptide. They also found that “highly purified” proteasomes are capable of peptide splicing and suggested that closely spaced threonines within the proteasome catalyze protein cleavage and peptide ligation. They estimate that only 1 spliced peptide is produced from 10,000 gp100 molecules but even this low efficiency is good enough to trigger CTL. This phenomenon expands enormously the universe of potential peptides (and will greatly complicate the prediction of MHC binding peptides).
PubMed An Antigenic Peptide Produced by Peptide Splicing in the Proteasome Vigneron N, Stroobant V, Chapiro J, Ooms A, Degiovanni G, Morel S, van der Bruggen P, Boon T, Van den Eynde BJ.
Science 304:587-23 APRIL 2004"